Psyllid ID: psy15598

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------26
Protein Sequence
MCEPTTSATSNPPKQQRFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQHQSPWPPVQHQL
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHcccccHHccccccccccHHHHHcEEccccccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccHHHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHccccccccccccccccccccccEEEcccccEccccccccHHHHHHHHHHHHccccHHHHHHHHcccHHHHHHHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHcccccHHHHHHHHHHcccccccccccHHHHHHHHHccHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
mcepttsatsnppkqqrfetlelgtdasgqqygevnqlggvfvngrplpnsVRMRIVELAqlgirpcdisrqlrvsHGCVSKILARYhetgsilpgaiggskprvttPKVVSYIKELkqkdpgifAWEIRDRLlsdgvcdkfnvpsvsSISRILRNKigssivqhhhhphiynsiypsypypsntsptvsctkvpigsltppprpqvcwpsshsvTDILSaaaglphqcnehhgnysnyYHMYlgqhqspwppvqhql
Flexible Loop (DISEMBL)
mcepttsatsnppkqqrFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGsilpgaiggskprvTTPKVVSYIKelkqkdpgiFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQHQSPWPPVQHQL
Low Complexity Region (SEG)
MCEPTTSATSNPPKQQRFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHiynsiypsypypsntsptVSCTKVPIGSLTPPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQHQSPWPPVQHQL
Disordered region (IsUnstruct)
*******************************YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILR***************************************************VCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQ************
Disordered Region (DISOPRED)
**************************************GGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH**********************VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL**************************************************************DI****************************************
Disordered Region (DISEMBL)
*************KQQRFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQHQS*********
Disordered Region (DISPRO)
******************************QYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS***********NSIYPSYPYPSNTSPTVSCTKVPIG*************************************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MCEPTTSATSNPPKQQRFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNYSNYYHMYLGQHQSPWPPVQHQL
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	258	2.2.26 [Sep-21-2011]
Q2VL56	341	Paired box protein Pax-9	N/A	N/A	0.693	0.524	0.690	4e-71
Q2VL57	341	Paired box protein Pax-9	N/A	N/A	0.693	0.524	0.690	5e-71
P55771	341	Paired box protein Pax-9	yes	N/A	0.693	0.524	0.690	5e-71
Q2VL60	341	Paired box protein Pax-9	N/A	N/A	0.693	0.524	0.690	5e-71
Q2VL58	341	Paired box protein Pax-9	yes	N/A	0.693	0.524	0.690	6e-71
Q2VL61	341	Paired box protein Pax-9	yes	N/A	0.693	0.524	0.690	6e-71
Q2VL62	341	Paired box protein Pax-9	yes	N/A	0.693	0.524	0.690	7e-71
Q2VL59	341	Paired box protein Pax-9	N/A	N/A	0.693	0.524	0.690	7e-71
Q2L4T2	342	Paired box protein Pax-9	yes	N/A	0.693	0.523	0.690	8e-71
Q2VL51	341	Paired box protein Pax-9	N/A	N/A	0.693	0.524	0.690	9e-71

>sp|Q2VL56|PAX9_SAGOE Paired box protein Pax-9 OS=Saguinus oedipus GN=PAX9 PE=3 SV=1

 Score =  268 bits (684), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQAHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.
Saguinus oedipus (taxid: 9490)

>sp|Q2VL57|PAX9_LEORO Paired box protein Pax-9 OS=Leontopithecus rosalia GN=PAX9 PE=3 SV=1

 Score =  267 bits (683), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Leontopithecus rosalia (taxid: 30588)

>sp|P55771|PAX9_HUMAN Paired box protein Pax-9 OS=Homo sapiens GN=PAX9 PE=1 SV=3

 Score =  267 bits (683), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPTPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Homo sapiens (taxid: 9606)

>sp|Q2VL60|PAX9_SAIBB Paired box protein Pax-9 OS=Saimiri boliviensis boliviensis GN=PAX9 PE=3 SV=1

 Score =  267 bits (683), Expect = 5e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Saimiri boliviensis boliviensis (taxid: 39432)

>sp|Q2VL58|PAX9_CALJA Paired box protein Pax-9 OS=Callithrix jacchus GN=PAX9 PE=3 SV=1

 Score =  267 bits (682), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLTQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Callithrix jacchus (taxid: 9483)

>sp|Q2VL61|PAX9_MACMU Paired box protein Pax-9 OS=Macaca mulatta GN=PAX9 PE=3 SV=1

 Score =  267 bits (682), Expect = 6e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPTPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Macaca mulatta (taxid: 9544)

>sp|Q2VL62|PAX9_PANTR Paired box protein Pax-9 OS=Pan troglodytes GN=PAX9 PE=3 SV=1

 Score =  267 bits (682), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPTPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Pan troglodytes (taxid: 9598)

>sp|Q2VL59|PAX9_CALGO Paired box protein Pax-9 OS=Callimico goeldii GN=PAX9 PE=3 SV=1

 Score =  267 bits (682), Expect = 7e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPNPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Callimico goeldii (taxid: 9495)

>sp|Q2L4T2|PAX9_RAT Paired box protein Pax-9 OS=Rattus norvegicus GN=Pax9 PE=2 SV=1

 Score =  266 bits (681), Expect = 8e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVALPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Rattus norvegicus (taxid: 10116)

>sp|Q2VL51|PAX9_LEPED Paired box protein Pax-9 OS=Lepilemur edwardsi GN=PAX9 PE=3 SV=1

 Score =  266 bits (681), Expect = 9e-71,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Transcription factor required for normal development of thymus, parathyroid glands, ultimobranchial bodies, teeth, skeletal elements of skull and larynx as well as distal limbs.

Lepilemur edwardsi (taxid: 122230)

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	258
91087217	251	PREDICTED: similar to Pax-1 protein [Tri	0.748	0.768	0.731	2e-78
270010988	280	pox meso [Tribolium castaneum]	0.720	0.664	0.751	3e-78
347976434	387	AGAP001493-PA [Anopheles gambiae str. PE	0.744	0.496	0.690	4e-76
312382242	439	hypothetical protein AND_05156 [Anophele	0.724	0.425	0.654	2e-73
242021507	306	Paired box protein Pax-1, putative [Pedi	0.751	0.633	0.700	9e-73
4996232	383	Pax1/9 [Ptychodera flava]	0.833	0.561	0.629	2e-72
301611748	360	PREDICTED: paired box protein Pax-9-like	0.689	0.494	0.694	2e-70
67043724	593	green fluorescent protein-paired-box gen	0.693	0.301	0.690	1e-69
351712895	383	Paired box protein Pax-9 [Heterocephalus	0.693	0.467	0.690	2e-69
431907339	401	Paired box protein Pax-9 [Pteropus alect	0.728	0.468	0.672	2e-69

>gi|91087217|ref|XP_975478.1| PREDICTED: similar to Pax-1 protein [Tribolium castaneum]

 Score =  298 bits (762), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 155/212 (73%), Positives = 170/212 (80%), Gaps = 19/212 (8%)

Query: 23  LGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSK 82
           + T+   QQYGEVNQLGGVFVNGRPLPNSVR+RIVEL+Q+GIRPCDISRQLRVSHGCVSK
Sbjct: 1   MDTEGQVQQYGEVNQLGGVFVNGRPLPNSVRLRIVELSQVGIRPCDISRQLRVSHGCVSK 60

Query: 83  ILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKF 142
           ILARYHETGSILPGAIGGSKPRVTTPKVV+YIK+LKQKDPGIFAWEIRDRLLSDG+CDK+
Sbjct: 61  ILARYHETGSILPGAIGGSKPRVTTPKVVAYIKDLKQKDPGIFAWEIRDRLLSDGICDKY 120

Query: 143 NVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPP 202
           NVPSVSSISRILRNKIGS +    H   +YN+IYPSYPYP                 TPP
Sbjct: 121 NVPSVSSISRILRNKIGSLVHPAPHSHSLYNAIYPSYPYPQQK------------LQTPP 168

Query: 203 PRPQV---CWPSSHSVTDIL----SAAAGLPH 227
           P+      CWPSSHSV+DIL    +AA   PH
Sbjct: 169 PQRHATAPCWPSSHSVSDILAGVHAAAFRTPH 200

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270010988|gb|EFA07436.1| pox meso [Tribolium castaneum]

 Score =  297 bits (760), Expect = 3e-78,   Method: Compositional matrix adjust.
 Identities = 154/205 (75%), Positives = 167/205 (81%), Gaps = 19/205 (9%)

Query: 30  QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89
           QQYGEVNQLGGVFVNGRPLPNSVR+RIVEL+Q+GIRPCDISRQLRVSHGCVSKILARYHE
Sbjct: 37  QQYGEVNQLGGVFVNGRPLPNSVRLRIVELSQVGIRPCDISRQLRVSHGCVSKILARYHE 96

Query: 90  TGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSS 149
           TGSILPGAIGGSKPRVTTPKVV+YIK+LKQKDPGIFAWEIRDRLLSDG+CDK+NVPSVSS
Sbjct: 97  TGSILPGAIGGSKPRVTTPKVVAYIKDLKQKDPGIFAWEIRDRLLSDGICDKYNVPSVSS 156

Query: 150 ISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRPQV-- 207
           ISRILRNKIGS +    H   +YN+IYPSYPYP                 TPPP+     
Sbjct: 157 ISRILRNKIGSLVHPAPHSHSLYNAIYPSYPYPQQK------------LQTPPPQRHATA 204

Query: 208 -CWPSSHSVTDIL----SAAAGLPH 227
            CWPSSHSV+DIL    +AA   PH
Sbjct: 205 PCWPSSHSVSDILAGVHAAAFRTPH 229

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347976434|ref|XP_001689344.2| AGAP001493-PA [Anopheles gambiae str. PEST] gi|333467323|gb|EGK96529.1| AGAP001493-PA [Anopheles gambiae str. PEST]

 Score =  290 bits (742), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 156/226 (69%), Positives = 168/226 (74%), Gaps = 34/226 (15%)

Query: 25  TDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKIL 84
           T+   QQYGEVNQLGGVFVNGRPLPNS RMRIVELA+LGIRPCDISRQLRVSHGCVSKIL
Sbjct: 32  TENQAQQYGEVNQLGGVFVNGRPLPNSTRMRIVELARLGIRPCDISRQLRVSHGCVSKIL 91

Query: 85  ARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNV 144
           ARYHETGSILPGAIGGSKPRVTTPKVV+YI+ELKQKDPGIFAWEIRDRLLSDGVCDK NV
Sbjct: 92  ARYHETGSILPGAIGGSKPRVTTPKVVTYIRELKQKDPGIFAWEIRDRLLSDGVCDKNNV 151

Query: 145 PSVSSISRILRNKIGS---------------------SIVQHHHHPHIYNSIYPSYPYPS 183
           PSVSSISRILRNK+G+                          H   H+YNSIYPSYPY +
Sbjct: 152 PSVSSISRILRNKLGNLAHHHHHPHHPHHPHAGTGGGGAHTPHAPAHLYNSIYPSYPYAA 211

Query: 184 NT-SPTVSCTKVPIGSLTPP--------PRPQVCWPSSHSVTDILS 220
           +T    +SC     GS +PP        P     WPSSHSVTDIL+
Sbjct: 212 STLKSEMSCG----GSPSPPTGATPIRSPHAHCPWPSSHSVTDILA 253

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312382242|gb|EFR27765.1| hypothetical protein AND_05156 [Anopheles darlingi]

 Score =  281 bits (719), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 155/237 (65%), Positives = 167/237 (70%), Gaps = 50/237 (21%)

Query: 30  QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89
           QQYGEVNQLGGVFVNGRPLPNS RMRIVELA+LGIRPCDISRQLRVSHGCVSKILARYHE
Sbjct: 81  QQYGEVNQLGGVFVNGRPLPNSTRMRIVELARLGIRPCDISRQLRVSHGCVSKILARYHE 140

Query: 90  TGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSS 149
           TGSILPGAIGGSKPRVTTPKVV+YI+ELKQKDPGIFAWEIRDRLLSDGVCDK NVPSVSS
Sbjct: 141 TGSILPGAIGGSKPRVTTPKVVTYIRELKQKDPGIFAWEIRDRLLSDGVCDKNNVPSVSS 200

Query: 150 ISRILRNKIGSSIVQH-------------------------------------HHHPHIY 172
           ISRILRNK+G     H                                     H   H+Y
Sbjct: 201 ISRILRNKLGGIGHHHHHHHHHHGGGGGGGGGGGGSGGGNGGSGGSGGGNHGTHPSAHLY 260

Query: 173 NSIYPSYPYPSNTSPT-VSCTKVPIGSLTPP--------PRPQVCWPSSHSVTDILS 220
           NSIYP+YPY + +  + +SC     GS +PP        P    CWPSSHSVTDIL+
Sbjct: 261 NSIYPTYPYTAGSLKSELSCG----GSPSPPTGTTPMRSPHAAHCWPSSHSVTDILA 313

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242021507|ref|XP_002431186.1| Paired box protein Pax-1, putative [Pediculus humanus corporis] gi|212516435|gb|EEB18448.1| Paired box protein Pax-1, putative [Pediculus humanus corporis]

 Score =  279 bits (713), Expect = 9e-73,   Method: Compositional matrix adjust.
 Identities = 152/217 (70%), Positives = 162/217 (74%), Gaps = 23/217 (10%)

Query: 26  DASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA 85
             S QQYGEVNQLGGVFVNGRPLPN+VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA
Sbjct: 5   QTSVQQYGEVNQLGGVFVNGRPLPNTVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA 64

Query: 86  RYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVP 145
           R+HETGSILPGAIGGSKPRVTTPKVVSYIK LKQKDPGIFAWEIRDRLLSDG+CDK+NVP
Sbjct: 65  RFHETGSILPGAIGGSKPRVTTPKVVSYIKGLKQKDPGIFAWEIRDRLLSDGICDKYNVP 124

Query: 146 SVSSISRILRNKIGSSI--------VQHHHHPHIYNSIYPSYPYPSNTSPTVSCTKVPIG 197
           SVSSISRILRNKIG+ +            H  H+YNS+Y SY Y   +         P+G
Sbjct: 125 SVSSISRILRNKIGALVHHHHHHHHSGPPHPSHLYNSLYSSYTYTGASGGPPPSHHQPLG 184

Query: 198 SLT---------------PPPRPQVCWPSSHSVTDIL 219
           S                 P   P  CWPSSHSVTDIL
Sbjct: 185 STKLPSSPPPPPSSHAHFPRAPPSHCWPSSHSVTDIL 221

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|4996232|dbj|BAA78380.1| Pax1/9 [Ptychodera flava]

 Score =  278 bits (710), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 153/243 (62%), Positives = 176/243 (72%), Gaps = 28/243 (11%)

Query: 30  QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89
           Q +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+E
Sbjct: 7   QTFGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNE 66

Query: 90  TGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSS 149
           TGSILPGAIGGSKPRVTTP VV++IKE KQ DPGIFAWEIRDRL++DGVCDK+NVPSVSS
Sbjct: 67  TGSILPGAIGGSKPRVTTPTVVNHIKEYKQHDPGIFAWEIRDRLMADGVCDKYNVPSVSS 126

Query: 150 ISRILRNKIGSSIVQHHHHPH---------IYNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           ISRILRNKIG++ +QH  H           IYN   P YPYP   +P+   +K P+ +  
Sbjct: 127 ISRILRNKIGNNNMQHLQHSSYDPTKDHRPIYN---PIYPYPCPGAPSTVNSK-PMATNP 182

Query: 201 PPPRPQVCWPSSHSVTDILSAAAGLPHQCNEHHGNY--------SNYYHMYLGQHQSPWP 252
            P R    WPSSHSV DIL    G   Q  EH G +        SN+ H  + ++  P P
Sbjct: 183 GPIR----WPSSHSVNDILGFRHG---QLIEHQGPFSVYPPPESSNHSHTAIAEYSRPPP 235

Query: 253 PVQ 255
           P  
Sbjct: 236 PTH 238

Source: Ptychodera flava

Species: Ptychodera flava

Genus: Ptychodera

Family: Ptychoderidae

Class: Enteropneusta

Phylum: Hemichordata

Superkingdom: Eukaryota

>gi|301611748|ref|XP_002935394.1| PREDICTED: paired box protein Pax-9-like [Xenopus (Silurana) tropicalis]

 Score =  271 bits (693), Expect = 2e-70,   Method: Compositional matrix adjust.
 Identities = 143/206 (69%), Positives = 159/206 (77%), Gaps = 28/206 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLTP 201
           RILRNKIG+   Q+H+  H           YN +Y SYP     SP  +  KVP    TP
Sbjct: 125 RILRNKIGNLAQQNHYESHKQHPAAASALPYNHLY-SYP-----SPIAAGAKVP----TP 174

Query: 202 PPRPQV--------CWPSSHSVTDIL 219
           P  P +         WPSSHSVTDIL
Sbjct: 175 PGMPSIPGTMGMPRTWPSSHSVTDIL 200

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|67043724|gb|AAY63958.1| green fluorescent protein-paired-box gene 9 fusion protein [Expression vector pEGFP-Pax9]

 Score =  268 bits (686), Expect = 1e-69,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 256 FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 315

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 316 SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 375

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 376 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 426

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 427 PPGVPAIPGSVALPRTWPSSHSVTDIL 453

Source: Expression vector pEGFP-Pax9

Species: Expression vector pEGFP-Pax9

Genus: N/A

Family: N/A

Order: N/A

Class: N/A

Phylum: N/A

>gi|351712895|gb|EHB15814.1| Paired box protein Pax-9 [Heterocephalus glaber]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 143/207 (69%), Positives = 158/207 (76%), Gaps = 28/207 (13%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct: 5   FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct: 65  SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query: 152 RILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVSCTKVPIGSLT 200
           RILRNKIG+   Q H+  +            YN IY SYP P     T +  KVP    T
Sbjct: 125 RILRNKIGNLAQQSHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAAAAKVP----T 175

Query: 201 PPPRPQV--------CWPSSHSVTDIL 219
           PP  P +         WPSSHSVTDIL
Sbjct: 176 PPGVPAIPGSVAMPRTWPSSHSVTDIL 202

Source: Heterocephalus glaber

Species: Heterocephalus glaber

Genus: Heterocephalus

Family: Bathyergidae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|431907339|gb|ELK11312.1| Paired box protein Pax-9 [Pteropus alecto]

 Score =  268 bits (685), Expect = 2e-69,   Method: Compositional matrix adjust.
 Identities = 146/217 (67%), Positives = 163/217 (75%), Gaps = 29/217 (13%)

Query: 23  LGTDASGQ-QYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVS 81
           LG +  G+  +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVS
Sbjct: 54  LGRNDCGEPAFGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVS 113

Query: 82  KILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDK 141
           KILARY+ETGSILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK
Sbjct: 114 KILARYNETGSILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDK 173

Query: 142 FNVPSVSSISRILRNKIGSSIVQHHHHPHI-----------YNSIYPSYPYPSNTSPTVS 190
           +NVPSVSSISRILRNKIG+   Q H+  +            YN IY SYP P     T +
Sbjct: 174 YNVPSVSSISRILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIY-SYPSPI----TAA 228

Query: 191 CTKVPIGSLTPPPRPQV--------CWPSSHSVTDIL 219
             KVP    TPP  P +         WPSSHSVTDIL
Sbjct: 229 AAKVP----TPPGVPAIPGSVAMPRTWPSSHSVTDIL 261

Source: Pteropus alecto

Species: Pteropus alecto

Genus: Pteropus

Family: Pteropodidae

Order: Chiroptera

Class: Mammalia

Phylum: Chordata

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	258
FB|FBgn0003129	370	Poxm "Pox meso" [Drosophila me	0.531	0.370	0.884	2.6e-67
UNIPROTKB|F1MH87	452	PAX1 "Uncharacterized protein"	0.802	0.457	0.633	1.3e-65
UNIPROTKB|F1PB32	534	PAX1 "Uncharacterized protein"	0.802	0.387	0.633	4.2e-65
MGI|MGI:97485	446	Pax1 "paired box gene 1" [Mus	0.802	0.464	0.628	8.7e-65
UNIPROTKB|P15863	534	PAX1 "Paired box protein Pax-1	0.759	0.367	0.655	1.1e-64
RGD|1588548	361	Pax1 "paired box 1" [Rattus no	0.736	0.526	0.665	2.3e-64
UNIPROTKB|F1SAU2	463	PAX1 "Uncharacterized protein"	0.748	0.416	0.660	2.9e-64
UNIPROTKB|F1MFP5	342	PAX9 "Uncharacterized protein"	0.713	0.538	0.673	1.6e-63
UNIPROTKB|F1PXE6	342	PAX9 "Uncharacterized protein"	0.713	0.538	0.673	1.6e-63
UNIPROTKB|P55771	341	PAX9 "Paired box protein Pax-9	0.713	0.539	0.673	1.6e-63

FB|FBgn0003129 Poxm "Pox meso" [Drosophila melanogaster (taxid:7227)]

 Score = 643 (231.4 bits), Expect = 2.6e-67, Sum P(2) = 2.6e-67
 Identities = 123/139 (88%), Positives = 132/139 (94%)

Query:    31 QYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90
             QYGEVNQLGGVFVNGRPLPN+ RMRIVELA+LGIRPCDISRQLRVSHGCVSKILARYHET
Sbjct:     9 QYGEVNQLGGVFVNGRPLPNATRMRIVELARLGIRPCDISRQLRVSHGCVSKILARYHET 68

Query:    91 GSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSI 150
             GSILPGAIGGSKPRVTTPKVV+YI+ELKQ+DPGIFAWEIRDRLLS+G+CDK NVPSVSSI
Sbjct:    69 GSILPGAIGGSKPRVTTPKVVNYIRELKQRDPGIFAWEIRDRLLSEGICDKTNVPSVSSI 128

Query:   151 SRILRNKIGSSIVQHHHHP 169
             SRILRNK+GS  + H H P
Sbjct:   129 SRILRNKLGS--LGHQHTP 145

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

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

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

GO:0003677 "DNA binding" evidence=IEA

GO:0007526 "larval somatic muscle development" evidence=IMP

UNIPROTKB|F1MH87 PAX1 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 629 (226.5 bits), Expect = 1.3e-65, Sum P(2) = 1.3e-65
 Identities = 138/218 (63%), Positives = 153/218 (70%)

Query:    12 PPKQQRFETLELGTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISR 71
             PP      +L  G  A  Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISR
Sbjct:    75 PPVFSPLPSLWPGASAE-QTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISR 133

Query:    72 QLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRD 131
             QLRVSHGCVSKILARY+ETGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRD
Sbjct:   134 QLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRD 193

Query:   132 RLLSDGVCDKFNVPSVSSISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXX 187
             RLL+DGVCDK+NVPSVSSISRILRNKIGS       +    P                  
Sbjct:   194 RLLADGVCDKYNVPSVSSISRILRNKIGSLAQPGPYEASKQPPPQPALPYNHIYQYPYPS 253

Query:   188 XVSCTKVPIGSL--TPPPRPQVC----WPSSHSVTDIL 219
              VS T   +GS    P     V     WPS+HSV++IL
Sbjct:   254 PVSSTGAKMGSHHGVPGTASHVSIPRSWPSAHSVSNIL 291

GO:0005634 "nucleus" evidence=IEA

GO:0061056 "sclerotome development" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

GO:0060017 "parathyroid gland development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0001756 "somitogenesis" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1PB32 PAX1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 627 (225.8 bits), Expect = 4.2e-65, Sum P(2) = 4.2e-65
 Identities = 138/218 (63%), Positives = 153/218 (70%)

Query:    13 PKQQRFETLEL-GTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISR 71
             P   R    +L G  A  Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISR
Sbjct:    70 PSPGRLGARQLAGPHAMEQTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISR 129

Query:    72 QLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRD 131
             QLRVSHGCVSKILARY+ETGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRD
Sbjct:   130 QLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRD 189

Query:   132 RLLSDGVCDKFNVPSVSSISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXX 187
             RLL+DGVCDK+NVPSVSSISRILRNKIGS       +    P                  
Sbjct:   190 RLLADGVCDKYNVPSVSSISRILRNKIGSLAQPGPYEASKQPPPQPALPYNHIYQYPYPS 249

Query:   188 XVSCTKVPIGSL--TPPPRPQVC----WPSSHSVTDIL 219
              VS T   +GS    P     V     WPS+HSV++IL
Sbjct:   250 PVSPTGTKMGSHHGVPGTAGHVSIPRSWPSAHSVSNIL 287

GO:0005634 "nucleus" evidence=IEA

GO:0061056 "sclerotome development" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

GO:0060017 "parathyroid gland development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0001756 "somitogenesis" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

MGI|MGI:97485 Pax1 "paired box gene 1" [Mus musculus (taxid:10090)]

 Score = 624 (224.7 bits), Expect = 8.7e-65, Sum P(2) = 8.7e-65
 Identities = 137/218 (62%), Positives = 154/218 (70%)

Query:    13 PKQQRFETLEL-GTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISR 71
             P  +R    +L G  A  Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISR
Sbjct:    70 PSPRRSGARQLAGPRAMEQTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISR 129

Query:    72 QLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRD 131
             QLRVSHGCVSKILARY+ETGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRD
Sbjct:   130 QLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRD 189

Query:   132 RLLSDGVCDKFNVPSVSSISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXX 187
             RLL+DGVCDK+NVPSVSSISRILRNKIGS       +    P                  
Sbjct:   190 RLLADGVCDKYNVPSVSSISRILRNKIGSLAQPGPYEASKQPPPQPALPYNHIYQYPYPS 249

Query:   188 XVSCTKVPIGSL--TPPPRPQVC----WPSSHSVTDIL 219
              VS T   +G+    P     V     WPS+HSV++IL
Sbjct:   250 PVSPTGTKMGTHPGVPGSAGHVSIPRSWPSAHSVSNIL 287

GO:0001501 "skeletal system development" evidence=IGI;IMP

GO:0001756 "somitogenesis" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=TAS

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007389 "pattern specification process" evidence=IMP

GO:0008283 "cell proliferation" evidence=IMP

GO:0009887 "organ morphogenesis" evidence=TAS

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IMP

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IMP

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

GO:0048538 "thymus development" evidence=IGI

GO:0060017 "parathyroid gland development" evidence=IGI

GO:0060349 "bone morphogenesis" evidence=IMP

UNIPROTKB|P15863 PAX1 "Paired box protein Pax-1" [Homo sapiens (taxid:9606)]

 Score = 624 (224.7 bits), Expect = 1.1e-64, Sum P(2) = 1.1e-64
 Identities = 135/206 (65%), Positives = 149/206 (72%)

Query:    24 GTDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKI 83
             G  A  Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKI
Sbjct:    91 GPLAMEQTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKI 150

Query:    84 LARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFN 143
             LARY+ETGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRDRLL+DGVCDK+N
Sbjct:   151 LARYNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRDRLLADGVCDKYN 210

Query:   144 VPSVSSISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSL 199
             VPSVSSISRILRNKIGS       +    P                   VS T   +GS 
Sbjct:   211 VPSVSSISRILRNKIGSLAQPGPYEASKQPPSQPTLPYNHIYQYPYPSPVSPTGAKMGSH 270

Query:   200 --TPPPRPQVC----WPSSHSVTDIL 219
                P     V     WPS+HSV++IL
Sbjct:   271 PGVPGTAGHVSIPRSWPSAHSVSNIL 296

GO:0003677 "DNA binding" evidence=IEA

GO:0001756 "somitogenesis" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IEA

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

GO:0048538 "thymus development" evidence=IEA

GO:0060017 "parathyroid gland development" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

GO:0061056 "sclerotome development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001501 "skeletal system development" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

RGD|1588548 Pax1 "paired box 1" [Rattus norvegicus (taxid:10116)]

 Score = 620 (223.3 bits), Expect = 2.3e-64, Sum P(2) = 2.3e-64
 Identities = 133/200 (66%), Positives = 147/200 (73%)

Query:    30 QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89
             Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+E
Sbjct:     1 QTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNE 60

Query:    90 TGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSS 149
             TGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRDRLL+DGVCDK+NVPSVSS
Sbjct:    61 TGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRDRLLADGVCDKYNVPSVSS 120

Query:   150 ISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSL--TPPP 203
             ISRILRNKIGS       +    P                   VS T   +GS    P  
Sbjct:   121 ISRILRNKIGSLAQPGPYEASKQPPPQPALPYNHIYQYPYPSPVSPTGTKMGSHPGVPGS 180

Query:   204 RPQVC----WPSSHSVTDIL 219
                V     WPS+HSV++IL
Sbjct:   181 AGHVSIPRSWPSAHSVSNIL 200

GO:0001501 "skeletal system development" evidence=ISO

GO:0001756 "somitogenesis" evidence=IEA;ISO

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

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

GO:0007389 "pattern specification process" evidence=ISO

GO:0008283 "cell proliferation" evidence=IEA;ISO

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IEA;ISO

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IEA;ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA;ISO

GO:0048538 "thymus development" evidence=IEA;ISO

GO:0060017 "parathyroid gland development" evidence=IEA;ISO

GO:0060349 "bone morphogenesis" evidence=IEA;ISO

GO:0061056 "sclerotome development" evidence=IEA

UNIPROTKB|F1SAU2 PAX1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 621 (223.7 bits), Expect = 2.9e-64, Sum P(2) = 2.9e-64
 Identities = 134/203 (66%), Positives = 148/203 (72%)

Query:    27 ASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 86
             A  Q YGEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILAR
Sbjct:    90 AMEQTYGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 149

Query:    87 YHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPS 146
             Y+ETGSILPGAIGGSKPRVTTP VV +I++ KQ DPGIFAWEIRDRLL+DGVCDK+NVPS
Sbjct:   150 YNETGSILPGAIGGSKPRVTTPNVVKHIRDYKQGDPGIFAWEIRDRLLADGVCDKYNVPS 209

Query:   147 VSSISRILRNKIGSSI----VQHHHHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSL--T 200
             VSSISRILRNKIGS       +    P                   VS T   +GS    
Sbjct:   210 VSSISRILRNKIGSLAQPGPYEASKQPPPQPALPYNHIYQYPYPSPVSPTGAKMGSHHGV 269

Query:   201 PPPRPQVC----WPSSHSVTDIL 219
             P     V     WPS+HSV++IL
Sbjct:   270 PGTAGHVSIPRSWPSAHSVSNIL 292

GO:0005634 "nucleus" evidence=IEA

GO:0061056 "sclerotome development" evidence=IEA

GO:0060349 "bone morphogenesis" evidence=IEA

GO:0060017 "parathyroid gland development" evidence=IEA

GO:0048538 "thymus development" evidence=IEA

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

GO:0043374 "CD8-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0043367 "CD4-positive, alpha-beta T cell differentiation" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0001756 "somitogenesis" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1MFP5 PAX9 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 648 (233.2 bits), Expect = 1.6e-63, P = 1.6e-63
 Identities = 136/202 (67%), Positives = 149/202 (73%)

Query:    32 YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
             +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct:     5 FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query:    92 SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
             SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct:    65 SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query:   152 RILRNKIGSSIVQHH------HHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSLTPPPRP 205
             RILRNKIG+   Q H      H P                    +  KVP    TPP  P
Sbjct:   125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIYSYPSPITAAAAKVP----TPPGVP 180

Query:   206 QV--------CWPSSHSVTDIL 219
              +         WPSSHSVTDIL
Sbjct:   181 AIPGSVAMPRTWPSSHSVTDIL 202

GO:0005634 "nucleus" evidence=IEA

GO:0071363 "cellular response to growth factor stimulus" evidence=IEA

GO:0060325 "face morphogenesis" evidence=IEA

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IEA

GO:0042481 "regulation of odontogenesis" evidence=IEA

GO:0042476 "odontogenesis" evidence=IEA

GO:0007492 "endoderm development" evidence=IEA

GO:0005739 "mitochondrion" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1PXE6 PAX9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 648 (233.2 bits), Expect = 1.6e-63, P = 1.6e-63
 Identities = 136/202 (67%), Positives = 149/202 (73%)

Query:    32 YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
             +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct:     5 FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query:    92 SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
             SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct:    65 SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query:   152 RILRNKIGSSIVQHH------HHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSLTPPPRP 205
             RILRNKIG+   Q H      H P                    +  KVP    TPP  P
Sbjct:   125 RILRNKIGNLAQQGHYDSYKQHQPAPQPALPYNHIYSYPSPITAAAAKVP----TPPGVP 180

Query:   206 QV--------CWPSSHSVTDIL 219
              +         WPSSHSVTDIL
Sbjct:   181 AIPGSVAMPRTWPSSHSVTDIL 202

GO:0005634 "nucleus" 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:0003677 "DNA binding" evidence=IEA

UNIPROTKB|P55771 PAX9 "Paired box protein Pax-9" [Homo sapiens (taxid:9606)]

 Score = 648 (233.2 bits), Expect = 1.6e-63, P = 1.6e-63
 Identities = 136/202 (67%), Positives = 149/202 (73%)

Query:    32 YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
             +GEVNQLGGVFVNGRPLPN++R+RIVELAQLGIRPCDISRQLRVSHGCVSKILARY+ETG
Sbjct:     5 FGEVNQLGGVFVNGRPLPNAIRLRIVELAQLGIRPCDISRQLRVSHGCVSKILARYNETG 64

Query:    92 SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
             SILPGAIGGSKPRVTTP VV +I+  KQ+DPGIFAWEIRDRLL+DGVCDK+NVPSVSSIS
Sbjct:    65 SILPGAIGGSKPRVTTPTVVKHIRTYKQRDPGIFAWEIRDRLLADGVCDKYNVPSVSSIS 124

Query:   152 RILRNKIGSSIVQHH------HHPHXXXXXXXXXXXXXXXXXXVSCTKVPIGSLTPPPRP 205
             RILRNKIG+   Q H      H P                    +  KVP    TPP  P
Sbjct:   125 RILRNKIGNLAQQGHYDSYKQHQPTPQPALPYNHIYSYPSPITAAAAKVP----TPPGVP 180

Query:   206 QV--------CWPSSHSVTDIL 219
              +         WPSSHSVTDIL
Sbjct:   181 AIPGSVAMPRTWPSSHSVTDIL 202

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

GO:0007492 "endoderm development" evidence=IEA

GO:0042476 "odontogenesis" evidence=IEA

GO:0042481 "regulation of odontogenesis" evidence=IEA

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

GO:0060325 "face morphogenesis" evidence=IEA

GO:0071363 "cellular response to growth factor stimulus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=NAS

GO:0007275 "multicellular organismal development" evidence=NAS

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA;NAS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

GO:0005739 "mitochondrion" evidence=IDA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P55771	PAX9_HUMAN	No assigned EC number	0.6908	0.6937	0.5249	yes	N/A
P47242	PAX9_MOUSE	No assigned EC number	0.6908	0.6937	0.5233	yes	N/A
P23757	POXM_DROME	No assigned EC number	0.8848	0.5310	0.3702	yes	N/A
Q2L4T2	PAX9_RAT	No assigned EC number	0.6908	0.6937	0.5233	yes	N/A
Q2VL62	PAX9_PANTR	No assigned EC number	0.6908	0.6937	0.5249	yes	N/A
Q2VL61	PAX9_MACMU	No assigned EC number	0.6908	0.6937	0.5249	yes	N/A
P55166	PAX9_CHICK	No assigned EC number	0.6859	0.6937	0.5280	yes	N/A
Q2VL58	PAX9_CALJA	No assigned EC number	0.6908	0.6937	0.5249	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	258
cd00131	128	cd00131, PAX, Paired Box domain	5e-82
pfam00292	125	pfam00292, PAX, 'Paired box' domain	3e-79
smart00351	125	smart00351, PAX, Paired Box domain	1e-78
pfam13384	50	pfam13384, HTH_23, Homeodomain-like domain	1e-05
pfam13565	74	pfam13565, HTH_32, Homeodomain-like domain	4e-05
pfam13551	109	pfam13551, HTH_29, Winged helix-turn helix	2e-04
cd00090	78	cd00090, HTH_ARSR, Arsenical Resistance Operon Rep	7e-04
COG3415	138	COG3415, COG3415, Transposase and inactivated deri	8e-04

>gnl|CDD|238076 cd00131, PAX, Paired Box domain

 Score =  241 bits (617), Expect = 5e-82
 Identities = 103/127 (81%), Positives = 113/127 (88%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
            G VNQLGGVFVNGRPLP+S+R RIVELAQ GIRPCDISRQLRVSHGCVSKIL RY+ETG
Sbjct: 2   QGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETG 61

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PGAIGGSKPRV TP+VV  I+  KQ++PG+FAWEIRDRLL +GVCDK NVPSVSSI+
Sbjct: 62  SIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSIN 121

Query: 152 RILRNKI 158
           RILRNK 
Sbjct: 122 RILRNKA 128

Length = 128

>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain

 Score =  234 bits (599), Expect = 3e-79
 Identities = 97/124 (78%), Positives = 107/124 (86%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
            G VNQLGGVFVNGRPLPN +R +IVELA  G+RPCDISRQLRVSHGCVSKIL RY ETG
Sbjct: 2   QGRVNQLGGVFVNGRPLPNHIRQKIVELAHSGVRPCDISRQLRVSHGCVSKILGRYQETG 61

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PG IGGSKP+V TP+VV  I E K+++PGIFAWEIRDRLL++GVCD  NVPSVSSIS
Sbjct: 62  SIRPGVIGGSKPKVATPEVVKKIAEYKRENPGIFAWEIRDRLLAEGVCDNDNVPSVSSIS 121

Query: 152 RILR 155
           RILR
Sbjct: 122 RILR 125

Length = 125

>gnl|CDD|128645 smart00351, PAX, Paired Box domain

 Score =  232 bits (594), Expect = 1e-78
 Identities = 100/124 (80%), Positives = 110/124 (88%)

Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +G VNQLGGVFVNGRPLP+  R RIVELAQ G+RPCDISRQL VSHGCVSKIL RY+ETG
Sbjct: 2   HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETG 61

Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PGAIGGSKP+V TPKVV  I + KQ++PGIFAWEIRDRLLS+GVCDK NVPSVSSI+
Sbjct: 62  SIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSIN 121

Query: 152 RILR 155
           RILR
Sbjct: 122 RILR 125

Length = 125

>gnl|CDD|222091 pfam13384, HTH_23, Homeodomain-like domain

 Score = 41.1 bits (97), Expect = 1e-05
 Identities = 14/39 (35%), Positives = 19/39 (48%)

Query: 53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
          R  I+ L   G+   +I+  L VS   V + L RY E G
Sbjct: 7  RAEILLLLAEGLSVKEIAELLGVSRRTVYRWLKRYREGG 45

Length = 50

>gnl|CDD|222226 pfam13565, HTH_32, Homeodomain-like domain

 Score = 40.4 bits (95), Expect = 4e-05
 Identities = 14/77 (18%), Positives = 24/77 (31%), Gaps = 6/77 (7%)

Query: 80  VSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIF--AWEIRDRLLSDG 137
           V + L RY E G+       G       P+ +  I     ++P          ++L    
Sbjct: 2   VYRWLKRYREEGAAGLVHRPGRPSNHRYPEELRAIVLTLIREPYADFGPTLAAEKLAELH 61

Query: 138 VCDKFNVPSVSSISRIL 154
                   S  ++ R L
Sbjct: 62  G----LKISRETLRRWL 74

Length = 74

>gnl|CDD|222216 pfam13551, HTH_29, Winged helix-turn helix

 Score = 39.6 bits (93), Expect = 2e-04
 Identities = 25/108 (23%), Positives = 50/108 (46%), Gaps = 7/108 (6%)

Query: 53  RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG--SILPGAIGGSKPRVTTPKV 110
           R + + L   G+    I+R L +S   V + L R++E G  ++      G      +P+ 
Sbjct: 1   RAQALLLLAEGVSVAQIARLLGLSRRTVYRWLKRFNEGGLAALKDRPRSGRPRNRLSPEQ 60

Query: 111 VSYIKEL--KQKDPGIFAWEIRDRLLSDGVCDKFNVP-SVSSISRILR 155
            + +  L  ++   G   W +   LL++ +  +F V  S S++ R+L+
Sbjct: 61  EAALVALAREKPPEGFARWTL--ELLAELLERRFGVTVSRSTVRRLLK 106

This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding. Length = 109

>gnl|CDD|238042 cd00090, HTH_ARSR, Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 12/50 (24%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 45 GRPLPNSVRMRIVE-LAQLGIRPCDISRQLRVSHGCVSKILARYHETGSI 93
           + L +  R+RI+  L +  +   +++ +L +S   VS+ L +  E G +
Sbjct: 1  LKALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLV 50

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions. Length = 78

>gnl|CDD|225949 COG3415, COG3415, Transposase and inactivated derivatives [DNA replication, recombination, and repair]

 Score = 38.5 bits (90), Expect = 8e-04
 Identities = 29/117 (24%), Positives = 55/117 (47%), Gaps = 16/117 (13%)

Query: 45  GRPLPNSVRMRIVEL-AQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKP 103
            +P  N +R R+V+     G+   + +++  VS   V + + RY ETG  LP      +P
Sbjct: 2   AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRP 61

Query: 104 R-VTTPKVVSYIKELKQKDPGIFAW---EIRDRLLSDGVCDKFNVP-SVSSISRILR 155
           R ++  ++   ++ L++KD     W   E+ + L       +F V    S++ R+L 
Sbjct: 62  RKLSEEQLEILLERLREKD-----WTLKELVEELGL-----EFGVWYHASAVRRLLH 108

Length = 138

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	258
KOG3517|consensus	334		100.0
PF00292	125	PAX: 'Paired box' domain; InterPro: IPR001523 The	100.0
cd00131	128	PAX Paired Box domain	99.97
smart00351	125	PAX Paired Box domain.	99.96
KOG3862|consensus	327		99.96
COG3415	138	Transposase and inactivated derivatives [DNA repli	99.71
KOG0849|consensus	354		99.69
PF13551	112	HTH_29: Winged helix-turn helix	99.69
PF01710	119	HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Tr	99.67
PF13565	77	HTH_32: Homeodomain-like domain	99.21
PF13011	85	LZ_Tnp_IS481: leucine-zipper of insertion element	99.03
PF13384	50	HTH_23: Homeodomain-like domain; PDB: 2X48_C.	98.97
PF13518	52	HTH_28: Helix-turn-helix domain	98.88
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	98.53
PRK09413	121	IS2 repressor TnpA; Reviewed	98.44
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	98.42
PF01527	76	HTH_Tnp_1: Transposase; InterPro: IPR002514 Transp	98.4
PF04218	53	CENP-B_N: CENP-B N-terminal DNA-binding domain; In	98.14
PF06056	58	Terminase_5: Putative ATPase subunit of terminase	98.06
COG2826	318	Tra8 Transposase and inactivated derivatives, IS30	97.96
COG2963	116	Transposase and inactivated derivatives [DNA repli	97.93
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	97.93
cd01104	68	HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain	97.7
PRK09409	301	IS2 transposase TnpB; Reviewed	97.69
smart00421	58	HTH_LUXR helix_turn_helix, Lux Regulon. lux regulo	97.62
PHA02517	277	putative transposase OrfB; Reviewed	97.45
PF13542	52	HTH_Tnp_ISL3: Helix-turn-helix domain of transposa	97.44
PF11427	50	HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C	97.4
TIGR02531	88	yecD_yerC TrpR-related protein YerC/YecD. This mod	97.39
cd06171	55	Sigma70_r4 Sigma70, region (SR) 4 refers to the mo	97.35
PF08281	54	Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013	97.28
PF04545	50	Sigma70_r4: Sigma-70, region 4; InterPro: IPR00763	97.26
cd04763	68	HTH_MlrA-like Helix-Turn-Helix DNA binding domain	97.19
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	97.19
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	97.12
cd06170	57	LuxR_C_like C-terminal DNA-binding domain of LuxR-	97.11
cd01105	88	HTH_GlnR-like Helix-Turn-Helix DNA binding domain	97.09
PRK00118	104	putative DNA-binding protein; Validated	97.08
PF13411	69	MerR_1: MerR HTH family regulatory protein; PDB: 2	97.04
cd04762	49	HTH_MerR-trunc Helix-Turn-Helix DNA binding domain	96.99
PF01498	72	HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Tr	96.97
PRK10141	117	DNA-binding transcriptional repressor ArsR; Provis	96.96
PF04552	160	Sigma54_DBD: Sigma-54, DNA binding domain; InterPr	96.92
PF13613	53	HTH_Tnp_4: Helix-turn-helix of DDE superfamily end	96.89
PF14493	91	HTH_40: Helix-turn-helix domain	96.88
cd04764	67	HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding dom	96.88
PHA02535	581	P terminase ATPase subunit; Provisional	96.83
PRK04217	110	hypothetical protein; Provisional	96.8
cd04765	99	HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding dom	96.79
smart00422	70	HTH_MERR helix_turn_helix, mercury resistance.	96.78
PF02796	45	HTH_7: Helix-turn-helix domain of resolvase; Inter	96.75
PF10668	60	Phage_terminase: Phage terminase small subunit; In	96.71
PRK13413	200	mpi multiple promoter invertase; Provisional	96.69
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	96.64
cd04773	108	HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding	96.62
PF09607	58	BrkDBD: Brinker DNA-binding domain; InterPro: IPR0	96.59
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	96.57
PF12759	46	HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR	96.56
PF07037	122	DUF1323: Putative transcription regulator (DUF1323	96.51
TIGR02395	429	rpoN_sigma RNA polymerase sigma-54 factor. A sigma	96.5
PF13309	64	HTH_22: HTH domain	96.5
PRK15418	318	transcriptional regulator LsrR; Provisional	96.48
cd04774	96	HTH_YfmP Helix-Turn-Helix DNA binding domain of th	96.48
PF05225	45	HTH_psq: helix-turn-helix, Psq domain; InterPro: I	96.47
PF00325	32	Crp: Bacterial regulatory proteins, crp family; In	96.45
TIGR01321	94	TrpR trp operon repressor, proteobacterial. This m	96.45
cd04761	49	HTH_MerR-SF Helix-Turn-Helix DNA binding domain of	96.44
TIGR03879	73	near_KaiC_dom probable regulatory domain. This mod	96.44
COG1725	125	Predicted transcriptional regulators [Transcriptio	96.38
cd01109	113	HTH_YyaN Helix-Turn-Helix DNA binding domain of th	96.32
cd04770	123	HTH_HMRTR Helix-Turn-Helix DNA binding domain of H	96.31
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	96.3
cd01106	103	HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain	96.29
PRK05932	455	RNA polymerase factor sigma-54; Reviewed	96.26
PHA02591	83	hypothetical protein; Provisional	96.25
TIGR00721	137	tfx DNA-binding protein, Tfx family. Tfx from Meth	96.23
PRK06759	154	RNA polymerase factor sigma-70; Validated	96.21
PF02954	42	HTH_8: Bacterial regulatory protein, Fis family; I	96.15
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	96.14
cd00592	100	HTH_MerR-like Helix-Turn-Helix DNA binding domain	96.1
cd04782	97	HTH_BltR Helix-Turn-Helix DNA binding domain of th	96.1
cd01279	98	HTH_HspR-like Helix-Turn-Helix DNA binding domain	96.09
cd04767	120	HTH_HspR-like_MBC Helix-Turn-Helix DNA binding dom	96.08
PF01371	87	Trp_repressor: Trp repressor protein; InterPro: IP	96.07
PRK09642	160	RNA polymerase sigma factor SigW; Reviewed	96.06
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	96.03
cd04783	126	HTH_MerR1 Helix-Turn-Helix DNA binding domain of t	96.02
PRK12469	481	RNA polymerase factor sigma-54; Provisional	96.01
TIGR01529	146	argR_whole arginine repressor. This model includes	96.0
cd01108	127	HTH_CueR Helix-Turn-Helix DNA binding domain of Cu	96.0
PRK11050	152	manganese transport regulator MntR; Provisional	96.0
PF06163	127	DUF977: Bacterial protein of unknown function (DUF	95.97
PRK09652	182	RNA polymerase sigma factor RpoE; Provisional	95.97
PRK09639	166	RNA polymerase sigma factor SigX; Provisional	95.94
cd04768	96	HTH_BmrR-like Helix-Turn-Helix DNA binding domain	95.94
TIGR02937	158	sigma70-ECF RNA polymerase sigma factor, sigma-70	95.94
PRK12537	182	RNA polymerase sigma factor; Provisional	95.93
PF08822	165	DUF1804: Protein of unknown function (DUF1804); In	95.93
PRK09047	161	RNA polymerase factor sigma-70; Validated	95.92
TIGR02044	127	CueR Cu(I)-responsive transcriptional regulator. T	95.92
PF12728	51	HTH_17: Helix-turn-helix domain	95.9
TIGR02989	159	Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodop	95.89
PRK11924	179	RNA polymerase sigma factor; Provisional	95.89
COG1508	444	RpoN DNA-directed RNA polymerase specialized sigma	95.89
cd04788	96	HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain	95.89
PHA00675	78	hypothetical protein	95.88
cd04766	91	HTH_HspR Helix-Turn-Helix DNA binding domain of th	95.86
TIGR02985	161	Sig70_bacteroi1 RNA polymerase sigma-70 factor, Ba	95.86
cd04780	95	HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding dom	95.86
TIGR01764	49	excise DNA binding domain, excisionase family. An	95.85
cd04787	133	HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain	95.85
PF00356	46	LacI: Bacterial regulatory proteins, lacI family;	95.85
PF00196	58	GerE: Bacterial regulatory proteins, luxR family;	95.85
TIGR02844	80	spore_III_D sporulation transcriptional regulator	95.81
TIGR02999	183	Sig-70_X6 RNA polymerase sigma factor, TIGR02999 f	95.79
cd04772	99	HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding d	95.77
PF01316	70	Arg_repressor: Arginine repressor, DNA binding dom	95.77
PHA00738	108	putative HTH transcription regulator	95.75
cd01110	139	HTH_SoxR Helix-Turn-Helix DNA binding domain of th	95.73
PRK12514	179	RNA polymerase sigma factor; Provisional	95.72
PRK13919	186	putative RNA polymerase sigma E protein; Provision	95.71
PRK12528	161	RNA polymerase sigma factor; Provisional	95.69
cd04789	102	HTH_Cfa Helix-Turn-Helix DNA binding domain of the	95.68
cd01282	112	HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding dom	95.65
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.64
COG1595	182	RpoE DNA-directed RNA polymerase specialized sigma	95.63
TIGR02043	131	ZntR Zn(II)-responsive transcriptional regulator.	95.61
TIGR02983	162	SigE-fam_strep RNA polymerase sigma-70 factor, sig	95.61
TIGR02952	170	Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02	95.6
PF07900	220	DUF1670: Protein of unknown function (DUF1670); In	95.57
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.57
cd01111	107	HTH_MerD Helix-Turn-Helix DNA binding domain of th	95.56
PRK01381	99	Trp operon repressor; Provisional	95.56
cd04784	127	HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain	95.55
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	95.54
cd04775	102	HTH_Cfa-like Helix-Turn-Helix DNA binding domain o	95.53
PRK03975	141	tfx putative transcriptional regulator; Provisiona	95.52
PRK09514	140	zntR zinc-responsive transcriptional regulator; Pr	95.51
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	95.5
TIGR02960	324	SigX5 RNA polymerase sigma-70 factor, TIGR02960 fa	95.5
PRK08241	339	RNA polymerase factor sigma-70; Validated	95.49
TIGR02047	127	CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional	95.48
PRK07037	163	extracytoplasmic-function sigma-70 factor; Validat	95.47
cd04786	131	HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding dom	95.46
PRK12519	194	RNA polymerase sigma factor; Provisional	95.46
cd04785	126	HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding do	95.44
PRK12547	164	RNA polymerase sigma factor; Provisional	95.44
PRK09644	165	RNA polymerase sigma factor SigM; Provisional	95.43
PRK12525	168	RNA polymerase sigma factor; Provisional	95.4
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.39
PRK12530	189	RNA polymerase sigma factor; Provisional	95.38
PRK12529	178	RNA polymerase sigma factor; Provisional	95.36
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	95.36
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	95.35
PRK09645	173	RNA polymerase sigma factor SigL; Provisional	95.32
PRK15043	243	transcriptional regulator MirA; Provisional	95.31
TIGR02957	281	SigX4 RNA polymerase sigma-70 factor, TIGR02957 fa	95.31
PRK09648	189	RNA polymerase sigma factor SigD; Reviewed	95.31
PRK10046	225	dpiA two-component response regulator DpiA; Provis	95.31
TIGR03209	142	P21_Cbot clostridium toxin-associated regulator Bo	95.29
PRK12516	187	RNA polymerase sigma factor; Provisional	95.27
PF12116	82	SpoIIID: Stage III sporulation protein D; InterPro	95.26
cd01107	108	HTH_BmrR Helix-Turn-Helix DNA binding domain of th	95.24
PRK09649	185	RNA polymerase sigma factor SigC; Reviewed	95.23
PRK12532	195	RNA polymerase sigma factor; Provisional	95.22
PRK12523	172	RNA polymerase sigma factor; Reviewed	95.22
PRK09415	179	RNA polymerase factor sigma C; Reviewed	95.21
PRK12522	173	RNA polymerase sigma factor; Provisional	95.2
TIGR02959	170	SigZ RNA polymerase sigma factor, SigZ family. Thi	95.17
PRK12536	181	RNA polymerase sigma factor; Provisional	95.16
TIGR02054	120	MerD mercuric resistence transcriptional repressor	95.15
PRK12520	191	RNA polymerase sigma factor; Provisional	95.14
cd04769	116	HTH_MerR2 Helix-Turn-Helix DNA binding domain of M	95.14
PRK05602	186	RNA polymerase sigma factor; Reviewed	95.13
TIGR02954	169	Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02	95.13
PF07638	185	Sigma70_ECF: ECF sigma factor	95.09
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	95.08
PRK09646	194	RNA polymerase sigma factor SigK; Reviewed	95.08
PF04297	101	UPF0122: Putative helix-turn-helix protein, YlxM /	95.07
PRK12512	184	RNA polymerase sigma factor; Provisional	95.05
PRK12511	182	RNA polymerase sigma factor; Provisional	95.05
PRK13749	121	transcriptional regulator MerD; Provisional	95.04
TIGR02947	193	SigH_actino RNA polymerase sigma-70 factor, TIGR02	95.03
PRK06811	189	RNA polymerase factor sigma-70; Validated	95.03
TIGR03001	244	Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxoco	95.03
PRK12539	184	RNA polymerase sigma factor; Provisional	95.02
PF04967	53	HTH_10: HTH DNA binding domain; InterPro: IPR00705	95.02
smart00342	84	HTH_ARAC helix_turn_helix, arabinose operon contro	95.01
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	95.01
PRK08301	234	sporulation sigma factor SigE; Reviewed	95.01
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	95.01
PRK13182	175	racA polar chromosome segregation protein; Reviewe	94.99
COG2390	321	DeoR Transcriptional regulator, contains sigma fac	94.98
PHA00542	82	putative Cro-like protein	94.96
PRK12534	187	RNA polymerase sigma factor; Provisional	94.95
PRK09637	181	RNA polymerase sigma factor SigZ; Provisional	94.95
PRK09647	203	RNA polymerase sigma factor SigE; Reviewed	94.93
PRK12524	196	RNA polymerase sigma factor; Provisional	94.92
PRK12526	206	RNA polymerase sigma factor; Provisional	94.92
PRK12540	182	RNA polymerase sigma factor; Provisional	94.89
TIGR02980	227	SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G	94.89
PRK12543	179	RNA polymerase sigma factor; Provisional	94.89
PRK12517	188	RNA polymerase sigma factor; Provisional	94.88
TIGR02051	124	MerR Hg(II)-responsive transcriptional regulator.	94.88
PRK06986	236	fliA flagellar biosynthesis sigma factor; Validate	94.88
COG0789	124	SoxR Predicted transcriptional regulators [Transcr	94.87
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.86
PRK12542	185	RNA polymerase sigma factor; Provisional	94.86
PRK12527	159	RNA polymerase sigma factor; Reviewed	94.85
PRK12533	216	RNA polymerase sigma factor; Provisional	94.85
TIGR02948	187	SigW_bacill RNA polymerase sigma-W factor. This si	94.84
TIGR01950	142	SoxR redox-sensitive transcriptional activator Sox	94.84
PRK12545	201	RNA polymerase sigma factor; Provisional	94.81
PRK10227	135	DNA-binding transcriptional regulator CueR; Provis	94.81
PRK09636	293	RNA polymerase sigma factor SigJ; Provisional	94.81
TIGR02984	189	Sig-70_plancto1 RNA polymerase sigma-70 factor, Pl	94.8
PRK06704	228	RNA polymerase factor sigma-70; Validated	94.79
PRK08583	257	RNA polymerase sigma factor SigB; Validated	94.78
PRK06930	170	positive control sigma-like factor; Validated	94.74
PF12298	172	Bot1p: Eukaryotic mitochondrial regulator protein	94.74
PF02001	106	DUF134: Protein of unknown function DUF134; InterP	94.74
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	94.71
TIGR02479	224	FliA_WhiG RNA polymerase sigma factor, FliA/WhiG f	94.71
COG1438	150	ArgR Arginine repressor [Transcription]	94.7
PRK09863	584	putative frv operon regulatory protein; Provisiona	94.64
PRK12531	194	RNA polymerase sigma factor; Provisional	94.63
PF13730	55	HTH_36: Helix-turn-helix domain	94.62
PRK12541	161	RNA polymerase sigma factor; Provisional	94.61
cd04777	107	HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding dom	94.6
PRK11923	193	algU RNA polymerase sigma factor AlgU; Provisional	94.59
PRK09640	188	RNA polymerase sigma factor SigX; Reviewed	94.58
TIGR02943	188	Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02	94.57
PRK11414	221	colanic acid/biofilm transcriptional regulator; Pr	94.57
PF04703	62	FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.	94.56
PRK03341	168	arginine repressor; Provisional	94.55
PRK12515	189	RNA polymerase sigma factor; Provisional	94.55
PRK15002	154	redox-sensitivie transcriptional activator SoxR; P	94.54
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	94.54
PRK15201	198	fimbriae regulatory protein FimW; Provisional	94.52
PRK11179	153	DNA-binding transcriptional regulator AsnC; Provis	94.5
PRK09638	176	RNA polymerase sigma factor SigY; Reviewed	94.5
TIGR02939	190	RpoE_Sigma70 RNA polymerase sigma factor RpoE. A s	94.5
PRK12544	206	RNA polymerase sigma factor; Provisional	94.49
PRK09635	290	sigI RNA polymerase sigma factor SigI; Provisional	94.49
TIGR02702	203	SufR_cyano iron-sulfur cluster biosynthesis transc	94.48
cd04779	134	HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding dom	94.47
PF01381	55	HTH_3: Helix-turn-helix; InterPro: IPR001387 This	94.47
PHA01976	67	helix-turn-helix protein	94.44
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	94.44
PRK05066	156	arginine repressor; Provisional	94.42
PRK10840	216	transcriptional regulator RcsB; Provisional	94.39
PF08765	108	Mor: Mor transcription activator family; InterPro:	94.39
PRK12513	194	RNA polymerase sigma factor; Provisional	94.38
TIGR02950	154	SigM_subfam RNA polymerase sigma factor, SigM fami	94.37
cd04781	120	HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding dom	94.37
PRK12546	188	RNA polymerase sigma factor; Provisional	94.35
PRK09651	172	RNA polymerase sigma factor FecI; Provisional	94.35
TIGR02859	198	spore_sigH RNA polymerase sigma-H factor. Members	94.35
PRK12538	233	RNA polymerase sigma factor; Provisional	94.34
PRK15411	207	rcsA colanic acid capsular biosynthesis activation	94.33
cd04790	172	HTH_Cfa-like_unk Helix-Turn-Helix DNA binding doma	94.32
PRK06474	178	hypothetical protein; Provisional	94.31
TIGR03338	212	phnR_burk phosphonate utilization associated trans	94.26
PRK11169	164	leucine-responsive transcriptional regulator; Prov	94.25
PRK12535	196	RNA polymerase sigma factor; Provisional	94.24
PRK04280	148	arginine repressor; Provisional	94.21
TIGR02835	234	spore_sigmaE RNA polymerase sigma-E factor. Member	94.18
PRK09641	187	RNA polymerase sigma factor SigW; Provisional	94.16
cd04776	118	HTH_GnyR Helix-Turn-Helix DNA binding domain of th	94.15
COG3355	126	Predicted transcriptional regulator [Transcription	94.15
PF05344	65	DUF746: Domain of Unknown Function (DUF746); Inter	94.14
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	94.13
PF07750	162	GcrA: GcrA cell cycle regulator; InterPro: IPR0116	94.1
PF11198	180	DUF2857: Protein of unknown function (DUF2857); In	94.08
COG2964	220	Uncharacterized protein conserved in bacteria [Fun	94.05
PF05930	51	Phage_AlpA: Prophage CP4-57 regulatory protein (Al	93.96
COG3677	129	Transposase and inactivated derivatives [DNA repli	93.96
TIGR03070	58	couple_hipB transcriptional regulator, y4mF family	93.92
COG2512	258	Predicted membrane-associated trancriptional regul	93.89
PRK05803	233	sporulation sigma factor SigK; Reviewed	93.87
COG1710	139	Uncharacterized protein conserved in archaea [Func	93.85
PF13565	77	HTH_32: Homeodomain-like domain	93.84
TIGR02297	287	HpaA 4-hydroxyphenylacetate catabolism regulatory	93.83
PRK04984	239	fatty acid metabolism regulator; Provisional	93.82
COG1321	154	TroR Mn-dependent transcriptional regulator [Trans	93.79
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	93.78
TIGR02885	231	spore_sigF RNA polymerase sigma-F factor. Members	93.77
PRK07408	256	RNA polymerase sigma factor SigF; Reviewed	93.74
PRK09954	362	putative kinase; Provisional	93.66
TIGR02941	255	Sigma_B RNA polymerase sigma-B factor. This sigma	93.63
PRK13509	251	transcriptional repressor UlaR; Provisional	93.62
PRK11303	328	DNA-binding transcriptional regulator FruR; Provis	93.57
PRK07670	251	RNA polymerase sigma factor SigD; Validated	93.55
PRK08295	208	RNA polymerase factor sigma-70; Validated	93.55
PRK05572	252	sporulation sigma factor SigF; Validated	93.55
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	93.52
PRK01905	77	DNA-binding protein Fis; Provisional	93.5
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	93.5
PRK00441	149	argR arginine repressor; Provisional	93.49
PRK05911	257	RNA polymerase sigma factor sigma-28; Reviewed	93.43
COG0735	145	Fur Fe2+/Zn2+ uptake regulation proteins [Inorgani	93.4
PRK11608	326	pspF phage shock protein operon transcriptional ac	93.32
smart00354	70	HTH_LACI helix_turn _helix lactose operon represso	93.32
PRK09191	261	two-component response regulator; Provisional	93.27
PF13936	44	HTH_38: Helix-turn-helix domain; PDB: 2W48_A.	93.27
TIGR02325	238	C_P_lyase_phnF phosphonates metabolism transcripti	93.23
PRK13503	278	transcriptional activator RhaS; Provisional	93.2
TIGR02337	118	HpaR homoprotocatechuate degradation operon regula	93.17
PRK09483	217	response regulator; Provisional	93.14
PRK12518	175	RNA polymerase sigma factor; Provisional	93.13
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	93.1
PRK10430	239	DNA-binding transcriptional activator DcuR; Provis	93.09
cd07153	116	Fur_like Ferric uptake regulator(Fur) and related	93.08
PRK06288	268	RNA polymerase sigma factor WhiG; Reviewed	93.08
PF13443	63	HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3	93.07
PRK10906	252	DNA-binding transcriptional repressor GlpR; Provis	93.05
PRK09643	192	RNA polymerase sigma factor SigM; Reviewed	93.02
PRK14999	241	histidine utilization repressor; Provisional	93.0
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	93.0
PRK13752	144	putative transcriptional regulator MerR; Provision	92.95
PHA02943	165	hypothetical protein; Provisional	92.95
PRK12427	231	flagellar biosynthesis sigma factor; Provisional	92.95
PRK11014	141	transcriptional repressor NsrR; Provisional	92.94
COG2345	218	Predicted transcriptional regulator [Transcription	92.94
PRK10703	341	DNA-binding transcriptional repressor PurR; Provis	92.93
COG1654	79	BirA Biotin operon repressor [Transcription]	92.89
PF07374	100	DUF1492: Protein of unknown function (DUF1492); In	92.87
TIGR02607	78	antidote_HigA addiction module antidote protein, H	92.86
PRK07122	264	RNA polymerase sigma factor SigF; Reviewed	92.85
TIGR02846	227	spore_sigmaK RNA polymerase sigma-K factor. The sp	92.85
PRK08215	258	sporulation sigma factor SigG; Reviewed	92.84
PF10654	126	DUF2481: Protein of unknown function (DUF2481) ; I	92.84
PRK09480	194	slmA division inhibitor protein; Provisional	92.83
COG1522	154	Lrp Transcriptional regulators [Transcription]	92.83
PRK11475	207	DNA-binding transcriptional activator BglJ; Provis	92.79
COG2771	65	CsgD DNA-binding HTH domain-containing proteins [T	92.77
TIGR02404	233	trehalos_R_Bsub trehalose operon repressor, B. sub	92.76
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	92.75
COG2197	211	CitB Response regulator containing a CheY-like rec	92.75
PRK11534	224	DNA-binding transcriptional regulator CsiR; Provis	92.74
COG5484	279	Uncharacterized conserved protein [Function unknow	92.73
COG3398	240	Uncharacterized protein conserved in archaea [Func	92.67
smart00529	96	HTH_DTXR Helix-turn-helix diphteria tox regulatory	92.66
PRK10100	216	DNA-binding transcriptional regulator CsgD; Provis	92.63
COG1802	230	GntR Transcriptional regulators [Transcription]	92.61
PRK00430	95	fis global DNA-binding transcriptional dual regula	92.57
PF08535	93	KorB: KorB domain; InterPro: IPR013741 This entry	92.56
PF13022	142	HTH_Tnp_1_2: Helix-turn-helix of insertion element	92.54
PF13592	60	HTH_33: Winged helix-turn helix	92.52
PRK09492	315	treR trehalose repressor; Provisional	92.51
PRK10572	290	DNA-binding transcriptional regulator AraC; Provis	92.49
PF07141	174	Phage_term_sma: Putative bacteriophage terminase s	92.49
PRK11402	241	DNA-binding transcriptional regulator FrlR; Provis	92.43
cd04778	219	HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding dom	92.42
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	92.38
PRK13719	217	conjugal transfer transcriptional regulator TraJ;	92.35
COG2188	236	PhnF Transcriptional regulators [Transcription]	92.33
PRK09764	240	DNA-binding transcriptional repressor MngR; Provis	92.3
COG2207	127	AraC AraC-type DNA-binding domain-containing prote	92.3
TIGR01636	134	phage_rinA phage transcriptional activator, RinA f	92.3
TIGR02018	230	his_ut_repres histidine utilization repressor, pro	92.27
PRK11512	144	DNA-binding transcriptional repressor MarR; Provis	92.27
PRK10079	241	phosphonate metabolism transcriptional regulator P	92.25
PRK09726	88	antitoxin HipB; Provisional	92.25
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	92.24
PRK10014	342	DNA-binding transcriptional repressor MalI; Provis	92.14
PRK10072	96	putative transcriptional regulator; Provisional	92.11
PF03444	78	HrcA_DNA-bdg: Winged helix-turn-helix transcriptio	92.11
PF01475	120	FUR: Ferric uptake regulator family; InterPro: IPR	92.08
PRK11922	231	RNA polymerase sigma factor; Provisional	92.07
TIGR02405	311	trehalos_R_Ecol trehalose operon repressor, proteo	92.06
PRK15369	211	two component system sensor kinase SsrB; Provision	91.98
PRK10411	240	DNA-binding transcriptional activator FucR; Provis	91.91
PF13404	42	HTH_AsnC-type: AsnC-type helix-turn-helix domain;	91.91
TIGR02394	285	rpoS_proteo RNA polymerase sigma factor RpoS. A si	91.91
PRK11523	253	DNA-binding transcriptional repressor ExuR; Provis	91.89
PRK10339	327	DNA-binding transcriptional repressor EbgR; Provis	91.83
TIGR02850	254	spore_sigG RNA polymerase sigma-G factor. Members	91.77
PF00126	60	HTH_1: Bacterial regulatory helix-turn-helix prote	91.76
PRK09526	342	lacI lac repressor; Reviewed	91.73
PRK10651	216	transcriptional regulator NarL; Provisional	91.7
TIGR02392	270	rpoH_proteo alternative sigma factor RpoH. A sigma	91.66
COG2522	119	Predicted transcriptional regulator [General funct	91.64
PRK10434	256	srlR DNA-bindng transcriptional repressor SrlR; Pr	91.61
PRK11361	457	acetoacetate metabolism regulatory protein AtoC; P	91.6
TIGR02393	238	RpoD_Cterm RNA polymerase sigma factor RpoD, C-ter	91.56
TIGR03020	247	EpsA transcriptional regulator EpsA. Proteins in t	91.56
PRK09791	302	putative DNA-binding transcriptional regulator; Pr	91.54
PRK09393	322	ftrA transcriptional activator FtrA; Provisional	91.48
PRK10225	257	DNA-binding transcriptional repressor UxuR; Provis	91.47
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	91.46
PF13601	80	HTH_34: Winged helix DNA-binding domain; PDB: 1UB9	91.39
PRK13502	282	transcriptional activator RhaR; Provisional	91.38
PRK10727	343	DNA-binding transcriptional regulator GalR; Provis	91.36
PRK13501	290	transcriptional activator RhaR; Provisional	91.33
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	91.32
PRK10401	346	DNA-binding transcriptional regulator GalS; Provis	91.28
TIGR03697	193	NtcA_cyano global nitrogen regulator NtcA, cyanoba	91.23
COG1191	247	FliA DNA-directed RNA polymerase specialized sigma	91.23
PRK15320	251	transcriptional activator SprB; Provisional	91.2
PF12844	64	HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_	91.18
PRK10371	302	DNA-binding transcriptional regulator MelR; Provis	91.15
PRK03837	241	transcriptional regulator NanR; Provisional	91.1
PF05263	130	DUF722: Protein of unknown function (DUF722); Inte	91.04
PRK12682	309	transcriptional regulator CysB-like protein; Revie	91.03
PRK09462	148	fur ferric uptake regulator; Provisional	90.99
TIGR02417	327	fruct_sucro_rep D-fructose-responsive transcriptio	90.98
PRK09464	254	pdhR transcriptional regulator PdhR; Reviewed	90.93
COG2186	241	FadR Transcriptional regulators [Transcription]	90.84
PRK09706	135	transcriptional repressor DicA; Reviewed	90.84
PRK15481	431	transcriptional regulatory protein PtsJ; Provision	90.81
TIGR02915	445	PEP_resp_reg putative PEP-CTERM system response re	90.79
PF13551	112	HTH_29: Winged helix-turn helix	90.78
PRK14987	331	gluconate operon transcriptional regulator; Provis	90.71
PRK00215	205	LexA repressor; Validated	90.71
PRK11639	169	zinc uptake transcriptional repressor; Provisional	90.63
PRK03573	144	transcriptional regulator SlyA; Provisional	90.57
COG1476	68	Predicted transcriptional regulators [Transcriptio	90.5
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	90.46
TIGR03541	232	reg_near_HchA LuxR family transcriptional regulato	90.45
TIGR02997	298	Sig70-cyanoRpoD RNA polymerase sigma factor, cyano	90.44
cd00093	58	HTH_XRE Helix-turn-helix XRE-family like proteins.	90.43
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	90.41
PRK09990	251	DNA-binding transcriptional regulator GlcC; Provis	90.33
cd06571	90	Bac_DnaA_C C-terminal domain of bacterial DnaA pro	90.26
smart00530	56	HTH_XRE Helix-turn-helix XRE-family like proteins.	90.24
PRK09978	274	DNA-binding transcriptional regulator GadX; Provis	90.22
PF13560	64	HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_	90.16
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	90.13
PRK12423	202	LexA repressor; Provisional	90.03
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	90.0
PRK03902	142	manganese transport transcriptional regulator; Pro	89.97
PF13744	80	HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_	89.97
PRK10820	520	DNA-binding transcriptional regulator TyrR; Provis	89.94
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	89.93
PRK15115	444	response regulator GlrR; Provisional	89.88
TIGR02787	251	codY_Gpos GTP-sensing transcriptional pleiotropic	89.83
TIGR02812	235	fadR_gamma fatty acid metabolism transcriptional r	89.8
PRK13918	202	CRP/FNR family transcriptional regulator; Provisio	89.79
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	89.78
TIGR01481	329	ccpA catabolite control protein A. Catabolite cont	89.78
PRK11569	274	transcriptional repressor IclR; Provisional	89.77
COG1349	253	GlpR Transcriptional regulators of sugar metabolis	89.75
PF12793	115	SgrR_N: Sugar transport-related sRNA regulator N-t	89.66
TIGR00637	99	ModE_repress ModE molybdate transport repressor do	89.63
cd01392	52	HTH_LacI Helix-turn-helix (HTH) DNA binding domain	89.63
PRK10403	215	transcriptional regulator NarP; Provisional	89.55
PRK10421	253	DNA-binding transcriptional repressor LldR; Provis	89.53
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	89.47
TIGR02974	329	phageshock_pspF psp operon transcriptional activat	89.46
PRK10360	196	DNA-binding transcriptional activator UhpA; Provis	89.45
cd00569	42	HTH_Hin_like Helix-turn-helix domain of Hin and re	89.45
PRK10188	240	DNA-binding transcriptional activator SdiA; Provis	89.4
COG1846	126	MarR Transcriptional regulators [Transcription]	89.39
PRK07500	289	rpoH2 RNA polymerase factor sigma-32; Reviewed	89.38
PRK11753	211	DNA-binding transcriptional dual regulator Crp; Pr	89.37
PRK11388	638	DNA-binding transcriptional regulator DhaR; Provis	89.29
COG3413	215	Predicted DNA binding protein [General function pr	89.19
PRK11013	309	DNA-binding transcriptional regulator LysR; Provis	89.16
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	89.15
COG2973	103	TrpR Trp operon repressor [Transcription]	88.98
PRK15185	309	transcriptional regulator HilD; Provisional	88.95
PRK15424	538	propionate catabolism operon regulatory protein Pr	88.86
COG1342	99	Predicted DNA-binding proteins [General function p	88.83
TIGR01884	203	cas_HTH CRISPR locus-related DNA-binding protein.	88.82
PRK05657	325	RNA polymerase sigma factor RpoS; Validated	88.82
PRK10423	327	transcriptional repressor RbsR; Provisional	88.81
PF14549	60	P22_Cro: DNA-binding transcriptional regulator Cro	88.74
PRK11161	235	fumarate/nitrate reduction transcriptional regulat	88.7
PRK11169	164	leucine-responsive transcriptional regulator; Prov	88.65
PF04645	181	DUF603: Protein of unknown function, DUF603; Inter	88.58
COG3311	70	AlpA Predicted transcriptional regulator [Transcri	88.57
smart00352	75	POU Found in Pit-Oct-Unc transcription factors.	88.44
PRK13870	234	transcriptional regulator TraR; Provisional	88.4
TIGR00498	199	lexA SOS regulatory protein LexA. LexA acts as a h	88.39
PRK10870	176	transcriptional repressor MprA; Provisional	88.36
PRK13777	185	transcriptional regulator Hpr; Provisional	88.35
PRK13500	312	transcriptional activator RhaR; Provisional	88.26
PF12833	81	HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_	88.15
PRK13890	120	conjugal transfer protein TrbA; Provisional	88.15
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	88.12
PRK10923	469	glnG nitrogen regulation protein NR(I); Provisiona	88.1
PRK04424	185	fatty acid biosynthesis transcriptional regulator;	88.03
COG1609	333	PurR Transcriptional regulators [Transcription]	87.94
TIGR01818	463	ntrC nitrogen regulation protein NR(I). This model	87.92
PF00376	38	MerR: MerR family regulatory protein; InterPro: IP	87.86
PRK11886	319	bifunctional biotin--[acetyl-CoA-carboxylase] synt	87.84
PRK15121	289	right oriC-binding transcriptional activator; Prov	87.8
COG4565	224	CitB Response regulator of citrate/malate metaboli	87.77
PF09862	113	DUF2089: Protein of unknown function (DUF2089); In	87.76
PRK10402	226	DNA-binding transcriptional activator YeiL; Provis	87.76
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	87.75
PRK15186	291	AraC family transcriptional regulator; Provisional	87.62
COG5352	169	Uncharacterized protein conserved in bacteria [Fun	87.55
PRK11139	297	DNA-binding transcriptional activator GcvA; Provis	87.55
TIGR02424	300	TF_pcaQ pca operon transcription factor PcaQ. Memb	87.52
COG1961	222	PinR Site-specific recombinases, DNA invertase Pin	87.46
PRK14165	217	winged helix-turn-helix domain-containing protein/	87.45
PRK09802	269	DNA-binding transcriptional regulator AgaR; Provis	87.42
COG1414	246	IclR Transcriptional regulator [Transcription]	87.42

>KOG3517|consensus

Probab=100.00  E-value=1.6e-45  Score=331.36  Aligned_cols=194  Identities=70%  Similarity=1.093  Sum_probs=179.4

Q ss_pred             CCCCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC
Q psy15598         28 SGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT  107 (258)
Q Consensus        28 ~~~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT  107 (258)
                      |+++|||||||||||||||++++++|.|||+|.+.|...|+|+|+|.||..||+||+.||.|+|++.|+.++|++||++|
T Consensus         1 ~~~~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTT   80 (334)
T KOG3517|consen    1 MEPSYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTT   80 (334)
T ss_pred             CCccccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCC
Confidence            68899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCCCCC---------CCCCCCCCC
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHP---------HIYNSIYPS  178 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~~~~---------~~~~~~~~~  178 (258)
                      +.++++|+.+++.+|.+++|||+|+|+++|+|++++++|+|+|+|+||++.+.+-+++.|+.         +.||.+|. 
T Consensus        81 P~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSSISRILRNKiGsLaqqg~y~t~kqp~~qpslpyN~~~~-  159 (334)
T KOG3517|consen   81 PKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSSISRILRNKIGSLAQQGTYGTVKQPSGQPSLPYNGGYS-  159 (334)
T ss_pred             hhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHHHHHHHHhhhcccccCCCcccccCCCCCCCccCCCCcc-
Confidence            99999999999999999999999999999999999999999999999999999999998874         78999875 


Q ss_pred             CCCCCCCCCCccCCCCCCCCCCCCC----CCCCCCCCCcchhhhhhccCC
Q psy15598        179 YPYPSNTSPTVSCTKVPIGSLTPPP----RPQVCWPSSHSVTDILSAAAG  224 (258)
Q Consensus       179 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~  224 (258)
                      |+++.+...  ...+++.++++|..    ..+.+||++|||++|||+++=
T Consensus       160 ~~~ss~~~~--~~a~~~~~~g~p~~~~h~~~~qswpsahSv~~ilgir~~  207 (334)
T KOG3517|consen  160 YPSSSSQNI--NLAKIGDPPGVPQQPGHVQQHQSWPSAHSVHHILGIRAY  207 (334)
T ss_pred             CCCCCccch--hhhhcCCCCCCCCCccccccccccccccchhhhhHHHHH
Confidence            666554443  37788888887764    678999999999999997653

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

Probab=100.00  E-value=6.5e-35  Score=240.02  Aligned_cols=125  Identities=76%  Similarity=1.261  Sum_probs=100.0

Q ss_pred             CcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH
Q psy15598         31 QYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV  110 (258)
Q Consensus        31 ~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~  110 (258)
                      ++++||||||+|+|||+|+.++|.+||+|+++|++.++||++|.||++||+||++||+|||++.|+..+|++|++.++++
T Consensus         1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v   80 (125)
T PF00292_consen    1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEV   80 (125)
T ss_dssp             S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCH
T ss_pred             CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHH
Confidence            35889999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILR  155 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLr  155 (258)
                      +.+|.+++.+||.+++|||+++|.++|+|..+++||.|+|+|+||
T Consensus        81 ~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRilr  125 (125)
T PF00292_consen   81 VEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRILR  125 (125)
T ss_dssp             HHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred             HHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhhC
Confidence            999999999999999999999999999999999999999999997

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

>cd00131 PAX Paired Box domain

Probab=99.97  E-value=3.7e-31  Score=217.98  Aligned_cols=125  Identities=82%  Similarity=1.295  Sum_probs=118.9

Q ss_pred             chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      +++||+||+|+|+++||.|+|.+||+++++|++.++||++|+||++||++|+++|+++|++.|++++|.+|++++++.+.
T Consensus         3 ~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~   82 (128)
T cd00131           3 GGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVK   82 (128)
T ss_pred             ccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHH
Confidence            57999999999999999999999999999999999999999999999999999999999999999888678988998889


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598        113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      +|+++++++|++|++||++.|.+.|++++.+.||.|||+|+|+++
T Consensus        83 ~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~  127 (128)
T cd00131          83 KIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK  127 (128)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence            999999999999999999999888998888889999999999975

>smart00351 PAX Paired Box domain

Probab=99.96  E-value=3.6e-29  Score=204.97  Aligned_cols=124  Identities=81%  Similarity=1.256  Sum_probs=118.5

Q ss_pred             cchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHH
Q psy15598         32 YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVV  111 (258)
Q Consensus        32 ~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~  111 (258)
                      ..++||+||.|+|+++||.|+|.+||.++++|++.++||++||||++||++|+++|+++|.+.|++++|.+|+++++++.
T Consensus         2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~   81 (125)
T smart00351        2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV   81 (125)
T ss_pred             CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence            46799999999999999999999999999999999999999999999999999999999999999888778999999999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598        112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILR  155 (258)
Q Consensus       112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLr  155 (258)
                      .+|+++++++|+++++||++.|.+.|+++..+.||.|||+|+|+
T Consensus        82 ~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~  125 (125)
T smart00351       82 KKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR  125 (125)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence            99999999999999999999999999998899999999999985

>KOG3862|consensus

Probab=99.96  E-value=6.1e-29  Score=225.98  Aligned_cols=179  Identities=58%  Similarity=0.879  Sum_probs=156.5

Q ss_pred             CCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598         30 QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK  109 (258)
Q Consensus        30 ~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e  109 (258)
                      -++++||||||||||||+++..+|.+|++|+++|...++|+++|.||..||++++-||.|+|+++++..+|++|++.++.
T Consensus         8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~   87 (327)
T KOG3862|consen    8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPK   87 (327)
T ss_pred             CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccch
Confidence            37899999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTV  189 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  189 (258)
                      +++.|..++++||.+++||||++|.++++|..++++|++.|+|++|++...+.....+...             ......
T Consensus        88 Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~~~s~v-------------sk~l~~  154 (327)
T KOG3862|consen   88 VVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGITHSCV-------------TKVLAR  154 (327)
T ss_pred             HHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccCCccchh-------------hccccC
Confidence            9999999999999999999999999999999999999999999999988876554443310             112223


Q ss_pred             cCCCCCCCCCCCCCCCCCCCCCCcchhhhhhc
Q psy15598        190 SCTKVPIGSLTPPPRPQVCWPSSHSVTDILSA  221 (258)
Q Consensus       190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  221 (258)
                      +++.+++....|+.+....-+.++||+.||++
T Consensus       155 ~h~a~~s~~~~P~~~~~~~s~~~~Si~~~~~~  186 (327)
T KOG3862|consen  155 GHTAVPSSASPPPSSVQSDSVGSYSINGLLGI  186 (327)
T ss_pred             cccccccCCCCCCCCcccCCCCceeecccccc
Confidence            35556666656666777777778999999884

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

Probab=99.71  E-value=1.4e-16  Score=133.63  Aligned_cols=115  Identities=23%  Similarity=0.275  Sum_probs=101.0

Q ss_pred             CCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15598         44 NGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDP  122 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP  122 (258)
                      |.++++.++|.+++.++ .+|+|+++||++||||.+||++|++||+++|.+.+...+++||+++++++...|++.+++..
T Consensus         1 ~~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~   80 (138)
T COG3415           1 MAKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD   80 (138)
T ss_pred             CCchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc
Confidence            56889999999999998 58999999999999999999999999999998755444444999999999999999988764


Q ss_pred             CCCHHHHHHHHH-hcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598        123 GIFAWEIRDRLL-SDGVCDKFNVPSVSSISRILRNKIGSSIVQ  164 (258)
Q Consensus       123 ~ita~EIr~~L~-~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~  164 (258)
                       +++.+++..|. +.|+..     +.++|+++|++.+..--++
T Consensus        81 -wTl~~~~~~l~~e~gv~y-----~~~~v~~~l~~~GlsykK~  117 (138)
T COG3415          81 -WTLKELVEELGLEFGVWY-----HASAVRRLLHELGLSYKKP  117 (138)
T ss_pred             -chHHHHHHHHhhhcCeEE-----eHHHHHHHHHHcCCCcCCC
Confidence             99999999987 689986     9999999999998875544

>KOG0849|consensus

Probab=99.69  E-value=1.2e-17  Score=158.32  Aligned_cols=131  Identities=64%  Similarity=1.082  Sum_probs=125.4

Q ss_pred             chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHH
Q psy15598         33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVV  111 (258)
Q Consensus        33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~  111 (258)
                      +++||+||+|+++++++.+.|..|+++...|.+.+.|+++|.||+.||.++++||.++|++.|+..+|++|+ +.+++++
T Consensus         1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~   80 (354)
T KOG0849|consen    1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVE   80 (354)
T ss_pred             CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhH
Confidence            479999999999999999999999999999999999999999999999999999999999999999988888 7779999


Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      .+|..++.++|.+++|||++.|...++|+.++.+|.++|+|.|++....+.+
T Consensus        81 ~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~  132 (354)
T KOG0849|consen   81 AKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQ  132 (354)
T ss_pred             HHHHHHHhcCCcccchhhhhcccCcccccCCCCCChhhhhHHhhcccccccc
Confidence            9999999999999999999999999999999999999999999988888776

>PF13551 HTH_29: Winged helix-turn helix

Probab=99.69  E-value=2.8e-16  Score=122.40  Aligned_cols=100  Identities=32%  Similarity=0.449  Sum_probs=86.6

Q ss_pred             HHHHHHHHHcCCC-HHHHHHHhCCCHHHHHHHHHHhhhhC--Cccc-CCCCCCCCCC-CCHHHHHHHHHHHHhCC-----
Q psy15598         53 RMRIVELAQLGIR-PCDISRQLRVSHGCVSKILARYHETG--SILP-GAIGGSKPRV-TTPKVVSYIKELKQKDP-----  122 (258)
Q Consensus        53 R~RIV~L~~~G~S-~~eIAr~LGVSrsTVsRwikRyrEtG--sl~p-k~rgG~RPrk-lT~e~~~~I~~lv~~nP-----  122 (258)
                      |.+||.++.+|++ ..+||+.||||++||++|+++|+++|  .+.+ ++++| +|+. +++++.+.|++++.++|     
T Consensus         1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g-~~~~~l~~~~~~~l~~~~~~~p~~g~~   79 (112)
T PF13551_consen    1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGG-RPRKRLSEEQRAQLIELLRENPPEGRS   79 (112)
T ss_pred             CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCC-CCCCCCCHHHHHHHHHHHHHCCCCCCC
Confidence            6789999999995 99999999999999999999999999  4556 45555 6766 89999999999999988     


Q ss_pred             CCCHHHHHHHH-H-hcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        123 GIFAWEIRDRL-L-SDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       123 ~ita~EIr~~L-~-~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      .++..+|++.| . ..|+.+     |.+||+|+|+++|
T Consensus        80 ~~t~~~l~~~l~~~~~~~~~-----s~~ti~r~L~~~G  112 (112)
T PF13551_consen   80 RWTLEELAEWLIEEEFGIDV-----SPSTIRRILKRAG  112 (112)
T ss_pred             cccHHHHHHHHHHhccCccC-----CHHHHHHHHHHCc
Confidence            57899999987 4 357765     9999999999875

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

Probab=99.67  E-value=4.7e-16  Score=126.22  Aligned_cols=103  Identities=24%  Similarity=0.291  Sum_probs=89.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      .||.|+|.+||..++.|.+.++||+.|+||++||++|++ ..++|++.++++++ +  ++.   .+.|.+++.++|++++
T Consensus         2 aYS~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~-~--Kid---~~~L~~~v~~~pd~tl   74 (119)
T PF01710_consen    2 AYSLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGR-K--KID---RDELKALVEENPDATL   74 (119)
T ss_pred             CCCHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hccccccccccccc-c--ccc---HHHHHHHHHHCCCcCH
Confidence            489999999999999999999999999999999999999 66799998887665 2  553   4568899999999999


Q ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCC
Q psy15598        127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHH  166 (258)
Q Consensus       127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~  166 (258)
                      .||+..|   |       ||.+||+++|++.+..+-+...
T Consensus        75 ~Ela~~l---~-------Vs~~ti~~~Lkrlg~t~KK~~~  104 (119)
T PF01710_consen   75 RELAERL---G-------VSPSTIWRALKRLGITRKKKTL  104 (119)
T ss_pred             HHHHHHc---C-------CCHHHHHHHHHHcCchhccCcc
Confidence            9998776   3       3999999999999998766553

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 [].

>PF13565 HTH_32: Homeodomain-like domain

Probab=99.21  E-value=5.9e-11  Score=87.90  Aligned_cols=71  Identities=31%  Similarity=0.362  Sum_probs=59.5

Q ss_pred             HHHHHHHHhhhhC-----CcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCCCCCCCCCCHHHHHH
Q psy15598         79 CVSKILARYHETG-----SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS-DGVCDKFNVPSVSSISR  152 (258)
Q Consensus        79 TVsRwikRyrEtG-----sl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~-~Gv~v~~~~pS~STI~R  152 (258)
                      ||++|+++|++.|     +..+++++| +|++ ++++++.|++++.++|.++..+|++.|.+ .|+.+   .||.+||+|
T Consensus         1 Tv~rw~~ry~~~G~~gL~~~~~~~~~G-rp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R   75 (77)
T PF13565_consen    1 TVYRWLKRYREEGLEGLKDRKRRPRPG-RPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYR   75 (77)
T ss_pred             CHHHHHHHHHhhCchhhhcccccCCCC-CCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHH
Confidence            8999999999999     333445566 7777 88888999999999999999999999985 57642   369999999


Q ss_pred             HH
Q psy15598        153 IL  154 (258)
Q Consensus       153 iL  154 (258)
                      +|
T Consensus        76 ~L   77 (77)
T PF13565_consen   76 IL   77 (77)
T ss_pred             hC
Confidence            87

>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481

Probab=99.03  E-value=2.4e-09  Score=83.32  Aligned_cols=80  Identities=30%  Similarity=0.390  Sum_probs=63.7

Q ss_pred             hhccCCcccCCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC--cccCC-CCCCCCCCCCHHH
Q psy15598         35 VNQLGGVFVNGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGS--ILPGA-IGGSKPRVTTPKV  110 (258)
Q Consensus        35 ~nq~~~~~~~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs--l~pk~-rgG~RPrklT~e~  110 (258)
                      ||.+    .|.+ |+..-|.++|.++ ++|.+.+++|+.||||+.|++||++||++.|.  +.++. ++.+.|..+.++.
T Consensus         1 Mn~H----~nA~-Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~   75 (85)
T PF13011_consen    1 MNSH----KNAR-LTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEV   75 (85)
T ss_pred             CCCC----CCCC-CCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHH
Confidence            4666    4444 9999999999987 67999999999999999999999999999985  33333 2334567788888


Q ss_pred             HHHHHHHHH
Q psy15598        111 VSYIKELKQ  119 (258)
Q Consensus       111 ~~~I~~lv~  119 (258)
                      ++.|+++.+
T Consensus        76 ~~~I~~lRr   84 (85)
T PF13011_consen   76 ERRIIELRR   84 (85)
T ss_pred             HHHHHHHhc
Confidence            888887753

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

Probab=98.97  E-value=4.7e-10  Score=77.06  Aligned_cols=44  Identities=30%  Similarity=0.462  Sum_probs=26.7

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         49 PNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +.+.|..||.++.+|++.++||+.||||++||++|+++|++.|.
T Consensus         3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~   46 (50)
T PF13384_consen    3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEGL   46 (50)
T ss_dssp             -------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred             chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence            56789999999999999999999999999999999999998883

>PF13518 HTH_28: Helix-turn-helix domain

Probab=98.88  E-value=3.4e-09  Score=72.71  Aligned_cols=41  Identities=34%  Similarity=0.516  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +|.+||+++.+|.|..+||++||||++||++|+++|++.|.
T Consensus         1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen    1 FRLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGGI   41 (52)
T ss_pred             CHHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence            37889999999999999999999999999999999999884

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

Probab=98.53  E-value=8.3e-08  Score=65.49  Aligned_cols=42  Identities=29%  Similarity=0.333  Sum_probs=26.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.++.+.|..|..++++|+|.++||+.||+|++||+++++|
T Consensus         2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR   43 (44)
T PF13936_consen    2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR   43 (44)
T ss_dssp             ----------HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred             ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence            457899999999999999999999999999999999999987

>PRK09413 IS2 repressor TnpA; Reviewed

Probab=98.44  E-value=1.6e-06  Score=70.58  Aligned_cols=49  Identities=18%  Similarity=0.198  Sum_probs=44.1

Q ss_pred             CCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         45 GRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+.||.+++..||..+ +.|.++++||+.||||.+||++|+++|++.|..
T Consensus        10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~   59 (121)
T PRK09413         10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLT   59 (121)
T ss_pred             CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccc
Confidence            4779999999999975 579999999999999999999999999987653

>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=98.42  E-value=1.7e-07  Score=63.98  Aligned_cols=41  Identities=27%  Similarity=0.327  Sum_probs=33.8

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.++.+....|++|+.+|++..+||++||||++||||+++.
T Consensus         4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~   44 (45)
T PF02796_consen    4 PKLSKEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK   44 (45)
T ss_dssp             SSSSHCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred             CCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            34777778999999999999999999999999999999863

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 ....

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

Probab=98.40  E-value=5.1e-07  Score=66.45  Aligned_cols=46  Identities=13%  Similarity=0.224  Sum_probs=38.2

Q ss_pred             cCCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         43 VNGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        43 ~~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ...+.||.++|.+||..+ ..|.++.+||+.+||+.+|+++|++.|.
T Consensus         2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~   48 (76)
T PF01527_consen    2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR   48 (76)
T ss_dssp             -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence            455789999999999998 7899999999999999999999999998

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.

>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=98.14  E-value=3.6e-06  Score=59.65  Aligned_cols=43  Identities=28%  Similarity=0.365  Sum_probs=35.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      -+.|+.+.+..||.++++|.+.++||+.|||+++||+.|++.-
T Consensus         4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~k   46 (53)
T PF04218_consen    4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKNK   46 (53)
T ss_dssp             SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred             CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence            3569999999999999999999999999999999999999874

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.

>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=98.06  E-value=6.5e-06  Score=59.65  Aligned_cols=40  Identities=23%  Similarity=0.205  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      |.|.++..|+-+|+++++||+.|||+++||+.|.+++.-.
T Consensus         1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~   40 (58)
T PF06056_consen    1 EVKEQARSLYLQGWSIKEIAEELGVPRSTVYSWKDRYKWD   40 (58)
T ss_pred             CHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHhhCcc
Confidence            4688999999999999999999999999999999999744

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

>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]

Probab=97.96  E-value=4.9e-05  Score=71.40  Aligned_cols=109  Identities=18%  Similarity=0.115  Sum_probs=85.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC---------cccCCCCCCCCCCCCHHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS---------ILPGAIGGSKPRVTTPKVVSYIKE  116 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs---------l~pk~rgG~RPrklT~e~~~~I~~  116 (258)
                      ..++.+.|.+|-.+.+.|+|.++||++||..++||+|=++|-...+.         +.-..++..++-.++++..+.|.+
T Consensus         6 ~hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e   85 (318)
T COG2826           6 KHLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLE   85 (318)
T ss_pred             hhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHH
Confidence            37999999999999999999999999999999999999888543331         111111212456688999999999


Q ss_pred             HHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        117 LKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       117 lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      .+++  .++..+|...|....       +|.+||+|+|.-...+...
T Consensus        86 ~L~~--~wSPEQI~g~l~~~~-------i~~eTIYr~ly~~~~~a~~  123 (318)
T COG2826          86 KLKS--KWSPEQIIGRLKKSK-------ISFETIYRWLYQGKSEALR  123 (318)
T ss_pred             HHHh--hCCHHHHHHHHHhcc-------cCHHHHHHHHhhccchhhh
Confidence            9887  789999999998653       4899999999876666555

>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=97.93  E-value=6.9e-05  Score=59.83  Aligned_cols=49  Identities=14%  Similarity=0.222  Sum_probs=44.5

Q ss_pred             CCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCC-CHHHHHHHHHHhhhhCCc
Q psy15598         45 GRPLPNSVRMRIVELAQ-LGIRPCDISRQLRV-SHGCVSKILARYHETGSI   93 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGV-SrsTVsRwikRyrEtGsl   93 (258)
                      -+.||.++|.+||.++. .|.++++||+.||| +.+++++|++.|.+.+..
T Consensus         5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~   55 (116)
T COG2963           5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGL   55 (116)
T ss_pred             cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccc
Confidence            46799999999999986 68999999999995 999999999999987754

>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=97.93  E-value=2.9e-05  Score=46.79  Aligned_cols=39  Identities=23%  Similarity=0.231  Sum_probs=35.2

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.++.+.+..|++++.+|.+..+||+.|+||++||++|+
T Consensus         4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~   42 (42)
T cd00569           4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL   42 (42)
T ss_pred             CcCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence            347788888999999999999999999999999999985

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

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

Probab=97.70  E-value=0.00027  Score=50.88  Aligned_cols=66  Identities=17%  Similarity=0.185  Sum_probs=45.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL  133 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L  133 (258)
                      ++..++|+.+||+.+|+++|.+++   |.+.+....+ ..+..++++...|..++. .+-.++..+|++.|
T Consensus         1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r~~~-~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~   67 (68)
T cd01104           1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQRTDG-GHRLYSEADVARLRLIRRLTSEGVRISQAAALA   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence            478899999999999999999765   4444333232 346777777666655543 22477888887655

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

>PRK09409 IS2 transposase TnpB; Reviewed

Probab=97.69  E-value=0.00021  Score=66.48  Aligned_cols=92  Identities=22%  Similarity=0.200  Sum_probs=69.4

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-
Q psy15598         58 ELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSD-  136 (258)
Q Consensus        58 ~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~-  136 (258)
                      .+...++++..+++.||||++|.|+|++++..-   .....   .+..-..+....|.++..+++......|...|... 
T Consensus         6 ~~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~---~~~~~---~~~~~~~~l~~~I~~i~~~~~~yG~Rri~~~L~~~g   79 (301)
T PRK09409          6 ALIARGWGVSLVSRCLRVSRAQLHVILRRTDDW---MDGRR---SRHTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQA   79 (301)
T ss_pred             HHHhcCCcHHHHHHhcCcChHHhhhhccccccc---ccccc---ccCcchHHHHHHHHHHHHhCccCCHHHHHHHHHhhh
Confidence            456788999999999999999999999986421   11111   11222345677788887788889999999999865 


Q ss_pred             ---CC-CCCCCCCCHHHHHHHHHhccCC
Q psy15598        137 ---GV-CDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       137 ---Gv-~v~~~~pS~STI~RiLrr~~~~  160 (258)
                         |+ .     ++..+|.|+|++.+..
T Consensus        80 ~~~g~~~-----v~~k~V~RlMr~~Gl~  102 (301)
T PRK09409         80 ELDGMPA-----INAKRVYRIMRQNALL  102 (301)
T ss_pred             cccCccc-----cCHHHHHHHHHHcCCc
Confidence               54 3     4999999999998876

>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon

Probab=97.62  E-value=0.00022  Score=48.14  Aligned_cols=42  Identities=21%  Similarity=0.294  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.+. |+.++..|++..+||+.|+||++||++++++..+
T Consensus         3 ~l~~~e~~-i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~   44 (58)
T smart00421        3 SLTPRERE-VLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMR   44 (58)
T ss_pred             CCCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            36776665 7788889999999999999999999999998753

lux regulon (activates the bioluminescence operon

>PHA02517 putative transposase OrfB; Reviewed

Probab=97.45  E-value=0.00037  Score=62.88  Aligned_cols=76  Identities=11%  Similarity=0.102  Sum_probs=57.0

Q ss_pred             hCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHhcCCCCCCCCCCHHHHH
Q psy15598         73 LRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK-DPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS  151 (258)
Q Consensus        73 LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~-nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~  151 (258)
                      ||||++|.|+|+++...     |..+.+ + ....++..+.|+++..+ ++....+.|...|.+.|+.+     |.+||+
T Consensus         1 l~vsrs~yY~~~~~~~~-----p~~~~~-~-~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~v-----s~~tV~   68 (277)
T PHA02517          1 LGIAPSTYYRCQQQRHH-----PDKRRA-R-AQHDDWLKSEILRVYDENHQVYGVRKVWRQLNREGIRV-----ARCTVG   68 (277)
T ss_pred             CCCChHHHHHHHhccCC-----cchhhh-h-hhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCccc-----CHHHHH
Confidence            68999999999987531     111111 1 12345567788888765 57889999999999889875     999999


Q ss_pred             HHHHhccCC
Q psy15598        152 RILRNKIGS  160 (258)
Q Consensus       152 RiLrr~~~~  160 (258)
                      |+|++.+..
T Consensus        69 Rim~~~gl~   77 (277)
T PHA02517         69 RLMKELGLA   77 (277)
T ss_pred             HHHHHcCCc
Confidence            999998874

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

Probab=97.44  E-value=0.00036  Score=47.99  Aligned_cols=44  Identities=25%  Similarity=0.326  Sum_probs=40.6

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .+..++..++..|+.++.+..+.++||+.+|||.+||.+++++|
T Consensus         8 ~~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~   51 (52)
T PF13542_consen    8 RYCRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY   51 (52)
T ss_pred             cCCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence            45568999999999999888999999999999999999999987

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

Probab=97.40  E-value=0.00038  Score=49.29  Aligned_cols=42  Identities=29%  Similarity=0.523  Sum_probs=32.4

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      |+.++..++.+|..+.+.|++..+||++++-|+.+|.++++.
T Consensus         2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~d   43 (50)
T PF11427_consen    2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKD   43 (50)
T ss_dssp             S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence            678999999999999999999999999999999999999875

>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD

Probab=97.39  E-value=0.00031  Score=55.02  Aligned_cols=36  Identities=17%  Similarity=0.288  Sum_probs=32.0

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...|..|+.+..+|++.++||+.||||++||+||.+
T Consensus        37 Ls~R~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R   72 (88)
T TIGR02531        37 LAQRLQVAKMLKQGKTYSDIEAETGASTATISRVKR   72 (88)
T ss_pred             hhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence            356788889999999999999999999999999664

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.

>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=97.35  E-value=0.00069  Score=44.71  Aligned_cols=42  Identities=26%  Similarity=0.250  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++.+.|..+...+.+|++..+||+.+|+|.+||++|+.+.++
T Consensus        11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~   52 (55)
T cd06171          11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK   52 (55)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            667777666666679999999999999999999999999764

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

>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=97.28  E-value=0.00062  Score=47.13  Aligned_cols=43  Identities=23%  Similarity=0.273  Sum_probs=32.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-+...+-+|++..+||+.+|+|.+||.+++.|-++
T Consensus        10 ~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~   52 (54)
T PF08281_consen   10 QLPERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARK   52 (54)
T ss_dssp             CS-HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence            3567777766666779999999999999999999999998753

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.

>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=97.26  E-value=0.00092  Score=45.86  Aligned_cols=42  Identities=29%  Similarity=0.279  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-|...+.+|++..+||+.||+|++||+++.++-.
T Consensus         4 ~L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al   45 (50)
T PF04545_consen    4 QLPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL   45 (50)
T ss_dssp             TS-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence            467888887777788999999999999999999999998864

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 ....

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

Probab=97.19  E-value=0.003  Score=45.84  Aligned_cols=66  Identities=15%  Similarity=0.213  Sum_probs=43.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL  133 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L  133 (258)
                      ++..++|+.+|||.+|++.|.+.+   |.+.+....+ ..+..+.++...|..... .+-.+++.+|+..|
T Consensus         1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r~~~-g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l   67 (68)
T cd04763           1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQRSDG-GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL   67 (68)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence            467899999999999999886553   5555544333 346788776665544422 22466777776544

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

>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=97.19  E-value=0.00051  Score=46.94  Aligned_cols=43  Identities=28%  Similarity=0.519  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.|.+|+.+..+| ++.++||+.|++|++||++-++..++.|-+
T Consensus         2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV   45 (47)
T PF01022_consen    2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV   45 (47)
T ss_dssp             HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence            5799999998765 799999999999999999999999998865

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 ....

>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=97.12  E-value=0.0016  Score=44.23  Aligned_cols=43  Identities=21%  Similarity=0.381  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+.+|+.... + +.+.++||+.+|+|.+||++.+++..+.|-+
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I   47 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI   47 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence            45677888765 3 5999999999999999999999999998865

...

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

Probab=97.11  E-value=0.0018  Score=43.88  Aligned_cols=39  Identities=21%  Similarity=0.187  Sum_probs=32.8

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ...+. |+.++..|++..+||+.|++|.+||++++++.++
T Consensus         3 ~~e~~-i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~   41 (57)
T cd06170           3 PRERE-VLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR   41 (57)
T ss_pred             HHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            33444 7777789999999999999999999999998753

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

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

Probab=97.09  E-value=0.0069  Score=46.67  Aligned_cols=71  Identities=18%  Similarity=0.072  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhcC
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSDG  137 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~G  137 (258)
                      +++..++|+.+|||.+|++.|-+    .|.+.|....+...+..++++...|..... .+-.+++.+|++.|....
T Consensus         1 ~~ti~evA~~~gvs~~tLR~ye~----~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~   72 (88)
T cd01105           1 VIGIGEVSKLTGVSPRQLRYWEE----KGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRR   72 (88)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcc
Confidence            46889999999999999998843    476666544322346788777766555533 335789999999887544

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.

>PRK00118 putative DNA-binding protein; Validated

Probab=97.08  E-value=0.0015  Score=52.69  Aligned_cols=45  Identities=18%  Similarity=0.130  Sum_probs=39.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      +..++...|.-++..+.+|+|.++||+.+|||++||++++.|-+.
T Consensus        15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArk   59 (104)
T PRK00118         15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEK   59 (104)
T ss_pred             hccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            345788888877777889999999999999999999999998653

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

Probab=97.04  E-value=0.001  Score=47.93  Aligned_cols=66  Identities=18%  Similarity=0.156  Sum_probs=43.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+||+.|.+++.    +.+....+ ..+..++++...|..+.. .+-.++..+|++.|.
T Consensus         1 yti~eva~~~gvs~~tlr~y~~~gl----l~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~   67 (69)
T PF13411_consen    1 YTIKEVAKLLGVSPSTLRYYEREGL----LPPPRDEN-GYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK   67 (69)
T ss_dssp             EEHHHHHHHTTTTHHHHHHHHHTTS----STTBESTT-SSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHhcC----cccccccC-ceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence            3678999999999999999977654    54444333 347788887776655533 124666777766664

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

Probab=96.99  E-value=0.0018  Score=42.52  Aligned_cols=44  Identities=14%  Similarity=0.143  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      ++..++|+.||||++||++|+++    |.+.+....+ +....+.++..
T Consensus         1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~~~~-~~~~~~~~ei~   44 (49)
T cd04762           1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIRTPG-GHRRFPEEDLE   44 (49)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc----CCCCceeCCC-CceecCHHHHH
Confidence            47789999999999999999986    4443332233 33445544433

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.

>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition

Probab=96.97  E-value=0.00061  Score=49.96  Aligned_cols=45  Identities=31%  Similarity=0.336  Sum_probs=21.8

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +.|+.++..+|.+++.+|...|...|+.+     |.+||.|+|++.+...
T Consensus         2 r~I~~~v~~~p~~s~~~i~~~l~~~~~~v-----S~~TI~r~L~~~g~~~   46 (72)
T PF01498_consen    2 RRIVRMVRRNPRISAREIAQELQEAGISV-----SKSTIRRRLREAGLKK   46 (72)
T ss_dssp             --------------HHHHHHHT---T--S------HHHHHHHHHHT-EEE
T ss_pred             cHHHHHHHHCCCCCHHHHHHHHHHccCCc-----CHHHHHHHHHHcCccc
Confidence            57888999999999999999998668876     9999999999987654

This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.

>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional

Probab=96.96  E-value=0.0015  Score=53.54  Aligned_cols=75  Identities=23%  Similarity=0.327  Sum_probs=56.5

Q ss_pred             CCCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         46 RPLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.+++..|.+|+.+..  .++++.+|++.|+++++||++-++..++.|-|...+.|..+--.+.+....++..++..
T Consensus        11 kaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~   87 (117)
T PRK10141         11 KILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ   87 (117)
T ss_pred             HHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH
Confidence            4578899999999885  35899999999999999999999999999988665554322233445555555554443

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

Probab=96.92  E-value=0.00096  Score=57.47  Aligned_cols=88  Identities=19%  Similarity=0.289  Sum_probs=28.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH-HhhhhC--Cc-----ccCCCCCCCCC-CCCHHHHHHHHHHHHh-CC--CCCHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILA-RYHETG--SI-----LPGAIGGSKPR-VTTPKVVSYIKELKQK-DP--GIFAWEIR  130 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwik-RyrEtG--sl-----~pk~rgG~RPr-klT~e~~~~I~~lv~~-nP--~ita~EIr  130 (258)
                      -++.++||..||++.|||+|.++ +|.++.  .+     -.......... ...+.+...|.+++.+ ++  -++=.+|.
T Consensus        49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~  128 (160)
T PF04552_consen   49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIA  128 (160)
T ss_dssp             ------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHH
T ss_pred             CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence            46889999999999999999765 566554  21     12211110111 1224467788888875 33  46788999


Q ss_pred             HHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598        131 DRLLSDGVCDKFNVPSVSSISRILR  155 (258)
Q Consensus       131 ~~L~~~Gv~v~~~~pS~STI~RiLr  155 (258)
                      +.|.+.|+.+     |++||...=.
T Consensus       129 ~~L~~~gi~i-----sRRTVaKYR~  148 (160)
T PF04552_consen  129 ELLKEEGIKI-----SRRTVAKYRE  148 (160)
T ss_dssp             HHHTTTTS--------HHHHHHHHH
T ss_pred             HHHHHcCCCc-----cHHHHHHHHH
Confidence            9999999986     9999976543

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.

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

Probab=96.89  E-value=0.0027  Score=44.58  Aligned_cols=43  Identities=16%  Similarity=0.266  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++..+ +.|.+..++|..||||++||+||++.+.+
T Consensus         2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~   45 (53)
T PF13613_consen    2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP   45 (53)
T ss_pred             CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence            46677776666664 68999999999999999999999999864

>PF14493 HTH_40: Helix-turn-helix domain

Probab=96.88  E-value=0.013  Score=45.26  Aligned_cols=84  Identities=19%  Similarity=0.086  Sum_probs=65.1

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRL  133 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L  133 (258)
                      ..-+.++++|+|..+||+.-+++.+||..-+.++...|...+-      ...++.+..+.|...+++.....++.|.+.|
T Consensus         4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~------~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l   77 (91)
T PF14493_consen    4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDI------EELLSEEEIKQIEDAIEKLGSEKLKPIKEAL   77 (91)
T ss_pred             HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH------HHhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence            4457788999999999999999999999999999998862111      1447778888898888887777787777766


Q ss_pred             HhcCCCCCCCCCCHHHHH
Q psy15598        134 LSDGVCDKFNVPSVSSIS  151 (258)
Q Consensus       134 ~~~Gv~v~~~~pS~STI~  151 (258)
                      .   -.     +|...|+
T Consensus        78 ~---~~-----~sy~~iR   87 (91)
T PF14493_consen   78 P---GD-----YSYFEIR   87 (91)
T ss_pred             C---CC-----CCHHHHH
Confidence            3   22     3666664

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

Probab=96.88  E-value=0.0068  Score=43.75  Aligned_cols=65  Identities=17%  Similarity=0.222  Sum_probs=42.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL  133 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L  133 (258)
                      ++..++|+.+|||.+|++.|.+++.   -..++..+  ..+..+.++...|...+. .+-..++.+|+..|
T Consensus         1 ~~i~evA~~~gvs~~tlR~~~~~g~---l~~~~~~~--g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l   66 (67)
T cd04764           1 YTIKEVSEIIGVKPHTLRYYEKEFN---LYIPRTEN--GRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL   66 (67)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhcC---CCCCCCCC--CceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence            4688999999999999999977643   11222222  346788777666655533 22467777776654

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.

>PHA02535 P terminase ATPase subunit; Provisional

Probab=96.83  E-value=0.0033  Score=63.97  Aligned_cols=42  Identities=17%  Similarity=0.109  Sum_probs=40.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .|+.|+|..++.++.+|.++++||++|||+.+||++|.++++
T Consensus         2 ~yt~EfK~~Av~Ly~~G~sv~eIA~~LGv~~~Tl~~W~kr~~   43 (581)
T PHA02535          2 AYDDDVRRAAKFLYWQGWTVAEIAEELGLKSRTIYSWKERDG   43 (581)
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHhcccc
Confidence            489999999999998899999999999999999999999986

>PRK04217 hypothetical protein; Provisional

Probab=96.80  E-value=0.0046  Score=50.34  Aligned_cols=45  Identities=13%  Similarity=0.089  Sum_probs=36.5

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ....++.+.|..+..+..+|++..+||+.||||++||++.+++-+
T Consensus        39 p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr   83 (110)
T PRK04217         39 PPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR   83 (110)
T ss_pred             CcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            345588888844444445999999999999999999999999864

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

Probab=96.79  E-value=0.018  Score=45.45  Aligned_cols=69  Identities=16%  Similarity=0.176  Sum_probs=51.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHhc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLLSD  136 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~~~  136 (258)
                      ++..++|+.+|||.+|++.|.+.+   |.+.+....+ ..+..++++...|..++.  ++-.+++.+|++.|...
T Consensus         1 yti~EvA~~~gVs~~tLR~ye~~~---gli~p~r~~~-g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~   71 (99)
T cd04765           1 FSIGEVAEILGLPPHVLRYWETEF---PQLKPVKRAG-GRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKED   71 (99)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHc---CCCCCcCCCC-CCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence            467899999999999999996663   4444433333 457788888887777653  45688999999988753

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.

>smart00422 HTH_MERR helix_turn_helix, mercury resistance

Probab=96.78  E-value=0.011  Score=42.38  Aligned_cols=50  Identities=14%  Similarity=0.136  Sum_probs=35.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC-CCCCCCCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG-AIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk-~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      ++..++|+.+|||.+|+++|.+    .|.+.+. ...+ ..+..+.++...|....
T Consensus         1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~-g~r~y~~~dl~~l~~i~   51 (70)
T smart00422        1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEG-GYRLYSDEDLERLRFIK   51 (70)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCC-CCEecCHHHHHHHHHHH
Confidence            4789999999999999999965    6777654 2222 34667777766655543

>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=96.75  E-value=0.0012  Score=44.85  Aligned_cols=43  Identities=28%  Similarity=0.363  Sum_probs=33.3

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      ||++++++..+.|.++..+.  .+..+|++.+   |       +|++||+|+|+.
T Consensus         2 Rp~~~~~~~~~~i~~l~~~G--~si~~IA~~~---g-------vsr~TvyR~l~~   44 (45)
T PF02796_consen    2 RPPKLSKEQIEEIKELYAEG--MSIAEIAKQF---G-------VSRSTVYRYLNK   44 (45)
T ss_dssp             SSSSSSHCCHHHHHHHHHTT----HHHHHHHT---T-------S-HHHHHHHHCC
T ss_pred             cCCCCCHHHHHHHHHHHHCC--CCHHHHHHHH---C-------cCHHHHHHHHhc
Confidence            88999998888999988774  7888887766   3       499999999964

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 ....

>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=96.71  E-value=0.003  Score=46.33  Aligned_cols=44  Identities=25%  Similarity=0.237  Sum_probs=34.5

Q ss_pred             CCCCCCHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         44 NGRPLPNSVRMRIVELAQL---GIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~---G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      |+|.-|. .|.+..+++.+   .+...+||++||||.+||++|-.+.+
T Consensus         1 M~r~Rsp-~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dk   47 (60)
T PF10668_consen    1 MARKRSP-NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDK   47 (60)
T ss_pred             CCCCCCc-CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcc
Confidence            3444333 67788888763   48999999999999999999998753

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 [].

>PRK13413 mpi multiple promoter invertase; Provisional

Probab=96.69  E-value=0.0027  Score=55.20  Aligned_cols=36  Identities=25%  Similarity=0.368  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .+.+|..++.+|+|.++||+.||||++||+|+++.+
T Consensus       161 ~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~  196 (200)
T PRK13413        161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTR  196 (200)
T ss_pred             hHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence            346788888899999999999999999999999864

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

Probab=96.64  E-value=0.0053  Score=42.92  Aligned_cols=49  Identities=24%  Similarity=0.413  Sum_probs=40.5

Q ss_pred             CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         47 PLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .++.+.+..|+..+. .+.+..+|++.++++++||++.+++..+.|-+..
T Consensus         3 ~~~~~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~   52 (78)
T cd00090           3 ALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVES   52 (78)
T ss_pred             cccChHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence            455566777888754 4499999999999999999999999999997643

ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.

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

Probab=96.62  E-value=0.025  Score=45.19  Aligned_cols=68  Identities=15%  Similarity=0.141  Sum_probs=49.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      ++..++|+.+|||.+|++.|.+    .|.+.|..+.++.-+..++++...|..... ..-.+++.+|++.|..
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~   69 (108)
T cd04773           1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ   69 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence            5789999999999999988844    577766544322457788877776655543 2236889999888864

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.

>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx

Probab=96.59  E-value=0.0038  Score=45.56  Aligned_cols=43  Identities=21%  Similarity=0.236  Sum_probs=31.4

Q ss_pred             CCCCCHHHHHHHHHHHH-cCC---CHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         45 GRPLPNSVRMRIVELAQ-LGI---RPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~-~G~---S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      -+.|+..++.++|+.++ .+.   ..+++|+.|+|++.+|.+|++.-
T Consensus         3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kqe   49 (58)
T PF09607_consen    3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQE   49 (58)
T ss_dssp             -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred             ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHHH
Confidence            36799999999999985 454   45999999999999999999764

100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.

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

Probab=96.57  E-value=0.0026  Score=45.46  Aligned_cols=48  Identities=27%  Similarity=0.398  Sum_probs=41.8

Q ss_pred             CCHHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         48 LPNSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      +++..|.+|+.+. . .+++..+||+.||++.+||++-++..++-|-|+.
T Consensus         7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~   56 (61)
T PF12840_consen    7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV   56 (61)
T ss_dssp             HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence            5678999999998 4 5799999999999999999999999999997743

...

>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA

Probab=96.56  E-value=0.0031  Score=43.95  Aligned_cols=39  Identities=28%  Similarity=0.318  Sum_probs=35.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +...++++||++..+|..++++||.|+||..||-|-+|.
T Consensus         6 ~kpgikeqIvema~nG~GiRdtaRvL~I~~nTVlrtLK~   44 (46)
T PF12759_consen    6 RKPGIKEQIVEMAFNGSGIRDTARVLKISINTVLRTLKN   44 (46)
T ss_pred             cCccHHHHHHHHHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence            456788999999999999999999999999999988774

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

Probab=96.51  E-value=0.005  Score=50.93  Aligned_cols=54  Identities=17%  Similarity=0.348  Sum_probs=37.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC--CCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV--TTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk--lT~e~~~~I~~lv  118 (258)
                      |+..|+|..+|+|+.||.||+++..=.-.-.|+-.|| |-+.  +++.+.++|...-
T Consensus         1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGG-rARLIhId~~V~efi~s~~   56 (122)
T PF07037_consen    1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGG-RARLIHIDEQVREFIRSIP   56 (122)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccc-cceeeeecHHHHHHHHhhH
Confidence            6789999999999999999999863111223433455 4443  5577777777664

The function of this family is unknown.

>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor

Probab=96.50  E-value=0.0086  Score=58.79  Aligned_cols=85  Identities=15%  Similarity=0.281  Sum_probs=61.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Cc-----ccCCCCC-C-CCCCCCHHHHHHHHHHHHhC-C--CCCHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SI-----LPGAIGG-S-KPRVTTPKVVSYIKELKQKD-P--GIFAWEIR  130 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl-----~pk~rgG-~-RPrklT~e~~~~I~~lv~~n-P--~ita~EIr  130 (258)
                      ++.++||..+||+.|||+|.++. |.++.  .+     -.....+ . .....+..+...|.+++... +  -++=.+|.
T Consensus       319 LtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI~~E~~~~PlSD~~I~  398 (429)
T TIGR02395       319 LTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKELIAAEDKRKPLSDQKIA  398 (429)
T ss_pred             CcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence            58899999999999999999874 55554  22     1111110 0 01244567888999998743 3  26788999


Q ss_pred             HHHHhcCCCCCCCCCCHHHHHHH
Q psy15598        131 DRLLSDGVCDKFNVPSVSSISRI  153 (258)
Q Consensus       131 ~~L~~~Gv~v~~~~pS~STI~Ri  153 (258)
                      +.|++.|+.+     |++||...
T Consensus       399 ~~L~~~Gi~I-----aRRTVaKY  416 (429)
T TIGR02395       399 ELLKEKGIKI-----ARRTVAKY  416 (429)
T ss_pred             HHHHhcCCCe-----ehHHHHHH
Confidence            9999999986     99999776

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

>PF13309 HTH_22: HTH domain

Probab=96.50  E-value=0.0039  Score=45.72  Aligned_cols=42  Identities=21%  Similarity=0.217  Sum_probs=35.3

Q ss_pred             CCCCCCHHHHHHHHHHHH-cCC-----CHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELAQ-LGI-----RPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~-~G~-----S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ....++.+.|..||.... .|.     +...+|+.||||+.|||++++
T Consensus        17 ~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr   64 (64)
T PF13309_consen   17 PPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR   64 (64)
T ss_pred             ChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence            445688899999998875 685     888999999999999999874

>PRK15418 transcriptional regulator LsrR; Provisional

Probab=96.48  E-value=0.0051  Score=57.94  Aligned_cols=43  Identities=23%  Similarity=0.332  Sum_probs=37.4

Q ss_pred             HHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +-.+|-.++ .+|++..|||++|||||.+|+|.+++-++.|-++
T Consensus        17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~   60 (318)
T PRK15418         17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR   60 (318)
T ss_pred             HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE
Confidence            455666665 5899999999999999999999999999999763

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

Probab=96.48  E-value=0.025  Score=44.38  Aligned_cols=66  Identities=12%  Similarity=0.224  Sum_probs=49.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hC-CCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KD-PGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~n-P~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|.+    .|.+.|....+ ..+..++.+...|..++. .+ -.++..+|+..|.
T Consensus         1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~~~-g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~   68 (96)
T cd04774           1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERSEG-RYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLE   68 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            4678999999999999999954    47776654433 567888887777766544 22 4789999988876

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.

>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=96.47  E-value=0.0086  Score=41.09  Aligned_cols=36  Identities=11%  Similarity=0.158  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.=...|+.+.+| +|.+++|+.|||+++|+++.++.
T Consensus         3 e~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g   39 (45)
T PF05225_consen    3 EDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG   39 (45)
T ss_dssp             HHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            3345566777777 99999999999999999977665

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.

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

Probab=96.45  E-value=0.0046  Score=39.94  Aligned_cols=29  Identities=28%  Similarity=0.418  Sum_probs=24.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      ++..|||..+|+++-||+|.++++++.|.
T Consensus         3 mtr~diA~~lG~t~ETVSR~l~~l~~~gl   31 (32)
T PF00325_consen    3 MTRQDIADYLGLTRETVSRILKKLERQGL   31 (32)
T ss_dssp             --HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHcCC
Confidence            67899999999999999999999998875

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 ....

>TIGR01321 TrpR trp operon repressor, proteobacterial

Probab=96.45  E-value=0.0048  Score=49.04  Aligned_cols=37  Identities=22%  Similarity=0.240  Sum_probs=30.6

Q ss_pred             HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ..|.+|+... +.|+|.++||+.+|||++||.|+-+-.
T Consensus        42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l   79 (94)
T TIGR01321        42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNL   79 (94)
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence            4677777644 568999999999999999999987654

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.

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

Probab=96.44  E-value=0.0073  Score=40.44  Aligned_cols=47  Identities=13%  Similarity=0.135  Sum_probs=33.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      ++..++|+.+||+.+||++|.++    |.+.+....| ..+..++++...|.
T Consensus         1 ~~~~e~a~~~gv~~~tlr~~~~~----g~l~~~~~~~-~~~~y~~~~v~~l~   47 (49)
T cd04761           1 YTIGELAKLTGVSPSTLRYYERI----GLLSPARTEG-GYRLYSDADLERLR   47 (49)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCEEeCHHHHHHhh
Confidence            47889999999999999999655    4444333333 44667777666654

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.

>TIGR03879 near_KaiC_dom probable regulatory domain

Probab=96.44  E-value=0.0066  Score=46.15  Aligned_cols=44  Identities=14%  Similarity=0.154  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598         48 LPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETG   91 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtG   91 (258)
                      ++...|...+... .+|+|.++||+.+|||.+||..|+++-...|
T Consensus        16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~   60 (73)
T TIGR03879        16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAG   60 (73)
T ss_pred             CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence            5666666555544 4899999999999999999999999854444

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.

>COG1725 Predicted transcriptional regulators [Transcription]

Probab=96.38  E-value=0.017  Score=48.13  Aligned_cols=107  Identities=17%  Similarity=0.210  Sum_probs=69.7

Q ss_pred             ccCCCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHH
Q psy15598         42 FVNGRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSY  113 (258)
Q Consensus        42 ~~~gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~  113 (258)
                      |-+.+|+...+..+|......|.        |+++.|..++|+..||.|-++...+.|-+....+.|   ...++...+.
T Consensus         6 f~s~~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G---~fV~~~~~~~   82 (125)
T COG1725           6 FDSSKPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKG---TFVTEDAKEI   82 (125)
T ss_pred             cCCCCCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCee---EEEcCCchhh
Confidence            45778888888888888876553        999999999999999999999999999886654333   4444332222


Q ss_pred             HHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        114 IKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       114 I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      +.+....--...+.++.+.++..|+       |...|..+|+...
T Consensus        83 ~~~~~~~~~~~~l~~~I~~~~~~G~-------s~eei~~~~~~~~  120 (125)
T COG1725          83 LDQLKRELAEEELEEFIEEAKALGL-------SLEEILELLKEIY  120 (125)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCC-------CHHHHHHHHHHHH
Confidence            2222211101122233344444554       7778877777544

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

Probab=96.32  E-value=0.063  Score=42.86  Aligned_cols=68  Identities=12%  Similarity=0.112  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      ++..++|+.+|||.+|++.|-+    .|.+.+..+.....+..++++...|..... ..-.+++.||++.|..
T Consensus         1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (113)
T cd01109           1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL   69 (113)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4788999999999999987754    577644333322457788877776655433 2357899999988863

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.

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

Probab=96.31  E-value=0.066  Score=43.14  Aligned_cols=68  Identities=16%  Similarity=0.227  Sum_probs=49.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||.+|++-    |.+.|.+.|..+..+.-|..++++...|..... .+-.+++.||++.+..
T Consensus         1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~   69 (123)
T cd04770           1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSL   69 (123)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            5789999999999999954    666788875444333567888877776655533 4457899999988863

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.

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

Probab=96.30  E-value=0.012  Score=43.35  Aligned_cols=45  Identities=16%  Similarity=0.333  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHc--C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQL--G--IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~~--G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ...+.+|+.++..  +  ++..+||+.|||++++|++.+.+..+.|.|.
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~   53 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC   53 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            4577888888753  4  8999999999999999999999999999874

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

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

Probab=96.29  E-value=0.027  Score=44.25  Aligned_cols=67  Identities=16%  Similarity=0.141  Sum_probs=46.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|.+    .|.+.+..+.+..-+..++++...|..+.. ..-.++..+|+..+.
T Consensus         1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~   68 (103)
T cd01106           1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLK   68 (103)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4788999999999999997765    576655433222346788877766544422 234788999888775

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

>PRK05932 RNA polymerase factor sigma-54; Reviewed

Probab=96.26  E-value=0.014  Score=57.81  Aligned_cols=83  Identities=19%  Similarity=0.309  Sum_probs=60.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Cc-----ccCC---CCCCCCCCCCHHHHHHHHHHHHh-CC--CCCHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SI-----LPGA---IGGSKPRVTTPKVVSYIKELKQK-DP--GIFAWEI  129 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl-----~pk~---rgG~RPrklT~e~~~~I~~lv~~-nP--~ita~EI  129 (258)
                      ++.++||..+|++.|||+|.++. |.++.  .+     -...   ..|  ....+..+...|.+++.. ++  -++=.+|
T Consensus       344 LtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g--~~~S~~~Ik~~Ik~lI~~Ed~~~PlSD~~I  421 (455)
T PRK05932        344 LVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGG--GEASSTAIRALIKKLIAAENPKKPLSDSKI  421 (455)
T ss_pred             ccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            48899999999999999999874 55543  21     1111   111  123446778899999884 33  3678899


Q ss_pred             HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598        130 RDRLLSDGVCDKFNVPSVSSISRI  153 (258)
Q Consensus       130 r~~L~~~Gv~v~~~~pS~STI~Ri  153 (258)
                      .+.|++.|+.+     |++||...
T Consensus       422 ~~~L~~~Gi~I-----aRRTVaKY  440 (455)
T PRK05932        422 AELLKEQGIDV-----ARRTVAKY  440 (455)
T ss_pred             HHHHHHcCCCe-----ehHHHHHH
Confidence            99999999986     99999776

>PHA02591 hypothetical protein; Provisional

Probab=96.25  E-value=0.009  Score=46.16  Aligned_cols=50  Identities=30%  Similarity=0.296  Sum_probs=39.2

Q ss_pred             chhhccCCc--ccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         33 GEVNQLGGV--FVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        33 ~~~nq~~~~--~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+=|.||+  |+-   --+|++.-.-+|.+.|+|..+||+.|||+..+|+++++
T Consensus        30 ~k~vqv~~~ryfi~---~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~   81 (83)
T PHA02591         30 QKVVQVGQTRYFVE---SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE   81 (83)
T ss_pred             HHhheeCCEEEEEe---ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            345566663  222   23578888888899999999999999999999999875

>TIGR00721 tfx DNA-binding protein, Tfx family

Probab=96.23  E-value=0.011  Score=49.76  Aligned_cols=42  Identities=26%  Similarity=0.430  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++. ...+|+.+..+|++..+||+.||+|++||+++.++.++
T Consensus         6 ~Lte-~qr~VL~Lr~~GlTq~EIAe~LgiS~stV~~~e~ra~k   47 (137)
T TIGR00721         6 FLTE-RQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAME   47 (137)
T ss_pred             CCCH-HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence            3444 44467777789999999999999999999999999764

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

>PRK06759 RNA polymerase factor sigma-70; Validated

Probab=96.21  E-value=0.013  Score=47.70  Aligned_cols=42  Identities=17%  Similarity=0.037  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+-+|++..+||+.||||.+||+.++.|-+
T Consensus       106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~  147 (154)
T PRK06759        106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQAL  147 (154)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477777777777778999999999999999999999999865

>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=96.15  E-value=0.014  Score=39.10  Aligned_cols=37  Identities=19%  Similarity=0.208  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      -.|.-|...++ .+....++|+.||||++|+++-+++|
T Consensus         5 ~E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~   42 (42)
T PF02954_consen    5 FEKQLIRQALERCGGNVSKAARLLGISRRTLYRKLKKY   42 (42)
T ss_dssp             HHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence            35666666665 57899999999999999999999886

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 ....

>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=96.14  E-value=0.0074  Score=41.87  Aligned_cols=41  Identities=24%  Similarity=0.371  Sum_probs=33.6

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|++++.   .+++..+||+.+|++++||+|+++...+.|-+.
T Consensus         6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~   49 (52)
T PF09339_consen    6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE   49 (52)
T ss_dssp             HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence            45666664   357899999999999999999999999998763

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.

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

Probab=96.10  E-value=0.093  Score=40.56  Aligned_cols=66  Identities=17%  Similarity=0.204  Sum_probs=47.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+||+.+||..|.+    .|.+.+....+ ..+..+.++...+...+. ....++..+|...+.
T Consensus         1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~   67 (100)
T cd00592           1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSEN-GYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD   67 (100)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            4788999999999999999965    46665544333 456788877766665543 225788888887776

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.

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

Probab=96.10  E-value=0.047  Score=42.71  Aligned_cols=67  Identities=18%  Similarity=0.140  Sum_probs=47.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|-+    .|.+.|..++.+.-|..++++...|..... ..-.+++.+|++.+.
T Consensus         1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~   68 (97)
T cd04782           1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLD   68 (97)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            4678999999999999987744    688877544322457788777665554433 334788999988775

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.

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

Probab=96.09  E-value=0.027  Score=44.25  Aligned_cols=66  Identities=12%  Similarity=0.145  Sum_probs=48.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|.    +.|.+.|....+ ..+..+..+...|...+.  .+-.+++.+|+..|.
T Consensus         2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~-g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~   69 (98)
T cd01279           2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNG-GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIE   69 (98)
T ss_pred             cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCC-CCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            478899999999999999884    367776643333 457788887777776644  335888988887775

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.

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

Probab=96.08  E-value=0.03  Score=46.27  Aligned_cols=65  Identities=12%  Similarity=0.139  Sum_probs=46.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|.++    |.+.+...+  ..|..++++...|..++.  .+-.+++.+|+..|.
T Consensus         2 ysI~eVA~~~GVs~~TLR~wE~~----GLl~p~r~~--G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~   68 (120)
T cd04767           2 YPIGVVAELLNIHPETLRIWERH----GLIKPARRN--GQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILS   68 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcCCC--CcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            57899999999999999977764    777665443  457788887776655543  224666666666554

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

>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=96.07  E-value=0.014  Score=45.67  Aligned_cols=39  Identities=15%  Similarity=0.200  Sum_probs=34.9

Q ss_pred             HHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         50 NSVRMRIVE-LAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        50 ~dlR~RIV~-L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ...|.+|+. +..+|++.++||+.+|||..||.|.-+-.+
T Consensus        35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk   74 (87)
T PF01371_consen   35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLK   74 (87)
T ss_dssp             HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            357899998 899999999999999999999999877665

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 ....

>PRK09642 RNA polymerase sigma factor SigW; Reviewed

Probab=96.06  E-value=0.016  Score=47.61  Aligned_cols=42  Identities=19%  Similarity=0.099  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+.+|+|..+||+.||||.+||...+.|.+
T Consensus       106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar  147 (160)
T PRK09642        106 ELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRAR  147 (160)
T ss_pred             hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            377777877777778999999999999999999998888865

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=96.03  E-value=0.0095  Score=40.81  Aligned_cols=47  Identities=26%  Similarity=0.333  Sum_probs=36.7

Q ss_pred             HHHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         50 NSVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        50 ~dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ..++..|+.. +..|  + +..++|+.|+||++||++.+++..+.|-+...
T Consensus         3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~   53 (60)
T smart00345        3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR   53 (60)
T ss_pred             HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3456666654 2333  4 89999999999999999999999999987533

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

Probab=96.02  E-value=0.092  Score=42.75  Aligned_cols=67  Identities=18%  Similarity=0.235  Sum_probs=47.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc-cCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL-PGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~-pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||.+||+    -|.+.|.+. +....+ .-|..++++...|..... .+-.+++.||++.|..
T Consensus         1 m~I~e~a~~~gvs~~tlR----~Ye~~GLl~~~~r~~~-gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   69 (126)
T cd04783           1 LTIGELAKAAGVNVETIR----YYQRRGLLPEPPRPEG-GYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL   69 (126)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            578899999999999994    446678886 333333 457788877666544432 3347889999888753

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.

>PRK12469 RNA polymerase factor sigma-54; Provisional

Probab=96.01  E-value=0.02  Score=57.16  Aligned_cols=83  Identities=20%  Similarity=0.339  Sum_probs=60.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Ccc-----c---CCCCCCCCCCCCHHHHHHHHHHHHh-CCC--CCHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SIL-----P---GAIGGSKPRVTTPKVVSYIKELKQK-DPG--IFAWEI  129 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl~-----p---k~rgG~RPrklT~e~~~~I~~lv~~-nP~--ita~EI  129 (258)
                      ++.++||..+|++.|||+|.++. |.++.  .+.     .   ...+|  ....+..++..|++++.. ++.  ++=.+|
T Consensus       370 LtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g--~~~Ss~~Ik~~Ik~lI~~Ed~~kPLSD~~I  447 (481)
T PRK12469        370 LVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGG--GECSAAAVRALIKEMIAAEQAGDPLSDVAL  447 (481)
T ss_pred             CcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence            48899999999999999999864 55544  221     1   11111  123456788899999884 443  678899


Q ss_pred             HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598        130 RDRLLSDGVCDKFNVPSVSSISRI  153 (258)
Q Consensus       130 r~~L~~~Gv~v~~~~pS~STI~Ri  153 (258)
                      .+.|++.|+.+     |++||...
T Consensus       448 ~~~L~~~GI~I-----ARRTVAKY  466 (481)
T PRK12469        448 AEMLAGRGVLI-----ARRTVAKY  466 (481)
T ss_pred             HHHHHhcCCCe-----echhHHHH
Confidence            99999999986     99999765

>TIGR01529 argR_whole arginine repressor

Probab=96.00  E-value=0.013  Score=49.55  Aligned_cols=49  Identities=20%  Similarity=0.162  Sum_probs=43.4

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ  164 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~  164 (258)
                      ...|.+++++++..++.||.+.|.+.|+.+     |.+||+|.|++.+..|...
T Consensus         4 ~~~i~~Li~~~~i~tqeeL~~~L~~~G~~v-----sqaTIsRdL~elglvk~~~   52 (146)
T TIGR01529         4 QERIKEIITEEKISTQEELVALLKAEGIEV-----TQATVSRDLRELGAVKVRD   52 (146)
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHhCCCc-----CHHHHHHHHHHcCCEEEEC
Confidence            456888889999999999999999999986     9999999999999987554

This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.

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

Probab=96.00  E-value=0.089  Score=43.01  Aligned_cols=67  Identities=18%  Similarity=0.208  Sum_probs=47.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++-|-+    .|.+.|..+..+.-|..++++...|..... .+-.+++.||+..+.
T Consensus         1 m~I~e~a~~~gvs~~tlRyYe~----~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T cd01108           1 MNIGEAAKLTGLSAKMIRYYEE----IGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5789999999999999875544    577764333222457788877766655543 345789999998775

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

>PRK11050 manganese transport regulator MntR; Provisional

Probab=96.00  E-value=0.044  Score=46.22  Aligned_cols=43  Identities=30%  Similarity=0.327  Sum_probs=35.0

Q ss_pred             HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ..|..++.  .+.+.++||+.|+||+++|++++++..+.|.+...
T Consensus        40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~   84 (152)
T PRK11050         40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR   84 (152)
T ss_pred             HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            34444443  46899999999999999999999999999977543

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

Probab=95.97  E-value=0.024  Score=47.36  Aligned_cols=52  Identities=23%  Similarity=0.305  Sum_probs=44.7

Q ss_pred             CCCCCCHHH----HHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         44 NGRPLPNSV----RMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        44 ~gR~~S~dl----R~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      |+++++.+.    ..+||++++ .| ++..+++..+|+++.||.+.++...++|.|..
T Consensus         1 Ma~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~   58 (127)
T PF06163_consen    1 MARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR   58 (127)
T ss_pred             CCCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence            677888764    577888876 56 89999999999999999999999999999843

>PRK09652 RNA polymerase sigma factor RpoE; Provisional

Probab=95.97  E-value=0.019  Score=47.41  Aligned_cols=42  Identities=21%  Similarity=0.261  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-.|++.++||+.||||.+||+.++.|-+
T Consensus       128 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~  169 (182)
T PRK09652        128 SLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAR  169 (182)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477777776666667999999999999999999999998865

>PRK09639 RNA polymerase sigma factor SigX; Provisional

Probab=95.94  E-value=0.019  Score=47.27  Aligned_cols=41  Identities=20%  Similarity=0.206  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+ +|++..+||+.||||.+||++.+.|-+
T Consensus       112 ~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~  152 (166)
T PRK09639        112 KMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAK  152 (166)
T ss_pred             cCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            48888888777878 999999999999999999999998875

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

Probab=95.94  E-value=0.049  Score=42.49  Aligned_cols=67  Identities=15%  Similarity=0.104  Sum_probs=48.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++-|-+    .|.+.|..+..+.-|..+.++...|..... .+-.+++.+|++.+.
T Consensus         1 ~ti~eva~~~gvs~~tLRyye~----~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~   68 (96)
T cd04768           1 LTIGEFAKLAGVSIRTLRHYDD----IGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLD   68 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            4688999999999999977765    487877554322457788877666655533 334789999988775

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.

>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family

Probab=95.94  E-value=0.02  Score=44.86  Aligned_cols=42  Identities=29%  Similarity=0.300  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+-.|++..+||+.||||++||++++++-+
T Consensus       110 ~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~  151 (158)
T TIGR02937       110 KLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR  151 (158)
T ss_pred             hCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777765555557899999999999999999999999875

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.

>PRK12537 RNA polymerase sigma factor; Provisional

Probab=95.93  E-value=0.019  Score=48.59  Aligned_cols=43  Identities=21%  Similarity=0.220  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-|+..+-+|++..+||+.||||.+||+.++.|-++
T Consensus       133 ~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~  175 (182)
T PRK12537        133 QLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK  175 (182)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence            4677777656666679999999999999999999999998763

>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24

Probab=95.93  E-value=0.021  Score=49.67  Aligned_cols=45  Identities=11%  Similarity=0.030  Sum_probs=42.4

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      ++.+.|.++-.++- ++++...||..+|||.+|++||.++-++.|+
T Consensus         3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GD   48 (165)
T PF08822_consen    3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGD   48 (165)
T ss_pred             CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence            67899999999986 8899999999999999999999999999996

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK09047 RNA polymerase factor sigma-70; Validated

Probab=95.92  E-value=0.021  Score=46.71  Aligned_cols=43  Identities=16%  Similarity=0.160  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..++...|.-++..+-+|++.++||+.||||.+||+..+.|-+
T Consensus       105 ~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  147 (161)
T PRK09047        105 QKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT  147 (161)
T ss_pred             HhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3477777776666678999999999999999999999988865

>TIGR02044 CueR Cu(I)-responsive transcriptional regulator

Probab=95.92  E-value=0.13  Score=42.08  Aligned_cols=67  Identities=15%  Similarity=0.159  Sum_probs=48.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |++.++|+.+|||..|++-|    .+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus         1 m~I~e~a~~~gvs~~tlRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T TIGR02044         1 MNIGQVAKLTGLSSKMIRYY----EEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            57899999999999998644    45677766444322457888887776655533 345789999998875

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.

>PF12728 HTH_17: Helix-turn-helix domain

Probab=95.90  E-value=0.01  Score=40.58  Aligned_cols=23  Identities=13%  Similarity=0.215  Sum_probs=21.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++..|+|+.||||++||++|+++
T Consensus         2 lt~~e~a~~l~is~~tv~~~~~~   24 (51)
T PF12728_consen    2 LTVKEAAELLGISRSTVYRWIRQ   24 (51)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHc
Confidence            57899999999999999999975

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

Probab=95.89  E-value=0.022  Score=46.52  Aligned_cols=43  Identities=26%  Similarity=0.271  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..+|.+.|.-++..+-+|++.++||+.||||.+||+..+.|-+
T Consensus       110 ~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar  152 (159)
T TIGR02989       110 EKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLR  152 (159)
T ss_pred             HHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3577788776666677999999999999999999999999876

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).

>PRK11924 RNA polymerase sigma factor; Provisional

Probab=95.89  E-value=0.02  Score=47.14  Aligned_cols=42  Identities=26%  Similarity=0.233  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+.+|++..+||+.||+|.+||++++.|.+
T Consensus       125 ~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~  166 (179)
T PRK11924        125 ALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR  166 (179)
T ss_pred             hCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            377777776666667999999999999999999999999875

>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]

Probab=95.89  E-value=0.033  Score=55.16  Aligned_cols=84  Identities=15%  Similarity=0.238  Sum_probs=61.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Ccc--------cCCCCCCCCCCCCHHHHHHHHHHHH-hCC--CCCHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SIL--------PGAIGGSKPRVTTPKVVSYIKELKQ-KDP--GIFAWEI  129 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl~--------pk~rgG~RPrklT~e~~~~I~~lv~-~nP--~ita~EI  129 (258)
                      +..++||..+|++.|||+|.++. |..+.  .++        -...+| .-.-.++.++..|++++. +++  -++=.+|
T Consensus       331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~g-g~~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kI  409 (444)
T COG1508         331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEG-GEASSTEAIKALIKKLIEAEDKKKPLSDSKI  409 (444)
T ss_pred             ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCC-CccccHHHHHHHHHHHHhhccCCCCCCHHHH
Confidence            68899999999999999998864 55544  321        111112 112234588999999987 455  4678889


Q ss_pred             HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598        130 RDRLLSDGVCDKFNVPSVSSISRI  153 (258)
Q Consensus       130 r~~L~~~Gv~v~~~~pS~STI~Ri  153 (258)
                      .+.|++.|+.+     +++||...
T Consensus       410 a~lLkekGi~i-----ARRTVAKY  428 (444)
T COG1508         410 AELLKEKGIDV-----ARRTVAKY  428 (444)
T ss_pred             HHHHHHcCCch-----hHHhHHHH
Confidence            99999999986     99999654

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

Probab=95.89  E-value=0.055  Score=42.22  Aligned_cols=67  Identities=13%  Similarity=0.128  Sum_probs=47.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |+..++|+.+|||.+|++.|-+    .|.+.|..+..+.-+..++++...|..... .+-.+++.||+..+.
T Consensus         1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~   68 (96)
T cd04788           1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALD   68 (96)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            5788999999999999987764    677766443222457788877665554433 234788999988775

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.

>PHA00675 hypothetical protein

Probab=95.88  E-value=0.019  Score=44.19  Aligned_cols=40  Identities=25%  Similarity=0.297  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         48 LPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      |....=.+|..+. .+|.|..+||+.||||++||+.|.+..
T Consensus        23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk   63 (78)
T PHA00675         23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYE   63 (78)
T ss_pred             cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccc
Confidence            7776667788888 799999999999999999999998654

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

Probab=95.86  E-value=0.04  Score=42.44  Aligned_cols=66  Identities=9%  Similarity=0.106  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+||+.|.+    .|-+.|....+ ..+..++.+...+...+.  .+-.++..+|+..|.
T Consensus         2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~   69 (91)
T cd04766           2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE   69 (91)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4788999999999999999854    58887754433 457788887777766654  335778887766653

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.

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

Probab=95.86  E-value=0.024  Score=45.67  Aligned_cols=42  Identities=19%  Similarity=0.169  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+-+|++..+||+.||||.+||+.++.|-+
T Consensus       113 ~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~  154 (161)
T TIGR02985       113 KLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKAL  154 (161)
T ss_pred             HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467666665555577999999999999999999999999865

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.

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

Probab=95.86  E-value=0.12  Score=40.60  Aligned_cols=68  Identities=16%  Similarity=0.202  Sum_probs=49.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK--DPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~--nP~ita~EIr~~L~~  135 (258)
                      ++..++|+.+|||.+||+.|.+    .|.+.|..+.+..-+..++++...|.....-  +-.++..+|+..|..
T Consensus         1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~   70 (95)
T cd04780           1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA   70 (95)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence            5788999999999999877766    5777664333323467888888877766442  247889999887765

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.

>TIGR01764 excise DNA binding domain, excisionase family

Probab=95.85  E-value=0.0098  Score=39.26  Aligned_cols=23  Identities=17%  Similarity=0.258  Sum_probs=20.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++..++|+.||||++||++|++.
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~   24 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHE   24 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHc
Confidence            57899999999999999999864

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).

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

Probab=95.85  E-value=0.11  Score=42.80  Aligned_cols=67  Identities=15%  Similarity=0.150  Sum_probs=48.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |++.++|+.+|||.+|++-|    .+.|.+.|....++.-|..++++...|..... .+-.+++.||++.|.
T Consensus         1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   68 (133)
T cd04787           1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILS   68 (133)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            57889999999999998444    56788877654322457788877666555432 335789999998886

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

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

Probab=95.85  E-value=0.031  Score=38.65  Aligned_cols=40  Identities=25%  Similarity=0.235  Sum_probs=31.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++||+..|||.+||+|.++.-                ...+++.+++|.+..++
T Consensus         1 Ti~dIA~~agvS~~TVSr~ln~~----------------~~vs~~tr~rI~~~a~~   40 (46)
T PF00356_consen    1 TIKDIAREAGVSKSTVSRVLNGP----------------PRVSEETRERILEAAEE   40 (46)
T ss_dssp             CHHHHHHHHTSSHHHHHHHHTTC----------------SSSTHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHhCC----------------CCCCHHHHHHHHHHHHH
Confidence            56899999999999999988642                23678888888877654

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 ....

>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=95.85  E-value=0.017  Score=40.68  Aligned_cols=40  Identities=20%  Similarity=0.259  Sum_probs=32.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +|...+ +|+.++..|++..+||+.++||.+||+..+++-.
T Consensus         4 LT~~E~-~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~   43 (58)
T PF00196_consen    4 LTEREL-EVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIM   43 (58)
T ss_dssp             S-HHHH-HHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred             cCHHHH-HHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHH
Confidence            344333 5888899999999999999999999999988865

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 ....

>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID

Probab=95.81  E-value=0.042  Score=42.38  Aligned_cols=57  Identities=14%  Similarity=0.128  Sum_probs=43.4

Q ss_pred             CCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~  119 (258)
                      |=.+-+.+|++++..| .+..+||+.+|||++||++.++.               .+..++++.++.|.+...
T Consensus         3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~---------------~~~~Vs~~Tr~rV~~aa~   60 (80)
T TIGR02844         3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTE---------------RLPEINPELAEEVKEVLD   60 (80)
T ss_pred             cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcC---------------CCCCCCHHHHHHHHHHHc
Confidence            3355678888887656 69999999999999999996521               112367888888888887

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.

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

Probab=95.79  E-value=0.026  Score=47.40  Aligned_cols=43  Identities=14%  Similarity=-0.026  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|+|..+||+.||||.+||...+.|-+.
T Consensus       134 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~  176 (183)
T TIGR02999       134 QVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARA  176 (183)
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3788888766666779999999999999999999999988653

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.

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

Probab=95.77  E-value=0.15  Score=40.09  Aligned_cols=67  Identities=19%  Similarity=0.235  Sum_probs=46.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS  135 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~  135 (258)
                      +..++|+.+|||.+|++.|    .+.|.+.+..+....-+..++++...|..+..-...+++.++++.+..
T Consensus         2 ~i~e~A~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~~~~   68 (99)
T cd04772           2 RTVDLARAIGLSPQTVRNY----ESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRIMRA   68 (99)
T ss_pred             CHHHHHHHHCcCHHHHHHH----HHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence            5789999999999999866    447877653332223577888877776655443247778887765553

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.

>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []

Probab=95.77  E-value=0.023  Score=42.80  Aligned_cols=51  Identities=22%  Similarity=0.139  Sum_probs=39.4

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      -...|.+++.++.-.+..||.+.|.+.|+.+     +.+||+|-|+..+..|....
T Consensus         6 R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~v-----TQaTiSRDLkeL~~vKv~~~   56 (70)
T PF01316_consen    6 RQELIKELISEHEISSQEELVELLEEEGIEV-----TQATISRDLKELGAVKVPDG   56 (70)
T ss_dssp             HHHHHHHHHHHS---SHHHHHHHHHHTT-T-------HHHHHHHHHHHT-EEEECT
T ss_pred             HHHHHHHHHHHCCcCCHHHHHHHHHHcCCCc-----chhHHHHHHHHcCcEEeeCC
Confidence            3678999999999889999999999999986     99999999999999987643

The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....

>PHA00738 putative HTH transcription regulator

Probab=95.75  E-value=0.016  Score=47.16  Aligned_cols=51  Identities=27%  Similarity=0.202  Sum_probs=44.1

Q ss_pred             CHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598         49 PNSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG   99 (258)
Q Consensus        49 S~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg   99 (258)
                      -+..|.+||.++..  ++++++|+..|++|++||++-++--++-|-|...+.|
T Consensus        10 ~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G   62 (108)
T PHA00738         10 AKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG   62 (108)
T ss_pred             CCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence            34689999998765  3899999999999999999999999999988766554

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

Probab=95.73  E-value=0.052  Score=45.34  Aligned_cols=66  Identities=18%  Similarity=0.184  Sum_probs=49.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||.+|++-|-+.    |.+.|....+ .-|..++++...|..+.. .+-.+++.||++.|.
T Consensus         2 ~~I~EvA~~~Gvs~~tLRyYE~~----GLl~p~r~~~-g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (139)
T cd01110           2 LSVGEVAKRSGVAVSALHFYEQK----GLIASWRNAG-NQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA   68 (139)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68899999999999999776654    7776643333 457788887776665544 345789999998875

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.

>PRK12514 RNA polymerase sigma factor; Provisional

Probab=95.72  E-value=0.027  Score=47.30  Aligned_cols=42  Identities=12%  Similarity=0.078  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|+|..+||+.||||.+||+..+.|.+
T Consensus       129 ~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar  170 (179)
T PRK12514        129 ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSL  170 (179)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence            377788877777778999999999999999999999998865

>PRK13919 putative RNA polymerase sigma E protein; Provisional

Probab=95.71  E-value=0.028  Score=47.40  Aligned_cols=43  Identities=19%  Similarity=0.119  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.+|||.+||+.++.|.++
T Consensus       135 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~  177 (186)
T PRK13919        135 ALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS  177 (186)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4777777666666789999999999999999999999988763

>PRK12528 RNA polymerase sigma factor; Provisional

Probab=95.69  E-value=0.031  Score=46.13  Aligned_cols=43  Identities=21%  Similarity=0.233  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus       113 ~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~  155 (161)
T PRK12528        113 GLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM  155 (161)
T ss_pred             HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666777655555679999999999999999999999998764

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

Probab=95.68  E-value=0.068  Score=42.21  Aligned_cols=66  Identities=12%  Similarity=0.037  Sum_probs=46.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|-+    .|.+.|....+ .-+..++++...|..... .+-.+++.+|+..+.
T Consensus         2 ~~i~eva~~~gvs~~tlR~ye~----~Gll~~~r~~~-g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~   68 (102)
T cd04789           2 YTISELAEKAGISRSTLLYYEK----LGLITGTRNAN-GYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ   68 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence            5789999999999999985544    58877643332 457788877766654422 334788888887663

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.

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

Probab=95.65  E-value=0.073  Score=42.66  Aligned_cols=67  Identities=18%  Similarity=0.229  Sum_probs=49.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||.+|++-|-+    .|-+.|....+ .-|..++++...|..... ..-.+++.||++.+..
T Consensus         1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~~~-g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~   68 (112)
T cd01282           1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERSAN-GYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC   68 (112)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            5788999999999999987755    48887644333 457888887776665544 3347899999987763

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.

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.64  E-value=0.035  Score=36.98  Aligned_cols=39  Identities=23%  Similarity=0.285  Sum_probs=32.9

Q ss_pred             HHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         56 IVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        56 IV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      |+....  .+++..+||+.|++|++||++.+++..+.|-+.
T Consensus         5 il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~   45 (53)
T smart00420        5 ILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT   45 (53)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            444432  468999999999999999999999999998775

>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]

Probab=95.63  E-value=0.025  Score=47.92  Aligned_cols=44  Identities=25%  Similarity=0.239  Sum_probs=39.6

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++.+.|.-++...-+|+|..+||+.+|||.+||..++.|-++
T Consensus       126 ~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~  169 (182)
T COG1595         126 ARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK  169 (182)
T ss_pred             HhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            35888999888888889999999999999999999999998764

>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator

Probab=95.61  E-value=0.071  Score=43.93  Aligned_cols=67  Identities=18%  Similarity=0.164  Sum_probs=49.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++.|-+    .|.+.|..+....-|..++++...|..+.. .+-.+++.||++.+.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~   69 (131)
T TIGR02043         2 FQIGELAKLCGVTSDTLRFYEK----NGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLS   69 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5789999999999999877664    477776544322457788877666655533 345889999998886

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.

>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family

Probab=95.61  E-value=0.029  Score=46.10  Aligned_cols=42  Identities=24%  Similarity=0.269  Sum_probs=35.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...|.-++..+-+|++..+||..||||.+||+.++.|-++
T Consensus       111 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~  152 (162)
T TIGR02983       111 LPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA  152 (162)
T ss_pred             CCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            566666666566679999999999999999999999998764

This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.

>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family

Probab=95.60  E-value=0.034  Score=45.80  Aligned_cols=43  Identities=16%  Similarity=0.108  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus       122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~  164 (170)
T TIGR02952       122 ILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIK  164 (170)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5777777666666779999999999999999999999988763

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.

>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function

Probab=95.57  E-value=0.13  Score=46.60  Aligned_cols=95  Identities=23%  Similarity=0.222  Sum_probs=64.7

Q ss_pred             HHHHHHHHH----HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhh-CCcccCCCCC-CCCCCCCHHHHHHHHHHHHhCCC
Q psy15598         52 VRMRIVELA----QLG--IRPCDISRQLRVSHGCVSKILARYHET-GSILPGAIGG-SKPRVTTPKVVSYIKELKQKDPG  123 (258)
Q Consensus        52 lR~RIV~L~----~~G--~S~~eIAr~LGVSrsTVsRwikRyrEt-Gsl~pk~rgG-~RPrklT~e~~~~I~~lv~~nP~  123 (258)
                      ...+|+.+.    ++|  ++..++|..|+||.+||++-++.|++. |.+.|...-- ...+.+  .+...|.++..+  .
T Consensus        88 r~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~--tHK~~ii~~~l~--g  163 (220)
T PF07900_consen   88 RKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGV--THKKIIIRLYLK--G  163 (220)
T ss_pred             HHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcc--hHHHHHHHHHHc--C
Confidence            345666654    344  699999999999999999999999987 8876653210 111222  355666666555  3


Q ss_pred             CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        124 IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       124 ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      ....||+++..          =|..+|-|.++.....
T Consensus       164 ~~~~eiar~t~----------HS~~av~rYi~~F~rV  190 (220)
T PF07900_consen  164 KPTPEIARRTN----------HSPEAVDRYIKDFKRV  190 (220)
T ss_pred             CCHHHHHHHhc----------cCHHHHHHHHHhhHHh
Confidence            56677877664          2888888888765443

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.57  E-value=0.11  Score=38.93  Aligned_cols=67  Identities=15%  Similarity=0.232  Sum_probs=46.6

Q ss_pred             HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy15598         53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD  121 (258)
Q Consensus        53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n  121 (258)
                      -.+|++++.   .+++..+||+.+|++++||++.++...+.|-+.....+|  .-.++......-..+....
T Consensus         7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~--~y~l~~~~~~~~~~~~~~~   76 (91)
T smart00346        7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNG--RYRLGPKVLELGQSYLSSL   76 (91)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCC--ceeecHHHHHHHHHHHhcC
Confidence            355666654   358999999999999999999999999999875432222  2345555555555554443

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

Probab=95.56  E-value=0.078  Score=42.46  Aligned_cols=68  Identities=15%  Similarity=0.048  Sum_probs=49.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||..|++.|-+    .|.+.|..+..+.-+..++++...|..... ..-.+++.+|++.|..
T Consensus         1 y~Ige~A~~~gvs~~tlR~ye~----~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~   69 (107)
T cd01111           1 YSISQLALDAGVSVHIVRDYLL----RGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA   69 (107)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence            4678999999999999876655    488876544322467788888777766544 3458889999888863

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,

>PRK01381 Trp operon repressor; Provisional

Probab=95.56  E-value=0.012  Score=47.32  Aligned_cols=54  Identities=20%  Similarity=0.326  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      ..|.+|+.+...| +|.++||+.+|||.+||.|--+-.+                ..+++.+++|..++..
T Consensus        42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk----------------~~~~~~k~~l~~~l~~   96 (99)
T PRK01381         42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLK----------------TAPPEFKEWLEQQLLK   96 (99)
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhc----------------cCCHHHHHHHHHHhcc
Confidence            4677888877665 9999999999999999988665543                1235667777666543

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

Probab=95.55  E-value=0.2  Score=40.73  Aligned_cols=67  Identities=12%  Similarity=0.136  Sum_probs=47.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++-|    .+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus         1 m~IgevA~~~gvs~~tLRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (127)
T cd04784           1 MKIGELAKKTGCSVETIRYY----EKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ   68 (127)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            57889999999999998554    44677765444322458888887765544422 233789999998875

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.

>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=95.54  E-value=0.03  Score=38.73  Aligned_cols=38  Identities=21%  Similarity=0.330  Sum_probs=31.4

Q ss_pred             HHHHHHH-H-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598         54 MRIVELA-Q-L-GIRPCDISRQLRVSHGCVSKILARYHETG   91 (258)
Q Consensus        54 ~RIV~L~-~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtG   91 (258)
                      .+|+.+. + . .++..++|+.|+||++||++-++.-++.|
T Consensus         3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            4566665 3 2 38999999999999999999999999988

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 ....

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

Probab=95.53  E-value=0.081  Score=41.72  Aligned_cols=66  Identities=18%  Similarity=0.132  Sum_probs=45.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|-+    .|-+.+....+ .-+..++++...|...+. .+-.++..+|+..+.
T Consensus         2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~r~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~   68 (102)
T cd04775           2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSARSEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA   68 (102)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCCCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence            5789999999999999965554    57774433223 447778777666555533 334788999987664

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

>PRK03975 tfx putative transcriptional regulator; Provisional

Probab=95.52  E-value=0.043  Score=46.52  Aligned_cols=43  Identities=23%  Similarity=0.242  Sum_probs=35.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ...++...| +|+.+..+|++..+||+.||+|++||++|.++-+
T Consensus         4 ~~~Lt~rqr-eVL~lr~~GlTq~EIAe~LGiS~~tVs~ie~ra~   46 (141)
T PRK03975          4 ESFLTERQI-EVLRLRERGLTQQEIADILGTSRANVSSIEKRAR   46 (141)
T ss_pred             ccCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            334555554 5667778999999999999999999999999865

>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional

Probab=95.51  E-value=0.073  Score=44.46  Aligned_cols=67  Identities=18%  Similarity=0.183  Sum_probs=49.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..||+.|-+    .|.+.|..+..+.-|..++++...|..+.. ..-.+++.||++.|.
T Consensus         2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   69 (140)
T PRK09514          2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS   69 (140)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5789999999999999987744    577776544332457888887776655533 344789999998875

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=95.50  E-value=0.15  Score=39.77  Aligned_cols=78  Identities=10%  Similarity=0.066  Sum_probs=52.4

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      +..+..+||+.+++|.+++.|..+++-  |.         .|...... -.+...+++ .+.+.+..+|+..+   |.. 
T Consensus        20 ~~~~~~~lA~~~~~S~~~l~r~f~~~~--g~---------s~~~~i~~~Rl~~a~~~L-~~~~~~i~~iA~~~---Gf~-   83 (107)
T PRK10219         20 QPLNIDVVAKKSGYSKWYLQRMFRTVT--HQ---------TLGDYIRQRRLLLAAVEL-RTTERPIFDIAMDL---GYV-   83 (107)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HccCCCHHHHHHHH---CCC-
Confidence            468999999999999999999999973  21         22222111 122233333 34567777776665   665 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+...|.+++.-+.
T Consensus        84 -----~~s~f~~~Fk~~~G~   98 (107)
T PRK10219         84 -----SQQTFSRVFRRQFDR   98 (107)
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 889999999876543

>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family

Probab=95.50  E-value=0.095  Score=48.17  Aligned_cols=89  Identities=18%  Similarity=0.119  Sum_probs=55.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc-ccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCC
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSI-LPGAIGGSKPRVTTPKVVSYIKELKQKDPGIF  125 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl-~pk~rgG~RPrklT~e~~~~I~~lv~~nP~it  125 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-++.=.- ....++...+.....+..+.|.+++..--.--
T Consensus       142 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD  221 (324)
T TIGR02960       142 YLPPRQRAVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYD  221 (324)
T ss_pred             hCCHHHhhHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCC
Confidence            47777777666667799999999999999999999999887753211 11111111123344555555555554322334


Q ss_pred             HHHHHHHHHh
Q psy15598        126 AWEIRDRLLS  135 (258)
Q Consensus       126 a~EIr~~L~~  135 (258)
                      ...|.+.|.+
T Consensus       222 ~~~l~~Lla~  231 (324)
T TIGR02960       222 LDALTALLHE  231 (324)
T ss_pred             HHHHHHHhcC
Confidence            5556665544

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK08241 RNA polymerase factor sigma-70; Validated

Probab=95.49  E-value=0.1  Score=48.44  Aligned_cols=89  Identities=15%  Similarity=0.083  Sum_probs=54.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-++.=.-......+..+.....+..+.+.+++..--.--.
T Consensus       153 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~  232 (339)
T PRK08241        153 HLPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDV  232 (339)
T ss_pred             hCCHHHhhhhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCH
Confidence            46777777666666799999999999999999999999887754211000001112334445555555565553222234


Q ss_pred             HHHHHHHHh
Q psy15598        127 WEIRDRLLS  135 (258)
Q Consensus       127 ~EIr~~L~~  135 (258)
                      ..+.+.|.+
T Consensus       233 ~~l~~lla~  241 (339)
T PRK08241        233 DALVALLTE  241 (339)
T ss_pred             HHHHHHhcC
Confidence            455555543

>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator

Probab=95.48  E-value=0.24  Score=40.59  Aligned_cols=67  Identities=19%  Similarity=0.166  Sum_probs=46.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |++.++|+.+|||..|++.|-+    .|.+.+..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus         1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~   68 (127)
T TIGR02047         1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLR   68 (127)
T ss_pred             CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            5788999999999999876644    577754333222457788877665554433 234789999988775

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.

>PRK07037 extracytoplasmic-function sigma-70 factor; Validated

Probab=95.47  E-value=0.041  Score=45.29  Aligned_cols=43  Identities=26%  Similarity=0.224  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++.++||+.||||.+||+..+.|-++
T Consensus       109 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~  151 (163)
T PRK07037        109 ELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV  151 (163)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666666655555679999999999999999999999887653

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

Probab=95.46  E-value=0.19  Score=41.62  Aligned_cols=88  Identities=14%  Similarity=0.141  Sum_probs=55.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhcCCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSDGVCDKF  142 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~Gv~v~~  142 (258)
                      |++.++|+.+|||.+|++-|-    +.|.+.|..+....-|..++++...|.-... ..-.+++.||++.|......   
T Consensus         1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~~~~---   73 (131)
T cd04786           1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASN---   73 (131)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCC---
Confidence            578899999999999986554    4677766444332457788776665544433 23478999999888632111   


Q ss_pred             CCCCHHHHHHHHHhccCC
Q psy15598        143 NVPSVSSISRILRNKIGS  160 (258)
Q Consensus       143 ~~pS~STI~RiLrr~~~~  160 (258)
                        .+...+...|.++..+
T Consensus        74 --~~~~~~~~~l~~k~~~   89 (131)
T cd04786          74 --WQHDELLAALERKVAD   89 (131)
T ss_pred             --CCHHHHHHHHHHHHHH
Confidence              1334555555544433

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

>PRK12519 RNA polymerase sigma factor; Provisional

Probab=95.46  E-value=0.029  Score=47.73  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++.++||+.||+|.+||..++.|.+
T Consensus       141 ~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  182 (194)
T PRK12519        141 QLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL  182 (194)
T ss_pred             hCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            467776665555567999999999999999999999998865

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

Probab=95.44  E-value=0.25  Score=40.28  Aligned_cols=67  Identities=18%  Similarity=0.186  Sum_probs=47.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||.+|++-|    .+.|.+.+..+..+.-|..++++...|..... ..-.+++.||++.+.
T Consensus         1 ~~I~e~a~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~   68 (126)
T cd04785           1 LSIGELARRTGVNVETIRYY----ESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLA   68 (126)
T ss_pred             CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            57889999999999998754    44677765433222457788887776655543 334788999988775

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.

>PRK12547 RNA polymerase sigma factor; Provisional

Probab=95.44  E-value=0.04  Score=45.83  Aligned_cols=43  Identities=16%  Similarity=0.176  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus       112 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~  154 (164)
T PRK12547        112 LLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN  154 (164)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            3666777666666679999999999999999999999998763

>PRK09644 RNA polymerase sigma factor SigM; Provisional

Probab=95.43  E-value=0.037  Score=45.92  Aligned_cols=44  Identities=14%  Similarity=0.030  Sum_probs=37.5

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++.+.|.-++..+-+|++..+||+.||+|.+||+.++.|-++
T Consensus       107 ~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~  150 (165)
T PRK09644        107 HTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK  150 (165)
T ss_pred             HhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            45778788766666779999999999999999999999998763

>PRK12525 RNA polymerase sigma factor; Provisional

Probab=95.40  E-value=0.044  Score=45.80  Aligned_cols=42  Identities=17%  Similarity=0.205  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||...+.|-.
T Consensus       118 ~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~  159 (168)
T PRK12525        118 GLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF  159 (168)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477887776666678999999999999999999999998865

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

Probab=95.39  E-value=0.03  Score=40.53  Aligned_cols=35  Identities=20%  Similarity=0.235  Sum_probs=31.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ..+++..+||+.+|+++++|++.+++..+.|-+..
T Consensus        20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~   54 (68)
T PF01978_consen   20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER   54 (68)
T ss_dssp             HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            45689999999999999999999999999998753

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.

>PRK12530 RNA polymerase sigma factor; Provisional

Probab=95.38  E-value=0.041  Score=47.11  Aligned_cols=42  Identities=17%  Similarity=0.177  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||..++.|-+
T Consensus       134 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr  175 (189)
T PRK12530        134 HLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR  175 (189)
T ss_pred             hCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777766666667999999999999999999999998865

>PRK12529 RNA polymerase sigma factor; Provisional

Probab=95.36  E-value=0.04  Score=46.67  Aligned_cols=42  Identities=19%  Similarity=0.241  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-|+...-+|++..+||+.||||.+||...+.|-.
T Consensus       127 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl  168 (178)
T PRK12529        127 TLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAY  168 (178)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477777766666677999999999999999999999988754

>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=95.36  E-value=0.042  Score=39.79  Aligned_cols=44  Identities=32%  Similarity=0.386  Sum_probs=34.4

Q ss_pred             HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC
Q psy15598         55 RIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI   98 (258)
Q Consensus        55 RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r   98 (258)
                      .|..+.++  ..+..+||+.|+||++||..-+++..+.|-+.-.+.
T Consensus        12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y   57 (60)
T PF01325_consen   12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY   57 (60)
T ss_dssp             HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence            44555543  479999999999999999999999999998754443

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 ....

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

Probab=95.35  E-value=0.056  Score=37.61  Aligned_cols=30  Identities=20%  Similarity=0.289  Sum_probs=28.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.++||+.|+||+.||++.+++..+.|-+.
T Consensus        27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~   56 (66)
T cd07377          27 SERELAEELGVSRTTVREALRELEAEGLVE   56 (66)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            489999999999999999999999999874

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

>PRK09645 RNA polymerase sigma factor SigL; Provisional

Probab=95.32  E-value=0.047  Score=45.49  Aligned_cols=42  Identities=21%  Similarity=0.199  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus       118 ~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  159 (173)
T PRK09645        118 QLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAL  159 (173)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777775555567999999999999999999988887765

>PRK15043 transcriptional regulator MirA; Provisional

Probab=95.31  E-value=0.075  Score=48.80  Aligned_cols=68  Identities=18%  Similarity=0.248  Sum_probs=50.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||..|++.|.+||   |.+.|....+ ..|..++++.+.|..++. .+-.++..+|+..|..
T Consensus         4 ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~-G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~   72 (243)
T PRK15043          4 YTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDG-GHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN   72 (243)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            688999999999999999998775   6776654444 457788887777665543 2336788888877753

>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family

Probab=95.31  E-value=0.13  Score=47.09  Aligned_cols=84  Identities=10%  Similarity=-0.018  Sum_probs=56.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      .++...|.-++...-.|++..|||+.||+|.+||+..+.|-+..=.  .. ..  +.....+++.+.+.+++..--.--.
T Consensus       108 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr--~~-~~--~~~~~~~~~~~~~~~f~~a~~~gD~  182 (281)
T TIGR02957       108 RLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLD--AR-RP--RFEVSREESRQLLERFVEAAQTGDL  182 (281)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH--hh-CC--CCCCChHHHHHHHHHHHHHHHhCCH
Confidence            4777888776666779999999999999999999999999875411  11 00  1223345555666666554333445


Q ss_pred             HHHHHHHHh
Q psy15598        127 WEIRDRLLS  135 (258)
Q Consensus       127 ~EIr~~L~~  135 (258)
                      ..+...|.+
T Consensus       183 ~~l~~lL~~  191 (281)
T TIGR02957       183 DGLLELLAE  191 (281)
T ss_pred             HHHHHHHhh
Confidence            666666654

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.

>PRK09648 RNA polymerase sigma factor SigD; Reviewed

Probab=95.31  E-value=0.046  Score=46.33  Aligned_cols=43  Identities=16%  Similarity=0.226  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-|+..+-+|++..+||+.||||.+||...+.|-++
T Consensus       139 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  181 (189)
T PRK09648        139 TLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALA  181 (189)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4677777666666779999999999999999999999988653

>PRK10046 dpiA two-component response regulator DpiA; Provisional

Probab=95.31  E-value=0.038  Score=48.06  Aligned_cols=47  Identities=11%  Similarity=0.076  Sum_probs=38.6

Q ss_pred             CCHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQL---GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~---G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++.....+|+.++.+   |.+.++||+.|+||..||.+.+..-.+.|.+.
T Consensus       159 ~~~Lt~r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~  208 (225)
T PRK10046        159 IDPLTLNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLII  208 (225)
T ss_pred             CCHHHHHHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEE
Confidence            333333388888877   48999999999999999999999999999653

>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR

Probab=95.29  E-value=0.023  Score=46.06  Aligned_cols=36  Identities=28%  Similarity=0.311  Sum_probs=30.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSK   82 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsR   82 (258)
                      .++.+.|.-|+..+-+|+|..+||+.||+|.+||++
T Consensus       107 ~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~~  142 (142)
T TIGR03209       107 ILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVYK  142 (142)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence            467777766666677999999999999999999974

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.

>PRK12516 RNA polymerase sigma factor; Provisional

Probab=95.27  E-value=0.046  Score=46.94  Aligned_cols=42  Identities=17%  Similarity=0.237  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++...-+|++..+||+.||||.+||...+.|-+
T Consensus       116 ~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar  157 (187)
T PRK12516        116 QLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR  157 (187)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777766666677999999999999999999999988865

>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D

Probab=95.26  E-value=0.027  Score=43.66  Aligned_cols=34  Identities=21%  Similarity=0.296  Sum_probs=23.3

Q ss_pred             HHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++.|+|+..    +...+++++|+.||||+|||++=+.
T Consensus         4 IeeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvt   41 (82)
T PF12116_consen    4 IEERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVT   41 (82)
T ss_dssp             HHHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHH
Confidence            455566543    4689999999999999999998664

It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.

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

Probab=95.24  E-value=0.13  Score=40.90  Aligned_cols=67  Identities=15%  Similarity=0.156  Sum_probs=48.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC-CCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG-SKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG-~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++-|.+    .|-+.|..+.+ +..|..++.+...|..... .+-.+++.+|...+.
T Consensus         1 ~~i~eva~~~gis~~tlR~ye~----~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~   69 (108)
T cd01107           1 FTIGEFAKLSNLSIKALRYYDK----IGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD   69 (108)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----cCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            4688999999999999977765    48787754321 2467888887777665543 234788889987665

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.

>PRK09649 RNA polymerase sigma factor SigC; Reviewed

Probab=95.23  E-value=0.045  Score=46.67  Aligned_cols=43  Identities=19%  Similarity=0.233  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-+.
T Consensus       130 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~  172 (185)
T PRK09649        130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD  172 (185)
T ss_pred             hCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4777777766666779999999999999999999999988764

>PRK12532 RNA polymerase sigma factor; Provisional

Probab=95.22  E-value=0.045  Score=46.73  Aligned_cols=42  Identities=19%  Similarity=0.219  Sum_probs=35.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       136 ~L~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  177 (195)
T PRK12532        136 NLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR  177 (195)
T ss_pred             hCCHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777766666677999999999999999999999988865

>PRK12523 RNA polymerase sigma factor; Reviewed

Probab=95.22  E-value=0.053  Score=45.37  Aligned_cols=42  Identities=24%  Similarity=0.218  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||+.||||.+||...+.|-.
T Consensus       119 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  160 (172)
T PRK12523        119 KLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL  160 (172)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            466777765555567999999999999999999999998865

>PRK09415 RNA polymerase factor sigma C; Reviewed

Probab=95.21  E-value=0.044  Score=46.34  Aligned_cols=43  Identities=21%  Similarity=0.151  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|.++
T Consensus       127 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~  169 (179)
T PRK09415        127 SLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE  169 (179)
T ss_pred             hCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4777777666666779999999999999999999999999764

>PRK12522 RNA polymerase sigma factor; Provisional

Probab=95.20  E-value=0.049  Score=45.55  Aligned_cols=43  Identities=16%  Similarity=0.063  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus       119 ~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~  161 (173)
T PRK12522        119 LLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK  161 (173)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4677777656655679999999999999999999999998753

>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family

Probab=95.17  E-value=0.056  Score=45.39  Aligned_cols=42  Identities=21%  Similarity=0.229  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+
T Consensus       100 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar  141 (170)
T TIGR02959       100 ELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGR  141 (170)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            577877766666678999999999999999999999988765

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).

>PRK12536 RNA polymerase sigma factor; Provisional

Probab=95.16  E-value=0.054  Score=45.79  Aligned_cols=42  Identities=21%  Similarity=0.283  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++.++||+.||||.+||...+.|-+
T Consensus       129 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar  170 (181)
T PRK12536        129 QLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGL  170 (181)
T ss_pred             HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            466666665555667999999999999999999999998865

>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD

Probab=95.15  E-value=0.13  Score=42.34  Aligned_cols=68  Identities=15%  Similarity=0.068  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      .+++.++|+.+|||..||+-|-+    .|.+.|..+..+.-|..++++...|.-... ..-.+++.+|+..|.
T Consensus         3 ~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~   71 (120)
T TIGR02054         3 AYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCR   71 (120)
T ss_pred             CCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            47899999999999999865544    588877655333567888887777666644 445788999988775

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.

>PRK12520 RNA polymerase sigma factor; Provisional

Probab=95.14  E-value=0.054  Score=46.09  Aligned_cols=42  Identities=17%  Similarity=0.187  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|+|..+||..||+|.+||...+.|-+
T Consensus       131 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar  172 (191)
T PRK12520        131 RLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRAR  172 (191)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            377777776666667999999999999999999999988865

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

Probab=95.14  E-value=0.27  Score=39.54  Aligned_cols=67  Identities=16%  Similarity=0.207  Sum_probs=48.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      ++..++|+.+|||..|++-|-    +.|.+.|..+.+ .-+..++.+...|..... .+=.++..||+..+..
T Consensus         1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~   68 (116)
T cd04769           1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG   68 (116)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            578899999999999986554    458887755554 457788877776554432 2247889999888764

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.

>PRK05602 RNA polymerase sigma factor; Reviewed

Probab=95.13  E-value=0.05  Score=46.04  Aligned_cols=43  Identities=23%  Similarity=0.298  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus       128 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (186)
T PRK05602        128 ALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRR  170 (186)
T ss_pred             hCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            4677777766666779999999999999999999999988653

>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family

Probab=95.13  E-value=0.053  Score=45.07  Aligned_cols=43  Identities=16%  Similarity=0.166  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus       119 ~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~  161 (169)
T TIGR02954       119 TLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK  161 (169)
T ss_pred             hCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4777777655566679999999999999999999999998763

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.

>PF07638 Sigma70_ECF: ECF sigma factor

Probab=95.09  E-value=0.056  Score=46.50  Aligned_cols=35  Identities=31%  Similarity=0.405  Sum_probs=29.9

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++|.+. -.|+|..|||+.||||.+||+|.++..+
T Consensus       141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR  176 (185)
T PF07638_consen  141 RRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR  176 (185)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4556554 5999999999999999999999988765

>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=95.08  E-value=0.042  Score=38.39  Aligned_cols=31  Identities=23%  Similarity=0.482  Sum_probs=28.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||+.++++++||++.+++..+.|-|.
T Consensus        22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~   52 (62)
T PF12802_consen   22 LTQSELAERLGISKSTVSRIVKRLEKKGLVE   52 (62)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            7999999999999999999999999999774

...

>PRK09646 RNA polymerase sigma factor SigK; Reviewed

Probab=95.08  E-value=0.057  Score=46.23  Aligned_cols=43  Identities=16%  Similarity=0.145  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||..++.|-+.
T Consensus       142 ~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~  184 (194)
T PRK09646        142 ALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLI  184 (194)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence            4777777655555679999999999999999999999988753

>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT)

Probab=95.07  E-value=0.033  Score=44.80  Aligned_cols=38  Identities=21%  Similarity=0.292  Sum_probs=28.0

Q ss_pred             HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +...+++.++ .+.+|.++||..+||||..|+.+++|-.
T Consensus        20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~   58 (101)
T PF04297_consen   20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE   58 (101)
T ss_dssp             HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3444666665 5789999999999999999999999965

Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.

>PRK12512 RNA polymerase sigma factor; Provisional

Probab=95.05  E-value=0.06  Score=45.36  Aligned_cols=42  Identities=24%  Similarity=0.258  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus       131 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~  172 (184)
T PRK12512        131 TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGL  172 (184)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            477777766666667999999999999999999999998865

>PRK12511 RNA polymerase sigma factor; Provisional

Probab=95.05  E-value=0.058  Score=46.23  Aligned_cols=43  Identities=19%  Similarity=0.241  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus       111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~  153 (182)
T PRK12511        111 DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA  153 (182)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence            5788888777666779999999999999999999999877653

>PRK13749 transcriptional regulator MerD; Provisional

Probab=95.04  E-value=0.16  Score=41.93  Aligned_cols=69  Identities=13%  Similarity=0.024  Sum_probs=52.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      .+++.++|+.+|||..||+-    |.+.|-+.|..+..+.-|..++++...|..+.. +.-.+++.||++.|..
T Consensus         3 ~~tIgelA~~~gvS~~tiR~----YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l   72 (121)
T PRK13749          3 AYTVSRLALDAGVSVHIVRD----YLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA   72 (121)
T ss_pred             CCcHHHHHHHHCCCHHHHHH----HHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence            37899999999999999854    455688766545323568889988888766655 4568999999988864

>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family

Probab=95.03  E-value=0.027  Score=48.00  Aligned_cols=42  Identities=21%  Similarity=0.203  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus       131 ~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  172 (193)
T TIGR02947       131 GLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGR  172 (193)
T ss_pred             hCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777776666677999999999999999999999988865

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.

>PRK06811 RNA polymerase factor sigma-70; Validated

Probab=95.03  E-value=0.061  Score=45.85  Aligned_cols=43  Identities=19%  Similarity=0.248  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus       131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~  173 (189)
T PRK06811        131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRK  173 (189)
T ss_pred             hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5777777655555679999999999999999999999988764

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

Probab=95.03  E-value=0.054  Score=49.01  Aligned_cols=42  Identities=19%  Similarity=0.120  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+-+|+|.++||..||||.+||...+.|-+
T Consensus       161 ~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr  202 (244)
T TIGR03001       161 ALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQAR  202 (244)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477778877777778999999999999999999999999875

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.

>PRK12539 RNA polymerase sigma factor; Provisional

Probab=95.02  E-value=0.058  Score=45.74  Aligned_cols=42  Identities=19%  Similarity=0.269  Sum_probs=36.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       131 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~  172 (184)
T PRK12539        131 RLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGL  172 (184)
T ss_pred             hCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777776666677999999999999999999999998865

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

Probab=95.02  E-value=0.087  Score=37.63  Aligned_cols=40  Identities=23%  Similarity=0.277  Sum_probs=32.0

Q ss_pred             CHHHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         49 PNSVRMRIVELAQLGI-------RPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~-------S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +...|.-+..+++.|.       +..++|+.||||++|++.-+++-.
T Consensus         2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae   48 (53)
T PF04967_consen    2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE   48 (53)
T ss_pred             CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4555666666677663       889999999999999999998864

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

>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein

Probab=95.01  E-value=0.16  Score=36.26  Aligned_cols=77  Identities=19%  Similarity=0.296  Sum_probs=53.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFN  143 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~  143 (258)
                      .+..+||+.+|+|.+++++.+++..  |. .++       ..+.......+.+++..+ .++..+|+..+   |+.    
T Consensus         2 ~~~~~la~~~~~s~~~l~~~f~~~~--~~-s~~-------~~~~~~r~~~a~~~l~~~-~~~~~~ia~~~---g~~----   63 (84)
T smart00342        2 LTLEDLAEALGMSPRHLQRLFKKET--GT-TPK-------QYLRDRRLERARRLLRDT-DLSVTEIALRV---GFS----   63 (84)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHh--Cc-CHH-------HHHHHHHHHHHHHHHHcC-CCCHHHHHHHh---CCC----
Confidence            5789999999999999999999763  11 000       112223345566666665 78888887766   553    


Q ss_pred             CCCHHHHHHHHHhccCC
Q psy15598        144 VPSVSSISRILRNKIGS  160 (258)
Q Consensus       144 ~pS~STI~RiLrr~~~~  160 (258)
                        |.+...|.+++.-+.
T Consensus        64 --s~~~f~r~Fk~~~g~   78 (84)
T smart00342       64 --SQSYFSRAFKKLFGV   78 (84)
T ss_pred             --ChHHHHHHHHHHHCc
Confidence              889999999876543

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=95.01  E-value=0.063  Score=39.03  Aligned_cols=38  Identities=21%  Similarity=0.258  Sum_probs=32.7

Q ss_pred             HHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         55 RIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        55 RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +|+.+..++ .+..+||+.||||++||++-+++.++.|-
T Consensus         4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~   42 (69)
T TIGR00122         4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV   42 (69)
T ss_pred             HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            466666554 68999999999999999999999999886

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.

>PRK08301 sporulation sigma factor SigE; Reviewed

Probab=95.01  E-value=0.048  Score=48.15  Aligned_cols=42  Identities=12%  Similarity=0.089  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+    .+|+|..+||+.||||.+||.+++.|-+
T Consensus       178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~  223 (234)
T PRK08301        178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRII  223 (234)
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46777666555555    4899999999999999999999988764

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=95.01  E-value=0.24  Score=40.29  Aligned_cols=86  Identities=12%  Similarity=0.118  Sum_probs=55.5

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHH-HHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVV-SYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~-~~I~~lv~~nP~ita~E  128 (258)
                      .+|+..+.    +..+..++|+.+|+|++++.|+.+++-  |.         .|.....+.+ .....++. +.+.+..+
T Consensus        12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~--G~---------s~~~~l~~~Rl~~A~~~L~-~t~~~i~e   79 (127)
T PRK11511         12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKET--GH---------SLGQYIRSRKMTEIAQKLK-ESNEPILY   79 (127)
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCCCCHHH
Confidence            34444443    458999999999999999999999974  21         1221111111 12223333 45677777


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      +.+...|.+++.-+.
T Consensus        80 IA~~~---Gf~------s~s~F~r~Fkk~~G~  102 (127)
T PRK11511         80 LAERY---GFE------SQQTLTRTFKNYFDV  102 (127)
T ss_pred             HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            76655   665      889999999877664

>PRK13182 racA polar chromosome segregation protein; Reviewed

Probab=94.99  E-value=0.088  Score=46.06  Aligned_cols=63  Identities=11%  Similarity=0.094  Sum_probs=45.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRD  131 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~  131 (258)
                      ++..++|+.+|||..||++|.+++.    +......+ ..+..++++...|..++. .+-+++..+|+.
T Consensus         1 mti~evA~~lGVS~~TLRrw~k~g~----L~~~R~~~-G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~   64 (175)
T PRK13182          1 MKTPFVAKKLGVSPKTVQRWVKQLN----LPCEKNEY-GHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK   64 (175)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHcCC----CCCCcCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence            4789999999999999999999753    32222222 347788887777766653 445788888865

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

Probab=94.98  E-value=0.047  Score=51.92  Aligned_cols=42  Identities=29%  Similarity=0.397  Sum_probs=35.8

Q ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      -.++-.++ .+|++..+||++|||||.+|+|.+++-++.|-|+
T Consensus        15 ~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~   57 (321)
T COG2390          15 LARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVK   57 (321)
T ss_pred             HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEE
Confidence            34444454 5899999999999999999999999999999764

>PHA00542 putative Cro-like protein

Probab=94.96  E-value=0.048  Score=41.60  Aligned_cols=32  Identities=19%  Similarity=0.230  Sum_probs=26.4

Q ss_pred             HHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         55 RIVEL-AQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        55 RIV~L-~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +++.+ ...|++..++|+.+|||++||++|.+.
T Consensus        22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g   54 (82)
T PHA00542         22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSG   54 (82)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            34444 457999999999999999999999754

>PRK12534 RNA polymerase sigma factor; Provisional

Probab=94.95  E-value=0.065  Score=45.28  Aligned_cols=43  Identities=16%  Similarity=0.052  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus       137 ~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~  179 (187)
T PRK12534        137 ELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA  179 (187)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence            4666777666666679999999999999999999999998763

>PRK09637 RNA polymerase sigma factor SigZ; Provisional

Probab=94.95  E-value=0.063  Score=45.80  Aligned_cols=43  Identities=16%  Similarity=0.151  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++.+.|.-++...-+|++..+||+.||||.+||++.+.|-+.
T Consensus       106 ~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~  148 (181)
T PRK09637        106 ALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV  148 (181)
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            5777777766666779999999999999999999999887653

>PRK09647 RNA polymerase sigma factor SigE; Reviewed

Probab=94.93  E-value=0.066  Score=46.79  Aligned_cols=42  Identities=26%  Similarity=0.297  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       138 ~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr  179 (203)
T PRK09647        138 SLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR  179 (203)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477777766666677999999999999999999999999975

>PRK12524 RNA polymerase sigma factor; Provisional

Probab=94.92  E-value=0.067  Score=45.87  Aligned_cols=42  Identities=21%  Similarity=0.283  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||..++.|-+
T Consensus       136 ~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~  177 (196)
T PRK12524        136 ALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK  177 (196)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            467777766666667999999999999999999999999865

>PRK12526 RNA polymerase sigma factor; Provisional

Probab=94.92  E-value=0.067  Score=46.47  Aligned_cols=43  Identities=19%  Similarity=0.193  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .|+...|.-|+..+-+|++..+||+.||||.+||..++.|-++
T Consensus       153 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~  195 (206)
T PRK12526        153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA  195 (206)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4777777666666779999999999999999999999888653

>PRK12540 RNA polymerase sigma factor; Provisional

Probab=94.89  E-value=0.067  Score=45.74  Aligned_cols=43  Identities=16%  Similarity=0.220  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus       111 ~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~  153 (182)
T PRK12540        111 KLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS  153 (182)
T ss_pred             hCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4677777777776789999999999999999999999888754

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

Probab=94.89  E-value=0.068  Score=46.89  Aligned_cols=42  Identities=24%  Similarity=0.243  Sum_probs=36.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+.+|++.++||+.||||.+||++++++-.
T Consensus       178 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ra~  219 (227)
T TIGR02980       178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRAL  219 (227)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477778877777677999999999999999999999998865

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.

>PRK12543 RNA polymerase sigma factor; Provisional

Probab=94.89  E-value=0.071  Score=44.97  Aligned_cols=42  Identities=19%  Similarity=0.198  Sum_probs=35.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus       117 ~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~  158 (179)
T PRK12543        117 KLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL  158 (179)
T ss_pred             hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            377777766666667999999999999999999999888864

>PRK12517 RNA polymerase sigma factor; Provisional

Probab=94.88  E-value=0.069  Score=45.83  Aligned_cols=43  Identities=19%  Similarity=0.142  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||..||||.+||+..+.|.+.
T Consensus       128 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~  170 (188)
T PRK12517        128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN  170 (188)
T ss_pred             hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            5777777766666679999999999999999999999998763

>TIGR02051 MerR Hg(II)-responsive transcriptional regulator

Probab=94.88  E-value=0.14  Score=41.70  Aligned_cols=66  Identities=14%  Similarity=0.082  Sum_probs=46.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++.++|+.+|||..|++.|    .+.|.+.+..+..+.-+..++++...|..+.. ..-.+++.||++.|.
T Consensus         1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~   67 (124)
T TIGR02051         1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLG   67 (124)
T ss_pred             CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            4679999999999999655    55677764333222457777777766655432 344789999998885

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.

>PRK06986 fliA flagellar biosynthesis sigma factor; Validated

Probab=94.88  E-value=0.06  Score=47.77  Aligned_cols=42  Identities=24%  Similarity=0.213  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+.+|+|..+||+.||||.+||+++++|-+
T Consensus       184 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  225 (236)
T PRK06986        184 SLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAI  225 (236)
T ss_pred             hCCHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            367777766666677999999999999999999999988865

>COG0789 SoxR Predicted transcriptional regulators [Transcription]

Probab=94.87  E-value=0.19  Score=39.90  Aligned_cols=68  Identities=18%  Similarity=0.182  Sum_probs=48.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||..|++-|    .+.|.+.|..+..+.-|..++++...+..+.. .+-.+++.+|++.|..
T Consensus         1 ~~I~eva~~~gvs~~tLRyY----E~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~   69 (124)
T COG0789           1 YTIGEVAKLTGVSVRTLRFY----ERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDL   69 (124)
T ss_pred             CcHHHHHHHhCCCHHHHHHH----HHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            47889999999999998654    45677766655422457888887665554433 2458899999988864

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.86  E-value=0.072  Score=36.16  Aligned_cols=35  Identities=23%  Similarity=0.385  Sum_probs=31.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+..+..+|++.|++|++||++.+++..+.|-+..
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~   42 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVES   42 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence            45689999999999999999999999999997753

>PRK12542 RNA polymerase sigma factor; Provisional

Probab=94.86  E-value=0.072  Score=45.11  Aligned_cols=42  Identities=19%  Similarity=0.137  Sum_probs=35.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus       122 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar  163 (185)
T PRK12542        122 ELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR  163 (185)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            477777766666677999999999999999999999988865

>PRK12527 RNA polymerase sigma factor; Reviewed

Probab=94.85  E-value=0.08  Score=43.55  Aligned_cols=42  Identities=21%  Similarity=0.249  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+
T Consensus       105 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~  146 (159)
T PRK12527        105 ELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM  146 (159)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            377777765555567999999999999999999999988764

>PRK12533 RNA polymerase sigma factor; Provisional

Probab=94.85  E-value=0.061  Score=47.73  Aligned_cols=43  Identities=26%  Similarity=0.186  Sum_probs=35.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus       134 ~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~  176 (216)
T PRK12533        134 KLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARR  176 (216)
T ss_pred             cCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666777666665679999999999999999999999887653

>TIGR02948 SigW_bacill RNA polymerase sigma-W factor

Probab=94.84  E-value=0.063  Score=44.95  Aligned_cols=43  Identities=30%  Similarity=0.285  Sum_probs=35.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-+...+-+|++..+||+.||+|.++|+..+.|-+.
T Consensus       136 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~  178 (187)
T TIGR02948       136 ALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGRE  178 (187)
T ss_pred             hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4666666655555679999999999999999999999998753

This sigma factor is restricted to certain lineages of the order Bacillales.

>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR

Probab=94.84  E-value=0.3  Score=41.11  Aligned_cols=66  Identities=17%  Similarity=0.167  Sum_probs=47.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++-|-+    .|.+.+....+ .-|..++++...|..+.. .+-.+++.+|++.+.
T Consensus         2 ~~IgevA~~~Gvs~~tLRyYE~----~GLl~~~r~~~-g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~   68 (142)
T TIGR01950         2 LTVGELAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALA   68 (142)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            6789999999999999866554    48887644333 347788777665555433 234788999998885

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.

>PRK12545 RNA polymerase sigma factor; Provisional

Probab=94.81  E-value=0.073  Score=46.07  Aligned_cols=42  Identities=21%  Similarity=0.235  Sum_probs=35.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus       139 ~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr  180 (201)
T PRK12545        139 HLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRAR  180 (201)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777777776677999999999999999999998887754

>PRK10227 DNA-binding transcriptional regulator CueR; Provisional

Probab=94.81  E-value=0.18  Score=41.95  Aligned_cols=67  Identities=16%  Similarity=0.212  Sum_probs=49.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |++.++|+.+|||..||+-    |.+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.+.
T Consensus         1 m~Ige~a~~~gvs~~tlRy----YE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~   68 (135)
T PRK10227          1 MNISDVAKITGLTSKAIRF----YEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (135)
T ss_pred             CCHHHHHHHHCcCHHHHHH----HHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            5788999999999999854    455677766544322458888888777766544 345889999988775

>PRK09636 RNA polymerase sigma factor SigJ; Provisional

Probab=94.81  E-value=0.21  Score=45.77  Aligned_cols=44  Identities=16%  Similarity=0.160  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      .++...|.-++...-+|++.+|||+.||+|.+||+..+.|-+..
T Consensus       115 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~  158 (293)
T PRK09636        115 RLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH  158 (293)
T ss_pred             hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            47888887666666799999999999999999999999998754

>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1

Probab=94.80  E-value=0.08  Score=44.30  Aligned_cols=42  Identities=24%  Similarity=0.301  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+-+|++..+||..||||.+||++-+.|.+
T Consensus       140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~  181 (189)
T TIGR02984       140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGL  181 (189)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            578887777766677999999999999999999999988865

This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).

>PRK06704 RNA polymerase factor sigma-70; Validated

Probab=94.79  E-value=0.062  Score=48.49  Aligned_cols=75  Identities=16%  Similarity=0.133  Sum_probs=49.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPG  123 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~  123 (258)
                      .++...|.-++...-+|+|.+|||+.+|+|.+||...+.|-++.=...- ..++ .+.-.....+..+..+.++||.
T Consensus       116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l-~~~~-~~~~~~~~~~~~~~~~~~~~~~  190 (228)
T PRK06704        116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS-EEGI-EIVEFTDDMEVVVTSIREERPE  190 (228)
T ss_pred             hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH-HhcC-CCCCccccHHHHHHHHHhcCHH
Confidence            4677777666666678999999999999999999999888764321000 0122 1222234456677777777774

>PRK08583 RNA polymerase sigma factor SigB; Validated

Probab=94.78  E-value=0.072  Score=47.86  Aligned_cols=42  Identities=14%  Similarity=0.065  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+-+|++..+||+.||||.+||++++++-.
T Consensus       205 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~  246 (257)
T PRK08583        205 VLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAI  246 (257)
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            366677765555567999999999999999999999998765

>PRK06930 positive control sigma-like factor; Validated

Probab=94.74  E-value=0.081  Score=45.74  Aligned_cols=42  Identities=14%  Similarity=0.218  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+.+|++..+||+.||||.+||..++.|-+
T Consensus       114 ~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~  155 (170)
T PRK06930        114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE  155 (170)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777766666678999999999999999999999998865

>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes

Probab=94.74  E-value=0.15  Score=44.62  Aligned_cols=52  Identities=17%  Similarity=0.126  Sum_probs=46.4

Q ss_pred             ccCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         42 FVNGRPLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        42 ~~~gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      |+....+|.++|..|+..+. +|++.++||..|||+...|.-+++-+.-.+..
T Consensus        11 f~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~   63 (172)
T PF12298_consen   11 FRSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIEKRW   63 (172)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence            66777899999999999985 78999999999999999999999998766554

This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].

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

Probab=94.74  E-value=0.08  Score=42.97  Aligned_cols=42  Identities=17%  Similarity=0.130  Sum_probs=36.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.|.-..|-..-.+|++..+.|++.|||++|+++++...+
T Consensus        41 ~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~AR   82 (106)
T PF02001_consen   41 VLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESAR   82 (106)
T ss_pred             EeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHH
Confidence            577888777766667999999999999999999999998865

>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=94.71  E-value=0.066  Score=38.10  Aligned_cols=41  Identities=22%  Similarity=0.396  Sum_probs=35.5

Q ss_pred             HHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         53 RMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        53 R~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+|+++++ .| .+..++|+.|+||..||+|=++...+.|.+
T Consensus         2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i   44 (57)
T PF08220_consen    2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI   44 (57)
T ss_pred             HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            456777775 34 799999999999999999999999999875

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

>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family

Probab=94.71  E-value=0.078  Score=46.60  Aligned_cols=43  Identities=14%  Similarity=0.120  Sum_probs=37.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|+|..+||+.+|||.+||++++++-.+
T Consensus       175 ~L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~  217 (224)
T TIGR02479       175 SLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALK  217 (224)
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4778888777777789999999999999999999999888653

Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.

>COG1438 ArgR Arginine repressor [Transcription]

Probab=94.70  E-value=0.073  Score=45.66  Aligned_cols=52  Identities=17%  Similarity=0.154  Sum_probs=47.0

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      +..+.|++++.++.--+..||.+.|++.|+++     +.+||+|-|+..+..|....
T Consensus         6 ~R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~v-----TQaTvSRDlkelglvKv~~~   57 (150)
T COG1438           6 ERLELIKEIITEEKISTQEELVELLQEEGIEV-----TQATVSRDLKELGLVKVRNE   57 (150)
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCeE-----ehHHHHHHHHHcCCEEecCC
Confidence            45788999999999899999999999999986     99999999999999988743

>PRK09863 putative frv operon regulatory protein; Provisional

Probab=94.64  E-value=0.29  Score=49.31  Aligned_cols=95  Identities=15%  Similarity=0.087  Sum_probs=61.6

Q ss_pred             HHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhh----hCC-cccCCCCCCCC-----C-------CCCHHHHHHH
Q psy15598         53 RMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHE----TGS-ILPGAIGGSKP-----R-------VTTPKVVSYI  114 (258)
Q Consensus        53 R~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrE----tGs-l~pk~rgG~RP-----r-------klT~e~~~~I  114 (258)
                      ..+|+.+.. +..+..++|+.||||.+||++-++.-.+    .|. +..+. +|-+=     .       ...++....+
T Consensus         6 ~~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~-~Gy~l~~~~~~~~~~~~~~~~~e~~~il   84 (584)
T PRK09863          6 ELKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGS-AKYHLEILNRRSLFQLLQKSDNEDRLLL   84 (584)
T ss_pred             HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecC-CceEEEeCCHHHHHHHHhcCCHHHHHHH
Confidence            455666654 5689999999999999999999986643    332 11221 23110     0       0122333344


Q ss_pred             HHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        115 KELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       115 ~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      ..++. +...+..++++.|.          ||.+||.+-|++...
T Consensus        85 ~~Ll~-~~~~~~~~La~~l~----------vS~sTi~~dl~~v~~  118 (584)
T PRK09863         85 LRLLL-NTFTPMAQLASALN----------LSRTWVAERLPRLNQ  118 (584)
T ss_pred             HHHHH-cCCccHHHHHHHhC----------CCHHHHHHHHHHHHH
Confidence            44554 55678888888884          599999999987665

>PRK12531 RNA polymerase sigma factor; Provisional

Probab=94.63  E-value=0.09  Score=45.00  Aligned_cols=42  Identities=14%  Similarity=0.137  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||..||||.+||..-+.|-+
T Consensus       141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~  182 (194)
T PRK12531        141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV  182 (194)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence            467777765555577999999999999999999998887765

>PF13730 HTH_36: Helix-turn-helix domain

Probab=94.62  E-value=0.054  Score=37.42  Aligned_cols=28  Identities=21%  Similarity=0.343  Sum_probs=26.3

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      |.+.||+.+|+|++||.++++.-++.|-
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~   54 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEKGL   54 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence            8899999999999999999999998774

>PRK12541 RNA polymerase sigma factor; Provisional

Probab=94.61  E-value=0.087  Score=43.42  Aligned_cols=43  Identities=21%  Similarity=0.125  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus       112 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~  154 (161)
T PRK12541        112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK  154 (161)
T ss_pred             HCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4777777766666679999999999999999999999998763

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

Probab=94.60  E-value=0.24  Score=39.10  Aligned_cols=65  Identities=17%  Similarity=0.270  Sum_probs=45.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++    -|.+.|-+.|...+|  -+..+++....|..... ++-.+++.||++.+.
T Consensus         1 m~Ige~a~~~gvs~~tlR----yYe~~GLl~p~~~~g--~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~   66 (107)
T cd04777           1 MKIGKFAKKNNITIDTVR----HYIDLGLLIPEKKGG--QYFFDEKCQDDLEFILELKGLGFSLIEIQKIFS   66 (107)
T ss_pred             CCHHHHHHHHCcCHHHHH----HHHHCCCcCCccCCC--ccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            578899999999999974    455678887754344  24577766655544433 334789999998885

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.

>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional

Probab=94.59  E-value=0.085  Score=44.79  Aligned_cols=42  Identities=21%  Similarity=0.270  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       138 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar  179 (193)
T PRK11923        138 QLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR  179 (193)
T ss_pred             hCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            366666665666577999999999999999999999988865

>PRK09640 RNA polymerase sigma factor SigX; Reviewed

Probab=94.58  E-value=0.032  Score=47.50  Aligned_cols=42  Identities=10%  Similarity=-0.050  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||..++.|-+
T Consensus       134 ~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  175 (188)
T PRK09640        134 HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRAL  175 (188)
T ss_pred             hcChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            356665554444567999999999999999999999999875

>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family

Probab=94.57  E-value=0.093  Score=44.93  Aligned_cols=42  Identities=21%  Similarity=0.297  Sum_probs=35.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++.++||+.||+|.+||...+.|-+
T Consensus       131 ~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar  172 (188)
T TIGR02943       131 HLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRAR  172 (188)
T ss_pred             hCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            466777766666667999999999999999999999888864

This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.

>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional

Probab=94.57  E-value=0.22  Score=43.61  Aligned_cols=65  Identities=14%  Similarity=0.106  Sum_probs=44.2

Q ss_pred             CCCCCHHHHHHHHHHHHc-----C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598         45 GRPLPNSVRMRIVELAQL-----G--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK  109 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~-----G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e  109 (258)
                      ...++..+-..|.+.+..     |  ++..++|++|||||++|+.-+++-...|-|...+..|-.-..++..
T Consensus         9 ~~~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~   80 (221)
T PRK11414          9 HISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR   80 (221)
T ss_pred             CCCHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCHH
Confidence            334444444444444333     3  4788999999999999999999999999887666555333334443

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

Probab=94.56  E-value=0.053  Score=39.89  Aligned_cols=43  Identities=16%  Similarity=0.219  Sum_probs=34.5

Q ss_pred             HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      +++|++.++   .+++.+|||+.+|+|+.+|++|+..-...|.|+.
T Consensus         2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~   47 (62)
T PF04703_consen    2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVER   47 (62)
T ss_dssp             HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred             cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            345666554   4689999999999999999999999999998853

>PRK03341 arginine repressor; Provisional

Probab=94.55  E-value=0.1  Score=45.33  Aligned_cols=53  Identities=13%  Similarity=0.058  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      .+-.+.|+++++++.-.+..||.+.|.+.|+.+     |.+||+|-|+.++..|....
T Consensus        14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-----TQaTiSRDl~eL~~~Kv~~~   66 (168)
T PRK03341         14 AARQARIVAILSRQSVRSQAELAALLADEGIEV-----TQATLSRDLDELGAVKLRGA   66 (168)
T ss_pred             HHHHHHHHHHHHHCCCccHHHHHHHHHHcCCcc-----cHHHHHHHHHHhcCEeeecC
Confidence            455778999999999999999999999999986     99999999999999986543

>PRK12515 RNA polymerase sigma factor; Provisional

Probab=94.55  E-value=0.099  Score=44.39  Aligned_cols=42  Identities=10%  Similarity=-0.027  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||+.||||.+||++.+.|-+
T Consensus       131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar  172 (189)
T PRK12515        131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR  172 (189)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            577787766666677999999999999999999999888765

>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional

Probab=94.54  E-value=0.41  Score=40.93  Aligned_cols=66  Identities=18%  Similarity=0.233  Sum_probs=48.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..||+.|    .+.|.+.+....+ .-|..++.+.+.|.-... ++-.+++.||++.|.
T Consensus        12 ~~IgevAk~~gvs~~TlRyY----E~~GLi~~~r~~~-g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~   78 (154)
T PRK15002         12 LTPGEVAKRSGVAVSALHFY----ESKGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG   78 (154)
T ss_pred             ccHHHHHHHHCcCHHHHHHH----HHCCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            79999999999999998654    5568777644333 347788777666654422 344789999998886

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=94.54  E-value=0.058  Score=35.57  Aligned_cols=32  Identities=25%  Similarity=0.353  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .++..+||+.+++|++||++.+++..+.|-+.
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~   39 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS   39 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            46889999999999999999999999999874

>PRK15201 fimbriae regulatory protein FimW; Provisional

Probab=94.52  E-value=0.11  Score=46.27  Aligned_cols=45  Identities=13%  Similarity=0.176  Sum_probs=38.4

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      -.+.+|...+ +|+.++.+|++.++||+.|+||.+||...+++-.+
T Consensus       130 ~~~~LSpREr-EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImk  174 (198)
T PRK15201        130 TTRHFSVTER-HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMR  174 (198)
T ss_pred             CCCCCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4556777666 68888999999999999999999999999988763

>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional

Probab=94.50  E-value=0.13  Score=43.05  Aligned_cols=42  Identities=19%  Similarity=0.292  Sum_probs=35.5

Q ss_pred             HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +=.+|+.+++ +| .|.++||+++|+|++||.+=+++.++.|.+
T Consensus        10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI   53 (153)
T PRK11179         10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGII   53 (153)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            4445666664 55 799999999999999999999999999965

>PRK09638 RNA polymerase sigma factor SigY; Reviewed

Probab=94.50  E-value=0.043  Score=45.74  Aligned_cols=43  Identities=16%  Similarity=0.197  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-.|++..+||+.||+|.+||+..+.|-++
T Consensus       126 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~  168 (176)
T PRK09638        126 KLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK  168 (176)
T ss_pred             cCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence            3777777666666678999999999999999999999988764

>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE

Probab=94.50  E-value=0.077  Score=44.54  Aligned_cols=43  Identities=28%  Similarity=0.342  Sum_probs=34.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||+|.+||+.++.|-++
T Consensus       138 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~  180 (190)
T TIGR02939       138 ALPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFRARE  180 (190)
T ss_pred             cCCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            3566666555555579999999999999999999999988753

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 RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.

>PRK12544 RNA polymerase sigma factor; Provisional

Probab=94.49  E-value=0.098  Score=45.80  Aligned_cols=43  Identities=14%  Similarity=0.168  Sum_probs=37.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..++.+.|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus       147 ~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr  189 (206)
T PRK12544        147 DGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRAR  189 (206)
T ss_pred             HhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            3577888877777777999999999999999999999988865

>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional

Probab=94.49  E-value=0.23  Score=46.05  Aligned_cols=106  Identities=11%  Similarity=0.032  Sum_probs=65.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      .++...|.-++...-.|++..+||+.||+|.+||+..+.|-++.  +... ..  +.....+++.+.+.+++..--.--.
T Consensus       118 ~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~--Lr~~-~~--~~~~~~~~~~~~~~~f~~a~~~gd~  192 (290)
T PRK09635        118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK--INES-RI--AASVEPAQHRVVTRAFIEACSNGDL  192 (290)
T ss_pred             hCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHH--HHhh-CC--CCCCChHHHHHHHHHHHHHHHhCCH
Confidence            57778777776666799999999999999999999999988754  1111 00  1122334555666666654334445


Q ss_pred             HHHHHHHHhc--CCCC---CCCCCCHHHHHHHHHhc
Q psy15598        127 WEIRDRLLSD--GVCD---KFNVPSVSSISRILRNK  157 (258)
Q Consensus       127 ~EIr~~L~~~--Gv~v---~~~~pS~STI~RiLrr~  157 (258)
                      ..|.+.|.++  |-..   ..-......|.++|...
T Consensus       193 ~~l~~ll~~d~~~~~~~~~~~~~~G~~~v~~~~~~~  228 (290)
T PRK09635        193 DTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRH  228 (290)
T ss_pred             HHHHHHhhhhhcCCCcCCCCccccCHHHHHHHHHHh
Confidence            6666666431  1111   00113677788887653

>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR

Probab=94.48  E-value=0.09  Score=46.00  Aligned_cols=43  Identities=16%  Similarity=0.171  Sum_probs=38.0

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|.+|+.++.  .+++..+||+.|||+.+||++.+++..+.|-|.
T Consensus         2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~   46 (203)
T TIGR02702         2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIE   46 (203)
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            5778888764  469999999999999999999999999999874

All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.

>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily

Probab=94.47  E-value=0.2  Score=41.89  Aligned_cols=67  Identities=16%  Similarity=0.187  Sum_probs=48.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      ++..++|+.+|||.+|++.|-    +.|.+.|....+ .-+..++++...|..... .+-.+++.+|++.+..
T Consensus         1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~-g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~   68 (134)
T cd04779           1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDS-NYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEE   68 (134)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            467899999999999998875    458887655433 346677776665554433 3347889999988864

Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.

>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=94.47  E-value=0.051  Score=37.24  Aligned_cols=26  Identities=19%  Similarity=0.399  Sum_probs=22.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.|++..++|+.+|||++||++|.+-
T Consensus         7 ~~gls~~~la~~~gis~~~i~~~~~g   32 (55)
T PF01381_consen    7 EKGLSQKELAEKLGISRSTISRIENG   32 (55)
T ss_dssp             HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence            57999999999999999999999764

; 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 ....

>PHA01976 helix-turn-helix protein

Probab=94.44  E-value=0.064  Score=38.29  Aligned_cols=33  Identities=15%  Similarity=0.254  Sum_probs=27.1

Q ss_pred             HHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         53 RMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        53 R~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+|..+.+ .|++..++|+.+|||+++|++|.+
T Consensus         4 ~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~   37 (67)
T PHA01976          4 AIQLIKARNARAWSAPELSRRAGVRHSLIYDFEA   37 (67)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            345555554 799999999999999999999864

>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities

Probab=94.44  E-value=0.071  Score=38.24  Aligned_cols=34  Identities=21%  Similarity=0.206  Sum_probs=28.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAI   98 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r   98 (258)
                      +..++|++|+||+.||++-+++..+.|-+.-.++
T Consensus        26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen   26 SERELAERYGVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence            8899999999999999999999999998754443

The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....

>PRK05066 arginine repressor; Provisional

Probab=94.42  E-value=0.11  Score=44.64  Aligned_cols=52  Identities=21%  Similarity=0.094  Sum_probs=46.3

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCC-CCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVC-DKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~-v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      +....|++++++++--+..||.+.|++.|+. +     +.+||+|-|+..+..|....
T Consensus         9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~~v-----TQATiSRDikeL~lvKv~~~   61 (156)
T PRK05066          9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNI-----NQSKVSRMLTKFGAVRTRNA   61 (156)
T ss_pred             HHHHHHHHHHhhCCCCCHHHHHHHHHHCCCCee-----cHHHHHHHHHHcCCEEeeCC
Confidence            3467899999999999999999999999998 6     99999999999999986543

>PRK10840 transcriptional regulator RcsB; Provisional

Probab=94.39  E-value=0.097  Score=44.84  Aligned_cols=41  Identities=17%  Similarity=0.149  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|.-.+ +|+.++.+|+|.++||+.|+||.+||...+++-.
T Consensus       150 ~Lt~rE~-evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~  190 (216)
T PRK10840        150 RLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM  190 (216)
T ss_pred             cCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4777665 7888899999999999999999999998888765

>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein

Probab=94.39  E-value=0.045  Score=43.76  Aligned_cols=48  Identities=17%  Similarity=0.236  Sum_probs=32.1

Q ss_pred             cCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         43 VNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        43 ~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      +++..+....|.+-|..--+|++..++|+.+|+|..+|++++++.+..
T Consensus        52 P~~~~~~~~~R~~~I~~~f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~   99 (108)
T PF08765_consen   52 PKCDRLLRALRNREIRREFNGMNVRELARKYGLSERQIYRIIKRVRRR   99 (108)
T ss_dssp             --SHHHHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred             eCccHHHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence            355555567776555544459999999999999999999999998743

It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.

>PRK12513 RNA polymerase sigma factor; Provisional

Probab=94.38  E-value=0.045  Score=46.58  Aligned_cols=42  Identities=17%  Similarity=0.096  Sum_probs=34.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       139 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~  180 (194)
T PRK12513        139 TLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYAL  180 (194)
T ss_pred             hCCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777765555567999999999999999999998888765

>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family

Probab=94.37  E-value=0.038  Score=44.85  Aligned_cols=41  Identities=22%  Similarity=0.173  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-++..+-+|++..+||+.||||.+||+..+.|.+
T Consensus       106 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~  146 (154)
T TIGR02950       106 LPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRAR  146 (154)
T ss_pred             CCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence            66666665555556899999999999999999999999875

This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.

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

Probab=94.37  E-value=0.26  Score=39.78  Aligned_cols=68  Identities=19%  Similarity=0.209  Sum_probs=48.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSD  136 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~  136 (258)
                      +++.++|+.+|||..|++-|-+    .|.+.|..+.+ .-|..++++...|..... ..-++++.+|++.+...
T Consensus         1 m~IgevA~~~gvs~~tlRyYe~----~GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~   69 (120)
T cd04781           1 LDIAEVARQSGLPASTLRYYEE----KGLIASIGRRG-LRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD   69 (120)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence            5788999999999999876655    47776654444 557888887776654422 23478899998877643

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

>PRK12546 RNA polymerase sigma factor; Provisional

Probab=94.35  E-value=0.098  Score=45.11  Aligned_cols=43  Identities=19%  Similarity=0.235  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus       113 ~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~  155 (188)
T PRK12546        113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA  155 (188)
T ss_pred             hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4677777777776789999999999999999999999988753

>PRK09651 RNA polymerase sigma factor FecI; Provisional

Probab=94.35  E-value=0.087  Score=44.25  Aligned_cols=42  Identities=24%  Similarity=0.238  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus       119 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~  160 (172)
T PRK09651        119 GLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT  160 (172)
T ss_pred             hCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            467777655555556999999999999999999999998865

>TIGR02859 spore_sigH RNA polymerase sigma-H factor

Probab=94.35  E-value=0.087  Score=44.61  Aligned_cols=41  Identities=12%  Similarity=0.133  Sum_probs=33.7

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         49 PNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..+.+..|+.++-+|++..+||+.||+|.+||+..+.|-+.
T Consensus       151 l~~~~~~i~~~~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~  191 (198)
T TIGR02859       151 LSDLEWKVLQSYLDGKSYQEIACDLNRHVKSIDNALQRVKR  191 (198)
T ss_pred             cCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44556666767779999999999999999999998888653

Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.

>PRK12538 RNA polymerase sigma factor; Provisional

Probab=94.34  E-value=0.087  Score=47.19  Aligned_cols=42  Identities=17%  Similarity=0.282  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus       171 ~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr  212 (233)
T PRK12538        171 RLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGR  212 (233)
T ss_pred             hCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366667765555567999999999999999999999998865

>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional

Probab=94.33  E-value=0.069  Score=46.82  Aligned_cols=40  Identities=18%  Similarity=0.200  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +|.-.+ +|+.++.+|++.++||++|+||.+||...+++-.
T Consensus       138 LT~RE~-eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~  177 (207)
T PRK15411        138 LSRTES-SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK  177 (207)
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence            666555 7899999999999999999999999999988865

>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators

Probab=94.32  E-value=0.28  Score=42.41  Aligned_cols=67  Identities=18%  Similarity=0.245  Sum_probs=47.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||++||+.|-+    .|.+.|..+..+.-|..++++...|..+.. .+-.+++.+|+..|.
T Consensus         2 ~~I~evA~~~gvs~~tLRyYe~----~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~   69 (172)
T cd04790           2 LTISQLARQFGLSRSTLLYYER----IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ   69 (172)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            5789999999999999876644    588877544322457788876666544433 334788889888775

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

>PRK06474 hypothetical protein; Provisional

Probab=94.31  E-value=0.073  Score=46.23  Aligned_cols=50  Identities=20%  Similarity=0.355  Sum_probs=43.6

Q ss_pred             CCCCCHHHHHHHHHHHHc-C--CCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598         45 GRPLPNSVRMRIVELAQL-G--IRPCDISRQL-RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~-G--~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..-++...|.+|+..+.. +  ++..+|++.+ +|+.+||||-++...+.|-|.
T Consensus         5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~   58 (178)
T PRK06474          5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILH   58 (178)
T ss_pred             HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence            445888999999998753 3  8999999999 799999999999999999764

>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator

Probab=94.26  E-value=0.21  Score=43.11  Aligned_cols=59  Identities=22%  Similarity=0.239  Sum_probs=42.1

Q ss_pred             HHHHHHHHH-HHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598         51 SVRMRIVEL-AQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK  109 (258)
Q Consensus        51 dlR~RIV~L-~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e  109 (258)
                      .+|.+|+.. +.-|  ++-.++|++||||+++|+.-+++....|-|...++.|-.=..++.+
T Consensus        19 ~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~   80 (212)
T TIGR03338        19 EIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISLA   80 (212)
T ss_pred             HHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence            345555553 2334  4778999999999999999999999999987666555332334444

This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=94.25  E-value=0.1  Score=44.28  Aligned_cols=42  Identities=21%  Similarity=0.279  Sum_probs=36.0

Q ss_pred             HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +=.+|+.+++ +| .+.++||+.+|+|++||++=++|..+.|.+
T Consensus        15 ~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI   58 (164)
T PRK11169         15 IDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI   58 (164)
T ss_pred             HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            4556777664 44 899999999999999999999999999965

>PRK12535 RNA polymerase sigma factor; Provisional

Probab=94.24  E-value=0.11  Score=45.10  Aligned_cols=43  Identities=21%  Similarity=0.254  Sum_probs=36.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-|+..+-+|++..+||+.||||.+||...+.|-+.
T Consensus       133 ~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~  175 (196)
T PRK12535        133 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA  175 (196)
T ss_pred             cCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            4677777766667779999999999999999999999887653

>PRK04280 arginine repressor; Provisional

Probab=94.21  E-value=0.12  Score=43.92  Aligned_cols=51  Identities=18%  Similarity=0.104  Sum_probs=45.6

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      -.+.|++++++++--+..||.+.|++.|+.+     +..||+|-|+..+..|....
T Consensus         5 R~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~v-----TQATiSRDikeL~lvKv~~~   55 (148)
T PRK04280          5 RHIKIREIITNNEIETQDELVDRLREEGFNV-----TQATVSRDIKELHLVKVPLP   55 (148)
T ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCe-----ehHHHHHHHHHcCCEEeecC
Confidence            3568999999999999999999999999986     99999999999999986543

>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor

Probab=94.18  E-value=0.11  Score=46.19  Aligned_cols=42  Identities=12%  Similarity=0.090  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+.    +|+|..+||+.+|||.+||.+++.|-+
T Consensus       178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~  223 (234)
T TIGR02835       178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRIL  223 (234)
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            367777766665552    799999999999999999999987754

Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.

>PRK09641 RNA polymerase sigma factor SigW; Provisional

Probab=94.16  E-value=0.12  Score=43.22  Aligned_cols=42  Identities=26%  Similarity=0.228  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus       136 ~L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar  177 (187)
T PRK09641        136 QLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGR  177 (187)
T ss_pred             hCCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            466666666655566999999999999999999999998875

>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR

Probab=94.15  E-value=0.29  Score=39.68  Aligned_cols=66  Identities=21%  Similarity=0.246  Sum_probs=48.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||..|++-|-    +.|.+.|...+  .-|..++++...|..... .+-.+++.+|++.+..
T Consensus         1 ~~Igeva~~~gvs~~tlRyYe----~~GLl~p~r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~   67 (118)
T cd04776           1 YTISELAREFDVTPRTLRFYE----DKGLLSPERRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL   67 (118)
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            467899999999999986554    45888775443  458888887777665433 3358899999888863

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.

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=94.15  E-value=0.14  Score=42.76  Aligned_cols=33  Identities=18%  Similarity=0.192  Sum_probs=30.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+++..+||..|+++++||+|-+++..+.|-+
T Consensus        40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV   72 (126)
T COG3355          40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLV   72 (126)
T ss_pred             cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCe
Confidence            346899999999999999999999999999976

>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons

Probab=94.14  E-value=0.097  Score=39.06  Aligned_cols=35  Identities=14%  Similarity=0.275  Sum_probs=31.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .+|.+.-.-+++.++|++||++..+|.+|+..|++
T Consensus         5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~   39 (65)
T PF05344_consen    5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ   39 (65)
T ss_pred             HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46667767899999999999999999999999985

>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=94.13  E-value=0.081  Score=37.27  Aligned_cols=33  Identities=24%  Similarity=0.307  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .++..+||+.+|+|++||++.+++..+.|-+..
T Consensus        25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~   57 (67)
T cd00092          25 PLTRQEIADYLGLTRETVSRTLKELEEEGLISR   57 (67)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            479999999999999999999999999998753

>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator

Probab=94.10  E-value=0.07  Score=46.04  Aligned_cols=39  Identities=28%  Similarity=0.299  Sum_probs=33.5

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHHHHHh
Q psy15598         49 PNSVRMRIVELAQLGIRPCDISRQLR-VSHGCVSKILARY   87 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~S~~eIAr~LG-VSrsTVsRwikRy   87 (258)
                      +++.-.++-+|+.+|+|.++||++|| ||++.|--.+.|.
T Consensus         4 tde~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl   43 (162)
T PF07750_consen    4 TDERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL   43 (162)
T ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence            45666778888999999999999999 9999998777774

These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].

>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins

Probab=94.08  E-value=1.2  Score=38.93  Aligned_cols=93  Identities=19%  Similarity=0.145  Sum_probs=62.8

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh---CCCC----C
Q psy15598         53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK---DPGI----F  125 (258)
Q Consensus        53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~---nP~i----t  125 (258)
                      +++|-.+...|-|..-+.+-||+|.+-|..+.+--   |.  + .+.| ||+.++++++..|-...++   .+..    .
T Consensus        77 ~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~ll---gi--~-~~~G-R~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~  149 (180)
T PF11198_consen   77 QQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLL---GI--P-VRKG-RPPALSEEEEAAIWRRWQQLMKKRGVDNLDS  149 (180)
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh---CC--C-CCCC-CCCCcCHHHHHHHHHHHHHHHhhcCCCCccc
Confidence            45555667889999999999999999998887664   21  1 2345 8999999888888777653   2222    2


Q ss_pred             --HHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        126 --AWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       126 --a~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                        .-|+.-.+. .-..     +|.++|+..++...
T Consensus       150 ~~~Le~~m~~A-e~~~-----isL~~iW~~i~~w~  178 (180)
T PF11198_consen  150 PDALELMMLLA-EETN-----ISLTVIWSLIQEWE  178 (180)
T ss_pred             hHHHHHHHHHH-HHhC-----CCHHHHHHHHHHHH
Confidence              223222232 2222     38999999998753

>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=94.05  E-value=0.1  Score=47.41  Aligned_cols=41  Identities=22%  Similarity=0.294  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598         51 SVRMRIVELAQLGI-----RPCDISRQLRVSHGCVSKILARYHETG   91 (258)
Q Consensus        51 dlR~RIV~L~~~G~-----S~~eIAr~LGVSrsTVsRwikRyrEtG   91 (258)
                      .-|+-|..|++.|.     ....+|+.|+||+.|||+++++++..|
T Consensus       174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k~~~  219 (220)
T COG2964         174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFKAGG  219 (220)
T ss_pred             HHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHhhcCC
Confidence            34444445567785     567799999999999999999998655

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

Probab=93.96  E-value=0.032  Score=38.80  Aligned_cols=23  Identities=17%  Similarity=0.374  Sum_probs=19.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++..++++.+|||++|+++|+++
T Consensus         4 l~~~ev~~~~g~s~~ti~~~~k~   26 (51)
T PF05930_consen    4 LRIKEVAELLGVSRSTIYRLIKD   26 (51)
T ss_dssp             E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred             ccHHHHHHHHCCCHHHHHHHHhc
Confidence            36789999999999999999994

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.

>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]

Probab=93.96  E-value=0.093  Score=43.70  Aligned_cols=46  Identities=24%  Similarity=0.293  Sum_probs=41.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ...+.+..++.++..|.+..++|+.++|+.++|.+|++++.+....
T Consensus        74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~  119 (129)
T COG3677          74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG  119 (129)
T ss_pred             cchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence            4578899999999999999999999999999999999999866543

>TIGR03070 couple_hipB transcriptional regulator, y4mF family

Probab=93.92  E-value=0.13  Score=34.82  Aligned_cols=30  Identities=13%  Similarity=0.220  Sum_probs=24.9

Q ss_pred             HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         56 IVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |-.+. +.|++..++|+.+|||++||++|.+
T Consensus         7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~   37 (58)
T TIGR03070         7 VRARRKALGLTQADLADLAGVGLRFIRDVEN   37 (58)
T ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            33343 4699999999999999999999974

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.

>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]

Probab=93.89  E-value=0.1  Score=48.22  Aligned_cols=57  Identities=26%  Similarity=0.328  Sum_probs=46.4

Q ss_pred             CCCCCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         44 NGRPLPNSVRMRIVELAQL-G-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~-G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +-..++.|.+.-|..+.+. | ...+|+.+.+|.|++||+|.+++-.+.|-++--+.|+
T Consensus       189 ~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~  247 (258)
T COG2512         189 NEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGR  247 (258)
T ss_pred             ccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCC
Confidence            4456888888766666654 4 7999999999999999999999999999886555543

>PRK05803 sporulation sigma factor SigK; Reviewed

Probab=93.87  E-value=0.12  Score=45.80  Aligned_cols=42  Identities=21%  Similarity=0.114  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+    .+|+|.++||..+|||.+||++++.|-+
T Consensus       175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~  220 (233)
T PRK05803        175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRAL  220 (233)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            57777776666655    4899999999999999999999987754

>COG1710 Uncharacterized protein conserved in archaea [Function unknown]

Probab=93.85  E-value=0.14  Score=42.69  Aligned_cols=44  Identities=25%  Similarity=0.366  Sum_probs=40.1

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+.|+...+.+|-+++++|++.++||+.|||...||+=.+++.+
T Consensus        91 prkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k  134 (139)
T COG1710          91 PRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLK  134 (139)
T ss_pred             CcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHHHHHHh
Confidence            45689999999999999999999999999999999999888764

>PF13565 HTH_32: Homeodomain-like domain

Probab=93.84  E-value=0.19  Score=36.76  Aligned_cols=41  Identities=37%  Similarity=0.486  Sum_probs=32.2

Q ss_pred             CCCCC-CHHHHHHHHHHHHc--CCCHHHHHHHh----C--C--CHHHHHHHH
Q psy15598         44 NGRPL-PNSVRMRIVELAQL--GIRPCDISRQL----R--V--SHGCVSKIL   84 (258)
Q Consensus        44 ~gR~~-S~dlR~RIV~L~~~--G~S~~eIAr~L----G--V--SrsTVsRwi   84 (258)
                      .|++. +.+.+..|++++.+  .++..+|+..|    |  +  |.+||+||+
T Consensus        26 ~Grp~~~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L   77 (77)
T PF13565_consen   26 PGRPRKDPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL   77 (77)
T ss_pred             CCCCCCcHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence            44443 58888999999875  48999988887    3  4  999999985

>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA

Probab=93.83  E-value=0.55  Score=42.05  Aligned_cols=86  Identities=17%  Similarity=0.190  Sum_probs=57.5

Q ss_pred             HHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~E  128 (258)
                      .+++..+    .+..+..++|+.+++|++++.|..+++.  |.         .|.. ++....+...+++ .+.+.+..|
T Consensus       189 ~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~--G~---------t~~~yi~~~Rl~~A~~lL-~~t~~sI~e  256 (287)
T TIGR02297       189 NRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFS--AL---------SPKRLIIERVMQEARRLL-LFTQHSINQ  256 (287)
T ss_pred             HHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHh--CC---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence            4555444    3568999999999999999999999974  21         1111 1111122222333 356788888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      |.+.-.|++|+.-+.
T Consensus       257 IA~~~---GF~------s~s~Fsr~FKk~~G~  279 (287)
T TIGR02297       257 IAYDL---GYK------DPAYFARFFQKETGL  279 (287)
T ss_pred             HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            87766   675      899999999987654

This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.

>PRK04984 fatty acid metabolism regulator; Provisional

Probab=93.82  E-value=0.16  Score=44.81  Aligned_cols=57  Identities=12%  Similarity=0.101  Sum_probs=42.3

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         44 NGRPLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..+..+......|.+.+..|       + +-.++|++|||||+||+.-+++....|-|.-.++.|
T Consensus         4 ~~~~~~~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G   68 (239)
T PRK04984          4 KAQSPAGFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   68 (239)
T ss_pred             cccCHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            34445555555555555443       4 688999999999999999999999999887655545

>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]

Probab=93.79  E-value=0.92  Score=38.75  Aligned_cols=101  Identities=26%  Similarity=0.165  Sum_probs=62.6

Q ss_pred             HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC--------
Q psy15598         52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD--------  121 (258)
Q Consensus        52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n--------  121 (258)
                      --..|..+.+ .| ....+||+.|+||.+||..-+++-.+.|-+.-.+.+|   -.+|+.=.+....+++.+        
T Consensus        11 YL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~g---i~LT~~G~~~a~~~~r~hrlle~fL~   87 (154)
T COG1321          11 YLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGG---VTLTEKGREKAKELLRKHRLLERFLV   87 (154)
T ss_pred             HHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCC---eEEChhhHHHHHHHHHHHHHHHHHHH
Confidence            3344444554 45 6889999999999999999999999999886555554   556654333322222221        


Q ss_pred             --CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        122 --PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       122 --P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                        =.+...+..+.....-..     +|..++.|+.+..+..
T Consensus        88 ~~lg~~~~~~~~ea~~leh~-----~s~~~~~rl~~~l~~~  123 (154)
T COG1321          88 DVLGLDWEEAHEEAEGLEHA-----LSDETAERLDELLGFP  123 (154)
T ss_pred             HHhCCCHHHHHHHHHHHhhc-----CCHHHHHHHHHHhCCC
Confidence              233333333222222222     4888998888877753

>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=93.78  E-value=0.096  Score=38.05  Aligned_cols=31  Identities=35%  Similarity=0.470  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||.|.++++++.|-+.
T Consensus        29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~   59 (76)
T PF13545_consen   29 LTQEEIADMLGVSRETVSRILKRLKDEGIIE   59 (76)
T ss_dssp             SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999999875

...

>TIGR02885 spore_sigF RNA polymerase sigma-F factor

Probab=93.77  E-value=0.17  Score=44.63  Aligned_cols=42  Identities=17%  Similarity=0.091  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+.+|++..+||+.||||..+|+++.++-.
T Consensus       183 ~L~~~e~~i~~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al  224 (231)
T TIGR02885       183 KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVL  224 (231)
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            456666655555566899999999999999999999998864

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.

>PRK07408 RNA polymerase sigma factor SigF; Reviewed

Probab=93.74  E-value=0.16  Score=46.03  Aligned_cols=42  Identities=14%  Similarity=0.080  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+-+|++..+||+.||||.++|++++++-.
T Consensus       203 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~  244 (256)
T PRK07408        203 QLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGL  244 (256)
T ss_pred             cCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366666666666667999999999999999999999998865

>PRK09954 putative kinase; Provisional

Probab=93.66  E-value=0.12  Score=48.42  Aligned_cols=43  Identities=19%  Similarity=0.291  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +...+|+.++++.  .+..+||+.|+||++||++.+++.++.|.+
T Consensus         3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i   47 (362)
T PRK09954          3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI   47 (362)
T ss_pred             hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence            4556788887643  799999999999999999999999998853

>TIGR02941 Sigma_B RNA polymerase sigma-B factor

Probab=93.63  E-value=0.16  Score=45.56  Aligned_cols=42  Identities=14%  Similarity=0.073  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+.+|++..+||+.||||.+||.+++.+-.
T Consensus       205 ~L~~~~r~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~  246 (255)
T TIGR02941       205 ILSEREKSIIHCTFEENLSQKETGERLGISQMHVSRLQRQAI  246 (255)
T ss_pred             cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366666665555557899999999999999999999988764

This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.

>PRK13509 transcriptional repressor UlaR; Provisional

Probab=93.62  E-value=0.15  Score=46.36  Aligned_cols=44  Identities=18%  Similarity=0.339  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+.+.+|+++++ .| ++..++|+.||||..||+|.++...+.|.+
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i   49 (251)
T PRK13509          4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKL   49 (251)
T ss_pred             HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            466778888876 34 799999999999999999999999988876

>PRK11303 DNA-binding transcriptional regulator FruR; Provisional

Probab=93.57  E-value=0.13  Score=46.45  Aligned_cols=44  Identities=16%  Similarity=0.165  Sum_probs=32.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      ++.++||+..|||++||+|.++.-.           + + ...+++.+++|.+..++
T Consensus         1 ~ti~dIA~~aGVS~~TVSrvLn~~~-----------~-~-~~Vs~~tr~rV~~~a~e   44 (328)
T PRK11303          1 MKLDEIARLAGVSRTTASYVINGKA-----------K-Q-YRVSDKTVEKVMAVVRE   44 (328)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCCC-----------C-C-CCcCHHHHHHHHHHHHH
Confidence            4789999999999999999996310           0 0 12567777777777654

>PRK07670 RNA polymerase sigma factor SigD; Validated

Probab=93.55  E-value=0.17  Score=45.37  Aligned_cols=41  Identities=17%  Similarity=0.208  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-|...+.+|++..+||+.||||.+||...+.|-+
T Consensus       202 L~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~  242 (251)
T PRK07670        202 LSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKAL  242 (251)
T ss_pred             CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            67777766666677999999999999999999999988865

>PRK08295 RNA polymerase factor sigma-70; Validated

Probab=93.55  E-value=0.18  Score=43.04  Aligned_cols=41  Identities=15%  Similarity=0.063  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++. +-+|++..+||..||||.+||...+.|-+
T Consensus       155 ~L~~~~r~vl~l-~~e~~s~~EIA~~lgis~~tV~~~l~rar  195 (208)
T PRK08295        155 LLSELEKEVLEL-YLDGKSYQEIAEELNRHVKSIDNALQRVK  195 (208)
T ss_pred             hCCHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777776666 77999999999999999999998888765

>PRK05572 sporulation sigma factor SigF; Validated

Probab=93.55  E-value=0.16  Score=45.64  Aligned_cols=42  Identities=14%  Similarity=0.140  Sum_probs=34.6

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+.+|++..+||+.||||.++|+++.++-.
T Consensus       202 ~L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral  243 (252)
T PRK05572        202 ELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKIL  243 (252)
T ss_pred             cCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366666655555566899999999999999999999998864

>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=93.52  E-value=0.2  Score=34.75  Aligned_cols=34  Identities=26%  Similarity=0.491  Sum_probs=30.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|++..+||+.+++++++|.+++++-.+.|-++
T Consensus        15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~   48 (59)
T PF01047_consen   15 NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE   48 (59)
T ss_dssp             HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence            3679999999999999999999999999999764

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 ....

>PRK01905 DNA-binding protein Fis; Provisional

Probab=93.50  E-value=0.2  Score=37.79  Aligned_cols=36  Identities=11%  Similarity=0.071  Sum_probs=30.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .+..|+.+++ .|-...++|+.||||++|+++.+++|
T Consensus        38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~   74 (77)
T PRK01905         38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQH   74 (77)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            4555666665 57789999999999999999999997

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=93.50  E-value=0.25  Score=38.31  Aligned_cols=41  Identities=24%  Similarity=0.323  Sum_probs=35.0

Q ss_pred             HHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|-+.
T Consensus         6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~   48 (108)
T smart00344        6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK   48 (108)
T ss_pred             HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            46777664 3 48999999999999999999999999999763

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

>PRK00441 argR arginine repressor; Provisional

Probab=93.49  E-value=0.21  Score=42.48  Aligned_cols=51  Identities=14%  Similarity=0.053  Sum_probs=45.3

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      -...|.++++++...+..||.+.|++.|+.+     |.+||+|-|+..+..|....
T Consensus         5 R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~v-----SqaTisRDl~~L~lvKv~~~   55 (149)
T PRK00441          5 RHAKILEIINSKEIETQEELAEELKKMGFDV-----TQATVSRDIKELKLIKVLSN   55 (149)
T ss_pred             HHHHHHHHHHHcCCCcHHHHHHHHHhcCCCc-----CHHHHHHHHHHcCcEEeECC
Confidence            4668889999999999999999999999986     99999999999999986543

>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed

Probab=93.43  E-value=0.19  Score=45.55  Aligned_cols=42  Identities=21%  Similarity=0.131  Sum_probs=35.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+.+|++..+||+.||||.++|++++.+-.
T Consensus       205 ~L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral  246 (257)
T PRK05911        205 ALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKAL  246 (257)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777765555667999999999999999999999998865

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

Probab=93.40  E-value=0.27  Score=41.34  Aligned_cols=54  Identities=22%  Similarity=0.186  Sum_probs=40.2

Q ss_pred             CCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        104 RVTTPKVVSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      -++|+. +..|.+++.+. -..++.+|.+.|.+.+..+     |.+||+|.|+-+...+.-
T Consensus        17 lr~T~q-R~~vl~~L~~~~~~~sAeei~~~l~~~~p~i-----slaTVYr~L~~l~e~Glv   71 (145)
T COG0735          17 LRLTPQ-RLAVLELLLEADGHLSAEELYEELREEGPGI-----SLATVYRTLKLLEEAGLV   71 (145)
T ss_pred             CCcCHH-HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCC-----CHhHHHHHHHHHHHCCCE
Confidence            446665 44555555544 3499999999999888775     999999999987766543

>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional

Probab=93.32  E-value=0.14  Score=48.16  Aligned_cols=37  Identities=8%  Similarity=0.012  Sum_probs=32.2

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ..|..|+.+++ .+....++|+.||||++|+||++++|
T Consensus       286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~  323 (326)
T PRK11608        286 QEKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKH  323 (326)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence            35777777776 58889999999999999999999998

>smart00354 HTH_LACI helix_turn _helix lactose operon repressor

Probab=93.32  E-value=0.2  Score=36.71  Aligned_cols=41  Identities=20%  Similarity=0.197  Sum_probs=31.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD  121 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n  121 (258)
                      +.++||+.+|||++||+++++.               ++. .+++....|.+..++-
T Consensus         2 t~~~iA~~~gvS~~TVSr~ln~---------------~~~-v~~~t~~~i~~~~~~~   42 (70)
T smart00354        2 TIKDVARLAGVSKATVSRVLNG---------------NGR-VSEETREKVLAAMEEL   42 (70)
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC---------------CCC-CCHHHHHHHHHHHHHh
Confidence            5789999999999999998731               222 4677777777776654

>PRK09191 two-component response regulator; Provisional

Probab=93.27  E-value=0.21  Score=43.54  Aligned_cols=44  Identities=16%  Similarity=0.073  Sum_probs=36.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      .++.+.|.-++...-+|++..+||+.+|+|.+||...+.|.++.
T Consensus        88 ~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~  131 (261)
T PRK09191         88 GLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE  131 (261)
T ss_pred             hCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            46777776666666799999999999999999999999888753

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

Probab=93.27  E-value=0.078  Score=35.92  Aligned_cols=41  Identities=34%  Similarity=0.402  Sum_probs=22.9

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      +.|+.+++..|..+..+  ..+..+|++.|.          .|.+||+|.|++
T Consensus         3 ~~Lt~~eR~~I~~l~~~--G~s~~~IA~~lg----------~s~sTV~relkR   43 (44)
T PF13936_consen    3 KHLTPEERNQIEALLEQ--GMSIREIAKRLG----------RSRSTVSRELKR   43 (44)
T ss_dssp             ---------HHHHHHCS-----HHHHHHHTT------------HHHHHHHHHH
T ss_pred             cchhhhHHHHHHHHHHc--CCCHHHHHHHHC----------cCcHHHHHHHhc
Confidence            34788888888888654  588999988873          399999999987

>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF

Probab=93.23  E-value=0.18  Score=44.22  Aligned_cols=52  Identities=15%  Similarity=0.170  Sum_probs=40.3

Q ss_pred             CHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         49 PNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      -..+...|.+...+|.        |-.++|++|||||.||++-+..-.+.|.|..+...|
T Consensus        10 y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~G   69 (238)
T TIGR02325        10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRG   69 (238)
T ss_pred             HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence            3455555656555442        889999999999999999999999999986655444

All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.

>PRK13503 transcriptional activator RhaS; Provisional

Probab=93.20  E-value=0.77  Score=40.83  Aligned_cols=78  Identities=14%  Similarity=0.135  Sum_probs=52.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      +..+..++|+.+++|+++++|..++.-  |.         .|.... ......-.+++ .+.+++..||+..+   |.. 
T Consensus       186 ~~~tl~~lA~~~~lS~~~l~r~Fk~~~--G~---------S~~~yi~~~Rl~~A~~LL-~~~~~sI~eIA~~~---GF~-  249 (278)
T PRK13503        186 EEVNWEALADQFSLSLRTLHRQLKQQT--GL---------TPQRYLNRLRLLKARHLL-RHSDASVTDIAYRC---GFG-  249 (278)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHh--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHHHHHHh---CCC-
Confidence            468999999999999999999999863  21         111111 11111112222 45678888888777   665 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+...|+.|+.-+.
T Consensus       250 -----~~s~F~r~FKk~~G~  264 (278)
T PRK13503        250 -----DSNHFSTLFRREFSW  264 (278)
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 888999999886654

>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR

Probab=93.17  E-value=0.56  Score=37.16  Aligned_cols=64  Identities=19%  Similarity=0.211  Sum_probs=44.5

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK  118 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv  118 (258)
                      .|+..+ . .+++..+||+.++++++||++.+++..+.|-|.-...... |  --.+|++-.+.+.+..
T Consensus        32 ~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~  100 (118)
T TIGR02337        32 RILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLS  100 (118)
T ss_pred             HHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhh
Confidence            344444 3 5689999999999999999999999999997743222111 2  2346777666655553

This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.

>PRK09483 response regulator; Provisional

Probab=93.14  E-value=0.19  Score=41.99  Aligned_cols=40  Identities=25%  Similarity=0.254  Sum_probs=34.0

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...+ +|+.++..|++.++||+.|++|.+||...+++-.
T Consensus       149 Lt~rE~-~vl~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~  188 (217)
T PRK09483        149 LSEREL-QIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMF  188 (217)
T ss_pred             cCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            665555 4667788999999999999999999999988875

>PRK12518 RNA polymerase sigma factor; Provisional

Probab=93.13  E-value=0.096  Score=43.56  Aligned_cols=42  Identities=19%  Similarity=0.123  Sum_probs=34.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus       120 ~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar  161 (175)
T PRK12518        120 TLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR  161 (175)
T ss_pred             hCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            366666654444467999999999999999999999998865

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

Probab=93.10  E-value=0.23  Score=39.01  Aligned_cols=43  Identities=23%  Similarity=0.302  Sum_probs=36.7

Q ss_pred             HHHHHHHHHHc---CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQL---GIRPCDISRQL-----RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~~---G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|..|++.+.+   .+|..+|.+.+     +||++||||.++.+.+.|.+.
T Consensus         2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~   52 (116)
T cd07153           2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR   52 (116)
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence            47788887642   38999999999     699999999999999999764

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK10430 DNA-binding transcriptional activator DcuR; Provisional

Probab=93.09  E-value=0.29  Score=42.84  Aligned_cols=46  Identities=9%  Similarity=0.100  Sum_probs=38.0

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         48 LPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        48 ~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ++...+..++.+..    .|++.++||+.|++|..||.+.+++-...|.+
T Consensus       159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~  208 (239)
T PRK10430        159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHIL  208 (239)
T ss_pred             CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence            55555555555554    79999999999999999999999999888865

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

Probab=93.08  E-value=0.29  Score=38.50  Aligned_cols=48  Identities=25%  Similarity=0.188  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        111 VSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       111 ~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      +..|.+.+.+. ..+++.||.+.|.+.+..+     |.+||+|.|+.+....+-
T Consensus         3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i-----~~~TVYR~L~~L~~~Gli   51 (116)
T cd07153           3 RLAILEVLLESDGHLTAEEIYERLRKKGPSI-----SLATVYRTLELLEEAGLV   51 (116)
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHhCCCE
Confidence            45566666654 4689999999999877664     999999999987777653

Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.

>PRK06288 RNA polymerase sigma factor WhiG; Reviewed

Probab=93.08  E-value=0.24  Score=44.98  Aligned_cols=42  Identities=14%  Similarity=0.203  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+-+|++..+||+.||||.+||++.+.|..
T Consensus       212 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~ra~  253 (268)
T PRK06288        212 TLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAV  253 (268)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777776666678999999999999999999998877654

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

Probab=93.07  E-value=0.11  Score=36.58  Aligned_cols=27  Identities=33%  Similarity=0.507  Sum_probs=20.6

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|++..++|+..|||++||++|++.
T Consensus         7 ~~~~it~~~La~~~gis~~tl~~~~~~   33 (63)
T PF13443_consen    7 AERGITQKDLARKTGISRSTLSRILNG   33 (63)
T ss_dssp             HHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence            457999999999999999999999873

>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional

Probab=93.05  E-value=0.17  Score=46.08  Aligned_cols=44  Identities=20%  Similarity=0.308  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+.|.+|+++++ .| .+..++|+.|+||..||+|.++...+.|.+
T Consensus         4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l   49 (252)
T PRK10906          4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI   49 (252)
T ss_pred             HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence            467788898886 45 799999999999999999999999999976

>PRK09643 RNA polymerase sigma factor SigM; Reviewed

Probab=93.02  E-value=0.26  Score=42.23  Aligned_cols=42  Identities=31%  Similarity=0.368  Sum_probs=33.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||..||||.+||..-+.|-+
T Consensus       134 ~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar  175 (192)
T PRK09643        134 RLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR  175 (192)
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777655544567999999999999999999988876654

>PRK14999 histidine utilization repressor; Provisional

Probab=93.00  E-value=0.21  Score=44.37  Aligned_cols=54  Identities=17%  Similarity=0.196  Sum_probs=40.8

Q ss_pred             CCCHHHHHHHHHHHHc-----C--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         47 PLPNSVRMRIVELAQL-----G--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~-----G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++-..+...|.+...+     |  + +-+++|++||||+.||++-+..-.+.|.|.-+...|
T Consensus        12 ply~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~GkG   73 (241)
T PRK14999         12 PFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVG   73 (241)
T ss_pred             cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCcE
Confidence            3444555555555554     4  2 889999999999999999999999999886555444

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=93.00  E-value=0.77  Score=34.06  Aligned_cols=41  Identities=20%  Similarity=0.393  Sum_probs=34.3

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|+.++ . .+++..+||+.+++|+++|++.+++..+.|-+.
T Consensus        13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~   55 (101)
T smart00347       13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR   55 (101)
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence            3455554 3 358999999999999999999999999999874

>PRK13752 putative transcriptional regulator MerR; Provisional

Probab=92.95  E-value=0.54  Score=39.63  Aligned_cols=67  Identities=13%  Similarity=0.011  Sum_probs=47.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++-|-    +.|.+.+..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus         8 ~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~   75 (144)
T PRK13752          8 LTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLR   75 (144)
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence            789999999999999986554    4577765433322457888887776655533 334788999988775

>PHA02943 hypothetical protein; Provisional

Probab=92.95  E-value=1.1  Score=38.82  Aligned_cols=56  Identities=25%  Similarity=0.378  Sum_probs=42.8

Q ss_pred             CCCCCCHHHH---HHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598         44 NGRPLPNSVR---MRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG   99 (258)
Q Consensus        44 ~gR~~S~dlR---~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg   99 (258)
                      |++..|+...   ..|+++.+.| .+.++||+.||+|.+-|+-++.-...+|-+.--.+|
T Consensus         1 MPr~~sd~v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G   60 (165)
T PHA02943          1 MPRGMSDTVHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG   60 (165)
T ss_pred             CCcchhHHHHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec
Confidence            4555666544   4556666677 679999999999999999999999999987543343

>PRK12427 flagellar biosynthesis sigma factor; Provisional

Probab=92.95  E-value=0.26  Score=44.10  Aligned_cols=43  Identities=9%  Similarity=0.108  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-|...+.+|++..+||+.||||.++|+++.++..+
T Consensus       183 ~L~~~er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~  225 (231)
T PRK12427        183 QLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ  225 (231)
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4667777666666778999999999999999999999988763

>PRK11014 transcriptional repressor NsrR; Provisional

Probab=92.94  E-value=0.22  Score=41.11  Aligned_cols=50  Identities=16%  Similarity=0.177  Sum_probs=39.1

Q ss_pred             CCHHHHHHHHHHHH-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         48 LPNSVRMRIVELAQ-LG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      ....+|..|..... .|  .+.++||+.+|||+..|.+.+++.+..|-+...+
T Consensus         7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~   59 (141)
T PRK11014          7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR   59 (141)
T ss_pred             HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence            34456666666543 44  5889999999999999999999999999875444

>COG2345 Predicted transcriptional regulator [Transcription]

Probab=92.94  E-value=0.25  Score=44.83  Aligned_cols=50  Identities=22%  Similarity=0.236  Sum_probs=42.9

Q ss_pred             CCCCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         45 GRPLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .-..+...|.+|+.+.+  .+++..+||++||||..+|++-+....+.|.+.
T Consensus         5 ~~~~~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~   56 (218)
T COG2345           5 LADPSGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVE   56 (218)
T ss_pred             ccCCCccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCccee
Confidence            33456678999999886  359999999999999999999999999999653

>PRK10703 DNA-binding transcriptional repressor PurR; Provisional

Probab=92.93  E-value=0.17  Score=45.95  Aligned_cols=41  Identities=12%  Similarity=0.140  Sum_probs=30.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+.++||++.|||++||+|.++..               + .++++.+++|.+..++
T Consensus         2 ~Ti~dIA~~agVS~~TVSrvLn~~---------------~-~vs~~tr~~V~~~a~e   42 (341)
T PRK10703          2 ATIKDVAKRAGVSTTTVSHVINKT---------------R-FVAEETRNAVWAAIKE   42 (341)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHH
Confidence            378999999999999999999531               1 1456666666666554

>COG1654 BirA Biotin operon repressor [Transcription]

Probab=92.89  E-value=0.34  Score=37.31  Aligned_cols=37  Identities=22%  Similarity=0.242  Sum_probs=31.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCC-cccCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGS-ILPGAIGG  100 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGs-l~pk~rgG  100 (258)
                      .|-.+||+.||+||.+|.+-+++-++.|- |+.....|
T Consensus        20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kG   57 (79)
T COG1654          20 VSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKG   57 (79)
T ss_pred             ccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCc
Confidence            79999999999999999999999999994 44333334

>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19

Probab=92.87  E-value=0.33  Score=38.28  Aligned_cols=38  Identities=13%  Similarity=0.033  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +.|.-+...+-++++..+||..|++|++|++||.++..
T Consensus        59 ~~r~iL~~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al   96 (100)
T PF07374_consen   59 DERLILRMRYINKLTWEQIAEELNISRRTYYRIHKKAL   96 (100)
T ss_pred             hHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34444444456899999999999999999999998864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.

>TIGR02607 antidote_HigA addiction module antidote protein, HigA family

Probab=92.86  E-value=0.29  Score=35.76  Aligned_cols=26  Identities=27%  Similarity=0.457  Sum_probs=23.5

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -+.|++..++|+.+|||++||++|.+
T Consensus        15 ~~~~~t~~~lA~~~gis~~tis~~~~   40 (78)
T TIGR02607        15 EPLGLSIRALAKALGVSRSTLSRIVN   40 (78)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            45799999999999999999999864

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.

>PRK07122 RNA polymerase sigma factor SigF; Reviewed

Probab=92.85  E-value=0.23  Score=45.36  Aligned_cols=42  Identities=24%  Similarity=0.280  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+.+|++..+||+.||||.++|++++++-.
T Consensus       215 ~L~~rer~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral  256 (264)
T PRK07122        215 ALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTL  256 (264)
T ss_pred             cCCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            356666655555566899999999999999999999988765

>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor

Probab=92.85  E-value=0.24  Score=43.77  Aligned_cols=42  Identities=24%  Similarity=0.116  Sum_probs=33.4

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-    +|+|..+||+.+|+|.+||.+++.|-+
T Consensus       174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl  219 (227)
T TIGR02846       174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL  219 (227)
T ss_pred             hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            467777755554443    899999999999999999999988754

The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.

>PRK08215 sporulation sigma factor SigG; Reviewed

Probab=92.84  E-value=0.24  Score=44.70  Aligned_cols=42  Identities=12%  Similarity=0.134  Sum_probs=33.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+.+|++..+||+.||||.++|+++.++-.
T Consensus       209 ~L~~~er~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al  250 (258)
T PRK08215        209 KLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAAL  250 (258)
T ss_pred             cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            466666655555456899999999999999999999988754

>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59

Probab=92.84  E-value=0.15  Score=42.07  Aligned_cols=36  Identities=17%  Similarity=0.282  Sum_probs=31.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ...|++.+.|++..+||..|+||++||.....+.+.
T Consensus        71 ~Efi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~  106 (126)
T PF10654_consen   71 REFIELRHAGLTCYAIADYFKISKSTVFNFTQNNKK  106 (126)
T ss_pred             HHHHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHH
Confidence            345677789999999999999999999999877654

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK09480 slmA division inhibitor protein; Provisional

Probab=92.83  E-value=0.23  Score=41.46  Aligned_cols=45  Identities=16%  Similarity=0.245  Sum_probs=37.4

Q ss_pred             ccCCCCCCHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         42 FVNGRPLPNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        42 ~~~gR~~S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      |.|.++-+.+.|.+|++..     +.   +.|.++||++.|||++|+|++.+.
T Consensus         1 ~~~~~~~~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~   53 (194)
T PRK09480          1 MAMKRPKKGERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS   53 (194)
T ss_pred             CCCcCCCchhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence            5688888889999998863     23   479999999999999999987655

>COG1522 Lrp Transcriptional regulators [Transcription]

Probab=92.83  E-value=0.24  Score=40.58  Aligned_cols=43  Identities=26%  Similarity=0.394  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ++-.+|+...+ + ..+.++||+.+|+|.+||.+-+++..+.|-+
T Consensus         8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI   52 (154)
T COG1522           8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI   52 (154)
T ss_pred             HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence            34446777665 3 3799999999999999999999999999954

>PRK11475 DNA-binding transcriptional activator BglJ; Provisional

Probab=92.79  E-value=0.19  Score=44.42  Aligned_cols=41  Identities=17%  Similarity=0.115  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|.-.+ +|+.++.+|++.++||++|+||.+||...+++-.
T Consensus       134 ~LT~RE~-eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~  174 (207)
T PRK11475        134 MLSPTER-EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVM  174 (207)
T ss_pred             CCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            3665555 7888999999999999999999999998888865

>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]

Probab=92.77  E-value=0.28  Score=34.03  Aligned_cols=34  Identities=26%  Similarity=0.293  Sum_probs=29.5

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+..+|.+..+||..+++|..||..-+++-.
T Consensus        11 ~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~   44 (65)
T COG2771          11 EILRLVAQGKSNKEIARILGISEETVKTHLRNIY   44 (65)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555778999999999999999999998888764

>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B

Probab=92.76  E-value=0.27  Score=43.31  Aligned_cols=36  Identities=25%  Similarity=0.177  Sum_probs=31.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      |-.++|++|||||.||++-++.-.+.|.|.-+...|
T Consensus        26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~G   61 (233)
T TIGR02404        26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQGKG   61 (233)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCce
Confidence            789999999999999999999999999986555444

subtilis-type. This family consists of repressors of the GntR 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 Gram-positive lineages and does not include the TreR from E. coli.

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

Probab=92.75  E-value=0.29  Score=32.96  Aligned_cols=42  Identities=21%  Similarity=0.238  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      +.+..|..++.++|.++..||++.+.          +|.+||++.|++....
T Consensus         3 ~~~~~Il~~l~~~~~~t~~ela~~~~----------is~~tv~~~l~~L~~~   44 (48)
T PF13412_consen    3 ETQRKILNYLRENPRITQKELAEKLG----------ISRSTVNRYLKKLEEK   44 (48)
T ss_dssp             HHHHHHHHHHHHCTTS-HHHHHHHHT----------S-HHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHhC----------CCHHHHHHHHHHHHHC
Confidence            34677888889999999999998883          4999999999986543

...

>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]

Probab=92.75  E-value=0.21  Score=44.04  Aligned_cols=35  Identities=17%  Similarity=0.314  Sum_probs=30.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|+.++.+|++.++||++|++|.+||...+.+-.
T Consensus       154 ~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~  188 (211)
T COG2197         154 LEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNIL  188 (211)
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence            35668889999999999999999999998888765

>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional

Probab=92.74  E-value=0.51  Score=41.24  Aligned_cols=58  Identities=10%  Similarity=0.105  Sum_probs=41.4

Q ss_pred             HHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598         52 VRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK  109 (258)
Q Consensus        52 lR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e  109 (258)
                      +|.+|+... .-|  ++..++|++||||+++|+--+++....|-|...++.|-.=+.++.+
T Consensus        16 i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~   76 (224)
T PRK11534         16 LKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQ   76 (224)
T ss_pred             HHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHH
Confidence            455555542 234  5789999999999999999999999999887666555332334444

>COG5484 Uncharacterized conserved protein [Function unknown]

Probab=92.73  E-value=0.14  Score=47.62  Aligned_cols=38  Identities=21%  Similarity=0.156  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +-|..+-.++-+||...+||..||||..||..|.+|+.
T Consensus         7 ~~r~~Akk~yl~gmk~~dIAeklGvspntiksWKrr~g   44 (279)
T COG5484           7 DKRIIAKKDYLKGMKLKDIAEKLGVSPNTIKSWKRRDG   44 (279)
T ss_pred             chHHHHHHHHHhhccHHHHHHHhCCChHHHHHHHHhcC
Confidence            44556666788999999999999999999999999863

>COG3398 Uncharacterized protein conserved in archaea [Function unknown]

Probab=92.67  E-value=0.89  Score=41.65  Aligned_cols=104  Identities=18%  Similarity=0.133  Sum_probs=78.4

Q ss_pred             CCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCC---CCCC----------CHHHHH
Q psy15598         48 LPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSK---PRVT----------TPKVVS  112 (258)
Q Consensus        48 ~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~R---Prkl----------T~e~~~  112 (258)
                      +-++.|.+|.....  -|++.+|+++-+++.|+|.+=-++-.+..+.++.++-+|..   |.-.          ..+.-+
T Consensus        98 ~~ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k  177 (240)
T COG3398          98 FLNSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSK  177 (240)
T ss_pred             HhhhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHH
Confidence            44578999999986  48999999999999999999888888888887766666521   2111          122336


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      .|...+++++..+..+|+.++.          +|..||.=.|++.-...
T Consensus       178 ~I~~eiq~~~~~t~~~ia~~l~----------ls~aTV~~~lk~l~~~G  216 (240)
T COG3398         178 AIIYEIQENKCNTNLLIAYELN----------LSVATVAYHLKKLEELG  216 (240)
T ss_pred             HHHHHHhcCCcchHHHHHHHcC----------ccHHHHHHHHHHHHHcC
Confidence            6777788888999988877763          48899988887665443

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

Probab=92.66  E-value=1.1  Score=33.91  Aligned_cols=32  Identities=22%  Similarity=0.362  Sum_probs=28.2

Q ss_pred             HHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         66 PCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        66 ~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      ..++|+.|+|+++||++.+++..+.|-+.-.+
T Consensus         2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~   33 (96)
T smart00529        2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP   33 (96)
T ss_pred             HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence            57999999999999999999999999775443

iron dependent repressor

>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional

Probab=92.63  E-value=0.2  Score=44.48  Aligned_cols=40  Identities=23%  Similarity=0.300  Sum_probs=34.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++. ...+|+.+..+|++.++||+.|+||.+||..++.+-.
T Consensus       156 Lt~-rE~~Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~  195 (216)
T PRK10100        156 LTH-REKEILNKLRIGASNNEIARSLFISENTVKTHLYNLF  195 (216)
T ss_pred             CCH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            665 3346888888899999999999999999999998875

>COG1802 GntR Transcriptional regulators [Transcription]

Probab=92.61  E-value=0.33  Score=42.77  Aligned_cols=65  Identities=18%  Similarity=0.158  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHH
Q psy15598         50 NSVRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        50 ~dlR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I  114 (258)
                      ..+|.+|+..- .-|  ++..+||++||||+..|+.-+.+....|-|.-.+++|-.=..++.+..+.|
T Consensus        23 ~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei   90 (230)
T COG1802          23 EELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI   90 (230)
T ss_pred             HHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence            46777777764 345  688999999999999999999999999988766666633344554444433

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

Probab=92.57  E-value=0.3  Score=38.57  Aligned_cols=38  Identities=16%  Similarity=0.110  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|..|..+++ .+....++|+.||||++|+++.+++|.
T Consensus        55 ~Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~g   93 (95)
T PRK00430         55 VEAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG   93 (95)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            34555556655 577899999999999999999999973

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

Probab=92.56  E-value=0.23  Score=38.35  Aligned_cols=84  Identities=19%  Similarity=0.258  Sum_probs=40.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCCC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS-DGVC  139 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~-~Gv~  139 (258)
                      +.|++..+||+.||.|++.|++.+.-..-...|...-..|   ..........|....+.+|    .++...+.. ..-.
T Consensus         1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~i~~~v~~g---~~~~~~a~~~L~~~~~~~~----~~~~~~v~~~~~~~   73 (93)
T PF08535_consen    1 EFGWTQEEIAKRLGKSRSWVSNHLALLDLPEEIKELVRSG---RISDIRALYELRKLAEKNP----EEVEALVAKAKEEG   73 (93)
T ss_dssp             HTT--HHHHHHHTT--HHHHHHHHGGGS--HHHHHHHHTT---S---HHHHHHHHHHHHH-H----HHHHHHH-HSTTS-
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHHHHcC---CCchHHHHHHHHHHHHhCH----HHHHHHHHHhcccc
Confidence            4699999999999999999999988653222221111122   2223333444445554543    344444422 2222


Q ss_pred             CCCCCCCHHHHHHHHHh
Q psy15598        140 DKFNVPSVSSISRILRN  156 (258)
Q Consensus       140 v~~~~pS~STI~RiLrr  156 (258)
                           ++..++.++.+.
T Consensus        74 -----~t~~~~~~~~~~   85 (93)
T PF08535_consen   74 -----LTRAAVKALRRE   85 (93)
T ss_dssp             ------SHHHHHHHHHH
T ss_pred             -----ccHHHHHHHHHH
Confidence                 377888555443

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.

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

Probab=92.54  E-value=0.45  Score=40.57  Aligned_cols=77  Identities=18%  Similarity=0.208  Sum_probs=40.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh--cCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS--DGVCDK  141 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~--~Gv~v~  141 (258)
                      .|..+||+.+||+++|+|+|.+.=+.                    ..++..++..+.=.-...++...|..  .|-.  
T Consensus        35 ~T~~eiAee~Gis~~tLYrWr~~~~~--------------------Fiey~n~la~~~~~~~~~eVy~~L~~~i~~~~--   92 (142)
T PF13022_consen   35 RTQAEIAEEVGISRSTLYRWRQQNKA--------------------FIEYKNELADRFLSSHREEVYTQLMKKIRGGQ--   92 (142)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHH-HH--------------------HHHHHHHHHHHHHHTTHHHHHHHHHHHHHSSS--
T ss_pred             chHHHHHHHhCCCHHHHHHHHhcCHH--------------------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCC--
Confidence            67999999999999999999965221                    11111222111111133344444432  1222  


Q ss_pred             CCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        142 FNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       142 ~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                         +|+..|.-+|++.|.-.+++.
T Consensus        93 ---~svKaieLflk~~GLLtDrq~  113 (142)
T PF13022_consen   93 ---PSVKAIELFLKRHGLLTDRQE  113 (142)
T ss_dssp             -----HHHHHHHHHHTT--EEEEE
T ss_pred             ---ccHHHHHHHHHHcCcccceee
Confidence               488888888888887665543

>PF13592 HTH_33: Winged helix-turn helix

Probab=92.52  E-value=0.22  Score=35.73  Aligned_cols=41  Identities=22%  Similarity=-0.024  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHHHHH-hcCCCCCCCCCCHHHHHHHHHhccCCCCCCCC
Q psy15598        121 DPGIFAWEIRDRLL-SDGVCDKFNVPSVSSISRILRNKIGSSIVQHH  166 (258)
Q Consensus       121 nP~ita~EIr~~L~-~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~  166 (258)
                      +..+++.+|++.+. +.|+..     |.++|++.|++++...-++..
T Consensus         2 ~~~wt~~~i~~~I~~~fgv~y-----s~~~v~~lL~r~G~s~~kp~~   43 (60)
T PF13592_consen    2 GGRWTLKEIAAYIEEEFGVKY-----SPSGVYRLLKRLGFSYQKPRP   43 (60)
T ss_pred             CCcccHHHHHHHHHHHHCCEE-----cHHHHHHHHHHcCCccccCCC
Confidence            45678999999998 589986     999999999999988665543

>PRK09492 treR trehalose repressor; Provisional

Probab=92.51  E-value=0.2  Score=44.97  Aligned_cols=23  Identities=30%  Similarity=0.388  Sum_probs=21.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++.++||+.+|||++||+|.++.
T Consensus         5 ~ti~dIA~~agVS~~TVSrvLn~   27 (315)
T PRK09492          5 LTIKDIARLSGVGKSTVSRVLNN   27 (315)
T ss_pred             CcHHHHHHHhCCCHHHHhHHhCC
Confidence            58899999999999999999964

>PRK10572 DNA-binding transcriptional regulator AraC; Provisional

Probab=92.49  E-value=0.9  Score=40.99  Aligned_cols=78  Identities=13%  Similarity=0.113  Sum_probs=52.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      +..+..++|+.+++|++++.|..++.-  |.         .|.. +...-...-..++ ....++..||+..+   |.. 
T Consensus       198 ~~isl~~lA~~~~lS~~~l~r~Fk~~~--G~---------tp~~~l~~~Rl~~A~~lL-~~t~~sI~eIA~~~---GF~-  261 (290)
T PRK10572        198 SEFDIESVAQHVCLSPSRLAHLFRQQL--GI---------SVLRWREDQRISRAKLLL-QTTRMPIATIGRNV---GYD-  261 (290)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHHHHHHh---CCC-
Confidence            568999999999999999999999973  21         1111 1111112222223 34678888887766   665 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+...|+.|+.-+.
T Consensus       262 -----d~s~Fsr~FKk~~G~  276 (290)
T PRK10572        262 -----DQLYFSRVFKKCTGA  276 (290)
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 788999999887654

>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins

Probab=92.49  E-value=0.26  Score=42.03  Aligned_cols=51  Identities=14%  Similarity=0.148  Sum_probs=43.0

Q ss_pred             ccCCc-ccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         37 QLGGV-FVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        37 q~~~~-~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      |.||. -+-++-|...+=.+||.++++|.+.++|+..|.||+.|.+.|...-
T Consensus         4 qnggrptilpkmYtE~Lve~II~~IE~dt~~sEIc~~L~isrKtFyeWrdtk   55 (174)
T PF07141_consen    4 QNGGRPTILPKMYTEPLVEQIIDKIESDTNDSEICTSLHISRKTFYEWRDTK   55 (174)
T ss_pred             cCCCCCcccHHhhhhHHHHHHHHHHHcCCcHHHHHHHHhccHHHHHHHHhhh
Confidence            45663 2355668888889999999999999999999999999999998754

This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.

>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional

Probab=92.43  E-value=0.3  Score=43.37  Aligned_cols=54  Identities=20%  Similarity=0.268  Sum_probs=41.3

Q ss_pred             CCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         47 PLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++-..+...|.+...+|.        |-.++|++|||||.||++-++.-.+.|.|.-....|
T Consensus         9 p~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~G   70 (241)
T PRK11402          9 LLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKG   70 (241)
T ss_pred             cHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            344455666666665542        789999999999999999999999999986554444

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

Probab=92.42  E-value=0.66  Score=41.79  Aligned_cols=67  Identities=16%  Similarity=0.180  Sum_probs=49.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+..|||.+||+-|-+    .|-+.|..+.+ +-+..++++.+.|..+.. ..-..++.+|++.|..
T Consensus         2 y~i~elA~~~Gvs~~tIR~Ye~----~GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~   69 (219)
T cd04778           2 YRIDDLARAAGTTVRNVRAYQD----RGLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA   69 (219)
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence            5789999999999999866554    47776654443 456889888887766655 3346778888887764

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

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

Probab=92.38  E-value=0.45  Score=37.09  Aligned_cols=33  Identities=15%  Similarity=0.090  Sum_probs=30.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..++..+||+.+|+|+.||+|.+++..+.|-|.
T Consensus        46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~   78 (95)
T TIGR01610        46 DRVTATVIAELTGLSRTHVSDAIKSLARRRIIF   78 (95)
T ss_pred             CccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence            468999999999999999999999999999885

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

>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional

Probab=92.35  E-value=0.25  Score=44.73  Aligned_cols=41  Identities=12%  Similarity=0.159  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|... ..|+.++.+|++.++||+.|+||.+||.+.+++-.
T Consensus       143 ~LS~RE-~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~  183 (217)
T PRK13719        143 KVTKYQ-NDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL  183 (217)
T ss_pred             CCCHHH-HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            344444 36888889999999999999999999999998876

>COG2188 PhnF Transcriptional regulators [Transcription]

Probab=92.33  E-value=0.3  Score=43.77  Aligned_cols=57  Identities=25%  Similarity=0.258  Sum_probs=44.8

Q ss_pred             CCCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         44 NGRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++.++-..++..|.+...+|.        +-.++|++|||||-||+|-++.-.+.|-|......|
T Consensus         4 ~~~plY~qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~G   68 (236)
T COG2188           4 SAMPLYQQIAEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKG   68 (236)
T ss_pred             ccCccHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCe
Confidence            344556667777777776653        789999999999999999999999999886554444

>PRK09764 DNA-binding transcriptional repressor MngR; Provisional

Probab=92.30  E-value=0.31  Score=43.34  Aligned_cols=53  Identities=21%  Similarity=0.140  Sum_probs=39.9

Q ss_pred             CCHHHHHHHHHHHHc-----CC---CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         48 LPNSVRMRIVELAQL-----GI---RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-----G~---S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +-..+...|.....+     |.   |-.++|++||||+.||++-+....+.|.|.-+.+.|
T Consensus         6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~G   66 (240)
T PRK09764          6 LYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSG   66 (240)
T ss_pred             HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            334555555555544     42   779999999999999999999999999886555444

>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]

Probab=92.30  E-value=2.2  Score=32.53  Aligned_cols=89  Identities=21%  Similarity=0.227  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHH
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEI  129 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EI  129 (258)
                      .....|......+.+..++|+.+|+|++++.+..++..  |.         .+.. +.......-.. +..+...+..+|
T Consensus        24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~--g~---------s~~~~~~~~Rl~~A~~-lL~~~~~~i~~i   91 (127)
T COG2207          24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKET--GT---------SPSQYLRQLRLEEARR-LLRSTDLSITEI   91 (127)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--CC---------CHHHHHHHHHHHHHHH-HHHcCCCCHHHH
Confidence            33344444334568999999999999999999988763  21         1111 11111122222 224445567777


Q ss_pred             HHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        130 RDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       130 r~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      +..+   |..      +.+...|..++.-+.
T Consensus        92 A~~~---Gf~------~~s~F~~~Fk~~~g~  113 (127)
T COG2207          92 ALRL---GYS------SPSHFSRAFKRLFGV  113 (127)
T ss_pred             HHHh---CcC------CHHHHHHHHHHHhCC
Confidence            6655   665      777788888876554

>TIGR01636 phage_rinA phage transcriptional activator, RinA family

Probab=92.30  E-value=0.38  Score=39.79  Aligned_cols=42  Identities=19%  Similarity=0.154  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHcCC--CHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGI--RPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~--S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++.+.|.-|...+-.+.  +..+||..|++|++||+++.+++..
T Consensus        83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~  126 (134)
T TIGR01636        83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIE  126 (134)
T ss_pred             CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            56666655555555554  9999999999999999999988753

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.

>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial

Probab=92.27  E-value=0.3  Score=43.07  Aligned_cols=36  Identities=17%  Similarity=0.156  Sum_probs=31.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      |-+++|++||||+.||++-+..-.+.|.+.-....|
T Consensus        27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~G   62 (230)
T TIGR02018        27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQGVG   62 (230)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence            889999999999999999999999999886555444

This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.

>PRK11512 DNA-binding transcriptional repressor MarR; Provisional

Probab=92.27  E-value=0.85  Score=37.47  Aligned_cols=55  Identities=16%  Similarity=0.167  Sum_probs=40.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKE  116 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~  116 (258)
                      .|.+.++||+.++++++||.+.+++..+.|-|.-...  .++ +--.+|++-.+.+.+
T Consensus        53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~  110 (144)
T PRK11512         53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ  110 (144)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence            5689999999999999999999999999998743322  221 122466665555444

>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional

Probab=92.25  E-value=0.18  Score=44.80  Aligned_cols=53  Identities=9%  Similarity=0.140  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHHHHHcCC---CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         48 LPNSVRMRIVELAQLGI---RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~---S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +..++|.+|...+..|.   |-.++|++|||||.||++-++.-.+.|.|.-+...|
T Consensus        17 i~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~G   72 (241)
T PRK10079         17 IAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVG   72 (241)
T ss_pred             HHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence            44566666643233452   789999999999999999999999999987555444

>PRK09726 antitoxin HipB; Provisional

Probab=92.25  E-value=0.32  Score=37.22  Aligned_cols=35  Identities=9%  Similarity=0.221  Sum_probs=28.3

Q ss_pred             HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+..+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus        12 ~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~   47 (88)
T PRK09726         12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3445555554 4699999999999999999999976

>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=92.24  E-value=0.43  Score=32.19  Aligned_cols=40  Identities=25%  Similarity=0.147  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      ++.+..|...+++++..+..+|.+.+.          +|.+||.+.+++.
T Consensus         2 D~~D~~Il~~Lq~d~r~s~~~la~~lg----------lS~~~v~~Ri~rL   41 (42)
T PF13404_consen    2 DELDRKILRLLQEDGRRSYAELAEELG----------LSESTVRRRIRRL   41 (42)
T ss_dssp             -HHHHHHHHHHHH-TTS-HHHHHHHHT----------S-HHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHcCCccHHHHHHHHC----------cCHHHHHHHHHHh
Confidence            456788999999999999999998883          4999999999864

...

>PRK10014 DNA-binding transcriptional repressor MalI; Provisional

Probab=92.14  E-value=0.25  Score=44.87  Aligned_cols=22  Identities=32%  Similarity=0.296  Sum_probs=20.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.++||+.+|||++||+|.++
T Consensus         7 ~Ti~dIA~~agVS~~TVSr~Ln   28 (342)
T PRK10014          7 ITIHDVALAAGVSVSTVSLVLS   28 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHHC
Confidence            6899999999999999999986

>PRK10072 putative transcriptional regulator; Provisional

Probab=92.11  E-value=0.26  Score=39.16  Aligned_cols=27  Identities=30%  Similarity=0.319  Sum_probs=24.3

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|++..++|+.+|||.+||++|.+.
T Consensus        43 ~~~glTQ~elA~~lGvS~~TVs~WE~G   69 (96)
T PRK10072         43 KGTGLKIDDFARVLGVSVAMVKEWESR   69 (96)
T ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence            357999999999999999999999764

>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress

Probab=92.11  E-value=0.85  Score=35.19  Aligned_cols=53  Identities=26%  Similarity=0.377  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHH-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCCCCC
Q psy15598         51 SVRMRIVELAQ-LG--IRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGGSKP  103 (258)
Q Consensus        51 dlR~RIV~L~~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG~RP  103 (258)
                      ++-..||+++. .|  +.-++||+.|++|..||++-....++-|-++  |.+.+|+.|
T Consensus         8 ~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriP   65 (78)
T PF03444_consen    8 EILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIP   65 (78)
T ss_pred             HHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCc
Confidence            34456777764 34  5779999999999999999999999999885  555666434

Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent

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

Probab=92.08  E-value=0.21  Score=39.84  Aligned_cols=48  Identities=27%  Similarity=0.234  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHhCC-CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        110 VVSYIKELKQKDP-GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       110 ~~~~I~~lv~~nP-~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      .+..|.+++.+.+ ..++.||.+.|.+.+..+     |.+||+|.|..+.....
T Consensus         9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~i-----s~~TVYR~L~~L~e~Gl   57 (120)
T PF01475_consen    9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRI-----SLATVYRTLDLLEEAGL   57 (120)
T ss_dssp             HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT-------HHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCc-----CHHHHHHHHHHHHHCCe
Confidence            3556666666544 788999999999888775     99999999998776654

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

>PRK11922 RNA polymerase sigma factor; Provisional

Probab=92.07  E-value=0.21  Score=44.27  Aligned_cols=41  Identities=20%  Similarity=0.209  Sum_probs=33.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-+...+-+|++..+||+.||||.+||+..+.|.+
T Consensus       150 L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar  190 (231)
T PRK11922        150 LPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR  190 (231)
T ss_pred             CCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            66666655444466899999999999999999999988764

>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial

Probab=92.06  E-value=0.23  Score=44.81  Aligned_cols=23  Identities=30%  Similarity=0.401  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++.++||+.+|||++||+|.++.
T Consensus         2 ~ti~dIA~~agVS~sTVSr~Ln~   24 (311)
T TIGR02405         2 LTIKDIARLAGVGKSTVSRVLNN   24 (311)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC
Confidence            47899999999999999999953

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

>PRK15369 two component system sensor kinase SsrB; Provisional

Probab=91.98  E-value=0.42  Score=38.68  Aligned_cols=41  Identities=24%  Similarity=0.235  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++.. ..+|+.++.+|++.++||+.+++|..||..++++-+.
T Consensus       150 lt~~-e~~vl~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~  190 (211)
T PRK15369        150 LTPR-ERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMR  190 (211)
T ss_pred             CCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            5544 3467777889999999999999999999999998763

>PRK10411 DNA-binding transcriptional activator FucR; Provisional

Probab=91.91  E-value=0.33  Score=43.92  Aligned_cols=44  Identities=25%  Similarity=0.351  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.+.+|++.++ . ..+..++|+.|+||..||+|.++...+.|.+.
T Consensus         4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~   49 (240)
T PRK10411          4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL   49 (240)
T ss_pred             HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44566777765 3 47999999999999999999999999888764

>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=91.91  E-value=0.54  Score=31.71  Aligned_cols=34  Identities=24%  Similarity=0.359  Sum_probs=25.4

Q ss_pred             HHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         54 MRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        54 ~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .+|+.+.+ +| .+..+||+.+|+|.+||.+=+++.
T Consensus         6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL   41 (42)
T PF13404_consen    6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL   41 (42)
T ss_dssp             HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence            46777765 44 799999999999999999877764

...

>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS

Probab=91.91  E-value=0.32  Score=44.61  Aligned_cols=42  Identities=10%  Similarity=0.019  Sum_probs=33.3

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|+..+    .+|+|..+||..||||.+||..++.+-+
T Consensus       222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAl  267 (285)
T TIGR02394       222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEAL  267 (285)
T ss_pred             cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            35666665444443    5899999999999999999999998865

A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).

>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional

Probab=91.89  E-value=0.42  Score=42.73  Aligned_cols=58  Identities=17%  Similarity=0.149  Sum_probs=42.0

Q ss_pred             cCCCCCCHHHHHHHHHHHHc-----C--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         43 VNGRPLPNSVRMRIVELAQL-----G--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        43 ~~gR~~S~dlR~RIV~L~~~-----G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ...++++..+-..|...+..     |  + +-+++|++||||+++|+--+++....|-|...++.|
T Consensus         4 ~~~~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G   69 (253)
T PRK11523          4 TEPRRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSG   69 (253)
T ss_pred             CCCCcHHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            34445555554444444433     4  3 468999999999999999999999999886665555

>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional

Probab=91.83  E-value=0.25  Score=44.88  Aligned_cols=42  Identities=26%  Similarity=0.252  Sum_probs=31.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~~~I~~lv~~  120 (258)
                      .+.++||+..|||++||+|.++..               +. ..+++.+++|.+..++
T Consensus         2 ~ti~dIA~~agVS~~TVSrvln~~---------------~~~~vs~~tr~rV~~~a~~   44 (327)
T PRK10339          2 ATLKDIAIEAGVSLATVSRVLNDD---------------PTLNVKEETKHRILEIAEK   44 (327)
T ss_pred             CCHHHHHHHhCCCHHhhhhhhcCC---------------CCCCcCHHHHHHHHHHHHH
Confidence            378999999999999999998542               11 2567777777777664

>TIGR02850 spore_sigG RNA polymerase sigma-G factor

Probab=91.77  E-value=0.4  Score=43.16  Aligned_cols=42  Identities=14%  Similarity=0.130  Sum_probs=34.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+.+|++.++||+.||||..+|+++.++-.
T Consensus       206 ~L~~rer~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ral  247 (254)
T TIGR02850       206 RLNEREKMILNMRFFEGKTQMEVAEEIGISQAQVSRLEKAAL  247 (254)
T ss_pred             cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            466666655555556899999999999999999999988864

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.

>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif

Probab=91.76  E-value=0.36  Score=34.22  Aligned_cols=36  Identities=17%  Similarity=0.147  Sum_probs=29.4

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      +++..+.+-.+...+|+.++||.++|++.+++.++.
T Consensus         5 ~~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~LE~~   40 (60)
T PF00126_consen    5 RYFLAVAETGSISAAAEELGISQSAVSRQIKQLEEE   40 (60)
T ss_dssp             HHHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHhhccchHHHHHHHHHHHH
Confidence            455555444499999999999999999999999863

These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....

>PRK09526 lacI lac repressor; Reviewed

Probab=91.73  E-value=0.27  Score=44.64  Aligned_cols=23  Identities=30%  Similarity=0.411  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.++||+..|||++||+|.++.
T Consensus         6 ~ti~dIA~~aGVS~~TVSrvLn~   28 (342)
T PRK09526          6 VTLYDVARYAGVSYQTVSRVLNQ   28 (342)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhcC
Confidence            58899999999999999999964

>PRK10651 transcriptional regulator NarL; Provisional

Probab=91.70  E-value=0.36  Score=39.65  Aligned_cols=40  Identities=23%  Similarity=0.294  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...+ +|+.++.+|++.++||+.|+||..||...+++-+
T Consensus       156 Lt~rE~-~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~  195 (216)
T PRK10651        156 LTPRER-DILKLIAQGLPNKMIARRLDITESTVKVHVKHML  195 (216)
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence            666554 7888889999999999999999999999999876

>TIGR02392 rpoH_proteo alternative sigma factor RpoH

Probab=91.66  E-value=0.32  Score=44.31  Aligned_cols=42  Identities=14%  Similarity=0.029  Sum_probs=32.4

Q ss_pred             CCCHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+  .+|+|.++||+.||||..+|+++.++-.
T Consensus       218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al  261 (270)
T TIGR02392       218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAM  261 (270)
T ss_pred             cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            36666665454445  2489999999999999999998887754

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.

>COG2522 Predicted transcriptional regulator [General function prediction only]

Probab=91.64  E-value=0.25  Score=40.87  Aligned_cols=39  Identities=21%  Similarity=0.371  Sum_probs=31.8

Q ss_pred             HHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         50 NSVRMRIVE-LAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        50 ~dlR~RIV~-L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..+|..+.. |.++|+|..+||+.||||++.|+++++-.+
T Consensus         8 PaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~kr   47 (119)
T COG2522           8 PAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKR   47 (119)
T ss_pred             HHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCC
Confidence            356666554 456899999999999999999999988753

>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional

Probab=91.61  E-value=0.34  Score=44.07  Aligned_cols=44  Identities=16%  Similarity=0.246  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+-|.+|+++++ .| ++..++|+.|+||+.||+|=++...+.|.+
T Consensus         4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l   49 (256)
T PRK10434          4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV   49 (256)
T ss_pred             HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            467788888886 45 799999999999999999999999989866

>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional

Probab=91.60  E-value=0.32  Score=46.66  Aligned_cols=38  Identities=16%  Similarity=0.117  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ...|..|..+++ .|....++|+.||||++|+||.+++|
T Consensus       416 ~~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~  454 (457)
T PRK11361        416 RVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY  454 (457)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence            346777777775 47899999999999999999999998

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

Probab=91.56  E-value=0.34  Score=43.15  Aligned_cols=42  Identities=10%  Similarity=0.057  Sum_probs=34.6

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+    .+|++..+||+.||||..+|+++.++-.
T Consensus       176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al  221 (238)
T TIGR02393       176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKAL  221 (238)
T ss_pred             hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46777776555555    4789999999999999999999988865

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.

>TIGR03020 EpsA transcriptional regulator EpsA

Probab=91.56  E-value=0.34  Score=44.37  Aligned_cols=42  Identities=17%  Similarity=0.133  Sum_probs=35.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .+|...+ .|+.+..+|++..+||+.|+||..||...+++-.+
T Consensus       190 ~LT~RE~-evl~l~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~  231 (247)
T TIGR03020       190 LITAREA-EILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFK  231 (247)
T ss_pred             CCCHHHH-HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5776555 56667789999999999999999999999998763

Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.

>PRK09791 putative DNA-binding transcriptional regulator; Provisional

Probab=91.54  E-value=0.75  Score=41.32  Aligned_cols=55  Identities=16%  Similarity=0.053  Sum_probs=37.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVV  111 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~  111 (258)
                      .+++..+.+-.+.+.+|+.|+||.++|++-+++.++ -|. +-.+  .+ |.-.+|++=+
T Consensus        10 L~~f~~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R--~~-r~~~lT~~G~   66 (302)
T PRK09791         10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFR--RS-KGVTLTDAGE   66 (302)
T ss_pred             HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEE--cC-CCceECccHH
Confidence            445555444449999999999999999999999986 443 2222  22 4455555433

>PRK09393 ftrA transcriptional activator FtrA; Provisional

Probab=91.48  E-value=1.2  Score=41.05  Aligned_cols=86  Identities=12%  Similarity=0.145  Sum_probs=56.3

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~ita~E  128 (258)
                      .++++.+.    +..+..++|+.+|+|.+++.|..+++-  |.         .|...-.+ -.....+++ .+.+.+..+
T Consensus       221 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~--g~---------s~~~~~~~~Rl~~A~~lL-~~~~~~i~~  288 (322)
T PRK09393        221 GPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT--GM---------TPAEWLLRERLARARDLL-ESSALSIDQ  288 (322)
T ss_pred             HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence            34455443    357999999999999999999999974  21         22222111 122222333 345788888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      +.+...|.+|+.-+.
T Consensus       289 IA~~~---Gf~------~~s~F~r~Fk~~~G~  311 (322)
T PRK09393        289 IAERA---GFG------SEESLRHHFRRRAAT  311 (322)
T ss_pred             HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            87665   665      889999999876543

>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional

Probab=91.47  E-value=0.48  Score=42.38  Aligned_cols=49  Identities=20%  Similarity=0.232  Sum_probs=37.9

Q ss_pred             HHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         52 VRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        52 lR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +|.+|+.. +.-|  + +-.++|++||||+++|+.-+++....|-|...++.|
T Consensus        18 l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G   70 (257)
T PRK10225         18 IRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAG   70 (257)
T ss_pred             HHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence            45555554 2334  4 578999999999999999999999999887666555

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=91.46  E-value=1.2  Score=35.08  Aligned_cols=57  Identities=12%  Similarity=0.173  Sum_probs=40.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC---CCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR---VTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr---klT~e~~~~I~~lv  118 (258)
                      .+.+..+||+.++++++||++.+++..+.|-|.-.+....+..   .+|++-...+.++.
T Consensus        42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~  101 (109)
T TIGR01889        42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLI  101 (109)
T ss_pred             CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHH
Confidence            3599999999999999999999999999997742222221222   26666666555554

This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.

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

Probab=91.39  E-value=0.48  Score=35.99  Aligned_cols=67  Identities=24%  Similarity=0.319  Sum_probs=46.6

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC-CCCCCCC---CCCHHHHHHHHHHH
Q psy15598         52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA-IGGSKPR---VTTPKVVSYIKELK  118 (258)
Q Consensus        52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~-rgG~RPr---klT~e~~~~I~~lv  118 (258)
                      +|..|+.+..  +.++.++|.+.+|++.+++++-++.-.+.|-|.-.+ ..+++|+   .+|++=++.+.+++
T Consensus         1 vRl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~   73 (80)
T PF13601_consen    1 VRLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV   73 (80)
T ss_dssp             HHHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred             CHHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence            4777877754  568999999999999999999999999999875333 2333665   47777666666654

>PRK13502 transcriptional activator RhaR; Provisional

Probab=91.38  E-value=1.5  Score=39.34  Aligned_cols=88  Identities=10%  Similarity=0.073  Sum_probs=58.5

Q ss_pred             HHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHHHHHHHHHHhCCCCCH
Q psy15598         52 VRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        52 lR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~~~I~~lv~~nP~ita  126 (258)
                      .-.+++.++    .+..+..++|+.+|+|.+.++|..+++-  |.         .+. -+...-...-++++ .+.+.+.
T Consensus       177 ~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~--G~---------t~~~yi~~~Rl~~A~~lL-~~t~~sI  244 (282)
T PRK13502        177 LLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQT--GM---------TINQYLRQVRICHAQYLL-QHSPLMI  244 (282)
T ss_pred             HHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence            335666664    3467999999999999999999999973  21         111 11111122223333 3457788


Q ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .||+..+   |..      +.+...|+.|+.-+.
T Consensus       245 ~eIA~~~---GF~------d~s~F~r~FKk~~G~  269 (282)
T PRK13502        245 SEISMQC---GFE------DSNYFSVVFTRETGM  269 (282)
T ss_pred             HHHHHHc---CCC------CHHHHHHHHHHHHCc
Confidence            8887766   775      889999999987654

>PRK10727 DNA-binding transcriptional regulator GalR; Provisional

Probab=91.36  E-value=0.33  Score=44.39  Aligned_cols=40  Identities=18%  Similarity=0.247  Sum_probs=30.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++||+..|||.+||+|.++.               +++ .+++.+++|.+..++
T Consensus         3 ti~dIA~~aGVS~~TVSrvLn~---------------~~~-Vs~~tr~rV~~~a~e   42 (343)
T PRK10727          3 TIKDVARLAGVSVATVSRVINN---------------SPK-ASEASRLAVHSAMES   42 (343)
T ss_pred             CHHHHHHHhCCCHHHHHHHhCC---------------CCC-CCHHHHHHHHHHHHH
Confidence            7899999999999999999953               112 566777777766654

>PRK13501 transcriptional activator RhaR; Provisional

Probab=91.33  E-value=1.8  Score=39.13  Aligned_cols=78  Identities=12%  Similarity=0.092  Sum_probs=53.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      +-.+..++|+.+++|+++++|..+++-  |.         .+.. +.......-.++ ..+.+.+..||+..+   |.. 
T Consensus       191 e~~sl~~lA~~~~lS~~~l~r~Fk~~~--G~---------T~~qyi~~~Ri~~A~~L-L~~t~~sI~eIA~~~---GF~-  254 (290)
T PRK13501        191 AYFDMADFCHKNQLVERSLKQLFRQQT--GM---------SISHYLRQIRLCHAKCL-LRGSEHRISDIAARC---GFE-  254 (290)
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHH-HHcCCCCHHHHHHHh---CCC-
Confidence            568999999999999999999999863  21         1111 111111122222 255678888887777   665 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+.-.|+.|+..+.
T Consensus       255 -----~~s~F~r~FKk~~G~  269 (290)
T PRK13501        255 -----DSNYFSAVFTREAGM  269 (290)
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 888999999887664

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

Probab=91.32  E-value=0.35  Score=43.27  Aligned_cols=41  Identities=12%  Similarity=0.235  Sum_probs=35.9

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|++++.   .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus        12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~   55 (248)
T TIGR02431        12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT   55 (248)
T ss_pred             HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            46777764   368999999999999999999999999999875

Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.

>PRK10401 DNA-binding transcriptional regulator GalS; Provisional

Probab=91.28  E-value=0.35  Score=44.25  Aligned_cols=41  Identities=22%  Similarity=0.262  Sum_probs=29.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+.++||+..|||++||+|.++..               + ..+++.+++|.+..++
T Consensus         2 ~ti~dIA~~aGVS~~TVSrvLn~~---------------~-~Vs~~tr~kV~~~a~e   42 (346)
T PRK10401          2 ITIRDVARQAGVSVATVSRVLNNS---------------A-LVSADTREAVMKAVSE   42 (346)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCC---------------C-CCCHHHHHHHHHHHHH
Confidence            478999999999999999999641               1 1455666666666544

>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial

Probab=91.23  E-value=0.27  Score=41.14  Aligned_cols=32  Identities=9%  Similarity=0.164  Sum_probs=29.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+++.||+|.++++++.|-+.-
T Consensus       144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~  175 (193)
T TIGR03697       144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI  175 (193)
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            58999999999999999999999999998743

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.

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

Probab=91.23  E-value=0.45  Score=43.79  Aligned_cols=42  Identities=21%  Similarity=0.309  Sum_probs=34.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.-.|.-+...+.++++.++||+.||||.+.|+++.++..
T Consensus       196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai  237 (247)
T COG1191         196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAI  237 (247)
T ss_pred             ccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence            455555555555567899999999999999999999999875

>PRK15320 transcriptional activator SprB; Provisional

Probab=91.20  E-value=0.43  Score=43.35  Aligned_cols=43  Identities=9%  Similarity=0.104  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      .+|.-.+ .|+.+..+|++.++||+.|++|.+||++..+|-.+.
T Consensus       164 ~LSdREI-EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeK  206 (251)
T PRK15320        164 GVTQAKY-ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYR  206 (251)
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHH
Confidence            3554443 677788899999999999999999999999998754

>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=91.18  E-value=0.37  Score=33.98  Aligned_cols=31  Identities=29%  Similarity=0.448  Sum_probs=22.5

Q ss_pred             HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         56 IVELA-QLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      |-.+. +.|++..++|+.+|++++++++|.+-
T Consensus         4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g   35 (64)
T PF12844_consen    4 LKELREEKGLTQKDLAEKLGISRSTISKIENG   35 (64)
T ss_dssp             HHHHHHHCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence            44444 36999999999999999999999754

>PRK10371 DNA-binding transcriptional regulator MelR; Provisional

Probab=91.15  E-value=1.7  Score=40.23  Aligned_cols=78  Identities=13%  Similarity=0.163  Sum_probs=51.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV-VSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~-~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      +..+..+||+.+|+|++++.|..++.  +|.         .+....... .....+++ .+++.+..||+..+   |.. 
T Consensus       206 ~~~tl~~lA~~~~~S~~~l~r~Fk~~--~G~---------t~~~~l~~~Rl~~A~~lL-~~~~~si~eIA~~~---Gf~-  269 (302)
T PRK10371        206 QALTINDVAEHVKLNANYAMGIFQRV--MQL---------TMKQYITAMRINHVRALL-SDTDKSILDIALTA---GFR-  269 (302)
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHH--hCC---------CHHHHHHHHHHHHHHHHH-hcCCCCHHHHHHHc---CCC-
Confidence            46899999999999999999999996  332         111111111 12222222 34577887876655   665 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+...|..++.-+.
T Consensus       270 -----~~s~F~r~Fk~~~G~  284 (302)
T PRK10371        270 -----SSSRFYSTFGKYVGM  284 (302)
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 888999999877553

>PRK03837 transcriptional regulator NanR; Provisional

Probab=91.10  E-value=0.31  Score=42.86  Aligned_cols=36  Identities=11%  Similarity=0.066  Sum_probs=31.9

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +..++|++||||+++|+.-+++....|-|...++.|
T Consensus        39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~G   74 (241)
T PRK03837         39 SERELMAFFGVGRPAVREALQALKRKGLVQISHGER   74 (241)
T ss_pred             CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCc
Confidence            789999999999999999999999999886655444

>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38

Probab=91.04  E-value=0.48  Score=39.74  Aligned_cols=42  Identities=19%  Similarity=0.271  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHH-H--cCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         48 LPNSVRMRIVELA-Q--LGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~--~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      +..+. .+||.+. .  .|++--+||..|+||.+|+++|...|+++
T Consensus        82 l~de~-k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~  126 (130)
T PF05263_consen   82 LIDEE-KRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKND  126 (130)
T ss_pred             hCHHH-HHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence            44443 4555654 3  46999999999999999999999999864

The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.

>PRK12682 transcriptional regulator CysB-like protein; Reviewed

Probab=91.03  E-value=0.69  Score=41.87  Aligned_cols=36  Identities=25%  Similarity=0.333  Sum_probs=30.9

Q ss_pred             HHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         55 RIV-ELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        55 RIV-~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      +++ .+++.|.+.+++|+.|+||.++|++.+++.++.
T Consensus         7 ~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~   43 (309)
T PRK12682          7 RFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEE   43 (309)
T ss_pred             HHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHH
Confidence            444 456678999999999999999999999999864

>PRK09462 fur ferric uptake regulator; Provisional

Probab=90.99  E-value=0.77  Score=38.23  Aligned_cols=52  Identities=23%  Similarity=0.191  Sum_probs=39.5

Q ss_pred             CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        106 TTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       106 lT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      +|+. +..|.+.+.+.  -.+++.||.+.|.+.+..+     |.+||+|.|..+....+-
T Consensus        15 ~T~q-R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i-----~~aTVYR~L~~L~e~Gli   68 (148)
T PRK09462         15 VTLP-RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI-----GLATVYRVLNQFDDAGIV   68 (148)
T ss_pred             CCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHCCCE
Confidence            5554 55666666543  3789999999999888765     999999999987766553

>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor

Probab=90.98  E-value=0.39  Score=43.42  Aligned_cols=43  Identities=16%  Similarity=0.156  Sum_probs=31.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++||+..|||.+||+|.++.-.             .....+++.+++|.+..++
T Consensus         1 ti~dIA~~aGVS~~TVSrvLn~~~-------------~~~~vs~~tr~rV~~~a~~   43 (327)
T TIGR02417         1 TLSDIAKLAGVSKTTASYVINGKA-------------KEYRISQETVERVMAVVRE   43 (327)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCCC-------------CCCccCHHHHHHHHHHHHH
Confidence            468999999999999999996310             0013567777777777665

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

>PRK09464 pdhR transcriptional regulator PdhR; Reviewed

Probab=90.93  E-value=0.29  Score=43.68  Aligned_cols=50  Identities=22%  Similarity=0.379  Sum_probs=39.2

Q ss_pred             HHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         51 SVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        51 dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .+|..|+.. +.-|  + +-.++|++||||+++|+--+++....|-|...+++|
T Consensus        18 ~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G   71 (254)
T PRK09464         18 QLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGG   71 (254)
T ss_pred             HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            455666554 2345  3 678999999999999999999999999887666555

>COG2186 FadR Transcriptional regulators [Transcription]

Probab=90.84  E-value=0.77  Score=41.43  Aligned_cols=56  Identities=23%  Similarity=0.261  Sum_probs=47.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         45 GRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .+.++.++=.+|.+++.+|.        +-+++|++|||||++|+--++.....|.|+.+...|
T Consensus         8 ~~~l~~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~G   71 (241)
T COG2186           8 RRRLADEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSG   71 (241)
T ss_pred             CCChHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCc
Confidence            34477888788888877653        689999999999999999999999999998877655

>PRK09706 transcriptional repressor DicA; Reviewed

Probab=90.84  E-value=0.47  Score=38.85  Aligned_cols=36  Identities=19%  Similarity=0.224  Sum_probs=29.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      +-.+|..+.+ .|++..++|+.+|||++||++|.+.-
T Consensus         6 ~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~   42 (135)
T PRK09706          6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDE   42 (135)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence            4455666654 69999999999999999999997653

>PRK15481 transcriptional regulatory protein PtsJ; Provisional

Probab=90.81  E-value=0.54  Score=45.00  Aligned_cols=36  Identities=17%  Similarity=0.221  Sum_probs=31.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +.+++|++|+||++||.+-+.+-.+.|-+...++.|
T Consensus        31 s~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~~G   66 (431)
T PRK15481         31 PVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNG   66 (431)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence            789999999999999999999999999775554444

>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator

Probab=90.79  E-value=0.41  Score=45.88  Aligned_cols=38  Identities=5%  Similarity=0.060  Sum_probs=31.7

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|..|...++ .+....++|+.|||||+|+||-+++|.
T Consensus       405 ~E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~  443 (445)
T TIGR02915       405 AEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHG  443 (445)
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            35666777665 578899999999999999999999983

Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).

>PF13551 HTH_29: Winged helix-turn helix

Probab=90.78  E-value=0.83  Score=34.97  Aligned_cols=40  Identities=28%  Similarity=0.400  Sum_probs=34.1

Q ss_pred             CCHHHHHHHHHHHHc----C---CCHHHHHHHh-------CCCHHHHHHHHHHh
Q psy15598         48 LPNSVRMRIVELAQL----G---IRPCDISRQL-------RVSHGCVSKILARY   87 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~----G---~S~~eIAr~L-------GVSrsTVsRwikRy   87 (258)
                      ++.+.+..|++++.+    |   ++..+|+..|       .+|.+||++|+++.
T Consensus        58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~  111 (112)
T PF13551_consen   58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA  111 (112)
T ss_pred             CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence            899999999999875    2   6788998865       69999999999873

>PRK14987 gluconate operon transcriptional regulator; Provisional

Probab=90.71  E-value=0.33  Score=44.07  Aligned_cols=41  Identities=15%  Similarity=0.090  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+.++||+..|||++||+|.++..               + ..+++.+++|.+..++
T Consensus         6 ~ti~dIA~~agVS~~TVSrvLn~~---------------~-~vs~~tr~rV~~~a~e   46 (331)
T PRK14987          6 PVLQDVADRVGVTKMTVSRFLRNP---------------E-QVSVALRGKIAAALDE   46 (331)
T ss_pred             CcHHHHHHHhCCCHHHhhhhhCCC---------------C-CCCHHHHHHHHHHHHH
Confidence            588999999999999999998531               1 2455666666655544

>PRK00215 LexA repressor; Validated

Probab=90.71  E-value=0.71  Score=40.11  Aligned_cols=33  Identities=21%  Similarity=0.195  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhCC-CHHHHHHHHHHhhhhCCcccC
Q psy15598         64 IRPCDISRQLRV-SHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        64 ~S~~eIAr~LGV-SrsTVsRwikRyrEtGsl~pk   96 (258)
                      .+.++||+.+|+ +++||++++++..+.|-+...
T Consensus        24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~   57 (205)
T PRK00215         24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRD   57 (205)
T ss_pred             CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeC
Confidence            589999999999 999999999999999987543

>PRK11639 zinc uptake transcriptional repressor; Provisional

Probab=90.63  E-value=0.64  Score=39.95  Aligned_cols=53  Identities=21%  Similarity=0.231  Sum_probs=39.2

Q ss_pred             CCHHHHHHHHHHHHhCC-CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598        106 TTPKVVSYIKELKQKDP-GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ  164 (258)
Q Consensus       106 lT~e~~~~I~~lv~~nP-~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~  164 (258)
                      .|+. +..|.+++.... .+++.+|.+.|.+.+..+     |.+||+|.|..+....+-.
T Consensus        24 ~T~q-R~~IL~~l~~~~~hlSa~eI~~~L~~~~~~i-----s~aTVYRtL~~L~e~Glv~   77 (169)
T PRK11639         24 LTPQ-RLEVLRLMSLQPGAISAYDLLDLLREAEPQA-----KPPTVYRALDFLLEQGFVH   77 (169)
T ss_pred             CCHH-HHHHHHHHHhcCCCCCHHHHHHHHHhhCCCC-----CcchHHHHHHHHHHCCCEE
Confidence            4444 455556655443 689999999999888765     9999999999877665533

>PRK03573 transcriptional regulator SlyA; Provisional

Probab=90.57  E-value=1  Score=36.76  Aligned_cols=55  Identities=15%  Similarity=0.215  Sum_probs=39.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKEL  117 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~l  117 (258)
                      |.+.++||+.++++++||.+.+++..+.|-|.-.+.... |  --.+|++=++.+.++
T Consensus        46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~  103 (144)
T PRK03573         46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV  103 (144)
T ss_pred             CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH
Confidence            589999999999999999999999999998743322111 2  234666655555444

>COG1476 Predicted transcriptional regulators [Transcription]

Probab=90.50  E-value=0.48  Score=35.67  Aligned_cols=32  Identities=22%  Similarity=0.368  Sum_probs=26.4

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .++..+. +.|++..+.|+.+|||+.||..|-+
T Consensus         4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk   36 (68)
T COG1476           4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEK   36 (68)
T ss_pred             hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence            4566665 4799999999999999999988744

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=90.46  E-value=0.55  Score=42.88  Aligned_cols=44  Identities=14%  Similarity=0.147  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.=.+|++++.   .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus        25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~   71 (271)
T PRK10163         25 ERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY   71 (271)
T ss_pred             HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            33456777774   358999999999999999999999999999874

>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated

Probab=90.45  E-value=0.63  Score=41.54  Aligned_cols=41  Identities=27%  Similarity=0.348  Sum_probs=34.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...| .|+.+..+|++..+||+.|+||.+||...+++-+
T Consensus       171 ~Lt~re~-evl~~~a~G~t~~eIa~~l~is~~Tv~~~l~~~~  211 (232)
T TIGR03541       171 VLSERER-EVLAWTALGRRQADIAAILGISERTVENHLRSAR  211 (232)
T ss_pred             cCCHHHH-HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            4666555 4566678999999999999999999999999875

Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family

Probab=90.44  E-value=0.54  Score=43.51  Aligned_cols=42  Identities=21%  Similarity=0.139  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+    .+++|..+||+.||||+.+|+.+.++-.
T Consensus       249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl  294 (298)
T TIGR02997       249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKAL  294 (298)
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            37777776555555    4789999999999999999999998865

This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).

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

Probab=90.43  E-value=0.48  Score=30.28  Aligned_cols=25  Identities=24%  Similarity=0.429  Sum_probs=22.6

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..|++..++|+.++++..+|++|.+
T Consensus        10 ~~~~s~~~~a~~~~~~~~~v~~~~~   34 (58)
T cd00093          10 EKGLTQEELAEKLGVSRSTISRIEN   34 (58)
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            4699999999999999999999854

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

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=90.41  E-value=0.57  Score=42.19  Aligned_cols=41  Identities=17%  Similarity=0.255  Sum_probs=35.6

Q ss_pred             HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|++++.  .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus        17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~   59 (257)
T PRK15090         17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVA   59 (257)
T ss_pred             HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            56777664  358999999999999999999999999999874

>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional

Probab=90.33  E-value=0.94  Score=40.28  Aligned_cols=36  Identities=17%  Similarity=0.154  Sum_probs=32.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +-.++|++|||||++|+--+++....|-|...++.|
T Consensus        33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G   68 (251)
T PRK09990         33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRG   68 (251)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            678999999999999999999999999887666555

>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins

Probab=90.26  E-value=1.1  Score=34.53  Aligned_cols=43  Identities=14%  Similarity=0.222  Sum_probs=32.8

Q ss_pred             CCCHHHHHHHHHHHH-cCCCHHHHHHHhC-CCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQ-LGIRPCDISRQLR-VSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~-~G~S~~eIAr~LG-VSrsTVsRwikRyrE   89 (258)
                      .++..-...+..+.+ -|+|..+|++.|| .+++||..-+++.++
T Consensus        27 ~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~   71 (90)
T cd06571          27 EIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEE   71 (90)
T ss_pred             CcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence            455544444444444 4999999999999 999999999999864

The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.

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

Probab=90.24  E-value=0.47  Score=30.09  Aligned_cols=25  Identities=24%  Similarity=0.412  Sum_probs=22.5

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+++..++|+.+||+..+|++|.+
T Consensus         8 ~~~~s~~~la~~~~i~~~~i~~~~~   32 (56)
T smart00530        8 EKGLTQEELAEKLGVSRSTLSRIEN   32 (56)
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4689999999999999999998864

>PRK09978 DNA-binding transcriptional regulator GadX; Provisional

Probab=90.22  E-value=2.9  Score=39.01  Aligned_cols=90  Identities=18%  Similarity=0.118  Sum_probs=58.9

Q ss_pred             CHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCC
Q psy15598         49 PNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPG  123 (258)
Q Consensus        49 S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~  123 (258)
                      ..+...+++..++    +.++..++|+.+|+|++++.|..++.   |.         .+.....+ -...-.+++ .+.+
T Consensus       140 ~~~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~---G~---------S~~~yl~~~Rl~~A~~LL-~~t~  206 (274)
T PRK09978        140 QPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE---ET---------SYSQLLTECRMQRALQLI-VIHG  206 (274)
T ss_pred             CHHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhc---CC---------CHHHHHHHHHHHHHHHHH-HcCC
Confidence            3455567777764    35799999999999999999988752   32         11111111 122222233 3456


Q ss_pred             CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        124 IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       124 ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .+..+|+..+   |..      +.+...|.+++.-+.
T Consensus       207 ~sI~eIA~~~---GF~------s~S~Fsr~FKk~~G~  234 (274)
T PRK09978        207 FSIKRVAVSC---GYH------SVSYFIYVFRNYYGM  234 (274)
T ss_pred             CCHHHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            7888887666   675      889999999987665

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

Probab=90.16  E-value=0.61  Score=33.18  Aligned_cols=24  Identities=29%  Similarity=0.458  Sum_probs=19.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .|+|..++|+.+|+|.++|++|.+
T Consensus        13 ~gls~~~lA~~~g~s~s~v~~iE~   36 (64)
T PF13560_consen   13 AGLSQAQLADRLGVSQSTVSRIER   36 (64)
T ss_dssp             HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHC
Confidence            599999999999999999988854

>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A

Probab=90.13  E-value=0.54  Score=33.22  Aligned_cols=32  Identities=25%  Similarity=0.466  Sum_probs=27.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ..++..+||+.+++++++|++.+++..+-|-|
T Consensus        17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv   48 (68)
T PF13463_consen   17 GPMTQSDLAERLGISKSTVSRIIKKLEEKGLV   48 (68)
T ss_dssp             S-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            45899999999999999999999999999987

>PRK12423 LexA repressor; Provisional

Probab=90.03  E-value=0.93  Score=39.76  Aligned_cols=48  Identities=21%  Similarity=0.248  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHHHHH-----cCC--CHHHHHHHhC-CCHHHHHHHHHHhhhhCCcccC
Q psy15598         48 LPNSVRMRIVELAQ-----LGI--RPCDISRQLR-VSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-----~G~--S~~eIAr~LG-VSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ++ ..|.+|++.+.     .|.  |.++||+.|| +|+++|++.+++..+.|.+...
T Consensus         4 lt-~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~   59 (202)
T PRK12423          4 LT-PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV   59 (202)
T ss_pred             CC-HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence            44 44556666543     344  9999999999 5999999999999999987543

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=90.00  E-value=1.1  Score=36.20  Aligned_cols=33  Identities=24%  Similarity=0.296  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .++..+||+.+++|+++|++.+++.++.|-+..
T Consensus        25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~   57 (130)
T TIGR02944        25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS   57 (130)
T ss_pred             CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence            379999999999999999999999999998743

The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.

>PRK03902 manganese transport transcriptional regulator; Provisional

Probab=89.97  E-value=1.4  Score=36.30  Aligned_cols=44  Identities=20%  Similarity=0.255  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.-..|..+.. . ..+.++||+.|+||.+||++.+++..+.|-|.
T Consensus         8 dyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~   53 (142)
T PRK03902          8 DYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI   53 (142)
T ss_pred             HHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence            34444555554 2 47899999999999999999999999999875

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

Probab=89.97  E-value=0.5  Score=35.58  Aligned_cols=30  Identities=27%  Similarity=0.448  Sum_probs=22.3

Q ss_pred             HHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         56 IVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        56 IV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |.++.+ .|++.+++|+.+||++++|+++.+
T Consensus        23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~   53 (80)
T PF13744_consen   23 IRELREERGLTQAELAERLGISQPRVSRLEN   53 (80)
T ss_dssp             HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence            444444 599999999999999999999875

>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional

Probab=89.94  E-value=0.48  Score=47.41  Aligned_cols=37  Identities=22%  Similarity=0.269  Sum_probs=31.3

Q ss_pred             HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .|..|.+++..+.+.+++|+.||||++|++|-+++|.
T Consensus       475 E~~~i~~~l~~~~~~~~aA~~LGisr~tL~rkl~~~g  511 (520)
T PRK10820        475 ERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYG  511 (520)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence            5666666666666899999999999999999999984

>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp

Probab=89.93  E-value=0.23  Score=37.44  Aligned_cols=31  Identities=26%  Similarity=0.439  Sum_probs=28.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||+.++++...|.+++++.++.|-+.
T Consensus        26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~   56 (83)
T PF02082_consen   26 VSSKEIAERLGISPSYLRKILQKLKKAGLIE   56 (83)
T ss_dssp             BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence            7999999999999999999999999999875

(strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.

>PRK15115 response regulator GlrR; Provisional

Probab=89.88  E-value=0.55  Score=45.00  Aligned_cols=37  Identities=16%  Similarity=0.005  Sum_probs=32.0

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .|..|..+++ .+....++|+.|||||+|+||-+++|.
T Consensus       399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~  436 (444)
T PRK15115        399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHE  436 (444)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            6777777765 478899999999999999999999984

>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY

Probab=89.83  E-value=0.65  Score=42.96  Aligned_cols=44  Identities=16%  Similarity=0.278  Sum_probs=36.7

Q ss_pred             HHHHHHHHc--C-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         54 MRIVELAQL--G-IRPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        54 ~RIV~L~~~--G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      .+|+...+.  | .+..++|+++|||+++|++-+++..+.|.++.++
T Consensus       186 ~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~  232 (251)
T TIGR02787       186 EHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS  232 (251)
T ss_pred             HHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence            455555543  4 6999999999999999999999999999987665

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

>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR

Probab=89.80  E-value=0.81  Score=40.28  Aligned_cols=51  Identities=14%  Similarity=0.130  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHH-HcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         50 NSVRMRIVELA-QLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        50 ~dlR~RIV~L~-~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..+|.+|+... .-|  + +-.++|++|||||++|+--+++-...|-|...++.|
T Consensus        13 ~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G   67 (235)
T TIGR02812        13 EYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   67 (235)
T ss_pred             HHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence            34666666653 345  5 688999999999999999999999999887665555

Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.

>PRK13918 CRP/FNR family transcriptional regulator; Provisional

Probab=89.79  E-value=0.53  Score=39.85  Aligned_cols=31  Identities=13%  Similarity=0.218  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+++.||+|.++++++.|.+.
T Consensus       150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~  180 (202)
T PRK13918        150 ATHDELAAAVGSVRETVTKVIGELSREGYIR  180 (202)
T ss_pred             CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence            4789999999999999999999999999885

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=89.78  E-value=0.77  Score=41.62  Aligned_cols=45  Identities=13%  Similarity=0.136  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+.-.+|++++.   .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus        10 l~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~   57 (263)
T PRK09834         10 LSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR   57 (263)
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            344466777763   248999999999999999999999999999875

>TIGR01481 ccpA catabolite control protein A

Probab=89.78  E-value=0.68  Score=41.79  Aligned_cols=23  Identities=26%  Similarity=0.423  Sum_probs=20.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.++||+..|||.+||+|.++.
T Consensus         2 ~ti~dIA~~agvS~~TVSrvLn~   24 (329)
T TIGR01481         2 VTIYDVAREAGVSMATVSRVVNG   24 (329)
T ss_pred             CcHHHHHHHhCCCHHHHHHHhCC
Confidence            47889999999999999999853

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.

>PRK11569 transcriptional repressor IclR; Provisional

Probab=89.77  E-value=0.71  Score=42.16  Aligned_cols=42  Identities=10%  Similarity=0.285  Sum_probs=36.2

Q ss_pred             HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      =.+|++++.   .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus        30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~   74 (274)
T PRK11569         30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR   74 (274)
T ss_pred             HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            356777764   358999999999999999999999999999875

>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]

Probab=89.75  E-value=0.6  Score=42.55  Aligned_cols=45  Identities=20%  Similarity=0.318  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         49 PNSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ..+-+.+|+++++ +| ++..++|+.|+||..||+|=++...+.|.+
T Consensus         3 ~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l   49 (253)
T COG1349           3 KEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLL   49 (253)
T ss_pred             hHHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcE
Confidence            4567788999986 46 799999999999999999999999999976

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

Probab=89.66  E-value=3.2  Score=33.79  Aligned_cols=40  Identities=23%  Similarity=0.348  Sum_probs=33.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc--ccCCCCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSI--LPGAIGGSKP  103 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl--~pk~rgG~RP  103 (258)
                      .+..++|..|.+|+.-|..+++++.+.|=|  .|+..+|.+.
T Consensus        20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S   61 (115)
T PF12793_consen   20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRS   61 (115)
T ss_pred             eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCC
Confidence            589999999999999999999999999965  5776555343

>TIGR00637 ModE_repress ModE molybdate transport repressor domain

Probab=89.63  E-value=2.1  Score=33.84  Aligned_cols=63  Identities=14%  Similarity=0.146  Sum_probs=45.1

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCC--CCCCCCCHHHHHHHH
Q psy15598         53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGG--SKPRVTTPKVVSYIK  115 (258)
Q Consensus        53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG--~RPrklT~e~~~~I~  115 (258)
                      ..+++..+.+--|.+.+|+.||||.+||++-+++.++ -|. +-.+..+|  ++...+|+.-+..+.
T Consensus         6 ~l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~   72 (99)
T TIGR00637         6 RVALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQ   72 (99)
T ss_pred             HHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHH
Confidence            4557777777889999999999999999999999986 343 22332221  255778877666553

ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.

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

Probab=89.63  E-value=0.2  Score=33.94  Aligned_cols=37  Identities=27%  Similarity=0.357  Sum_probs=26.7

Q ss_pred             HHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         68 DISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        68 eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +||+.+|||++||++|++.               ++ ..++.....|.+..++
T Consensus         2 ~lA~~~gvs~~tvs~~l~g---------------~~-~vs~~~~~~i~~~~~~   38 (52)
T cd01392           2 DIARAAGVSVATVSRVLNG---------------KP-RVSEETRERVLAAAEE   38 (52)
T ss_pred             cHHHHHCcCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence            7999999999999999853               11 2455666666666554

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

>PRK10403 transcriptional regulator NarP; Provisional

Probab=89.55  E-value=0.74  Score=37.64  Aligned_cols=40  Identities=15%  Similarity=0.155  Sum_probs=33.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++.... .|+.++..|.+.++||+.+++|.+||...+++-+
T Consensus       154 Lt~~e~-~vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~  193 (215)
T PRK10403        154 LTEREL-DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLL  193 (215)
T ss_pred             CCHHHH-HHHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence            565444 5777888999999999999999999999988875

>PRK10421 DNA-binding transcriptional repressor LldR; Provisional

Probab=89.53  E-value=0.75  Score=41.10  Aligned_cols=50  Identities=30%  Similarity=0.392  Sum_probs=38.3

Q ss_pred             HHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         51 SVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        51 dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .+|..|+.. +.-|  + +-.++|++||||+++|+.-+++-...|-|.-.++.|
T Consensus        10 ~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G   63 (253)
T PRK10421         10 RVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGG   63 (253)
T ss_pred             HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            345555554 2335  4 578999999999999999999999999887665555

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=89.47  E-value=1.6  Score=35.06  Aligned_cols=32  Identities=19%  Similarity=0.297  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..+..+||+.+++++++|+++++...+.|-+.
T Consensus        25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~   56 (132)
T TIGR00738        25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVE   56 (132)
T ss_pred             cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            47999999999999999999999999999774

This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.

>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF

Probab=89.46  E-value=0.59  Score=44.12  Aligned_cols=36  Identities=6%  Similarity=-0.037  Sum_probs=29.7

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .|..|...++ .|...+++|+.||||++|+|+.+++|
T Consensus       293 E~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~  329 (329)
T TIGR02974       293 EIELLQQALAEAQFNQRKAAELLGLTYHQLRGLLRKH  329 (329)
T ss_pred             HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            4555555555 58899999999999999999999986

Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH

>PRK10360 DNA-binding transcriptional activator UhpA; Provisional

Probab=89.45  E-value=0.81  Score=37.49  Aligned_cols=41  Identities=24%  Similarity=0.245  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...+ .|+.++.+|++.++||+.|++|.+||...+++.++
T Consensus       138 Lt~~E~-~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~  178 (196)
T PRK10360        138 LTKRER-QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLME  178 (196)
T ss_pred             CCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            444333 56777778999999999999999999999998763

>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=89.45  E-value=1.3  Score=25.67  Aligned_cols=41  Identities=34%  Similarity=0.416  Sum_probs=28.8

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHH
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL  154 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiL  154 (258)
                      |++.++++....|.+...+  ..+..++.+.+   |       +|.+||++++
T Consensus         2 r~~~~~~~~~~~i~~~~~~--~~s~~~ia~~~---~-------is~~tv~~~~   42 (42)
T cd00569           2 RPPKLTPEQIEEARRLLAA--GESVAEIARRL---G-------VSRSTLYRYL   42 (42)
T ss_pred             CCCcCCHHHHHHHHHHHHc--CCCHHHHHHHH---C-------CCHHHHHHhC
Confidence            5667777777777777653  44777787666   3       3899998864

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

>PRK10188 DNA-binding transcriptional activator SdiA; Provisional

Probab=89.40  E-value=0.7  Score=41.67  Aligned_cols=41  Identities=15%  Similarity=0.198  Sum_probs=34.4

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|...+ .|+.+..+|++..+||..|+||..||..-+++-+
T Consensus       179 ~LT~rE~-evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~  219 (240)
T PRK10188        179 NFSKREK-EILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ  219 (240)
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4665554 5777778999999999999999999999988876

>COG1846 MarR Transcriptional regulators [Transcription]

Probab=89.39  E-value=2.1  Score=32.53  Aligned_cols=71  Identities=17%  Similarity=0.163  Sum_probs=44.8

Q ss_pred             CCHHHHHHHHHHHHcCCCH-HHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQLGIRP-CDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~-~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv  118 (258)
                      ++...-.-+..+...+-.. .+||+.++|++++|.+.+++..+.|-|.-...... |  --.+|++-.+.+.+..
T Consensus        20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~   94 (126)
T COG1846          20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLL   94 (126)
T ss_pred             CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhc
Confidence            3433333333344444444 99999999999999999999999997743322211 2  2246666666655554

>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed

Probab=89.38  E-value=0.81  Score=42.37  Aligned_cols=41  Identities=24%  Similarity=0.107  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-|...+-  +|+|..+||+.||||+.+|+++.++..
T Consensus       228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al  270 (289)
T PRK07500        228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARAL  270 (289)
T ss_pred             CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55555544444333  799999999999999999999998865

>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional

Probab=89.37  E-value=0.44  Score=40.52  Aligned_cols=31  Identities=26%  Similarity=0.359  Sum_probs=28.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+..+||..+|+++.||+|.++++++.|.+.
T Consensus       169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~  199 (211)
T PRK11753        169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLIS  199 (211)
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            4679999999999999999999999999774

>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional

Probab=89.29  E-value=0.48  Score=48.15  Aligned_cols=41  Identities=17%  Similarity=0.185  Sum_probs=34.7

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +....|..|+..++ .|-..+++|+.|||||+|+||-+++|.
T Consensus       588 l~~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~  629 (638)
T PRK11388        588 LAELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHG  629 (638)
T ss_pred             HHHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcC
Confidence            44557777888776 577899999999999999999999985

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

Probab=89.19  E-value=1.1  Score=39.56  Aligned_cols=42  Identities=19%  Similarity=0.226  Sum_probs=37.0

Q ss_pred             CCCHHHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGI-------RPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~-------S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .|+...+.-+..+++.|.       +.+++|++||||++|+...++|-.
T Consensus       155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe  203 (215)
T COG3413         155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE  203 (215)
T ss_pred             cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            688888888888888774       889999999999999999998865

>PRK11013 DNA-binding transcriptional regulator LysR; Provisional

Probab=89.16  E-value=1.7  Score=39.43  Aligned_cols=57  Identities=19%  Similarity=0.179  Sum_probs=39.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVSY  113 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~~  113 (258)
                      .+++..+.+-.|.+.+|+.|+||.++|++.+++.++. |. +-.+  .+ +.-.+|+.-+.+
T Consensus         9 L~~f~av~~~gS~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R--~~-~~v~LT~~G~~l   67 (309)
T PRK11013          9 IEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER--VR-GRLHPTVQGLRL   67 (309)
T ss_pred             HHHHHHHHHhCcHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeee--cC-CCcccCHHHHHH
Confidence            4455555555599999999999999999999999863 42 2222  23 446677654333

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

Probab=89.15  E-value=1.1  Score=32.96  Aligned_cols=45  Identities=16%  Similarity=0.161  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHHHhCCC--CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        108 PKVVSYIKELKQKDPG--IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~--ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ++.++.|..++.+++.  +++.||++.|   |       ++.++|+|+|..+..+..
T Consensus         5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l---g-------l~~~~v~r~L~~L~~~G~   51 (68)
T smart00550        5 DSLEEKILEFLENSGDETSTALQLAKNL---G-------LPKKEVNRVLYSLEKKGK   51 (68)
T ss_pred             hHHHHHHHHHHHHCCCCCcCHHHHHHHH---C-------CCHHHHHHHHHHHHHCCC
Confidence            4567888888888766  9999998888   3       488999999987766644

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

>COG2973 TrpR Trp operon repressor [Transcription]

Probab=88.98  E-value=1.2  Score=35.89  Aligned_cols=31  Identities=29%  Similarity=0.411  Sum_probs=25.4

Q ss_pred             HHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHH
Q psy15598         52 VRMRIVELAQL-GIRPCDISRQLRVSHGCVSK   82 (258)
Q Consensus        52 lR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsR   82 (258)
                      .|.+||...-+ .+|.++|+..||||..||-|
T Consensus        48 ~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITR   79 (103)
T COG2973          48 TRVRIVEELLRGELSQREIAQKLGVSIATITR   79 (103)
T ss_pred             HHHHHHHHHHhccccHHHHHHHhCcchhhhcc
Confidence            56777776654 58999999999999999854

>PRK15185 transcriptional regulator HilD; Provisional

Probab=88.95  E-value=2.4  Score=40.30  Aligned_cols=87  Identities=11%  Similarity=0.101  Sum_probs=55.3

Q ss_pred             HHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCH
Q psy15598         52 VRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        52 lR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita  126 (258)
                      ...+|...++    +.++..++|+.+++|++++.|..+.   .|.         .+.. +...-.....+++ .+.+.+.
T Consensus       207 ~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~---~G~---------S~~~yl~~~Ri~~A~~LL-~~t~~sI  273 (309)
T PRK15185        207 LKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAE---EGT---------SFSDIYLSARMNQAAKLL-RIGNHNV  273 (309)
T ss_pred             HHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH---cCC---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence            4445555543    4579999999999999999998874   342         1111 1111111112223 3457788


Q ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .+|+..+   |..      |.+...|.+++..+.
T Consensus       274 seIA~~~---GFs------s~S~FsR~FKk~~G~  298 (309)
T PRK15185        274 NAVALKC---GYD------STSYFIQCFKKYFKT  298 (309)
T ss_pred             HHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            8887766   665      889999999887654

>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional

Probab=88.86  E-value=0.73  Score=46.75  Aligned_cols=39  Identities=8%  Similarity=0.015  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ...|..|...++ .|-...++|+.|||||+|+||.+++|.
T Consensus       496 ~~Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g  535 (538)
T PRK15424        496 RLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEA  535 (538)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            346777777765 577899999999999999999999985

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

Probab=88.83  E-value=1.1  Score=36.07  Aligned_cols=42  Identities=10%  Similarity=0.056  Sum_probs=32.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.|.-..|-..-.+|++..++|.+.|||++|+++.++..+
T Consensus        33 ~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR   74 (99)
T COG1342          33 ILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSAR   74 (99)
T ss_pred             eecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHHHH
Confidence            355665544433345899999999999999999999998875

>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein

Probab=88.82  E-value=0.98  Score=39.49  Aligned_cols=42  Identities=17%  Similarity=0.293  Sum_probs=35.7

Q ss_pred             HHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..+|+....+  +.+.++||+.+++|++||++.+++..+.|-+.
T Consensus       145 ~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~  188 (203)
T TIGR01884       145 ELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVE  188 (203)
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            4566666653  57999999999999999999999999999874

Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.

>PRK05657 RNA polymerase sigma factor RpoS; Validated

Probab=88.82  E-value=0.84  Score=43.11  Aligned_cols=42  Identities=14%  Similarity=0.114  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+    .+|++..+||+.||||++||..++.|-+
T Consensus       262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl  307 (325)
T PRK05657        262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEAL  307 (325)
T ss_pred             cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            46666776555432    4799999999999999999999988865

>PRK10423 transcriptional repressor RbsR; Provisional

Probab=88.81  E-value=0.74  Score=41.40  Aligned_cols=19  Identities=32%  Similarity=0.422  Sum_probs=17.7

Q ss_pred             HHHHHHhCCCHHHHHHHHH
Q psy15598         67 CDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        67 ~eIAr~LGVSrsTVsRwik   85 (258)
                      ++||+..|||++||+|.++
T Consensus         2 ~dIA~~agVS~~TVSrvLn   20 (327)
T PRK10423          2 KDVARLAGVSTSTVSHVIN   20 (327)
T ss_pred             hhHHHHhCCcHHHHHHHhC
Confidence            6899999999999999996

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

Probab=88.74  E-value=0.43  Score=34.85  Aligned_cols=19  Identities=26%  Similarity=0.319  Sum_probs=17.3

Q ss_pred             CHHHHHHHhCCCHHHHHHH
Q psy15598         65 RPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRw   83 (258)
                      +.+++|+.||||+++|+.|
T Consensus        11 ~~~~lAkalGVs~~aVs~W   29 (60)
T PF14549_consen   11 GQSKLAKALGVSPQAVSQW   29 (60)
T ss_dssp             SHHHHHHHHTS-HHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHh
Confidence            7789999999999999999

>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional

Probab=88.70  E-value=0.54  Score=40.94  Aligned_cols=33  Identities=21%  Similarity=0.435  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ++..+||..||+++.||+|.++++++.|.++-.
T Consensus       185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~  217 (235)
T PRK11161        185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK  217 (235)
T ss_pred             ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence            578999999999999999999999999988533

>PRK11169 leucine-responsive transcriptional regulator; Provisional

Probab=88.65  E-value=0.69  Score=39.21  Aligned_cols=47  Identities=19%  Similarity=0.071  Sum_probs=40.4

Q ss_pred             CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        106 TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       106 lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ..++.+..|++.+++|+.++..||++.|.          +|.+||+++++++..+..
T Consensus        11 ~lD~~D~~IL~~Lq~d~R~s~~eiA~~lg----------lS~~tv~~Ri~rL~~~Gv   57 (164)
T PRK11169         11 DLDRIDRNILNELQKDGRISNVELSKRVG----------LSPTPCLERVRRLERQGF   57 (164)
T ss_pred             hHHHHHHHHHHHhccCCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCCC
Confidence            34678899999999999999999999883          499999999999877765

>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species

Probab=88.58  E-value=0.71  Score=40.62  Aligned_cols=37  Identities=19%  Similarity=0.292  Sum_probs=32.7

Q ss_pred             HHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         56 IVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        56 IV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      -|.++.+| ++..+||+.||||+..|.+..++|...++
T Consensus        11 Yi~yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~   48 (181)
T PF04645_consen   11 YIFYFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSED   48 (181)
T ss_pred             HHHHHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCC
Confidence            46677888 89999999999999999999999987654

>COG3311 AlpA Predicted transcriptional regulator [Transcription]

Probab=88.57  E-value=1  Score=34.11  Aligned_cols=23  Identities=9%  Similarity=0.192  Sum_probs=20.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ...|++..+|+|++||||+++.-
T Consensus        15 rl~ev~~~~GlSrstiYr~i~~~   37 (70)
T COG3311          15 RLPEVAQLTGLSRSTIYRLIKDG   37 (70)
T ss_pred             hHHHHHHHHCccHHHHHHHHccC
Confidence            56789999999999999999874

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

Probab=88.44  E-value=1.3  Score=34.01  Aligned_cols=34  Identities=18%  Similarity=0.261  Sum_probs=27.4

Q ss_pred             HHHHHHHHH-HcCCCHHHHHHHhC------CCHHHHHHHHH
Q psy15598         52 VRMRIVELA-QLGIRPCDISRQLR------VSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~-~~G~S~~eIAr~LG------VSrsTVsRwik   85 (258)
                      +..++..+. +.|++..++|+.+|      +|.+||+||-+
T Consensus        12 ~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es   52 (75)
T smart00352       12 FAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA   52 (75)
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence            445555554 47999999999999      59999999866

>PRK13870 transcriptional regulator TraR; Provisional

Probab=88.40  E-value=0.88  Score=40.93  Aligned_cols=41  Identities=15%  Similarity=-0.006  Sum_probs=33.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|.-.+ .++....+|++..|||..||||.+||..-+++-+
T Consensus       173 ~LT~RE~-E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~  213 (234)
T PRK13870        173 WLDPKEA-TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM  213 (234)
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            4555444 4666677999999999999999999999998876

>TIGR00498 lexA SOS regulatory protein LexA

Probab=88.39  E-value=0.87  Score=39.35  Aligned_cols=45  Identities=16%  Similarity=0.244  Sum_probs=35.0

Q ss_pred             HHHHHHHHHHH-----cC--CCHHHHHHHhCCC-HHHHHHHHHHhhhhCCccc
Q psy15598         51 SVRMRIVELAQ-----LG--IRPCDISRQLRVS-HGCVSKILARYHETGSILP   95 (258)
Q Consensus        51 dlR~RIV~L~~-----~G--~S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~p   95 (258)
                      +...+|+..+.     .|  .+.++||+.||++ ++||++.+++..+.|-+..
T Consensus         6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~   58 (199)
T TIGR00498         6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIER   58 (199)
T ss_pred             HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEec
Confidence            34445555543     23  5788999999998 9999999999999998753

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

>PRK10870 transcriptional repressor MprA; Provisional

Probab=88.36  E-value=1.6  Score=37.52  Aligned_cols=56  Identities=20%  Similarity=0.251  Sum_probs=40.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCC---CCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSK---PRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~R---PrklT~e~~~~I~~lv  118 (258)
                      +.+..+||+.++++++||.+.+++..+.|-|+-.+.+..+   --.+|++=.+.+.+..
T Consensus        71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~  129 (176)
T PRK10870         71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL  129 (176)
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            4788999999999999999999999999987533322212   2237777666665553

>PRK13777 transcriptional regulator Hpr; Provisional

Probab=88.35  E-value=2.7  Score=36.96  Aligned_cols=57  Identities=12%  Similarity=0.007  Sum_probs=41.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv  118 (258)
                      .|.+.++||+.++++++||.+.+++..+.|-|.-.+.... |  --.+|++-++.+.++.
T Consensus        58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~  117 (185)
T PRK13777         58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM  117 (185)
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            5899999999999999999999999999998752222211 2  2236776666555553

>PRK13500 transcriptional activator RhaR; Provisional

Probab=88.26  E-value=3.6  Score=38.04  Aligned_cols=88  Identities=9%  Similarity=0.067  Sum_probs=58.1

Q ss_pred             HHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCH
Q psy15598         52 VRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        52 lR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita  126 (258)
                      .-.+++..++    +..+..++|+.+++|.+++.|+.|++-  |.         .|.. +.........+++ .+.+.+.
T Consensus       207 ~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~t--G~---------T~~~yi~~~RL~~A~~LL-~~t~~sI  274 (312)
T PRK13500        207 LLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQT--GM---------TINQYLRQVRVCHAQYLL-QHSRLLI  274 (312)
T ss_pred             HHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence            3455666654    357999999999999999999999973  22         1111 1111122222222 3457788


Q ss_pred             HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .||+..+   |..      +.+...|+.|+.-+.
T Consensus       275 ~eIA~~~---GF~------d~s~Fsr~FKk~~G~  299 (312)
T PRK13500        275 SDISTEC---GFE------DSNYFSVVFTRETGM  299 (312)
T ss_pred             HHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            8887766   665      788999999887654

>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B

Probab=88.15  E-value=1.3  Score=32.44  Aligned_cols=72  Identities=22%  Similarity=0.293  Sum_probs=44.9

Q ss_pred             HHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCH
Q psy15598         69 ISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSV  147 (258)
Q Consensus        69 IAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~  147 (258)
                      +|+.||||.+++.++.++..  |.         .+.. +...-...+.+++.++++.+..||+..+   |..      +.
T Consensus         1 lA~~~~~s~~~l~~~f~~~~--g~---------s~~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~---Gf~------~~   60 (81)
T PF12833_consen    1 LADELGMSERYLSRIFKKET--GM---------SFKQYLRELRLQRAKELLRQNTDLSIAEIAEEC---GFS------SQ   60 (81)
T ss_dssp             HHHHCTS-HHHHHHHHHHHH--SS----------HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHT---T-S------SH
T ss_pred             ChHHhCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHHHhhcccHHHHHHHc---CCC------CH
Confidence            68999999999999999974  21         1111 2222234444555455788888886655   665      88


Q ss_pred             HHHHHHHHhccCC
Q psy15598        148 SSISRILRNKIGS  160 (258)
Q Consensus       148 STI~RiLrr~~~~  160 (258)
                      +...|.+++.-+.
T Consensus        61 ~~f~~~fk~~~g~   73 (81)
T PF12833_consen   61 SHFSRAFKRYFGM   73 (81)
T ss_dssp             HHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHCc
Confidence            8888888876543

...

>PRK13890 conjugal transfer protein TrbA; Provisional

Probab=88.15  E-value=0.9  Score=37.10  Aligned_cols=36  Identities=14%  Similarity=0.137  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .-+=.+|..+. +.|++..++|+.+|||++|+++|.+
T Consensus         4 ~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~   40 (120)
T PRK13890          4 YIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTT   40 (120)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            33344555655 4799999999999999999998874

>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria

Probab=88.12  E-value=2.2  Score=31.40  Aligned_cols=33  Identities=21%  Similarity=0.261  Sum_probs=28.9

Q ss_pred             cCC--CHHHHHHHhCCC-HHHHHHHHHHhhhhCCcc
Q psy15598         62 LGI--RPCDISRQLRVS-HGCVSKILARYHETGSIL   94 (258)
Q Consensus        62 ~G~--S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~   94 (258)
                      .|.  |.+|||+.||++ .+||++.++.-.+-|.|.
T Consensus        22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~   57 (65)
T PF01726_consen   22 NGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR   57 (65)
T ss_dssp             HSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence            575  779999999996 999999999999999874

The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.

>PRK10923 glnG nitrogen regulation protein NR(I); Provisional

Probab=88.10  E-value=0.88  Score=44.00  Aligned_cols=38  Identities=11%  Similarity=0.061  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .-.|..|...++ .|....++|+.|||||+|+||-+++|
T Consensus       428 ~~E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~  466 (469)
T PRK10923        428 ELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKEL  466 (469)
T ss_pred             HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence            336666776665 48889999999999999999999988

>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional

Probab=88.03  E-value=0.79  Score=39.95  Aligned_cols=45  Identities=11%  Similarity=0.001  Sum_probs=37.2

Q ss_pred             CHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         49 PNSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ..+-+.+|++++. .| .+..++|+.|+||..||+|=+....+.|.+
T Consensus         5 ~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~   51 (185)
T PRK04424          5 KKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR   51 (185)
T ss_pred             HHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence            3566677887775 45 699999999999999999999998877754

>COG1609 PurR Transcriptional regulators [Transcription]

Probab=87.94  E-value=0.89  Score=42.62  Aligned_cols=40  Identities=18%  Similarity=0.217  Sum_probs=32.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++||+..|||++||+|.++.-               + ..+++.+++|.+.+++
T Consensus         2 TikDVA~~AGVS~sTVSrvln~~---------------~-~Vs~eTr~kV~~a~~e   41 (333)
T COG1609           2 TIKDVAKLAGVSKATVSRVLNGS---------------P-YVSEETREKVLAAIKE   41 (333)
T ss_pred             CHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHH
Confidence            67899999999999999988752               1 3667778888877664

>TIGR01818 ntrC nitrogen regulation protein NR(I)

Probab=87.92  E-value=0.84  Score=43.90  Aligned_cols=38  Identities=11%  Similarity=-0.012  Sum_probs=31.2

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .-.|..|....+ .|....++|+.|||||+|+||-++++
T Consensus       425 ~~E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~  463 (463)
T TIGR01818       425 EFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLKEL  463 (463)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence            335666777665 58899999999999999999999864

This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.

>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=87.86  E-value=0.56  Score=31.02  Aligned_cols=25  Identities=16%  Similarity=0.166  Sum_probs=19.1

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ++.++|+.+|||.+||+.|-+.    |.+
T Consensus         1 ti~e~A~~~gvs~~tlR~ye~~----Gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSPRTLRYYERE----GLL   25 (38)
T ss_dssp             EHHHHHHHHTS-HHHHHHHHHT----TSS
T ss_pred             CHHHHHHHHCCCHHHHHHHHHC----CCC
Confidence            4679999999999999777554    655

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 ....

>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional

Probab=87.84  E-value=1.1  Score=41.87  Aligned_cols=39  Identities=15%  Similarity=0.171  Sum_probs=33.5

Q ss_pred             HHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         54 MRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        54 ~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      .+|+.+..+  ..+..+||++||||++||++-+++.++.|-
T Consensus         7 ~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~   47 (319)
T PRK11886          7 LQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGL   47 (319)
T ss_pred             HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            356666654  479999999999999999999999999997

>PRK15121 right oriC-binding transcriptional activator; Provisional

Probab=87.80  E-value=4  Score=37.24  Aligned_cols=86  Identities=7%  Similarity=0.014  Sum_probs=52.7

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV-VSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~-~~~I~~lv~~nP~ita~E  128 (258)
                      .++++.++    +..+..++|+.+|+|+.++.|..++..  |.         .+....... ......++ ...+.+..+
T Consensus         8 ~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~--g~---------s~~~yi~~~Rl~~A~~~L-~~~~~~i~~   75 (289)
T PRK15121          8 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVT--GH---------AIGAYIRARRLSKAAVAL-RLTSRPILD   75 (289)
T ss_pred             HHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence            34444443    468999999999999999999999873  21         111111111 11111222 234677777


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      |.++..|.+++.-+.
T Consensus        76 iA~~~---Gf~------s~~~f~r~Fk~~~g~   98 (289)
T PRK15121         76 IALQY---RFD------SQQTFTRAFKKQFAQ   98 (289)
T ss_pred             HHHHH---CCC------CHHHHHHHHHHHHCc
Confidence            76655   664      788888888776554

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

Probab=87.77  E-value=1.9  Score=39.38  Aligned_cols=49  Identities=12%  Similarity=0.169  Sum_probs=41.0

Q ss_pred             CCCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         46 RPLPNSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +=++...-++|.+.++   .+.|..++|+.+|+||.|++|++.-....|-++
T Consensus       153 kGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~  204 (224)
T COG4565         153 KGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILE  204 (224)
T ss_pred             CCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeee
Confidence            3456667777888876   578999999999999999999999988888653

>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins

Probab=87.76  E-value=7.3  Score=32.04  Aligned_cols=80  Identities=15%  Similarity=-0.022  Sum_probs=54.5

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      .++.+...=|...+...=+.+++++.||||..||+.=+.+-.+.=.+.+      -+..-....+..|.+.+++ -.+++
T Consensus        33 ~L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~------~~~~~~~~~~~~IL~~L~~-GeIs~  105 (113)
T PF09862_consen   33 RLSPEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGYEE------DEEEEEEDERKEILDKLEK-GEISV  105 (113)
T ss_pred             cCCHHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC------CcccccchhHHHHHHHHHc-CCCCH
Confidence            4777777766667778889999999999999999988877654311100      1122233446677777664 47888


Q ss_pred             HHHHHHH
Q psy15598        127 WEIRDRL  133 (258)
Q Consensus       127 ~EIr~~L  133 (258)
                      .|-.+.|
T Consensus       106 eeA~~~L  112 (113)
T PF09862_consen  106 EEALEIL  112 (113)
T ss_pred             HHHHHHh
Confidence            7776655

>PRK10402 DNA-binding transcriptional activator YeiL; Provisional

Probab=87.76  E-value=1.1  Score=39.22  Aligned_cols=32  Identities=19%  Similarity=0.214  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+..+||..+|+|+.||+|.++++++.|.+..
T Consensus       170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~  201 (226)
T PRK10402        170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK  201 (226)
T ss_pred             chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence            47799999999999999999999999998743

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.75  E-value=1.1  Score=36.27  Aligned_cols=36  Identities=17%  Similarity=0.226  Sum_probs=29.7

Q ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ....+.++ .+-.|..+||..|+|||+.|+.-++|-.
T Consensus        22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~   58 (105)
T COG2739          22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTE   58 (105)
T ss_pred             HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHH
Confidence            34455554 5789999999999999999999999864

>PRK15186 AraC family transcriptional regulator; Provisional

Probab=87.62  E-value=2.8  Score=39.21  Aligned_cols=84  Identities=15%  Similarity=0.089  Sum_probs=52.7

Q ss_pred             HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Q psy15598         56 IVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS  135 (258)
Q Consensus        56 IV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~  135 (258)
                      |.....+.++..++|+.+|+|++|++|..++.  .++..         ..+...-...-..++ .+...+..+|+..+  
T Consensus       190 I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~--g~s~~---------~~~~~~Rl~~A~~lL-~~~~~sI~~IA~~~--  255 (291)
T PRK15186        190 IISDISRKWALKDISDSLYMSCSTLKRKLKQE--NTSFS---------EVYLNARMNKATKLL-RNSEYNITRVAYMC--  255 (291)
T ss_pred             HHhCccCCCCHHHHHHHHCcCHHHHHHHHHHc--CCCHH---------HHHHHHHHHHHHHHH-HcCCCCHHHHHHHh--
Confidence            33334467999999999999999999998862  22211         111111111122223 33456777776666  


Q ss_pred             cCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        136 DGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       136 ~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                       |..      |.+...|.+|+.-+.
T Consensus       256 -GY~------s~S~Fsr~FK~~~G~  273 (291)
T PRK15186        256 -GYD------SASYFTCVFKKHFKT  273 (291)
T ss_pred             -CCC------CHHHHHHHHHHHHCc
Confidence             665      889999999887654

>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=87.55  E-value=0.69  Score=39.70  Aligned_cols=42  Identities=26%  Similarity=0.327  Sum_probs=31.3

Q ss_pred             HHHHH-HHHHHHcCCCHHHHHHHhC-CCHHHHHHHHHHhhhhCC
Q psy15598         51 SVRMR-IVELAQLGIRPCDISRQLR-VSHGCVSKILARYHETGS   92 (258)
Q Consensus        51 dlR~R-IV~L~~~G~S~~eIAr~LG-VSrsTVsRwikRyrEtGs   92 (258)
                      |.|.. +-+|+.+|+|.++||++|| ||++.|---+.|..=.|.
T Consensus         5 dERve~LkKLWseGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR   48 (169)
T COG5352           5 DERVETLKKLWSEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGR   48 (169)
T ss_pred             HHHHHHHHHHHHcccCHHHHHHHhcCcchhhhheeeeecccccc
Confidence            44544 4456789999999999998 999999766666654444

>PRK11139 DNA-binding transcriptional activator GcvA; Provisional

Probab=87.55  E-value=2.8  Score=37.50  Aligned_cols=57  Identities=16%  Similarity=0.163  Sum_probs=40.2

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHH
Q psy15598         53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~  112 (258)
                      ..+++..+.+--+.+.+|+.|+||.++|++-+++.++. |. +-.  |.| +.-.+|+.=+.
T Consensus        10 ~l~~f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~--R~~-r~l~lT~~G~~   68 (297)
T PRK11139         10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFR--RRN-RSLLLTEEGQR   68 (297)
T ss_pred             HHHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCchheE--ecC-CceeECHhHHH
Confidence            44566666666799999999999999999999999864 32 222  223 45666655333

>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ

Probab=87.52  E-value=2.1  Score=38.24  Aligned_cols=58  Identities=14%  Similarity=0.095  Sum_probs=39.4

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .+++..+.+-.|.+.+|+.|+||.++|++.+++.++ -|. +-.+  .+ +.-.+|+.-+.++
T Consensus         8 l~~f~~v~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R--~~-~~~~lT~~G~~l~   67 (300)
T TIGR02424         8 LQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFER--DR-RGIRLTRYGELFL   67 (300)
T ss_pred             HHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEE--cC-CCccccHhHHHHH
Confidence            345555555569999999999999999999999986 443 2233  22 4456666544333

Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.

>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]

Probab=87.46  E-value=0.89  Score=39.98  Aligned_cols=47  Identities=23%  Similarity=0.309  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         46 RPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +....+.+..|+.+...| .+.++||+.+++++.||++|++.....+.
T Consensus       159 ~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~  206 (222)
T COG1961         159 RKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG  206 (222)
T ss_pred             ccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhhhcccc
Confidence            567778888999999999 79999999999999999999999875554

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

Probab=87.45  E-value=1  Score=40.70  Aligned_cols=55  Identities=15%  Similarity=0.167  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l  117 (258)
                      +.|.++||+.|++|++||++++++..+.|-+.....+...--.+|++-+..+.+.
T Consensus        21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~   75 (217)
T PRK14165         21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNE   75 (217)
T ss_pred             CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHH
Confidence            4789999999999999999999999999987432211112334666555554333

>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional

Probab=87.42  E-value=1.1  Score=41.12  Aligned_cols=45  Identities=20%  Similarity=0.213  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+.+.+|+++++.  -++..++|+.|+||..||+|=+..-.+.|.+.
T Consensus        16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~   62 (269)
T PRK09802         16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV   62 (269)
T ss_pred             HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence            3556777777753  37999999999999999999999998888764

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=87.42  E-value=1.3  Score=40.05  Aligned_cols=44  Identities=18%  Similarity=0.367  Sum_probs=36.1

Q ss_pred             HHHHHHHH-c--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         54 MRIVELAQ-L--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        54 ~RIV~L~~-~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      .+|++++. .  +++..+||+.+|++++||+|.+....+.|-++-..
T Consensus         7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~   53 (246)
T COG1414           7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP   53 (246)
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            45666664 2  35799999999999999999999999999875443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	258
1k78_A	149	Pax5(1-149)+ets-1(331-440)+dna Length = 149		2e-50
2k27_A	159	Solution Structure Of Human Pax8 Paired Box Domain		3e-49
6pax_A	133	Crystal Structure Of The Human Pax-6 Paired Domain-		1e-47
1pdn_C	128	Crystal Structure Of A Paired Domain-Dna Complex At		8e-47

>pdb|1K78|A Chain A, Pax5(1-149)+ets-1(331-440)+dna Length = 149

Iteration: 1
 Score =  195 bits (495), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 94/127 (74%), Positives = 108/127 (85%)
Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +G VNQLGGVFVNGRPLP+ VR RIVELA  G+RPCDISRQLRVSHGCVSKIL RY+ETG
Sbjct: 17  HGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 76
Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PG IGGSKP+V TPKVV  I E K+++P +FAWEIRDRLL++ VCD   VPSVSSI+
Sbjct: 77  SIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSIN 136
Query: 152 RILRNKI 158
           RI+R K+
Sbjct: 137 RIIRTKV 143

>pdb|2K27|A Chain A, Solution Structure Of Human Pax8 Paired Box Domain Length = 159

Iteration: 1
 Score =  191 bits (485), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 91/127 (71%), Positives = 107/127 (84%)
Query: 32  YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETG 91
           +G +NQLGG FVNGRPLP  VR RIV+LA  G+RPCDISRQLRVSHGCVSKIL RY+ETG
Sbjct: 10  HGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETG 69
Query: 92  SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151
           SI PG IGGSKP+V TPKVV  I + K+++P +FAWEIRDRLL++GVCD   VPSVSSI+
Sbjct: 70  SIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSIN 129
Query: 152 RILRNKI 158
           RI+R K+
Sbjct: 130 RIIRTKV 136

>pdb|6PAX|A Chain A, Crystal Structure Of The Human Pax-6 Paired Domain-Dna Complex Reveals A General Model For Pax Protein-Dna Interactions Length = 133

Iteration: 1
 Score =  186 bits (471), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 92/122 (75%), Positives = 103/122 (84%)
Query: 35  VNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94
           VNQLGGVFVNGRPLP+S R RIVELA  G RPCDISR L+VS+GCVSKIL RY+ TGSI 
Sbjct: 5   VNQLGGVFVNGRPLPDSTRQRIVELAHSGARPCDISRILQVSNGCVSKILGRYYATGSIR 64
Query: 95  PGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL 154
           P AIGGSKPRV TP+VVS I + KQ+ P IFAWEIRDRLLS+GVC   N+PSVSSI+R+L
Sbjct: 65  PRAIGGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVL 124
Query: 155 RN 156
           RN
Sbjct: 125 RN 126

>pdb|1PDN|C Chain C, Crystal Structure Of A Paired Domain-Dna Complex At 2.5 Angstroms Resolution Reveals Structural Basis For Pax Developmental Mutations Length = 128

Iteration: 1
 Score =  183 bits (464), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 83/125 (66%), Positives = 106/125 (84%)
Query: 33  GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92
           G VNQLGGVF+NGRPLPN++R++IVE+A  GIRPC ISRQLRVSHGCVSKIL RY ETGS
Sbjct: 3   GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGS 62
Query: 93  ILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISR 152
           I PG IGGSKPR+ TP++ + I+E K+  PG+F+WEIR++L+ +GVCD+   PSVS+ISR
Sbjct: 63  IRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISR 122
Query: 153 ILRNK 157
           ++R +
Sbjct: 123 LVRGR 127
  Database: pdbaa

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	258
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	1e-57
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	2e-55
2k27_A	159	Paired box protein PAX-8; paired domain, solution	2e-54
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	8e-11
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	6e-07
1u78_A	141	TC3 transposase, transposable element TC3 transpos	8e-05

>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 Length = 128

 Score =  179 bits (454), Expect = 1e-57
 Identities = 83/125 (66%), Positives = 106/125 (84%)

Query: 33  GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92
           G VNQLGGVF+NGRPLPN++R++IVE+A  GIRPC ISRQLRVSHGCVSKIL RY ETGS
Sbjct: 3   GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGS 62

Query: 93  ILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISR 152
           I PG IGGSKPR+ TP++ + I+E K+  PG+F+WEIR++L+ +GVCD+   PSVS+ISR
Sbjct: 63  IRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISR 122

Query: 153 ILRNK 157
           ++R +
Sbjct: 123 LVRGR 127

>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 Length = 149

 Score =  174 bits (441), Expect = 2e-55
 Identities = 95/136 (69%), Positives = 109/136 (80%)

Query: 26  DASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA 85
             S   +G VNQLGGVFVNGRPLP+ VR RIVELA  G+RPCDISRQLRVSHGCVSKIL 
Sbjct: 11  RTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILG 70

Query: 86  RYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVP 145
           RY+ETGSI PG IGGSKP+V TPKVV  I E K+++P +FAWEIRDRLL++ VCD   VP
Sbjct: 71  RYYETGSIKPGVIGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVP 130

Query: 146 SVSSISRILRNKIGSS 161
           SVSSI+RI+R K+   
Sbjct: 131 SVSSINRIIRTKVQQP 146

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens} Length = 159

 Score =  171 bits (435), Expect = 2e-54
 Identities = 96/157 (61%), Positives = 114/157 (72%), Gaps = 11/157 (7%)

Query: 25  TDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKIL 84
            ++    +G +NQLGG FVNGRPLP  VR RIV+LA  G+RPCDISRQLRVSHGCVSKIL
Sbjct: 3   HNSIRSGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKIL 62

Query: 85  ARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNV 144
            RY+ETGSI PG IGGSKP+V TPKVV  I + K+++P +FAWEIRDRLL++GVCD   V
Sbjct: 63  GRYYETGSIRPGVIGGSKPKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTV 122

Query: 145 PSVSSISRILRNKIG-----------SSIVQHHHHPH 170
           PSVSSI+RI+R K+                 HHHH H
Sbjct: 123 PSVSSINRIIRTKVQQPFNLPMDSGAPGGGSHHHHHH 159

>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 Length = 194

 Score = 58.7 bits (141), Expect = 8e-11
 Identities = 14/98 (14%), Positives = 29/98 (29%), Gaps = 4/98 (4%)

Query: 112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNV----PSVSSISRILRNKIGSSIVQHHH 167
           + ++ L Q+DP   A  ++  L    +  +  V     + S +S+ L         +   
Sbjct: 18  AVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAA 77

Query: 168 HPHIYNSIYPSYPYPSNTSPTVSCTKVPIGSLTPPPRP 205
               Y             +      + P G   P  + 
Sbjct: 78  LYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKG 115

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens} Length = 221

 Score = 48.1 bits (113), Expect = 6e-07
 Identities = 8/46 (17%), Positives = 18/46 (39%), Gaps = 4/46 (8%)

Query: 114 IKELKQKDPGIFAWEIRDRLLSDGVCDKFNV----PSVSSISRILR 155
           +  +  +DP   A  I+  +    +  +  V     + S +S+ L 
Sbjct: 21  VDRMLSEDPWRAAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLN 66

>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 Length = 141

 Score = 40.8 bits (95), Expect = 8e-05
 Identities = 12/113 (10%), Positives = 38/113 (33%), Gaps = 15/113 (13%)

Query: 45  GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR 104
           G  L ++ R ++  +  L +   ++SR++  S  C+   L      G+         + +
Sbjct: 4   GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR----APRRK 59

Query: 105 VTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVP-SVSSISRILRN 156
             + +    +                    +  + ++  +  S  +I  +++ 
Sbjct: 60  ALSVRDERNVIRAASNSCKT----------ARDIRNELQLSASKRTILNVIKR 102

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	258
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	99.91
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	99.89
2k27_A	159	Paired box protein PAX-8; paired domain, solution	99.85
1u78_A	141	TC3 transposase, transposable element TC3 transpos	99.68
3hot_A	345	Transposable element mariner, complete CDS; protei	99.44
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	98.91
2jn6_A	97	Protein CGL2762, transposase; GFT PSI-2, protein s	98.67
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	98.65
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	98.55
2glo_A	59	Brinker CG9653-PA; protein-DNA complex, helix-turn	98.48
2rn7_A	108	IS629 ORFA; helix, all alpha, unknown function, st	98.35
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	98.25
4fcy_A	529	Transposase; rnaseh, DDE transposase, DNA binding	98.21
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	97.97
2pjp_A	121	Selenocysteine-specific elongation factor; SELB, p	97.68
2jrt_A	95	Uncharacterized protein; solution, structure, NESG	97.65
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	97.47
2ao9_A	155	Phage protein; structural genomics, nine-fold NCS.	97.23
1jhg_A	101	Trp operon repressor; complex (regulatory protein-	97.23
3jth_A	98	Transcription activator HLYU; transcription factor	97.21
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	97.17
2o8x_A	70	Probable RNA polymerase sigma-C factor; promoter r	97.17
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	97.12
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	97.1
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	97.04
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	96.97
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	96.97
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	96.96
3hug_A	92	RNA polymerase sigma factor; ECF sigma factor, zin	96.96
2kko_A	108	Possible transcriptional regulatory protein (possi	96.96
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	96.91
2jpc_A	61	SSRB; DNA binding protein, structural genomics, PS	96.89
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	96.88
1p4w_A	99	RCSB; solution structure, DNA binding domain, DNA	96.86
2oa4_A	101	SIR5; structure, structural genomics, PSI-2, prote	96.84
1ku3_A	73	Sigma factor SIGA; helix-turn-helix, transcription	96.83
2p7v_B	68	Sigma-70, RNA polymerase sigma factor RPOD; RSD, r	96.82
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	96.73
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	96.73
1fse_A	74	GERE; helix-turn-helix DNA-binding protein transcr	96.71
1s7o_A	113	Hypothetical UPF0122 protein SPY1201/SPYM3_0842/SP	96.71
1je8_A	82	Nitrate/nitrite response regulator protein NARL; p	96.7
3neu_A	125	LIN1836 protein; structural genomics, PSI-2, prote	96.68
1y0u_A	96	Arsenical resistance operon repressor, putative; s	96.68
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	96.67
3uj3_X	193	DNA-invertase; helix-turn-helix, site-specific rec	96.66
1tty_A	87	Sigma-A, RNA polymerase sigma factor RPOD; helix-t	96.62
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	96.6
3kor_A	119	Possible Trp repressor; putative DNA-binding Trp r	96.55
3frw_A	107	Putative Trp repressor protein; structural genomic	96.53
1zx4_A	192	P1 PARB, plasmid partition PAR B protein, PARB; tr	96.52
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	96.49
2w7n_A	101	TRFB transcriptional repressor protein; INCP, plas	96.43
3mzy_A	164	RNA polymerase sigma-H factor; PSI, MCSG, structur	96.42
2vz4_A	108	Tipal, HTH-type transcriptional activator TIPA; tr	96.41
3c57_A	95	Two component transcriptional regulatory protein;	96.4
1x3u_A	79	Transcriptional regulatory protein FIXJ; helix-tur	96.38
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	96.38
1xsv_A	113	Hypothetical UPF0122 protein SAV1236; helix-turn-h	96.37
2jml_A	81	DNA binding domain/transcriptional regulator; anti	96.34
2zkz_A	99	Transcriptional repressor PAGR; protein-DNA, HTH m	96.34
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	96.3
1tc3_C	51	Protein (TC3 transposase); DNA binding, helix-turn	96.29
3e7l_A	63	Transcriptional regulator (NTRC family); sigma43 a	96.26
1q06_A	135	Transcriptional regulator CUER; MERR family transc	96.23
2rnj_A	91	Response regulator protein VRAR; HTH LUXR-type dom	96.22
3ulq_B	90	Transcriptional regulatory protein COMA; tetratric	96.19
1g2h_A	61	Transcriptional regulatory protein TYRR homolog; p	96.14
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	96.12
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	96.12
3gp4_A	142	Transcriptional regulator, MERR family; structural	96.11
3plo_X	193	DNA-invertase; resolvase, helix-turn-helix, serine	96.1
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	96.09
1gdt_A	183	GD resolvase, protein (gamma delta resolvase); pro	96.07
1or7_A	194	Sigma-24, RNA polymerase sigma-E factor; regulatio	96.05
1jko_C	52	HIN recombinase, DNA-invertase HIN; water-mediated	96.03
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	96.01
1b4a_A	149	Arginine repressor; helix turn helix; 2.50A {Geoba	95.97
2vxz_A	165	Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Py	95.97
2l0k_A	93	Stage III sporulation protein D; SPOIIID, solution	95.95
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	95.95
3ic7_A	126	Putative transcriptional regulator; helix-turn-hel	95.92
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	95.9
2r0q_C	209	Putative transposon TN552 DNA-invertase BIN3; site	95.89
1r8d_A	109	Transcription activator MTAN; protein-DNA complex,	95.84
1z4h_A	66	TORI, TOR inhibition protein; winged helix, revers	95.84
1ntc_A	91	Protein (nitrogen regulation protein (NTRC)); heli	95.82
3by6_A	126	Predicted transcriptional regulator; structural ge	95.81
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	95.79
1rp3_A	239	RNA polymerase sigma factor sigma-28 (FLIA); trans	95.79
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	95.78
1umq_A	81	Photosynthetic apparatus regulatory protein; DNA-b	95.75
4ham_A	134	LMO2241 protein; structural genomics, PSI-biology,	95.7
2dg6_A	222	Putative transcriptional regulator; winged-helix m	95.65
1u78_A	141	TC3 transposase, transposable element TC3 transpos	95.64
3lsg_A	103	Two-component response regulator YESN; structural	95.58
2b0l_A	102	GTP-sensing transcriptional pleiotropic repressor;	95.57
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	95.57
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	95.53
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	95.49
2w48_A	315	Sorbitol operon regulator; SORC, activator, repres	95.47
1j9i_A	68	GPNU1 DBD;, terminase small subunit; DNA binding d	95.41
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	95.4
3iuo_A	122	ATP-dependent DNA helicase RECQ; C-terminal, GI PS	95.37
3gpv_A	148	Transcriptional regulator, MERR family; protein st	95.36
1uxc_A	65	FRUR (1-57), fructose repressor; DNA-binding prote	95.35
1sfx_A	109	Conserved hypothetical protein AF2008; structural	95.32
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	95.26
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	95.25
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	95.24
2w25_A	150	Probable transcriptional regulatory protein; trans	95.23
3hh0_A	146	Transcriptional regulator, MERR family; protein st	95.23
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	95.22
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	95.22
3i4p_A	162	Transcriptional regulator, ASNC family; PSI, struc	95.21
3mn2_A	108	Probable ARAC family transcriptional regulator; st	95.2
2k27_A	159	Paired box protein PAX-8; paired domain, solution	95.2
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	95.18
1neq_A	74	DNA-binding protein NER; NMR {Enterobacteria phage	95.16
2lfw_A	157	PHYR sigma-like domain; signal transduction, respo	95.14
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	95.12
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	95.1
3t72_q	99	RNA polymerase sigma factor RPOD, DNA-directed RN	95.09
3u1d_A	151	Uncharacterized protein; GNTR-superfamily, structu	95.0
2q1z_A	184	RPOE, ECF SIGE; ECF sigma factor, cupin fold, zinc	94.99
3kz3_A	80	Repressor protein CI; five helix bundle, DNA-bindi	94.98
1x57_A	91	Endothelial differentiation-related factor 1; HMBF	94.98
3eet_A	272	Putative GNTR-family transcriptional regulator; st	94.92
1eto_A	98	FIS, factor for inversion stimulation; transcripti	94.92
1r69_A	69	Repressor protein CI; gene regulating protein; 2.0	94.92
2b5a_A	77	C.BCLI; helix-turn-helix motif, gene regulation; 1	94.91
1rzs_A	61	Antirepressor, regulatory protein CRO; helix-turn-	94.89
3bhq_A	211	Transcriptional regulator; bacterial RE proteins,	94.81
2q0o_A	236	Probable transcriptional activator protein TRAR; h	94.8
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	94.8
3b7h_A	78	Prophage LP1 protein 11; structural genomics, PSI2	94.78
1zug_A	71	Phage 434 CRO protein; gene regulating protein, tr	94.77
2wiu_B	88	HTH-type transcriptional regulator HIPB; transfera	94.74
3hrs_A	214	Metalloregulator SCAR; DTXR/MNTR family member, tr	94.74
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	94.73
2r1j_L	68	Repressor protein C2; protein-DNA complex, helix-t	94.73
2a6c_A	83	Helix-turn-helix motif; putative transcriptional r	94.73
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	94.69
3r0a_A	123	Putative transcriptional regulator; structural gen	94.64
1y7y_A	74	C.AHDI; helix-turn-helix, DNA-binding protein, tra	94.59
1k78_A	149	Paired box protein PAX5; paired domain, ETS domain	94.55
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	94.53
1l3l_A	234	Transcriptional activator protein TRAR; helix-turn	94.51
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	94.5
2hoe_A	380	N-acetylglucosamine kinase; TM1224, structural gen	94.48
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	94.45
1bl0_A	129	Protein (multiple antibiotic resistance protein),	94.43
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	94.43
2qq9_A	226	Diphtheria toxin repressor; regulator, DTXR, helix	94.42
2kpj_A	94	SOS-response transcriptional repressor, LEXA; NESG	94.42
3s8q_A	82	R-M controller protein; protein-DNA complex, helix	94.41
2qvo_A	95	Uncharacterized protein AF_1382; PSI, structural g	94.4
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	94.4
1adr_A	76	P22 C2 repressor; transcription regulation; NMR {E	94.39
2hin_A	71	GP39, repressor protein; transcription factor, dim	94.39
1uly_A	192	Hypothetical protein PH1932; helix-turn-helix, str	94.37
2ewt_A	71	BLDD, putative DNA-binding protein; the DNA-bindin	94.33
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	94.32
2cob_A	70	LCOR protein; MLR2, KIAA1795, helix-turn-helix, st	94.3
2xi8_A	66	Putative transcription regulator; HTH DNA-binding	94.3
3f6w_A	83	XRE-family like protein; helix-turn-helix, DNA bin	94.25
3sxy_A	218	Transcriptional regulator, GNTR family; transcript	94.14
2k9q_A	77	Uncharacterized protein; all helix, helix-turn-hel	94.14
2h09_A	155	Transcriptional regulator MNTR; transcription regu	94.14
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	94.13
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	94.12
2eth_A	154	Transcriptional regulator, putative, MAR family; M	94.12
3b73_A	111	PHIH1 repressor-like protein; winged-helix-turn-he	94.12
2ef8_A	84	C.ECOT38IS, putative transcription factor; helix-t	94.11
3clo_A	258	Transcriptional regulator; NP_811094.1, bacterial	94.1
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	94.08
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	94.06
3edp_A	236	LIN2111 protein; APC88337, listeria innocua CLIP11	94.05
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	94.05
2zhg_A	154	Redox-sensitive transcriptional activator SOXR; ox	94.02
3bd1_A	79	CRO protein; transcription factor, helix-turn-heli	94.01
2l8n_A	67	Transcriptional repressor CYTR; bacterial gene rep	93.99
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	93.93
3v4g_A	180	Arginine repressor; vibrio vulnificus CMCP6, virul	93.88
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	93.88
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	93.87
2cw1_A	65	SN4M; lambda CRO fold, de novo protein; NMR {Synth	93.85
2ict_A	94	Antitoxin HIGA; helix-turn-helix, structural genom	93.82
3omt_A	73	Uncharacterized protein; structural genomics, PSI-	93.77
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	93.75
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	93.75
2pg4_A	95	Uncharacterized protein; structural genomics, join	93.74
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	93.73
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	93.73
1rr7_A	129	Middle operon regulator; MOR, transcription; 2.20A	93.73
2pij_A	67	Prophage PFL 6 CRO; transcription factor, helix-tu	93.73
2p5k_A	64	Arginine repressor; DNA-binding domain, winged hel	93.72
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	93.69
3lap_A	170	Arginine repressor; arginine repressor, DNA bindin	93.68
3szt_A	237	QCSR, quorum-sensing control repressor; quorum sen	93.67
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	93.66
1l0o_C	243	Sigma factor; bergerat fold, helix-turn-helix, pro	93.64
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	93.64
4g6q_A	182	Putative uncharacterized protein; structural genom	93.63
3qao_A	249	LMO0526 protein, MERR-like transcriptional regulat	93.62
1z6r_A	406	MLC protein; transcriptional repressor, ROK family	93.61
2gxg_A	146	146AA long hypothetical transcriptional regulator;	93.59
3fmy_A	73	HTH-type transcriptional regulator MQSA (YGIT/B302	93.55
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	93.52
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	93.51
3ihu_A	222	Transcriptional regulator, GNTR family; YP_298823.	93.5
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	93.5
3t76_A	88	VANU, transcriptional regulator vanug; structural	93.48
1hw1_A	239	FADR, fatty acid metabolism regulator protein; hel	93.47
3g5g_A	99	Regulatory protein; transcriptional regulator, hel	93.46
3vib_A	210	MTRR; helix-turn-helix motif, DNA binding, DNA bin	93.42
2dg7_A	195	Putative transcriptional regulator; helix-turn-hel	93.41
1lmb_3	92	Protein (lambda repressor); protein-DNA complex, d	93.4
3c7j_A	237	Transcriptional regulator, GNTR family; structural	93.32
3bs3_A	76	Putative DNA-binding protein; XRE-family, structur	93.3
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	93.27
2fq4_A	192	Transcriptional regulator, TETR family; DNA-bindin	93.27
3qq6_A	78	HTH-type transcriptional regulator SINR; helix-tur	93.25
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	93.22
1mkm_A	249	ICLR transcriptional regulator; structural genomic	93.21
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	93.21
3op9_A	114	PLI0006 protein; structural genomics, PSI-2, prote	93.16
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	93.15
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	93.13
2di3_A	239	Bacterial regulatory proteins, GNTR family; helix-	93.13
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	93.07
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	93.06
3kp7_A	151	Transcriptional regulator TCAR; multiple drug resi	93.02
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	93.0
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	92.94
3eus_A	86	DNA-binding protein; structural genomics, PSI2,MCS	92.93
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	92.93
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	92.92
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	92.9
1fx7_A	230	Iron-dependent repressor IDER; DTXR, iron-dependen	92.89
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	92.86
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.86
1z05_A	429	Transcriptional regulator, ROK family; structural	92.85
1ku9_A	152	Hypothetical protein MJ223; putative transcription	92.83
2wv0_A	243	YVOA, HTH-type transcriptional repressor YVOA; DNA	92.8
1jhf_A	202	LEXA repressor; LEXA SOS repressor, hydrolase; 1.8	92.8
3qp6_A	265	CVIR transcriptional regulator; quorum sensing, ag	92.79
3s2w_A	159	Transcriptional regulator, MARR family; structural	92.77
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	92.75
2nnn_A	140	Probable transcriptional regulator; structural gen	92.66
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	92.64
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	92.64
2ovg_A	66	Phage lambda CRO; transcription factor, helix-turn	92.62
2fe3_A	145	Peroxide operon regulator; oxidative stress regula	92.6
2l1p_A	83	DNA-binding protein SATB1; PSI-biology, NESG, stru	92.59
3bja_A	139	Transcriptional regulator, MARR family, putative;	92.59
2p4w_A	202	Transcriptional regulatory protein ARSR family; ar	92.57
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	92.41
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	92.35
3f52_A	117	CLP gene regulator (CLGR); helix-turn-helix motif,	92.32
2jvl_A	107	TRMBF1; coactivator, helix-turn-helix, Pro binding	92.25
2ppx_A	99	AGR_C_3184P, uncharacterized protein ATU1735; HTH-	92.25
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	92.25
1pdn_C	128	Protein (PRD paired); protein-DNA complex, double	92.24
2hs5_A	239	Putative transcriptional regulator GNTR; APC6050,	92.24
3bwg_A	239	Uncharacterized HTH-type transcriptional regulato;	92.23
4ghj_A	101	Probable transcriptional regulator; structural gen	92.2
3nqo_A	189	MARR-family transcriptional regulator; structural	92.18
2o03_A	131	Probable zinc uptake regulation protein FURB; DNA-	92.16
1z91_A	147	Organic hydroperoxide resistance transcriptional;	92.11
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	92.11
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	92.1
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	92.07
1yyv_A	131	Putative transcriptional regulator; reductive meth	92.04
3cwr_A	208	Transcriptional regulator, TETR family; YP_425770.	92.02
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	92.02
1qpz_A	340	PURA, protein (purine nucleotide synthesis repress	91.99
2zb9_A	214	Putative transcriptional regulator; transcription	91.96
1bia_A	321	BIRA bifunctional protein; transcription regulatio	91.95
4aik_A	151	Transcriptional regulator SLYA; transcription, tra	91.93
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	91.92
1b0n_A	111	Protein (SINR protein); transcription regulator, a	91.91
3ivp_A	126	Putative transposon-related DNA-binding protein; A	91.9
1mzb_A	136	Ferric uptake regulation protein; ferric uptake re	91.9
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	91.85
2p8t_A	200	Hypothetical protein PH0730; pyrococcus horikoshii	91.72
4fe7_A	412	Xylose operon regulatory protein; HTH_ARAC, helix-	91.7
3lwj_A	202	Putative TETR-family transcriptional regulator; st	91.7
2l49_A	99	C protein; P2 bacteriophage, P2 C, direct repeats,	91.63
3f8m_A	248	GNTR-family protein transcriptional regulator; PHN	91.59
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	91.57
3vk0_A	114	NHTF, transcriptional regulator; HTH motif, XRE tr	91.55
2hsg_A	332	Glucose-resistance amylase regulator; CCPA, transc	91.55
3hta_A	217	EBRA repressor; TETR family, DNA binding protein,	91.55
3o9x_A	133	Uncharacterized HTH-type transcriptional regulato;	91.55
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	91.51
2bnm_A	198	Epoxidase; oxidoreductase, cupin, HTH, cation-depe	91.46
3dv8_A	220	Transcriptional regulator, CRP/FNR family; cyclic	91.45
3f3x_A	144	Transcriptional regulator, MARR family, putative;	91.38
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	91.37
3vp5_A	189	Transcriptional regulator; heme, sensor protein, T	91.35
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	91.29
2eby_A	113	Putative HTH-type transcriptional regulator YBAQ;	91.23
3cec_A	104	Putative antidote protein of plasmid maintenance;	91.19
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	91.19
3cjd_A	198	Transcriptional regulator, TETR family; YP_510936.	91.13
2xig_A	150	Ferric uptake regulation protein; hpfur, transcrip	91.12
2hku_A	215	A putative transcriptional regulator; structural g	91.11
2dg8_A	193	Putative TETR-family transcriptional regulatory P;	91.09
3kz9_A	206	SMCR; transcriptional regulator, quorum S DNA-bind	91.05
3df8_A	111	Possible HXLR family transcriptional factor; APC89	91.02
2fxa_A	207	Protease production regulatory protein HPR; protea	90.96
2oz6_A	207	Virulence factor regulator; winged helix, helix-tu	90.89
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	90.84
3ryp_A	210	Catabolite gene activator; CAMP receptor protein (	90.81
2wui_A	210	MEXZ, transcriptional regulator; gene regulation,	90.72
2g7u_A	257	Transcriptional regulator; ICLR family, structural	90.7
3gbg_A	276	TCP pilus virulence regulatory protein; cupin, hel	90.67
2v7f_A	150	RPS19, RPS19E SSU ribosomal protein S19E; diamond	90.61
2d6y_A	202	Putative TETR family regulatory protein; helix-tur	90.6
1y9q_A	192	Transcriptional regulator, HTH_3 family; transcrip	90.59
2pex_A	153	Transcriptional regulator OHRR; transcription regu	90.58
1d5y_A	292	ROB transcription factor; protein-DNA complex, DNA	90.54
3geu_A	189	Intercellular adhesion protein R; TETR family, int	90.52
2o38_A	120	Hypothetical protein; alpha-beta, helix-turn-helix	90.5
2i10_A	202	Putative TETR transcriptional regulator; structura	90.47
4dyq_A	140	Gene 1 protein; GP1, octamer, DNA-binding, viral p	90.44
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	90.36
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	90.32
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	90.28
3iwz_A	230	CAP-like, catabolite activation-like protein; XCC,	90.27
3qkx_A	188	Uncharacterized HTH-type transcriptional regulato;	90.27
1ft9_A	222	Carbon monoxide oxidation system transcription reg	90.27
3k69_A	162	Putative transcription regulator; putative transcr	90.25
3lhq_A	220	Acrab operon repressor (TETR/ACRR family); structu	90.21
4ev0_A	216	Transcription regulator, CRP family; CAMP binding,	90.21
2zcw_A	202	TTHA1359, transcriptional regulator, FNR/CRP famil	90.21
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	90.19
3dkw_A	227	DNR protein; CRP-FNR, HTH, beta barrel, dimerizati	90.14
4ets_A	162	Ferric uptake regulation protein; metal binding pr	90.11
3egq_A	170	TETR family transcriptional regulator; DNA-binding	90.08
2f07_A	197	YVDT; helix-turn-helix, transcription; HET: BTB; 2	90.07
3h5t_A	366	Transcriptional regulator, LACI family; DNA-depend	90.05
2w57_A	150	Ferric uptake regulation protein; gene regulation,	90.04
3kjx_A	344	Transcriptional regulator, LACI family; LACL famil	90.02
3e97_A	231	Transcriptional regulator, CRP/FNR family; YP_6044	89.99
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	89.99
3b81_A	203	Transcriptional regulator, ACRR family; NP_350189.	89.97
2eh3_A	179	Transcriptional regulator; all alpha proteins, tet	89.91
2w57_A	150	Ferric uptake regulation protein; gene regulation,	89.87
2fmy_A	220	COOA, carbon monoxide oxidation system transcripti	89.86
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	89.84
3b02_A	195	Transcriptional regulator, CRP family; structural	89.82
2xdn_A	210	HTH-type transcriptional regulator TTGR; transcrip	89.79
2gqq_A	163	Leucine-responsive regulatory protein; helix-turn-	89.78
1p6r_A	82	Penicillinase repressor; transcription regulation,	89.76
3cdl_A	203	Transcriptional regulator AEFR; APC88582, TETR, ps	89.75
3trb_A	104	Virulence-associated protein I; mobIle and extrach	89.74
3d0s_A	227	Transcriptional regulatory protein; CAMP receptor	89.73
2x48_A	55	CAG38821; archeal virus, viral protein; 2.60A {Sul	89.72
1zyb_A	232	Transcription regulator, CRP family; NP_813211.1,	89.7
3knw_A	212	Putative transcriptional regulator (TETR/ACRR FAM;	89.69
2fjr_A	189	Repressor protein CI; genetic switch, regulation,	89.64
3anp_C	204	Transcriptional repressor, TETR family; all alpha	89.58
3mwm_A	139	ZUR, putative metal uptake regulation protein; FUR	89.56
3loc_A	212	HTH-type transcriptional regulator RUTR; helix-tur	89.55
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	89.53
2bgc_A	238	PRFA; bacterial infection, human pathogen, transcr	89.5
3mlf_A	111	Transcriptional regulator; structural genomics, he	89.5
3lmm_A	583	Uncharacterized protein; multi-domained alpha-beta	89.5
1l9z_H	438	Sigma factor SIGA; helix-turn-helix, coiled-coil,	89.47
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	89.43
1r8e_A	278	Multidrug-efflux transporter regulator; protein-DN	89.4
3bqz_B	194	HTH-type transcriptional regulator QACR; multidrug	89.39
3q0w_A	236	HTH-type transcriptional regulator EThr; TETR fami	89.38
3ppb_A	195	Putative TETR family transcription regulator; DNA-	89.37
3dew_A	206	Transcriptional regulator, TETR family; S genomics	89.33
1zs4_A	83	Regulatory protein CII; helix-turn-helix, transcri	89.33
3eyy_A	145	Putative iron uptake regulatory protein; NUR, nick	89.32
4a0z_A	190	Transcription factor FAPR; lipid homeostasis; HET:	89.29
1a04_A	215	Nitrate/nitrite response regulator protein NARL; s	89.21
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	89.19
2gau_A	232	Transcriptional regulator, CRP/FNR family; structu	89.17
1pb6_A	212	Hypothetical transcriptional regulator YCDC; helix	89.11
3c3w_A	225	Two component transcriptional regulatory protein;	89.06
3mky_B	189	Protein SOPB; partition, F plasmid, centromere, DN	89.05
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	89.0
3la7_A	243	Global nitrogen regulator; activator, DNA-binding,	88.98
3vpr_A	190	Transcriptional regulator, TETR family; all alpha,	88.93
3crj_A	199	Transcription regulator; APC88200, TETR, structura	88.88
3kxa_A	141	NGO0477 protein, putative uncharacterized protein;	88.87
3e6c_C	250	CPRK, cyclic nucleotide-binding protein; CPRK, hal	88.86
3f1b_A	203	TETR-like transcriptional regulator; APC5888, rhod	88.83
3pas_A	195	TETR family transcription regulator; structural ge	88.78
2g7s_A	194	Transcriptional regulator, TETR family; APC5906, P	88.77
2oer_A	214	Probable transcriptional regulator; helix-turn-hel	88.74
2np5_A	203	Transcriptional regulator; TETR family, structural	88.72
1ixc_A	294	CBNR, LYSR-type regulatory protein; long alpha hel	88.71
3bru_A	222	Regulatory protein, TETR family; structural genomi	88.68
2id3_A	225	Putative transcriptional regulator; structural gen	88.65
3lfp_A	98	CSP231I C protein; transcriptional regulator, DNA	88.62
2o7t_A	199	Transcriptional regulator; transcription regulator	88.6
3hhg_A	306	Transcriptional regulator, LYSR family; transcript	88.6
3kcc_A	260	Catabolite gene activator; helix-turn-helix, CAMP,	88.54
3gzi_A	218	Transcriptional regulator, TETR family; TETR famil	88.54
3bdn_A	236	Lambda repressor; repressor, allostery; HET: DNA;	88.5
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	88.49
3dcf_A	218	Transcriptional regulator of the TETR/ACRR family;	88.45
2ibd_A	204	Possible transcriptional regulator; probable trans	88.4
3g1o_A	255	Transcriptional regulatory repressor protein (TETR	88.4
4fx0_A	148	Probable transcriptional repressor protein; helix-	88.39
3dpj_A	194	Transcription regulator, TETR family; APC88616, si	88.38
2auw_A	170	Hypothetical protein NE0471; alpha-beta structure,	88.37
2ofy_A	86	Putative XRE-family transcriptional regulator; tra	88.32
2jj7_A	186	Hemolysin II regulatory protein; DNA-binding prote	88.32
2nx4_A	194	Transcriptional regulator, TETR family protein; HT	88.31
4aci_A	191	HTH-type transcriptional repressor ACNR; aconitase	88.26
2zcx_A	231	SCO7815, TETR-family transcriptional regulator; he	88.22
3jsj_A	190	Putative TETR-family transcriptional regulator; DN	88.15
3cta_A	230	Riboflavin kinase; structural genomics, transferas	88.11
3ljl_A	156	Transcriptional regulator LUXT; structural genomic	88.03
3bjb_A	207	Probable transcriptional regulator, TETR family P;	88.02
1iuf_A	144	Centromere ABP1 protein; riken structural genomics	87.99
2qtq_A	213	Transcriptional regulator, TETR family; transcript	87.94
3mnl_A	203	KSTR, transcriptional regulatory protein (probably	87.88
2hyt_A	197	TETR-family transcriptional regulator; structural	87.88
3on4_A	191	Transcriptional regulator, TETR family; structural	87.81
2gfn_A	209	HTH-type transcriptional regulator PKSA related P;	87.78
3n0r_A	286	Response regulator; sigma factor, receiver, two-co	87.78
3qbm_A	199	TETR transcriptional regulator; DNA/RNA-binding th	87.75
2qlz_A	232	Transcription factor PF0095; 2.50A {Pyrococcus fur	87.73
2esn_A	310	Probable transcriptional regulator; PA0477, APC582	87.72
3nnr_A	228	Transcriptional regulator, TETR family; TETR-famil	87.64
1vi0_A	206	Transcriptional regulator; structural genomics; HE	87.6
3bni_A	229	Putative TETR-family transcriptional regulator; st	87.59
2qko_A	215	Possible transcriptional regulator, TETR family P;	87.53
1okr_A	123	MECI, methicillin resistance regulatory protein ME	87.5
3c2b_A	221	Transcriptional regulator, TETR family; structural	87.45
2gen_A	197	Probable transcriptional regulator; APC6095, TETR	87.45
3col_A	196	Putative transcription regulator; structural genom	87.4
3fx3_A	237	Cyclic nucleotide-binding protein; helix_TURN_heli	87.34
2ras_A	212	Transcriptional regulator, TETR family; bacterial	87.34
3kkc_A	177	TETR family transcriptional regulator; APC20805, s	87.32
3e7q_A	215	Transcriptional regulator; structural genomics, PS	87.25
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	87.23
1ylf_A	149	RRF2 family protein; structural genomics, transcri	87.17
2v57_A	190	TETR family transcriptional repressor LFRR; DNA-bi	87.17
3he0_A	196	Transcriptional regulator, TETR family; ACRR, vibr	87.16
1rkt_A	205	Protein YFIR; transcription regulator, structural	87.16
3rh2_A	212	Hypothetical TETR-like transcriptional regulator;	87.14
1hqc_A	324	RUVB; extended AAA-ATPase domain, complex with nuc	87.1
1hlv_A	131	CENP-B, major centromere autoantigen B; helix-turn	87.05
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	87.02
2a6h_F	423	RNA polymerase sigma factor RPOD; RNA polymerase h	86.96
2g3b_A	208	Putative TETR-family transcriptional regulator; tr	86.95
2w53_A	219	Repressor, SMet; antibiotic resistance, multi-drug	86.73
3npi_A	251	TETR family regulatory protein; structural genomic	86.72
2o0m_A	345	Transcriptional regulator, SORC family; structural	86.63
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	86.59
3eup_A	204	Transcriptional regulator, TETR family; structural	86.59
2lnb_A	80	Z-DNA-binding protein 1; structural genomics, nort	86.56
3mvp_A	217	TETR/ACRR transcriptional regulator; PSI, MCSG, st	86.54
1ojl_A	304	Transcriptional regulatory protein ZRAR; response	86.51
3ccy_A	203	Putative TETR-family transcriptional regulator; AP	86.47
1ui5_A	215	A-factor receptor homolog; helix-turn-helix, alpha	86.47
3nrg_A	217	TETR family transcriptional regulator; structural	86.43
2yve_A	185	Transcriptional regulator; helix-turn-helix, TETR-	86.38
3f0c_A	216	TETR-molecule A, transcriptional regulator; MCSG,P	86.33
2guh_A	214	Putative TETR-family transcriptional regulator; he	86.31
2qwt_A	196	Transcriptional regulator, TETR family; structural	86.25
1yio_A	208	Response regulatory protein; transcription regulat	86.2
2zcm_A	192	Biofilm operon icaabcd HTH-type negative transcri	86.14
3klo_A	225	Transcriptional regulator VPST; REC domain, HTH do	86.07
1yg2_A	179	Gene activator APHA; virulence factor, winged heli	86.05
3g7r_A	221	Putative transcriptional regulator; TETR, all-heli	86.02
2iu5_A	195	DHAS, YCEG, HTH-type dhaklm operon transcriptional	85.99
2wus_R	112	RODZ, putative uncharacterized protein; structural	85.86
3rd3_A	197	Probable transcriptional regulator; 2.40A {Pseudom	85.77
2qib_A	231	TETR-family transcriptional regulator; HTH DNA bin	85.74
3fxq_A	305	LYSR type regulator of TSAMBCD; transcriptional re	85.66
3v6g_A	208	Probable transcriptional regulatory protein (PROB	85.66
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	85.63
2ijl_A	135	AGR_C_4647P, molybdenum-binding transcriptional re	85.61
3s5r_A	216	Transcriptional regulator TETR family; DNA/RNA-bin	85.45
2of7_A	260	Putative TETR-family transcriptional regulator; AP	85.44
2o3f_A	111	Putative HTH-type transcriptional regulator YBBH;	85.37
1hsj_A	487	Fusion protein consisting of staphylococcus access	85.24
2of5_A	114	Death domain-containing protein cradd; death domai	85.22
3him_A	211	Probable transcriptional regulator; TETR, bacteria	85.22
2oi8_A	216	Putative regulatory protein SCO4313; TETR, structu	85.2
2hyj_A	200	Putative TETR-family transcriptional regulator; HT	85.18
1xwr_A	97	Regulatory protein CII; all-alpha fold, DNA bindin	85.17
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	85.1
2elh_A	87	CG11849-PA, LD40883P; structural genomics, NPPSFA,	85.06
3nxc_A	212	HTH-type protein SLMA; nucleoid occlusion, cell di	85.03
1t33_A	224	Putative transcriptional repressor (TETR/ACRR FAM;	84.95
3fzv_A	306	Probable transcriptional regulator; LYSR, structur	84.92
2rek_A	199	Putative TETR-family transcriptional regulator; su	84.78
2fbq_A	235	Probable transcriptional regulator; PA3006, APC589	84.75
3szp_A	291	Transcriptional regulator, LYSR family; winged hel	84.73

>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=99.91  E-value=7.4e-24  Score=164.88  Aligned_cols=126  Identities=66%  Similarity=1.188  Sum_probs=108.2

Q ss_pred             chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      |++|++||+|.|++.|+.++|.+|+.++.+|++.++||+.||||++||++|+++|+++|.+.+++++|.++++++++.+.
T Consensus         3 ~~~~~~gg~~~m~~~~s~~~r~~i~~~~~~g~s~~~ia~~lgis~~Tv~~w~~~~~~~g~~~~~~~~g~~~~~l~~~~~~   82 (128)
T 1pdn_C            3 GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIEN   82 (128)
T ss_dssp             EEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHH
T ss_pred             chHhhhcccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhhCCcccccCCCCCCCcCCHHHHH
Confidence            78999999999999999999999999999999999999999999999999999999999887776655467788888899


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      .|.+++.++|.++.++|++.|.+.|+......+|.+||+|+|++++
T Consensus        83 ~i~~~~~~~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~~~~  128 (128)
T 1pdn_C           83 RIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGRD  128 (128)
T ss_dssp             HHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC----
T ss_pred             HHHHHHHhCcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHHhcC
Confidence            9999999999999999999998778731111259999999998753

>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=99.89  E-value=1.6e-22  Score=164.58  Aligned_cols=132  Identities=69%  Similarity=1.111  Sum_probs=109.5

Q ss_pred             cCCCCCCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC
Q psy15598         25 TDASGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR  104 (258)
Q Consensus        25 ~~~~~~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr  104 (258)
                      ..+.-++.+++|++||+|.|++.|+.++|.+||.++.+|++.++||+.||||++||++|+++|++.|.+.+++++|++++
T Consensus        10 ~~~~~~~~~~~~~~gg~~~~~~~~s~e~r~~iv~~~~~G~s~~~iA~~lgis~~TV~rw~~~~~~~G~~~~~~r~gr~~~   89 (149)
T 1k78_A           10 PRTSRTGHGGVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPGVIGGSKPK   89 (149)
T ss_dssp             ---------CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCCCCCCCCCS
T ss_pred             CccccCCCCCccCCCceecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCCCccCCCCCCCC
Confidence            44556777999999999999999999999999999999999999999999999999999999999998877776664478


Q ss_pred             CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-----CCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        105 VTTPKVVSYIKELKQKDPGIFAWEIRDRLLSD-----GVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       105 klT~e~~~~I~~lv~~nP~ita~EIr~~L~~~-----Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +++++..+.|.+++.++|.+++++|++.|.+.     |+.     +|.+||+|+|++....+
T Consensus        90 ~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~-----~S~sTV~r~L~~~~~~~  146 (149)
T 1k78_A           90 VATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTV-----PSVSSINRIIRTKVQQP  146 (149)
T ss_dssp             SSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTS-----CCHHHHHHHHHCC----
T ss_pred             CCCHHHHHHHHHHHHhCcchhHHHHHHHHHHhcccccCCC-----cCHHHHHHHHHHHhcCC
Confidence            89999999999999999999999999999765     454     59999999999877643

>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=99.85  E-value=1.1e-20  Score=155.70  Aligned_cols=139  Identities=65%  Similarity=1.081  Sum_probs=118.2

Q ss_pred             CCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598         30 QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK  109 (258)
Q Consensus        30 ~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e  109 (258)
                      .+...++++|+++.|++.|+.++|.+|+.++.+|++.++||+.||||++||++|+++|++.|.+.+++++|.++++++++
T Consensus         8 ~~~~~~~~~g~~~~~~~~~s~e~r~~ii~l~~~G~s~~~IA~~lgis~~TV~rwl~r~~~~G~~~~~~r~gr~~~~~~~~   87 (159)
T 2k27_A            8 SGHGGLNQLGGAFVNGRPLPEVVRQRIVDLAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPK   87 (159)
T ss_dssp             CSCSSCCCCCCTTSSSCSSCHHHHHHHHHHHHHTCCHHHHHHHHTCCSHHHHHHHCCSSTTSCCCCCCCCCCCCCCCCTT
T ss_pred             hcchhhhhcCCcCCCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHhcCCccCCCCCCCCCCCCCHH
Confidence            34467899999999999999999999999999999999999999999999999999999999887777666447788888


Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHH  168 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~~~  168 (258)
                      ..+.|.++++++|.+++++|++.|.+.+++.....+|.+||+|+|++......+..+.+
T Consensus        88 ~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~~~~~~~~  146 (159)
T 2k27_A           88 VVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPFNLPMDS  146 (159)
T ss_dssp             HHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCCSCCCCCC
T ss_pred             HHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCCccCcccC
Confidence            89999999999999999999999986553111112699999999999888766665543

>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=99.68  E-value=5.4e-16  Score=123.15  Aligned_cols=102  Identities=16%  Similarity=0.222  Sum_probs=89.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGI  124 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~i  124 (258)
                      ++.++.+.|.+|+.++.+|++.++||+.||||++||++|+++|.+.|....   .| +|++++++.+..|.++ ..+|.+
T Consensus         4 ~~~~s~~~r~~i~~~~~~G~s~~~ia~~lgis~~Tv~r~~~~~~~~g~~~~---~g-r~~~l~~~~~~~i~~~-~~~~~~   78 (141)
T 1u78_A            4 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGTSKR---AP-RRKALSVRDERNVIRA-ASNSCK   78 (141)
T ss_dssp             SCCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHSGGGTTCCCC---CC-CCCSSCHHHHHHHHHH-HHHCCC
T ss_pred             cccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHcccccCCcCC---CC-CCCcCCHHHHHHHHHH-HhCCCC
Confidence            457999999999999999999999999999999999999999998886532   45 7888999988888888 677899


Q ss_pred             CHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        125 FAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       125 ta~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      ++.+|++.|   |+.+     |.+||+|+|++.+.
T Consensus        79 s~~~i~~~l---g~~~-----s~~tV~r~l~~~g~  105 (141)
T 1u78_A           79 TARDIRNEL---QLSA-----SKRTILNVIKRSGV  105 (141)
T ss_dssp             CHHHHHHHT---TCCS-----CHHHHHHHHHHTC-
T ss_pred             CHHHHHHHH---CCCc-----cHHHHHHHHHHCCC
Confidence            999998877   6654     99999999999876

>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=99.44  E-value=6.7e-13  Score=119.75  Aligned_cols=101  Identities=16%  Similarity=0.162  Sum_probs=87.2

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhC-------CCHHHHHHHHHHhhhhC--CcccCCCCCCCCCCCCHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLR-------VSHGCVSKILARYHETG--SILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LG-------VSrsTVsRwikRyrEtG--sl~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      -.+...++|.+|+.++.+|++.++||+.|+       ||++||++|+++|++ |  .+.+++++| ||+++++   +.|.
T Consensus         4 ~~~~~~~~R~~i~~~~~~G~s~~~~~~~l~~~~g~~~vs~~tv~~w~~r~~~-g~~~l~~~~r~g-rp~~~~~---~~i~   78 (345)
T 3hot_A            4 FVPNKEQTRTVLIFCFHLKKTAAESHRMLVEAFGEQVPTVKTCERWFQRFKS-GDFDVDDKEHGK-PPKRYED---AELQ   78 (345)
T ss_dssp             -CCCHHHHHHHHHHHHHTTCCHHHHHHHHHHHTCSCSCCHHHHHHHHHHHTT-CCCCCSCCCCCC-CCCSSCH---HHHH
T ss_pred             ccccHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCcHHHHHHHHHHHhC-CCccccCCCCCC-CCCcccH---HHHH
Confidence            345678999999999999999999999977       999999999999997 6  467888888 8888876   5566


Q ss_pred             HHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        116 ELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       116 ~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      ++++.+|..+..+|++.|   +       +|.+||+|+|++.+..
T Consensus        79 ~~v~~~~~~t~~~ia~~l---~-------vs~~tV~r~L~~~g~~  113 (345)
T 3hot_A           79 ALLDEDDAQTQKQLAEQL---E-------VSQQAVSNRLREMGKI  113 (345)
T ss_dssp             HHHHHCSCCCHHHHHHHT---T-------SCHHHHHHHHHHTTCE
T ss_pred             HHHHhCccchHHHHHHHH---C-------CCHHHHHHHHHHhCCe
Confidence            778899999999999887   2       4999999999998775

>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=98.91  E-value=2.1e-09  Score=70.02  Aligned_cols=47  Identities=19%  Similarity=0.331  Sum_probs=43.5

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +.++.+.|..|+.++.+|++..+||+.||||++||++|+++|++.|.
T Consensus         4 ~~l~~~~~~~i~~~~~~g~s~~~IA~~lgis~~Tv~~~~~~~~~~g~   50 (51)
T 1tc3_C            4 SALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSYGT   50 (51)
T ss_dssp             CCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCSTTTTC
T ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhhHHhcCC
Confidence            45899999999999999999999999999999999999999987763

>2jn6_A Protein CGL2762, transposase; GFT PSI-2, protein structure, structural genomics, protein structure initiative; NMR {Corynebacterium glutamicum} SCOP: a.4.1.19

Probab=98.67  E-value=4.1e-08  Score=74.40  Aligned_cols=47  Identities=13%  Similarity=0.237  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         46 RPLPNSVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +.||.++|..+|.++. . |.+..+||+.||||++||++|+++|.+.|.
T Consensus         4 ~~ys~e~k~~~v~~~~~~~g~s~~~ia~~~gIs~~tl~rW~~~~~~~g~   52 (97)
T 2jn6_A            4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHN   52 (97)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCST
T ss_pred             CCCCHHHHHHHHHHHHHcCCChHHHHHHHHCcCHHHHHHHHHHHhhcCc
Confidence            5799999999999985 5 899999999999999999999999997764

>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=98.65  E-value=5e-07  Score=71.28  Aligned_cols=110  Identities=15%  Similarity=0.096  Sum_probs=75.8

Q ss_pred             CCCCCHHHHHHHHHHH-HcCCCH-HHHHHHhCCCHHHHHHHHHHhhh-------hCCcccCCCCCCCCCCCCHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELA-QLGIRP-CDISRQLRVSHGCVSKILARYHE-------TGSILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~-~~G~S~-~eIAr~LGVSrsTVsRwikRyrE-------tGsl~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      .+.|+.++|.+||.++ +.|.+. ++||+.|||+++||++|++.+..       .+...+.. .+ ......++.++.|.
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~gvs~stl~~~~~~~~~~~~~~~~~~~~~~~~-kr-~r~~~~~~~E~~L~   82 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNKRAILASERKYGVASTCR-KT-NKLSPYDKLEGLLI   82 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTHHHHHHHHHHHGGGGGTC-CC-CCCCTTHHHHHHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHhCCCHHHHHHHHhchhhhcchhhhccccchhh-cc-cCCCCCHHHHHHHH
Confidence            4579999999999998 677665 49999999999999999998765       34322221 12 22446677888888


Q ss_pred             HHHHh----CCCCCHHHHHHHH---H-hcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        116 ELKQK----DPGIFAWEIRDRL---L-SDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       116 ~lv~~----nP~ita~EIr~~L---~-~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      .++.+    +-.++...|++..   . ..|+.  +-.+|..-+.++.++++
T Consensus        83 ~Wi~~~~~~g~pvs~~~I~~kA~~i~~~~g~~--~f~~S~gWl~~F~~Rh~  131 (131)
T 1hlv_A           83 AWFQQIRAAGLPVKGIILKEKALRIAEELGMD--DFTASNGWLDRFRRRRS  131 (131)
T ss_dssp             HHHHHHGGGTCCCCHHHHHHHHHHHHHHHTCT--TCCCCHHHHHHHHHHTC
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHhCCC--CCCCCHHHHHHHHHhcC
Confidence            88763    2235655554333   2 23553  12369999999998864

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=98.55  E-value=1.4e-07  Score=70.81  Aligned_cols=48  Identities=10%  Similarity=0.110  Sum_probs=44.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      .+.|+.+++..+|.++..|.+..+||+.||||++||++|+++|.+.+.
T Consensus        20 ~~~ys~e~k~~~v~~~~~g~s~~~iA~~~gIs~sTl~rW~k~~~~~~~   67 (87)
T 2elh_A           20 LRSLTPRDKIHAIQRIHDGESKASVARDIGVPESTLRGWCKNEDKLRF   67 (87)
T ss_dssp             CSSCCHHHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHhccc
Confidence            458999999999999988999999999999999999999999987553

>2glo_A Brinker CG9653-PA; protein-DNA complex, helix-turn-helix motif, transcription/DNA complex; NMR {Drosophila melanogaster}

Probab=98.48  E-value=1.8e-07  Score=65.47  Aligned_cols=47  Identities=11%  Similarity=0.111  Sum_probs=42.6

Q ss_pred             CCCCCHHHHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598         45 GRPLPNSVRMRIVELAQLGIR----PCDISRQLRVSHGCVSKILARYHETG   91 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S----~~eIAr~LGVSrsTVsRwikRyrEtG   91 (258)
                      .+.||.++|.+|+++++.|.+    ..+||+.|||+.+||++|+++|.+.+
T Consensus         3 r~~ys~efK~~~~~~~~~g~s~~~~~~~vA~~~gIs~~tl~~W~~~~~~~~   53 (59)
T 2glo_A            3 RRIFTPHFKLQVLESYRNDNDCKGNQRATARKYNIHRRQIQKWLQCESNLR   53 (59)
T ss_dssp             CCCCCHHHHHHHHHHHHHCTTTTTCHHHHHHHTTSCHHHHHHHHTTHHHHH
T ss_pred             CCcCCHHHHHHHHHHHHcCCCcchHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence            357999999999887888999    99999999999999999999998754

>2rn7_A IS629 ORFA; helix, all alpha, unknown function, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri}

Probab=98.35  E-value=4e-07  Score=70.03  Aligned_cols=49  Identities=12%  Similarity=0.196  Sum_probs=43.6

Q ss_pred             CCCCCCHHHHHHHHHHHH-cC-------CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         44 NGRPLPNSVRMRIVELAQ-LG-------IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~-~G-------~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +.+.||.++|.++|.++. .|       .+..+||+.||||.+||++|+++|.+.|.
T Consensus         3 ~~~~ys~e~K~~~v~~~~~~~~~~~s~g~s~~~va~~~gIs~~tl~~W~~~~~~~~~   59 (108)
T 2rn7_A            3 KNTRFSPEVRQRAVRMVLESQGEYDSQWATICSIAPKIGCTPETLRVWVRQHERDTG   59 (108)
T ss_dssp             SSCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHTSCHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcccccccccccHHHHHHHHCcCHHHHHHHHHHHHhccc
Confidence            456799999999999884 44       89999999999999999999999998765

>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=98.25  E-value=4.9e-07  Score=59.45  Aligned_cols=42  Identities=7%  Similarity=0.100  Sum_probs=37.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++.+.+..|+.++.+|.+..+||+.||||++||++|++++.
T Consensus         5 ~~~~~~~~~i~~l~~~g~s~~~ia~~lgvs~~Tv~r~l~~~~   46 (52)
T 1jko_C            5 AINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYFPASS   46 (52)
T ss_dssp             SSCTTHHHHHHHHHHTTCCHHHHHHTTSCCHHHHHHHSCTTC
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHcc
Confidence            466777788999988999999999999999999999998753

>4fcy_A Transposase; rnaseh, DDE transposase, DNA binding protein-DNA complex; HET: DNA; 3.71A {Enterobacteria phage MU} PDB: 2ezk_A 2ezl_A 2ezh_A 2ezi_A

Probab=98.21  E-value=8.6e-06  Score=77.92  Aligned_cols=103  Identities=10%  Similarity=0.048  Sum_probs=67.1

Q ss_pred             HHHHHHHH----HHcCCCH----HHHHHHhCCCHHHHHHHHHHhhhhCC------cccCCCCC---CCCCCCCHHHHHHH
Q psy15598         52 VRMRIVEL----AQLGIRP----CDISRQLRVSHGCVSKILARYHETGS------ILPGAIGG---SKPRVTTPKVVSYI  114 (258)
Q Consensus        52 lR~RIV~L----~~~G~S~----~eIAr~LGVSrsTVsRwikRyrEtGs------l~pk~rgG---~RPrklT~e~~~~I  114 (258)
                      .|..||..    ...|.+.    .++|+.+|||++|++||+++|+..|.      +.|+..+.   .+...++++..+.|
T Consensus        33 ~r~~~i~~v~~l~~~g~~~~~a~~~~a~~~gvS~~Tl~rW~~~y~~~~~~~gl~~L~~~~~~~~~~~~~~~~~~~~~~~i  112 (529)
T 4fcy_A           33 KWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVDGRGASRRNVHKSEFDEDAWQFL  112 (529)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHHHHTTSCHHHHHHHHHHHHTSCGGGHHHHHC------------CCCCHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHhhCcccCceecccCCCCCCCCCCcCcCCHHHHHHH
Confidence            44455554    3467764    45799999999999999999976542      34443221   12344678888888


Q ss_pred             HHHHHhCCCCCHHH----HHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        115 KELKQKDPGIFAWE----IRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       115 ~~lv~~nP~ita~E----Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      .+.....+..+...    +...+.+.|+.+    ||.+||+|+|++..
T Consensus       113 ~~~yl~~~~~s~~~~~~~~~~~~~~~g~~~----PS~~tv~r~l~~~~  156 (529)
T 4fcy_A          113 IADYLRPEKPAFRKCYERLELAAREHGWSI----PSRATAFRRIQQLD  156 (529)
T ss_dssp             HHHHTSTTCCCHHHHHHHHHHHHHHHTCCC----CCHHHHHHHHHHHC
T ss_pred             HHHHhCcCCCCHHHHHHHHHHHHHHcCCCC----CCHHHHHHHHHhcC
Confidence            87766555556544    445555678876    89999999998743

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=97.97  E-value=5.6e-06  Score=56.18  Aligned_cols=39  Identities=26%  Similarity=0.290  Sum_probs=34.3

Q ss_pred             CC--HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LP--NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S--~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++  .+....|+.++.+|++..+||+.||||++||++|+++
T Consensus        14 l~~~~~~~~~i~~l~~~g~s~~eIA~~lgis~~TV~~~l~~   54 (55)
T 2x48_A           14 VESEDDLVSVAHELAKMGYTVQQIANALGVSERKVRRYLES   54 (55)
T ss_dssp             ECSHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHTC
T ss_pred             HhcCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence            56  6777788888889999999999999999999999864

>2pjp_A Selenocysteine-specific elongation factor; SELB, protein-RNA complex, elongation factor, winged- helix, bulge, translation/RNA complex; 2.30A {Escherichia coli}

Probab=97.68  E-value=1.9e-05  Score=62.59  Aligned_cols=100  Identities=15%  Similarity=0.086  Sum_probs=79.8

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEI  129 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EI  129 (258)
                      +++.+|+..+. .+.++.++|..|+++..++..|++...+.|.+.+...+.--......+..+.|.+++..++.+++.++
T Consensus         7 ~l~~~i~~~~~~~p~~~~~la~~~~~~~~~~~~~l~~l~~~G~l~~i~~~~~~~~~~~~~~~~~l~~~~~~~~~it~ae~   86 (121)
T 2pjp_A            7 AIWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVKDRYYRNDRIVEFANMIRDLDQECGSTCAADF   86 (121)
T ss_dssp             HHHHHHGGGCSSSCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEETTEEEEHHHHHHHHHHHHHHHHHHSSEEHHHH
T ss_pred             HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceECHHHHHHHHHHHHHHHHHCCCccHHHH
Confidence            57788888886 67899999999999999999999999999987655433212233446667788888888999999999


Q ss_pred             HHHHHhcCCCCCCCCCCHH---HHHHHHHhccCC
Q psy15598        130 RDRLLSDGVCDKFNVPSVS---SISRILRNKIGS  160 (258)
Q Consensus       130 r~~L~~~Gv~v~~~~pS~S---TI~RiLrr~~~~  160 (258)
                      ++.|   |       +|+.   +|-.+|.+.+.-
T Consensus        87 Rd~l---g-------~sRK~ai~lLE~~Dr~g~T  110 (121)
T 2pjp_A           87 RDRL---G-------VGRKLAIQILEYFDRIGFT  110 (121)
T ss_dssp             HHHH---T-------SCHHHHHHHHHHHHHHTSE
T ss_pred             HHHH---C-------CcHHHHHHHHHHHhhcCCe
Confidence            9999   4       3888   888888877654

>2jrt_A Uncharacterized protein; solution, structure, NESG, PSI, target RHR5, structural genomics, protein structure initiative; NMR {Rhodobacter sphaeroides}

Probab=97.65  E-value=8.9e-05  Score=57.48  Aligned_cols=50  Identities=14%  Similarity=0.094  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         44 NGRPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .-+..+.+++.+||..+..| .|.+++|+.++||.++|++|.+.|.+.|..
T Consensus        29 ~~rrWs~~~Kl~VV~~~~~g~~s~~e~arry~Is~s~i~~W~r~~~~~G~~   79 (95)
T 2jrt_A           29 DTRRWVASRKAAVVKAVIHGLITEREALDRYSLSEEEFALWRSAVAAHGEK   79 (95)
T ss_dssp             SCCCCCHHHHHHHHHHHHTTSSCHHHHHHHTTCCHHHHHHHHHHTTTCCTT
T ss_pred             hhhccCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhHH
Confidence            44569999999999998765 799999999999999999999999988853

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=97.47  E-value=0.00069  Score=55.06  Aligned_cols=113  Identities=13%  Similarity=0.044  Sum_probs=74.5

Q ss_pred             CCCCCCHHHHHHHHHHH-H--cCCCHHHHHH----Hh--CCCHHHHHHHHHHhhhhCCc-c--cCCCCCCCCCCCCHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-Q--LGIRPCDISR----QL--RVSHGCVSKILARYHETGSI-L--PGAIGGSKPRVTTPKVV  111 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-~--~G~S~~eIAr----~L--GVSrsTVsRwikRyrEtGsl-~--pk~rgG~RPrklT~e~~  111 (258)
                      .-+.|+.+.|.+|++.+ +  .+++..++|+    .|  +||++||++|++.-.+--.. .  +..+.. +.....++.+
T Consensus         8 ~R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~is~stis~ilk~k~~~l~~~~~~~~~~kr-~r~~~~~~le   86 (144)
T 1iuf_A            8 KRRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKDISQPSVSQILSSKYSYLDNTVEKPWDVKR-NRPPKYPLLE   86 (144)
T ss_dssp             SSSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSCCSSSSTTHHHHHHHHHTTTSCSSSSSSSC-CCCCSCHHHH
T ss_pred             cCccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCCCcHHHHHHHHhhHHHHhhhcccccccccC-CCCCCCHHHH
Confidence            44579999999999999 4  3589999999    99  99999999999986552211 1  111111 2234568888


Q ss_pred             HHHHHHHHh---CCCCCHHHHHHHHHh----c----CCCCCCCCCCHHHHHHHHHhccC
Q psy15598        112 SYIKELKQK---DPGIFAWEIRDRLLS----D----GVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       112 ~~I~~lv~~---nP~ita~EIr~~L~~----~----Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      +.+..++.+   +..++-..|++....    .    |..  .-..|..-+.++.++++.
T Consensus        87 ~~L~~Wi~~~~~~~~it~~~I~~kA~~i~~~l~~~~~~~--~f~~S~GWL~~Fk~Rh~i  143 (144)
T 1iuf_A           87 AALFEWQVQQGDDATLSGETIKRAAAILWHKIPEYQDQP--VPNFSNGWLEGFRKRHIL  143 (144)
T ss_dssp             HHHHHHHHHTCTTCCCSSHHHHHHHHHHHHHCSSSSCCC--CCSCCSHHHHHHHHHTSC
T ss_pred             HHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHhhccCCCC--CCCcCHHHHHHHHHHcCC
Confidence            888888876   334554444333321    1    211  123588888888887653

>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=97.23  E-value=0.00036  Score=58.71  Aligned_cols=43  Identities=7%  Similarity=0.013  Sum_probs=37.8

Q ss_pred             CCCCCHHHHHHHHHHHH-c--------CCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         45 GRPLPNSVRMRIVELAQ-L--------GIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~-~--------G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      -|.|+.+++..++.+.. .        |.+..+||+.||||++|+++|++.+
T Consensus        21 ~r~yt~EfK~aAv~l~~~~~~~p~~~~~lTv~eIA~~LGIS~~TLyrW~k~~   72 (155)
T 2ao9_A           21 KQKLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRTKN   72 (155)
T ss_dssp             HTTSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHHHC
T ss_pred             hhhcCHHHHHHHHHHHHccccccccccCCCHHHHHHHhCCCHHHHHHHHHcC
Confidence            56799999999987753 2        6899999999999999999999964

>1jhg_A Trp operon repressor; complex (regulatory protein-peptide), DNA-binding regulatory complex (regulatory protein-peptide) complex; HET: TRP; 1.30A {Escherichia coli} SCOP: a.4.12.1 PDB: 1co0_A* 1mi7_R 1p6z_R 1wrp_R* 1zt9_A* 2oz9_R* 3ssw_R 3wrp_A 1rcs_A* 1wrs_R* 1wrt_R 2xdi_A 3ssx_R* 1trr_A* 1tro_A*

Probab=97.23  E-value=0.0008  Score=52.86  Aligned_cols=36  Identities=17%  Similarity=0.277  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         52 VRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        52 lR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .|..|+.+..+| ++.++||+.+|||++||+|+ +|..
T Consensus        46 ~R~~l~~~L~~ge~TQREIA~~lGiS~stISRi-~r~L   82 (101)
T 1jhg_A           46 TRVRIIEELLRGEMSQRELKNELGAGIATITRG-SNSL   82 (101)
T ss_dssp             HHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHH-HHHH
T ss_pred             HHHHHHHHHHcCCcCHHHHHHHHCCChhhhhHH-HHHH
Confidence            346777777788 99999999999999999999 7765

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

Probab=97.21  E-value=0.00025  Score=53.08  Aligned_cols=70  Identities=16%  Similarity=0.211  Sum_probs=50.4

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l  117 (258)
                      ++...|.+|+.+..+ +++..+||+.+|+|++||++-++...+.|-+.....+...--.++++....+.+.
T Consensus        20 l~~~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~   90 (98)
T 3jth_A           20 MANERRLQILCMLHNQELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKL   90 (98)
T ss_dssp             HCSHHHHHHHHHTTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHH
Confidence            566789999998765 4799999999999999999999999999987544333212223444444444443

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

Probab=97.17  E-value=0.00026  Score=52.28  Aligned_cols=71  Identities=18%  Similarity=0.152  Sum_probs=49.9

Q ss_pred             CCHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      ++...|.+|+.+..+  +.+..+||+.||+|++||++.+++..+.|-+.-...++..--.++++....+.+.+
T Consensus        21 l~~~~~~~il~~l~~~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l   93 (99)
T 3cuo_A           21 MSHPKRLLILCMLSGSPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATL   93 (99)
T ss_dssp             HCSHHHHHHHHHHTTCCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHH
T ss_pred             hCChHHHHHHHHHHhCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHH
Confidence            455788889988754  48999999999999999999999999999875332222111234554444444443

>2o8x_A Probable RNA polymerase sigma-C factor; promoter recognition, transcription regulation, helix-turn-H motif, transcription; 3.00A {Mycobacterium tuberculosis}

Probab=97.17  E-value=0.00089  Score=46.53  Aligned_cols=43  Identities=19%  Similarity=0.233  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-+...+.+|++..+||+.||||.+||++++.+.++
T Consensus        15 ~L~~~~r~il~l~~~~g~s~~eIA~~lgis~~tv~~~~~ra~~   57 (70)
T 2o8x_A           15 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD   57 (70)
T ss_dssp             SSCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4777777555555679999999999999999999999999764

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

Probab=97.12  E-value=0.00049  Score=49.31  Aligned_cols=45  Identities=9%  Similarity=0.247  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHH-c--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         51 SVRMRIVELAQ-L--GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        51 dlR~RIV~L~~-~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      +.|.+|++++. +  .++..+||+.||||++||++.++..++.|.|..
T Consensus        10 ~~~~~IL~~L~~~~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~   57 (67)
T 2heo_A           10 NLEQKILQVLSDDGGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSS   57 (67)
T ss_dssp             HHHHHHHHHHHHHCSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEec
Confidence            46778988875 3  379999999999999999999999999998753

>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=97.10  E-value=0.00042  Score=56.33  Aligned_cols=43  Identities=16%  Similarity=0.152  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCC-CHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRV-SHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGV-SrsTVsRwikRyrE   89 (258)
                      .|+.++-.+|.+++..|.+.++||+.+|| |++||++|+++..+
T Consensus        12 k~t~e~~e~I~~~i~~G~sl~~i~~~~~~ps~~T~~~W~~~~~e   55 (140)
T 4dyq_A           12 DYMPEVADDICSLLSSGESLLKVCKRPGMPDKSTVFRWLAKHED   55 (140)
T ss_dssp             SCCTTHHHHHHHHHHTTCCHHHHHTSTTCCCHHHHHHHHHHCHH
T ss_pred             CCCHHHHHHHHHHHHCCCcHHHHHhcCCCCCHHHHHHHHHcCHH
Confidence            58999999999999999999999999999 99999999999754

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

Probab=97.04  E-value=0.00049  Score=51.92  Aligned_cols=51  Identities=20%  Similarity=0.296  Sum_probs=44.4

Q ss_pred             CCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         47 PLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      .++...|.+|+.+..+| ++..+||+.+|+|++||++-+++..+.|-|....
T Consensus        19 ~l~~~~r~~Il~~L~~~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~   70 (102)
T 3pqk_A           19 TLSHPVRLMLVCTLVEGEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRR   70 (102)
T ss_dssp             HHCSHHHHHHHHHHHTCCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEEC
T ss_pred             HcCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            35678899999998765 7999999999999999999999999999875433

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

Probab=96.97  E-value=0.00086  Score=50.87  Aligned_cols=48  Identities=15%  Similarity=0.232  Sum_probs=42.5

Q ss_pred             CHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         49 PNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ....+.+|+.++. +|.+..+||+.||||+++|++-+.+..+.|.|.-.
T Consensus        15 ~~~~~~~IL~lL~~~g~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~   63 (82)
T 1oyi_A           15 NAEIVCEAIKTIGIEGATAAQLTRQLNMEKREVNKALYDLQRSAMVYSS   63 (82)
T ss_dssp             SHHHHHHHHHHHSSSTEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEC
T ss_pred             hHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            3478899999875 68999999999999999999999999999988543

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

Probab=96.97  E-value=0.00068  Score=51.47  Aligned_cols=72  Identities=14%  Similarity=0.128  Sum_probs=51.1

Q ss_pred             CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      .++...|.+|+.+... +.+.++||+.||+|++||++.+++..+.|-|.....++..--.++++....+...+
T Consensus        17 ~l~~~~r~~IL~~L~~~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~gr~~~y~l~~~~~~~~~~~~   89 (114)
T 2oqg_A           17 ALSDETRWEILTELGRADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKVGREIRYRALGAELNKTARTL   89 (114)
T ss_dssp             HTTCHHHHHHHHHHHHSCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             HhCChHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecCCEEEEEechHHHHHHHHHH
Confidence            3556788899988754 58999999999999999999999999999875332221111235555444444443

>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=96.96  E-value=0.00093  Score=50.13  Aligned_cols=47  Identities=19%  Similarity=0.368  Sum_probs=40.6

Q ss_pred             CCHHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQ-LG----IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G----~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++.+...+|++++. .|    ++..+||+.||||++||.+.+.+.++.|.|.
T Consensus         7 ~~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~   58 (81)
T 1qbj_A            7 IYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   58 (81)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cchHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            45677788888875 45    7999999999999999999999999999874

>3hug_A RNA polymerase sigma factor; ECF sigma factor, zinc binding anti-sigma factor, oxidative transcription regulation; 2.35A {Mycobacterium tuberculosis}

Probab=96.96  E-value=0.0015  Score=48.67  Aligned_cols=42  Identities=21%  Similarity=0.183  Sum_probs=36.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||.+++.|-+
T Consensus        37 ~L~~~~r~vl~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~   78 (92)
T 3hug_A           37 QLSAEHRAVIQRSYYRGWSTAQIATDLGIAEGTVKSRLHYAV   78 (92)
T ss_dssp             TSCHHHHHHHHHHHTSCCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            367777766666678999999999999999999999998865

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

Probab=96.96  E-value=0.00018  Score=55.43  Aligned_cols=49  Identities=18%  Similarity=0.163  Sum_probs=41.6

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ++...|.+|+.++.+ +++.++||+.||||++||++.+++.++.|-|...
T Consensus        22 l~~~~r~~IL~~L~~~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~   71 (108)
T 2kko_A           22 LANGRRLQILDLLAQGERAVEAIATATGMNLTTASANLQALKSGGLVEAR   71 (108)
T ss_dssp             HTTSTTHHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             hCCHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            445667888888764 4799999999999999999999999999987543

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

Probab=96.91  E-value=0.0019  Score=47.00  Aligned_cols=42  Identities=19%  Similarity=0.249  Sum_probs=37.2

Q ss_pred             HHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      |.+|+.++.  ..++.++||+.||||++||++.+++..+.|-+.
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~   45 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQ   45 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            667888765  348999999999999999999999999999875

>2jpc_A SSRB; DNA binding protein, structural genomics, PSI-2, protein structure initiative; NMR {Salmonella typhimurium}

Probab=96.89  E-value=0.0013  Score=44.88  Aligned_cols=36  Identities=19%  Similarity=0.213  Sum_probs=32.0

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..|+.++.+|++.++||+.||||.+||+..+++-.+
T Consensus         4 ~~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~~~~~   39 (61)
T 2jpc_A            4 RQVLKLIDEGYTNHGISEKLHISIKTVETHRMNMMR   39 (61)
T ss_dssp             HHHHHHHHTSCCSHHHHHHTCSCHHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            467777889999999999999999999999998763

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

Probab=96.88  E-value=0.00039  Score=54.23  Aligned_cols=72  Identities=10%  Similarity=0.146  Sum_probs=53.5

Q ss_pred             CCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      .++...|.+|+.+..+| ++..+||+.||||++||++-++...+.|-|.....+..+--.++++....+.+++
T Consensus        14 al~~~~R~~Il~~L~~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~~   86 (118)
T 3f6o_A           14 ALADPTRRAVLGRLSRGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHKQGRVRTCAIEKEPFTAVEAWL   86 (118)
T ss_dssp             HHTSHHHHHHHHHHHTCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECSHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHhCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEecCCEEEEEECHHHHHHHHHHH
Confidence            46778999999998754 7999999999999999999999999999885443332122335555555554443

>1p4w_A RCSB; solution structure, DNA binding domain, DNA binding protein; NMR {Erwinia amylovora} SCOP: a.4.6.2

Probab=96.86  E-value=0.0022  Score=49.43  Aligned_cols=44  Identities=16%  Similarity=0.145  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ...++...| +|+.++.+|++.++||+.|+||.+||+..+++-.+
T Consensus        32 ~~~Lt~re~-~Vl~l~~~G~s~~EIA~~L~iS~~TV~~~l~ri~~   75 (99)
T 1p4w_A           32 DKRLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMM   75 (99)
T ss_dssp             SSSCCHHHH-HHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            456888877 56667779999999999999999999999998763

>2oa4_A SIR5; structure, structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; NMR {Silicibacter pomeroyi} SCOP: a.4.12.3

Probab=96.84  E-value=0.0013  Score=51.77  Aligned_cols=48  Identities=15%  Similarity=0.120  Sum_probs=40.2

Q ss_pred             CCCCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         45 GRPLPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      -|.-....+..||..+.. ++|..|+|+.|+||.++|.+|.+.|++.|.
T Consensus        31 ~rRWva~rK~~VV~~v~~g~lS~~EAa~ry~Is~~ei~~W~r~y~~~G~   79 (101)
T 2oa4_A           31 TRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGK   79 (101)
T ss_dssp             CSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCS
T ss_pred             HHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhH
Confidence            334444568889998875 589999999999999999999999998885

>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=96.83  E-value=0.0026  Score=45.33  Aligned_cols=43  Identities=9%  Similarity=0.009  Sum_probs=35.9

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-+...+-    +|++..+||+.+|||.+||++++.+-.+
T Consensus        10 ~L~~~er~il~l~~~l~~~~~~s~~eIA~~l~is~~tV~~~~~ra~~   56 (73)
T 1ku3_A           10 KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALR   56 (73)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHhcccCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            477888866666565    8999999999999999999999888653

>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=96.82  E-value=0.0021  Score=45.22  Aligned_cols=43  Identities=12%  Similarity=0.053  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-+...+    .+|++..+||+.+|||.+||..++.+-.+
T Consensus         5 ~L~~~er~il~l~~~l~~~~g~s~~eIA~~lgis~~tV~~~~~ra~~   51 (68)
T 2p7v_B            5 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALR   51 (68)
T ss_dssp             CCCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36777775555555    48999999999999999999999998764

>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=96.73  E-value=0.0013  Score=48.62  Aligned_cols=47  Identities=19%  Similarity=0.368  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHHH-cC----CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQ-LG----IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G----~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++.+...+|+.++. .|    ++..+||+.||||++||.+.+.+.++.|.|.
T Consensus        11 ~~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~   62 (77)
T 1qgp_A           11 IYQDQEQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQ   62 (77)
T ss_dssp             HHHHHHHHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            34566678887764 34    7999999999999999999999999999873

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

Probab=96.73  E-value=0.0015  Score=49.81  Aligned_cols=49  Identities=29%  Similarity=0.297  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         47 PLPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .++...|.+|+.++.+ +++..+||+.+|+|++||++.+++.++.|-+.-
T Consensus        22 ~l~~~~r~~IL~~L~~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~   71 (106)
T 1r1u_A           22 ALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKA   71 (106)
T ss_dssp             HTCSHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HhCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            3567789999988754 579999999999999999999999999998753

>1fse_A GERE; helix-turn-helix DNA-binding protein transcriptional regulat transcription; 2.05A {Bacillus subtilis} SCOP: a.4.6.2

Probab=96.71  E-value=0.0027  Score=44.47  Aligned_cols=42  Identities=19%  Similarity=0.184  Sum_probs=35.1

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..++...+ .|+.++.+|++..+||+.||||.+||++++++-.
T Consensus        10 ~~L~~~e~-~il~~~~~g~s~~eIA~~l~is~~tV~~~~~~~~   51 (74)
T 1fse_A           10 PLLTKRER-EVFELLVQDKTTKEIASELFISEKTVRNHISNAM   51 (74)
T ss_dssp             CCCCHHHH-HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            34666666 5566678899999999999999999999999965

>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=96.71  E-value=0.0032  Score=49.54  Aligned_cols=42  Identities=17%  Similarity=0.065  Sum_probs=37.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+.+|++..+||+.+|||.+||++++.+-+
T Consensus        22 ~L~~~~r~vl~l~y~~g~s~~EIA~~lgiS~~tV~~~l~ra~   63 (113)
T 1s7o_A           22 LLTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTE   63 (113)
T ss_dssp             GSCHHHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            478888876666678999999999999999999999999976

>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=96.70  E-value=0.0026  Score=46.75  Aligned_cols=42  Identities=21%  Similarity=0.288  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...| +|+.++.+|++.++||+.||||.+||++.+++-++
T Consensus        21 ~Lt~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   62 (82)
T 1je8_A           21 QLTPRER-DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK   62 (82)
T ss_dssp             GSCHHHH-HHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             cCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4677666 55556779999999999999999999999998763

>3neu_A LIN1836 protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, unknown function; 1.58A {Listeria innocua}

Probab=96.68  E-value=0.01  Score=46.99  Aligned_cols=100  Identities=16%  Similarity=0.190  Sum_probs=62.3

Q ss_pred             CCCCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIK  115 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~  115 (258)
                      ..++...+...|...+..|       + |.+++|++||||+.||++.+++..+.|-+...++.|.  .+.. ......+.
T Consensus        11 ~~~~~~~i~~~i~~~I~~g~~~~g~~Lps~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G~--~V~~~~~~~~~~~   88 (125)
T 3neu_A           11 DKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS--FVTSDKALFDQLK   88 (125)
T ss_dssp             SSCHHHHHHHHHHHHHHTTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEE--EECCCHHHHHHHH
T ss_pred             CCcHHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCeEEEecCCEE--EEecCchhhHHHH
Confidence            3455666667777776654       2 6999999999999999999999999998865554441  1111 22122111


Q ss_pred             HH-HHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598        116 EL-KQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       116 ~l-v~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      .. +..    .+..+...+...|+       +...|.+.+...
T Consensus        89 ~~~~~~----~le~~~~~~~~~g~-------~~~ei~~l~~~~  120 (125)
T 3neu_A           89 KELADA----ITERFLEEAKSIGL-------DDQTAIELLIKR  120 (125)
T ss_dssp             HHHHHH----HHHHHHHHHHHTTC-------CHHHHHHHHHHH
T ss_pred             HHHHHH----HHHHHHHHHHHcCC-------CHHHHHHHHHHH
Confidence            11 111    23344555555565       667777777654

>1y0u_A Arsenical resistance operon repressor, putative; structural genomics, protein structure initiative, PSI; HET: MSE; 1.60A {Archaeoglobus fulgidus} SCOP: a.4.5.5

Probab=96.68  E-value=0.0022  Score=47.87  Aligned_cols=47  Identities=21%  Similarity=0.208  Sum_probs=41.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++...|.+|+.+++.+++..+||+.|+||++||++.++...+.|-+.
T Consensus        28 l~~~~r~~Il~~L~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~   74 (96)
T 1y0u_A           28 VTNPVRRKILRMLDKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIE   74 (96)
T ss_dssp             HSCHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hCCHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            45677888998884458999999999999999999999999999874

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

Probab=96.67  E-value=0.0015  Score=51.34  Aligned_cols=49  Identities=20%  Similarity=0.195  Sum_probs=42.2

Q ss_pred             CCHHHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         48 LPNSVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ++...|.+|+.++. . +++.++||+.||+|++||++.++..++.|-+.-.
T Consensus        39 l~~~~rl~IL~~L~~~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~   89 (122)
T 1u2w_A           39 IADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFR   89 (122)
T ss_dssp             HHSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             hCCHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            45677889998875 4 5899999999999999999999999999987544

>3uj3_X DNA-invertase; helix-turn-helix, site-specific recombinase, recombination; 3.51A {Enterobacteria phage MU} PDB: 3plo_X

Probab=96.66  E-value=0.00028  Score=59.36  Aligned_cols=44  Identities=14%  Similarity=0.040  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      .++.+...+|++++.+|++..+||+.||||++||+||+++..+.
T Consensus       142 ~~~~~~~~~i~~l~~~G~s~~~Ia~~l~vs~~Tvyr~l~~~~~~  185 (193)
T 3uj3_X          142 KLTKAEWEQAGRLLAQGIPRKQVALIYDVALSTLYKKHPAKRAH  185 (193)
T ss_dssp             --------------------------------------------
T ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHhhhc
Confidence            35666777899999999999999999999999999999987643

>1tty_A Sigma-A, RNA polymerase sigma factor RPOD; helix-turn-helix, transcription; NMR {Thermotoga maritima} SCOP: a.4.13.2

Probab=96.62  E-value=0.0042  Score=45.96  Aligned_cols=43  Identities=9%  Similarity=0.009  Sum_probs=36.4

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-|+..+-    +|+|..+||+.||||.+||+.++.|-..
T Consensus        18 ~L~~~er~vl~l~~~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~   64 (87)
T 1tty_A           18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            478888866666665    8999999999999999999999998764

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

Probab=96.60  E-value=0.00055  Score=56.38  Aligned_cols=75  Identities=17%  Similarity=0.226  Sum_probs=57.0

Q ss_pred             CCCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         46 RPLPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++...|.+|+.++.. .++..+||+.||+|++||++-++..++.|-|...+.+..+--.++++....+.+.+..
T Consensus        53 ~aL~~p~R~~IL~~L~~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~Gr~~~y~lt~~~~~~l~~~l~~  128 (151)
T 3f6v_A           53 EVAAEPTRRRLVQLLTSGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDGRFRYYRLDPQGLAQLRALFDS  128 (151)
T ss_dssp             HHHTSHHHHHHHHHGGGCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHHHH
T ss_pred             HHhCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHHH
Confidence            34677899999999865 5899999999999999999999999999988644333212234677766666666543

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

Probab=96.55  E-value=0.0035  Score=50.61  Aligned_cols=39  Identities=15%  Similarity=0.267  Sum_probs=33.8

Q ss_pred             CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         49 PNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        49 S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      +...|.+|+.+..+|++.++||+.+|+|..||.|..+..
T Consensus        61 aLs~R~eV~klL~~G~syreIA~~~g~S~aTIsRv~r~L   99 (119)
T 3kor_A           61 SLSQRLQVAKMIKQGYTYATIEQESGASTATISRVKRSL   99 (119)
T ss_dssp             HHHHHHHHHHHHHHTCCHHHHHHHHCCCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence            345679999999999999999999999999999955544

>3frw_A Putative Trp repressor protein; structural genomics, APC21159, PSI-2, P structure initiative; 2.05A {Ruminococcus obeum atcc 29174} PDB: 3g1c_A

Probab=96.53  E-value=0.0035  Score=49.77  Aligned_cols=39  Identities=18%  Similarity=0.165  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ...|.+|+.+..+|++.++|++.+|+|.+||.|..+-.+
T Consensus        45 laqR~~Ia~lL~~G~SyreIa~~tG~StaTIsRv~r~L~   83 (107)
T 3frw_A           45 LSQRFEVAKMLTDKRTYLDISEKTGASTATISRVNRSLN   83 (107)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCccHHHHHHHHHHHH
Confidence            457899999999999999999999999999999887765

>1zx4_A P1 PARB, plasmid partition PAR B protein, PARB; translation; HET: CIT; 2.98A {Enterobacteria phage P1} PDB: 2ntz_A

Probab=96.52  E-value=0.0045  Score=53.58  Aligned_cols=48  Identities=15%  Similarity=0.210  Sum_probs=39.6

Q ss_pred             CCCCCCH-HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh-hhC
Q psy15598         44 NGRPLPN-SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH-ETG   91 (258)
Q Consensus        44 ~gR~~S~-dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr-EtG   91 (258)
                      ..|++|. ++-.++..++..|++..+||+.||||+.+|+||+++.+ +.|
T Consensus         4 Take~sl~eiG~ria~~y~~g~tQ~eIA~~lGiSr~~VSR~L~~A~~~~~   53 (192)
T 1zx4_A            4 TALQHSIREIGLRLMRMKNDGMSQKDIAAKEGLSQAKVTRALQAASAPEE   53 (192)
T ss_dssp             -CCSSCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHTSCHH
T ss_pred             ccccccHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHhccchh
Confidence            3566676 45577778888999999999999999999999999987 444

>2w7n_A TRFB transcriptional repressor protein; INCP, plasmid, repressor, DNA-binding, transcription/DNA; HET: BRU; 1.85A {Escherichia coli}

Probab=96.43  E-value=0.0058  Score=47.84  Aligned_cols=37  Identities=19%  Similarity=0.257  Sum_probs=32.4

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      .+|..++ .+|++..+||+.||||+.+|+|.+++.++.
T Consensus        24 ~~~A~lyYv~g~tQ~eIA~~lGiSR~~VsrlL~~Ar~~   61 (101)
T 2w7n_A           24 IEIARGVLVDGKPQATFATSLGLTRGAVSQAVHRVWAA   61 (101)
T ss_dssp             HHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            4566665 589999999999999999999999999865

>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=96.42  E-value=0.0048  Score=48.33  Aligned_cols=41  Identities=10%  Similarity=0.092  Sum_probs=35.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++ ++-+|++..+||+.||||.+||++++.|-+
T Consensus       109 ~L~~~~r~v~~-~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  149 (164)
T 3mzy_A          109 NFSKFEKEVLT-YLIRGYSYREIATILSKNLKSIDNTIQRIR  149 (164)
T ss_dssp             HSCHHHHHHHH-HHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            47788887666 777999999999999999999999998865

>2vz4_A Tipal, HTH-type transcriptional activator TIPA; transcription, resistance, antibiotic; 2.90A {Streptomyces lividans}

Probab=96.41  E-value=0.011  Score=45.68  Aligned_cols=68  Identities=10%  Similarity=0.055  Sum_probs=48.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++..++|+.+|||.+|++.|-+.    |.+.|..+..+.-+..++++...|..... .+-.+++.+|+..|.
T Consensus         1 ~~~i~e~A~~~gvs~~tLR~ye~~----Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~   69 (108)
T 2vz4_A            1 SYSVGQVAGFAGVTVRTLHHYDDI----GLLVPSERSHAGHRRYSDADLDRLQQILFYRELGFPLDEVAALLD   69 (108)
T ss_dssp             CBCHHHHHHHHTCCHHHHHHHHHH----TSSCCSEECSSCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHT
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHC----CCCCCCccCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            468899999999999999988654    87766543212347788877665554432 234788889988774

>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=96.40  E-value=0.0074  Score=45.46  Aligned_cols=42  Identities=17%  Similarity=0.275  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|. |+.++.+|++.++||+.||||.+||+..+++-++
T Consensus        27 ~Lt~~e~~-vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   68 (95)
T 3c57_A           27 GLTDQERT-LLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLLA   68 (95)
T ss_dssp             CCCHHHHH-HHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            47777774 5555689999999999999999999999988764

>1x3u_A Transcriptional regulatory protein FIXJ; helix-turn-helix; NMR {Sinorhizobium meliloti}

Probab=96.38  E-value=0.0057  Score=43.52  Aligned_cols=41  Identities=20%  Similarity=0.200  Sum_probs=33.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...| .|+.++.+|++..+||+.||||.+||++++.+-++
T Consensus        17 L~~~e~-~vl~l~~~g~s~~eIA~~l~is~~tV~~~~~r~~~   57 (79)
T 1x3u_A           17 LSERER-QVLSAVVAGLPNKSIAYDLDISPRTVEVHRANVMA   57 (79)
T ss_dssp             HCHHHH-HHHHHHTTTCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            455555 45555678999999999999999999999998764

>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=96.38  E-value=0.002  Score=47.36  Aligned_cols=72  Identities=15%  Similarity=0.077  Sum_probs=50.4

Q ss_pred             CCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      .++...|.+|+....  .+++.++||+.+++|++||++.+++..+.|-+.-..  ..+ ..--.+|++-.+.+.++.
T Consensus        12 ~l~~~~~~~iL~~L~~~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~~~~~~~r~~~~~lt~~g~~~~~~~~   88 (100)
T 1ub9_A           12 ILGNPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             HHHSHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             ccCChHHHHHHHHHHhcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCCcceEEEEECHHHHHHHHHHH
Confidence            345567888888653  468999999999999999999999999999874211  112 112236776555554443

>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=96.37  E-value=0.0058  Score=47.86  Aligned_cols=42  Identities=19%  Similarity=0.111  Sum_probs=36.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-+...+.+|++..+||+.||||.+||++++.|-+
T Consensus        25 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgiS~~tV~~~l~ra~   66 (113)
T 1xsv_A           25 LLTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTG   66 (113)
T ss_dssp             GSCHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            477777766666667999999999999999999999999875

>2jml_A DNA binding domain/transcriptional regulator; anti-repressor, MERR, carotenogenesis; HET: DNA; NMR {Myxococcus xanthus}

Probab=96.34  E-value=0.0081  Score=44.03  Aligned_cols=68  Identities=16%  Similarity=0.155  Sum_probs=46.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC-CCCCCCCCHHHHHHHHHHHH-h-CCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG-GSKPRVTTPKVVSYIKELKQ-K-DPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg-G~RPrklT~e~~~~I~~lv~-~-nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||.+|++.|.++   .|.+.|.... + .-+..++++...|..++. . +-.+++.+|++.|..
T Consensus         6 ~~i~e~A~~~gvs~~tlR~ye~~---~gl~~p~r~~~~-g~R~Y~~~dl~~l~~I~~l~~~~G~sl~ei~~~l~~   76 (81)
T 2jml_A            6 LRIRTIARMTGIREATLRAWERR---YGFPRPLRSEGN-NYRVYSREEVEAVRRVARLIQEEGLSVSEAIAQVKT   76 (81)
T ss_dssp             EEHHHHHHTTSTTHHHHHHHHHH---TCCSCCBSSSCS-SSCEECHHHHHHHHHHHHHHHHTSTHHHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHHh---CCCCCCcCCCCC-CeeecCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHc
Confidence            57899999999999999988665   2555554332 3 456788877765544432 1 346778888777754

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

Probab=96.34  E-value=0.002  Score=48.82  Aligned_cols=47  Identities=21%  Similarity=0.386  Sum_probs=39.7

Q ss_pred             CCCHHHHHHHH-HHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         47 PLPNSVRMRIV-ELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        47 ~~S~dlR~RIV-~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+++..|.+|+ .+.. .+++.++||+.+|+|++||++-++..++. -+.
T Consensus        23 aL~~~~Rl~IL~~l~~~~~~~~~ela~~l~is~stvs~hL~~L~~~-lv~   71 (99)
T 2zkz_A           23 TMAHPMRLKIVNELYKHKALNVTQIIQILKLPQSTVSQHLCKMRGK-VLK   71 (99)
T ss_dssp             HHCSHHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHBTT-TBE
T ss_pred             HhCCHHHHHHHHHHHHCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH-hhh
Confidence            35678899999 4554 45899999999999999999999999988 654

>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=96.30  E-value=0.013  Score=40.09  Aligned_cols=45  Identities=20%  Similarity=0.088  Sum_probs=37.0

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      ...|..++..+..+++.||.+.|.+.|..+     |.+||+|.|+..+..
T Consensus         7 ~~~i~~ll~~~~~~t~~el~~~l~~~~~~v-----s~~Tv~R~L~~lg~v   51 (64)
T 2p5k_A            7 HIKIREIITSNEIETQDELVDMLKQDGYKV-----TQATVSRDIKELHLV   51 (64)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHHTTCCC-----CHHHHHHHHHHHTCE
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHHHHhCCCc-----CHHHHHHHHHHcCCE
Confidence            345667777888899999999999888775     999999999966543

>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=96.29  E-value=0.015  Score=36.66  Aligned_cols=45  Identities=11%  Similarity=0.144  Sum_probs=36.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      ||..++++....|..+..+  .++..+|++.|.          +|.+||+++|++..
T Consensus         2 R~~~l~~~~~~~i~~~~~~--g~s~~~IA~~lg----------is~~Tv~~~~~~~~   46 (51)
T 1tc3_C            2 RGSALSDTERAQLDVMKLL--NVSLHEMSRKIS----------RSRHCIRVYLKDPV   46 (51)
T ss_dssp             CSCCCCHHHHHHHHHHHHT--TCCHHHHHHHHT----------CCHHHHHHHHHCST
T ss_pred             CCCCCCHHHHHHHHHHHHc--CCCHHHHHHHHC----------cCHHHHHHHHhhHH
Confidence            7788898888788877654  578999988873          49999999998654

>3e7l_A Transcriptional regulator (NTRC family); sigma43 activator, AAA+ ATPase, response regulator, transcriptional activator, ATP-binding; 2.25A {Aquifex aeolicus} PDB: 4fth_A

Probab=96.26  E-value=0.0076  Score=42.32  Aligned_cols=38  Identities=5%  Similarity=0.033  Sum_probs=31.6

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      -.|..|..+++ .+...+++|+.||||++|+++++++|.
T Consensus        19 ~E~~~i~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~g   57 (63)
T 3e7l_A           19 FEKIFIEEKLREYDYDLKRTAEEIGIDLSNLYRKIKSLN   57 (63)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHTCCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            35666666665 577899999999999999999999984

>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=96.23  E-value=0.032  Score=44.89  Aligned_cols=67  Identities=13%  Similarity=0.136  Sum_probs=47.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++.|-+    .|.+.|..+..+.-|..++++...|..... .+-.+++.+|++.|.
T Consensus         1 ~~I~e~A~~~gvs~~tLR~ye~----~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~   68 (135)
T 1q06_A            1 MNISDVAKITGLTSKAIRFYEE----KGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (135)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----TTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence            5788999999999999987754    577765433222457788877665554432 234789999998886

>2rnj_A Response regulator protein VRAR; HTH LUXR-type domain, DNA binding domain, activator, antibiotic resistance, cytoplasm, DNA-binding; NMR {Staphylococcus aureus}

Probab=96.22  E-value=0.0047  Score=45.86  Aligned_cols=42  Identities=14%  Similarity=0.097  Sum_probs=34.9

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|. |+.++.+|++..+||+.||||.+||+.++++-++
T Consensus        29 ~Lt~~e~~-vl~l~~~g~s~~eIA~~l~is~~tV~~~l~r~~~   70 (91)
T 2rnj_A           29 MLTEREME-ILLLIAKGYSNQEIASASHITIKTVKTHVSNILS   70 (91)
T ss_dssp             GCCSHHHH-HHHHHHTTCCTTHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            36666664 5555689999999999999999999999998764

>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=96.19  E-value=0.0093  Score=44.89  Aligned_cols=42  Identities=17%  Similarity=0.184  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...+ .|+.++.+|++..+||+.|+||.+||...+++-.+
T Consensus        29 ~Lt~rE~-~Vl~l~~~G~s~~eIA~~L~iS~~TV~~~~~~i~~   70 (90)
T 3ulq_B           29 VLTPREC-LILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFN   70 (90)
T ss_dssp             CCCHHHH-HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            4676666 46677779999999999999999999999988753

>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=96.14  E-value=0.0081  Score=42.11  Aligned_cols=41  Identities=15%  Similarity=0.105  Sum_probs=33.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +....|..|..+++.....+++|+.||||++|+++++++|.
T Consensus        18 l~~~Er~~I~~aL~~~gn~~~aA~~LGIsr~tL~rklkk~g   58 (61)
T 1g2h_A           18 IGFYEAQVLKLFYAEYPSTRKLAQRLGVSHTAIANKLKQYG   58 (61)
T ss_dssp             CSHHHHHHHHHHHHHSCSHHHHHHHTTSCTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            55667777777776446889999999999999999999984

>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=96.12  E-value=0.0067  Score=44.70  Aligned_cols=48  Identities=13%  Similarity=0.257  Sum_probs=39.3

Q ss_pred             CCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         47 PLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .++...+..++.+..  .+.+..+||+.||||++||++.+++..+.|-+.
T Consensus        18 ~l~~~~~~~l~~l~~~~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~   67 (109)
T 2d1h_A           18 KITDTDVAVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVV   67 (109)
T ss_dssp             TCCHHHHHHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            456665555656654  468999999999999999999999999999774

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

Probab=96.12  E-value=0.0059  Score=46.88  Aligned_cols=46  Identities=15%  Similarity=0.257  Sum_probs=40.1

Q ss_pred             CHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         49 PNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        49 S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ....|.+|+.++.+ +.+.++||+.|+||++||++.+++..+.|.+.
T Consensus        30 ~~~~~~~il~~L~~~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~   76 (119)
T 2lkp_A           30 ATPSRLMILTQLRNGPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVV   76 (119)
T ss_dssp             CCHHHHHHHHHHHHCCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEE
T ss_pred             CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            34677888887765 79999999999999999999999999999764

>3gp4_A Transcriptional regulator, MERR family; structural genomics, DNA-BI transcription regulator, PSI-2; 1.85A {Listeria monocytogenes str}

Probab=96.11  E-value=0.048  Score=44.38  Aligned_cols=67  Identities=19%  Similarity=0.105  Sum_probs=48.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +++.++|+.+|||..|++.|-+.    |.+.|..+..+.-|..++++...|..++. ..-.+++.+|++.|.
T Consensus         3 ~~I~e~A~~~gvs~~tLR~Ye~~----GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~   70 (142)
T 3gp4_A            3 LNIKEASEKSGVSADTIRYYERI----GLIPPIHRNESGVRKFGAEDLRWILFTRQMRRAGLSIEALIDYLA   70 (142)
T ss_dssp             BCHHHHHHHHTSCHHHHHHHHHH----TSSCCCCBCTTSCBCBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            68899999999999999877554    77877334322457788877665544432 334889999988875

>1r1t_A Transcriptional repressor SMTB; zinc, transcriptional regulation, winged HTH protein, DNA binding, transcription repressor; 1.70A {Synechococcus elongatus pcc 7942} SCOP: a.4.5.5 PDB: 1r23_A 1smt_A 1r22_A

Probab=96.09  E-value=0.0037  Score=49.33  Aligned_cols=48  Identities=21%  Similarity=0.274  Sum_probs=41.7

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++...|.+|+.+..+ +++..+||+.||+|++||++.+++.++.|-+.-
T Consensus        43 L~~~~rl~IL~~L~~~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~   91 (122)
T 1r1t_A           43 LADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSY   91 (122)
T ss_dssp             HCCHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            556678889988765 589999999999999999999999999998753

>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=96.07  E-value=0.0053  Score=51.05  Aligned_cols=33  Identities=18%  Similarity=0.396  Sum_probs=30.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..|.+++.+|++..+||+.||||++||++|+++
T Consensus       149 ~~i~~~~~~G~s~~~Ia~~l~is~~tv~r~l~~  181 (183)
T 1gdt_A          149 DAVLNMWQQGLGASHISKTMNIARSTVYKVINE  181 (183)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhh
Confidence            468888899999999999999999999999975

>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=96.05  E-value=0.0097  Score=48.32  Aligned_cols=42  Identities=26%  Similarity=0.320  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...|.-++..+-+|+|..+||+.||||.+||.+++.|-++
T Consensus       141 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~  182 (194)
T 1or7_A          141 LPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRARE  182 (194)
T ss_dssp             SCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHhHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            677777655555679999999999999999999999998753

>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=96.03  E-value=0.0038  Score=40.32  Aligned_cols=45  Identities=20%  Similarity=0.205  Sum_probs=34.4

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      ||+.++++....|.++..+.  .+..+|++.|   |       +|.+||+|+|++..
T Consensus         2 Rp~~~~~~~~~~i~~l~~~g--~s~~~ia~~l---g-------vs~~Tv~r~l~~~~   46 (52)
T 1jko_C            2 RPRAINKHEQEQISRLLEKG--HPRQQLAIIF---G-------IGVSTLYRYFPASS   46 (52)
T ss_dssp             CCCSSCTTHHHHHHHHHHTT--CCHHHHHHTT---S-------CCHHHHHHHSCTTC
T ss_pred             CCCCCCHHHHHHHHHHHHcC--CCHHHHHHHH---C-------CCHHHHHHHHHHcc
Confidence            77788877777888876653  7888887665   4       49999999998654

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

Probab=96.01  E-value=0.0044  Score=47.16  Aligned_cols=46  Identities=20%  Similarity=0.239  Sum_probs=39.3

Q ss_pred             HHHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         51 SVRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        51 dlR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      +.+.+|+... ..|  ++.++||+.||||++||++-+++..+.|-+.-.
T Consensus        18 ~~~l~Il~~l~~~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           18 DDVIDVLRILLDKGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             STTHHHHHHHHHHCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             hHHHHHHHHHHHcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4677888775 444  799999999999999999999999999987544

>1b4a_A Arginine repressor; helix turn helix; 2.50A {Geobacillus stearothermophilus} SCOP: a.4.5.3 d.74.2.1 PDB: 1f9n_A

Probab=95.97  E-value=0.012  Score=48.93  Aligned_cols=52  Identities=17%  Similarity=0.092  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      +-.+.|++++.++...+..||++.|++.|+.+     |.+||+|-|++++..|....
T Consensus         5 ~R~~~I~~li~~~~~~tq~eL~~~L~~~G~~V-----tqaTisRDL~eL~~vKv~~~   56 (149)
T 1b4a_A            5 QRHIKIREIIMSNDIETQDELVDRLREAGFNV-----TQATVSRDIKEMQLVKVPMA   56 (149)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCC-----CHHHHHHHHHHTTCEEEECS
T ss_pred             HHHHHHHHHHHHCCCccHHHHHHHHHHcCCCc-----CHHHHHHHHHHcCCeEEECC
Confidence            34678999999999999999999999999986     99999999999999987653

>2vxz_A Pyrsv_GP04; viral protein, SSPF, ORF165A; 1.7A {Pyrobaculum spherical virus}

Probab=95.97  E-value=0.024  Score=47.74  Aligned_cols=102  Identities=15%  Similarity=0.126  Sum_probs=67.6

Q ss_pred             CCCCCCH---HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH
Q psy15598         44 NGRPLPN---SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        44 ~gR~~S~---dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~  119 (258)
                      |++..+.   +.|.+|+++..+| .+..+||+.||+|.+.|.-.+.-...+|-+..-++|..+--.+.+.  +++. .+.
T Consensus         1 MPrk~Td~v~erk~~ILE~Lk~G~~~t~~Iak~LGlShg~aq~~Ly~LeREG~V~~Vk~GK~ayw~L~~s--~y~~-kV~   77 (165)
T 2vxz_A            1 MPIGHSREVLVRLRDILALLADGCKTTSLIQQRLGLSHGRAKALIYVLEKEGRVTRVAFGNVALVCLSMD--QYRQ-LVD   77 (165)
T ss_dssp             ----CCHHHHHHHHHHHHHHTTCCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSCEEEEETTEEEEESCHH--HHHH-HHH
T ss_pred             CCcchhHHHHHHHHHHHHHHHhCCccHHHHHHHhCCcHHHHHHHHHHHHhcCceEEEEEccEEEEEecHH--HHHH-HHH
Confidence            4455555   5678899988877 6999999999999999999999999999875444443222334433  2322 111


Q ss_pred             hCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        120 KDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       120 ~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      .    ..+|+-..|.+.|+..    ++.+-..|.+..
T Consensus        78 d----ilrel~~~l~s~gvk~----i~p~~l~~li~~  106 (165)
T 2vxz_A           78 G----MIREVERLVTTNKLKF----ISPPRLHDLIIK  106 (165)
T ss_dssp             H----HHHHHHHHHHHTTCSE----ECHHHHHHHHHH
T ss_pred             H----HHHHHHHHHHHcCCee----eCcHHHHHHHHh
Confidence            1    2345555566778876    788877777654

>2l0k_A Stage III sporulation protein D; SPOIIID, solution structure, DNA binding, bacillus subti transcription factor, transcription; NMR {Bacillus subtilis}

Probab=95.95  E-value=0.0085  Score=46.06  Aligned_cols=39  Identities=18%  Similarity=0.118  Sum_probs=32.5

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +..+-+.+|++++. .+.+..+||+.+|||.+||+|+++.
T Consensus         4 ~~~~R~~~I~~~l~~~~~ti~dlA~~~gVS~~TVsR~L~~   43 (93)
T 2l0k_A            4 YIKERTIKIGKYIVETKKTVRVIAKEFGVSKSTVHKDLTE   43 (93)
T ss_dssp             THHHHHHHHHHHHHHHCCCHHHHHHHHTSCHHHHHHHHTT
T ss_pred             cHHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence            44566677888775 5899999999999999999999864

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=95.95  E-value=0.0075  Score=48.25  Aligned_cols=55  Identities=16%  Similarity=0.122  Sum_probs=41.6

Q ss_pred             CCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         46 RPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .++...+...|...+..|.        +.+++|++||||++||++-+++..+.|-+...++.|
T Consensus         3 ~~~~~~i~~~i~~~I~~g~l~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g~G   65 (129)
T 2ek5_A            3 VPLYKQIASLIEDSIVDGTLSIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRGIG   65 (129)
T ss_dssp             CCHHHHHHHHHHHHHHTTSSCTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETTTE
T ss_pred             CcHHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCE
Confidence            3444555555666655442        899999999999999999999999999886555444

>3ic7_A Putative transcriptional regulator; helix-turn-helix, structural genomics, PSI-2, protein struct initiative; 2.82A {Bacteroides thetaiotaomicron}

Probab=95.92  E-value=0.0074  Score=47.89  Aligned_cols=103  Identities=15%  Similarity=0.125  Sum_probs=64.7

Q ss_pred             CCCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      ...++...+-..|...+..|.        +.+++|+.||||+.||++-+++..+.|-+...++.|   ....+.....+.
T Consensus         8 ~~~~~~~~i~~~l~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~~~G---~~V~~~~~~~~~   84 (126)
T 3ic7_A            8 ESRAIYLQIADRICDDILLGQYEEEGRIPSVREYASIVEVNANTVMRSYEYLQSQEVIYNKRGIG---FFVASGAKMLIH   84 (126)
T ss_dssp             ----CTTHHHHHHHHHHHTTSSCBTSEECCTTTTTTCC-CCSGGGHHHHHHHHTTTSEEEETTTE---EEECTTHHHHHH
T ss_pred             CCCCHHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEcCCc---cEEccCcHHHHH
Confidence            345566666667777665542        788999999999999999999999999886555444   222333344444


Q ss_pred             HHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        116 ELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       116 ~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      +..+.. -...+..+...+...|+       +...+...+..
T Consensus        85 ~~~~~~~~~~~le~~~~~~~~~~~-------~~~~l~~l~~~  119 (126)
T 3ic7_A           85 SLRKEQFLKEEVGSFFRQLYTLGI-------SIKEIEKMYYE  119 (126)
T ss_dssp             HHHHTTCCCCCSHHHHHHHHHTTC-------CHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCC-------CHHHHHHHHHH
Confidence            544332 23345566666666665       56677666654

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

Probab=95.90  E-value=0.013  Score=42.40  Aligned_cols=44  Identities=20%  Similarity=0.446  Sum_probs=38.6

Q ss_pred             HHHHHHHHHHHc----CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQL----GIRPCDISRQL-----RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~----G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|..|++++.+    .++..+|++.|     +||.+||||.++.+.+.|-+.
T Consensus        17 ~~r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~   69 (83)
T 2fu4_A           17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVT   69 (83)
T ss_dssp             HHHHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeE
Confidence            577888888742    47999999999     999999999999999999874

>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=95.89  E-value=0.0073  Score=51.28  Aligned_cols=35  Identities=20%  Similarity=0.321  Sum_probs=31.2

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|++++.+|++..+||+.||||++||+||+++..
T Consensus       166 ~~i~~~~~~G~s~~~Ia~~l~is~~tv~r~l~~~~  200 (209)
T 2r0q_C          166 HRVVEMLEEGQAISKIAKEVNITRQTVYRIKHDNG  200 (209)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHTTCC
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhccc
Confidence            46778888999999999999999999999998653

>1r8d_A Transcription activator MTAN; protein-DNA complex, transcription/DNA complex; 2.70A {Bacillus subtilis} SCOP: a.6.1.3 PDB: 1jbg_A

Probab=95.84  E-value=0.024  Score=43.75  Aligned_cols=67  Identities=15%  Similarity=0.103  Sum_probs=47.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|.+    .|.+.|..+..+..+..++++...|..... .+-.+++.+|+..|.
T Consensus         3 ~~i~e~A~~~gvs~~tLR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~~I~~~l~   70 (109)
T 1r8d_A            3 YQVKQVAEISGVSIRTLHHYDN----IELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLD   70 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHHH----TTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----CCCCCCCeECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence            5789999999999999998854    587766543222347788887766554432 233778899988775

>1z4h_A TORI, TOR inhibition protein; winged helix, reverse turn, protein binding, DNA binding protein; NMR {Escherichia coli}

Probab=95.84  E-value=0.0051  Score=43.61  Aligned_cols=51  Identities=12%  Similarity=0.127  Sum_probs=35.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      ++..+||+.||||++|||+|+++-    .+ |+  +.|+ +-+-...+++++|.+....
T Consensus        11 l~~~eva~~lgvsrstiy~~~~~g----~f-P~piklG~-~~~w~~~ev~~Wl~~~~~~   63 (66)
T 1z4h_A           11 VDLKFIMADTGFGKTFIYDRIKSG----DL-PKAKVIHG-RARWLYRDHCEFKNKLLSR   63 (66)
T ss_dssp             ECHHHHHHHHSSCHHHHHHHHHHH----HC-CCSEESSS-CEEEEHHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHCC----CC-CCCEEeCC-CeEEeHHHHHHHHHHHHHh
Confidence            578999999999999999999963    33 33  2343 3344446667777665543

>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=95.82  E-value=0.0096  Score=44.76  Aligned_cols=38  Identities=11%  Similarity=0.003  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|..|..+++ .|...+++|+.||||++|+++++++|.
T Consensus        51 ~E~~~i~~aL~~~~gn~~~aA~~LGIsr~tL~rklkk~~   89 (91)
T 1ntc_A           51 LERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHhC
Confidence            35566666665 467888999999999999999999984

>3by6_A Predicted transcriptional regulator; structural genomics, PSI-2, MCSG, structure initiative, midwest center for structural genomic binding; 2.20A {Oenococcus oeni}

Probab=95.81  E-value=0.016  Score=45.98  Aligned_cols=53  Identities=13%  Similarity=0.036  Sum_probs=40.3

Q ss_pred             CCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         48 LPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +...+...|...+..|       + +.+++|+.||||+.||++-+++..+.|.+...++.|
T Consensus        12 ~~~~i~~~l~~~I~~g~~~~G~~lPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   72 (126)
T 3by6_A           12 VYLQLVDRIKNEVATDVLSANDQLPSVRETALQEKINPNTVAKAYKELEAQKVIRTIPGKG   72 (126)
T ss_dssp             HHHHHHHHHHHHHHTTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            3444555555555544       2 899999999999999999999999999886555444

>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=95.79  E-value=0.039  Score=41.67  Aligned_cols=79  Identities=13%  Similarity=0.123  Sum_probs=53.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVC  139 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~  139 (258)
                      .+..+..+||+.+|+|++++++..++.-  |.         .|.... ..-.+...+++. +++.+..||+..+   |..
T Consensus        19 ~~~~~~~~lA~~~~~S~~~l~r~fk~~~--G~---------s~~~~~~~~Rl~~A~~lL~-~~~~si~~IA~~~---Gf~   83 (108)
T 3oou_A           19 SEGMSLKTLGNDFHINAVYLGQLFQKEM--GE---------HFTDYLNRYRVNYAKEELL-QTKDNLTIIAGKS---GYT   83 (108)
T ss_dssp             TSCCCHHHHHHHHTSCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHT---TCC
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCCCCHHHHHHHc---CCC
Confidence            3568999999999999999999999874  21         111111 111222333333 4677888886655   775


Q ss_pred             CCCCCCCHHHHHHHHHhccCC
Q psy15598        140 DKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       140 v~~~~pS~STI~RiLrr~~~~  160 (258)
                            +.+...|.+++.-+.
T Consensus        84 ------~~s~F~r~Fk~~~G~   98 (108)
T 3oou_A           84 ------DMAYFYRQFKKHTGE   98 (108)
T ss_dssp             ------CHHHHHHHHHHHHSS
T ss_pred             ------ChHHHHHHHHHHhCc
Confidence                  889999999876543

>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=95.79  E-value=0.015  Score=48.33  Aligned_cols=43  Identities=19%  Similarity=0.209  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..++...|.-|+..+-+|++..+||+.||||.+||++++.|-+
T Consensus       186 ~~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~~V~~~~~ra~  228 (239)
T 1rp3_A          186 SKLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKAL  228 (239)
T ss_dssp             TTSCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHH
T ss_pred             HcCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3478888866666667999999999999999999999998865

>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=95.78  E-value=0.029  Score=44.97  Aligned_cols=43  Identities=16%  Similarity=0.297  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+.+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus         7 ~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   51 (151)
T 2cyy_A            7 EIDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVI   51 (151)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            34557887765 4 4899999999999999999999999999976

>4ham_A LMO2241 protein; structural genomics, PSI-biology, midwest center for structu genomics, MCSG, winged helix-turn-helix, four helix bundle; 1.91A {Listeria monocytogenes}

Probab=95.70  E-value=0.16  Score=40.25  Aligned_cols=54  Identities=20%  Similarity=0.249  Sum_probs=40.3

Q ss_pred             CCCHHHHHHHHHHHHc-----C--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         47 PLPNSVRMRIVELAQL-----G--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~-----G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      |+-..+...|......     |  + +.+++|++||||+.||++-+++-...|-+...++.|
T Consensus        14 PlY~QI~~~i~~~I~~G~l~pG~~LPser~La~~~gVSr~tVReAl~~L~~eGlv~~~~g~G   75 (134)
T 4ham_A           14 PIYEQIVQKIKEQVVKGVLQEGEKILSIREFASRIGVNPNTVSKAYQELERQEVIITVKGKG   75 (134)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CHHHHHHHHHHHHHHcCCCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCcE
Confidence            4444455555555443     4  2 789999999999999999999999999886555444

>2dg6_A Putative transcriptional regulator; winged-helix motif, MERR family, gene regulation; 2.20A {Streptomyces coelicolor}

Probab=95.65  E-value=0.099  Score=45.79  Aligned_cols=87  Identities=14%  Similarity=0.100  Sum_probs=54.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hC-CCCCHHHHHHHHHh--cCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KD-PGIFAWEIRDRLLS--DGVC  139 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~n-P~ita~EIr~~L~~--~Gv~  139 (258)
                      +++.++|+.+|||.+||+.|-+    .|.+.|..+..+.-+..++++...|..++. .+ -.+++.+|++.|..  .|-.
T Consensus         1 ~~IgevA~~~Gvs~~TLRyYE~----~GLl~p~~R~~~gyR~Y~~~dl~~L~~I~~lr~~~G~sL~eIk~~l~~~~~~~~   76 (222)
T 2dg6_A            1 MRLADLSKRSGVSTATIKYYLR----EGLLPPGRQVNATTAEYDEDHLRRLRLVRALIQVGKVPVATAREVLGHVDDDSL   76 (222)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHH----HTSSCCC---------CCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHTCCSS
T ss_pred             CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCeeCCCCceeeCHHHHHHHHHHHHHHHcCCCCHHHHHHHHHhhhcCCC
Confidence            5789999999999999987754    477766444322457788888777766644 22 37899999998874  2321


Q ss_pred             CCCCCCCHHHHHHHHHhccCC
Q psy15598        140 DKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       140 v~~~~pS~STI~RiLrr~~~~  160 (258)
                            +...+...+......
T Consensus        77 ------~~~~~l~~~~~~l~~   91 (222)
T 2dg6_A           77 ------GRTVRLGAALWALPQ   91 (222)
T ss_dssp             ------CHHHHHHHHHTTSCC
T ss_pred             ------CHHHHHHHHHHHhcc
Confidence                  445565666554443

>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=95.64  E-value=0.024  Score=43.94  Aligned_cols=42  Identities=17%  Similarity=0.219  Sum_probs=36.0

Q ss_pred             CCCCHHHHHHHHHHHHc-CCCHHHHHHHhC--CCHHHHHHHHHHh
Q psy15598         46 RPLPNSVRMRIVELAQL-GIRPCDISRQLR--VSHGCVSKILARY   87 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~-G~S~~eIAr~LG--VSrsTVsRwikRy   87 (258)
                      +.++.+....|+.+..+ ..+..+|+..||  ||.+||++|+++.
T Consensus        59 ~~l~~~~~~~i~~~~~~~~~s~~~i~~~lg~~~s~~tV~r~l~~~  103 (141)
T 1u78_A           59 KALSVRDERNVIRAASNSCKTARDIRNELQLSASKRTILNVIKRS  103 (141)
T ss_dssp             CSSCHHHHHHHHHHHHHCCCCHHHHHHHTTCCSCHHHHHHHHHHT
T ss_pred             CcCCHHHHHHHHHHHhCCCCCHHHHHHHHCCCccHHHHHHHHHHC
Confidence            45888888888887554 589999999999  8999999999874

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

Probab=95.58  E-value=0.053  Score=40.47  Aligned_cols=77  Identities=17%  Similarity=0.166  Sum_probs=52.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCC
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDK  141 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~  141 (258)
                      ..+..+||+.+|+|++++.+..++.-  |.         .|.... ..-.....+++. +++.+..||+..+   |..  
T Consensus        19 ~~~~~~lA~~~~~S~~~l~r~fk~~~--g~---------s~~~~~~~~Rl~~A~~lL~-~~~~si~~iA~~~---Gf~--   81 (103)
T 3lsg_A           19 QFTLSVLSEKLDLSSGYLSIMFKKNF--GI---------PFQDYLLQKRMEKAKLLLL-TTELKNYEIAEQV---GFE--   81 (103)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHT---TCS--
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-CCCCCHHHHHHHh---CCC--
Confidence            68999999999999999999999974  21         111111 111222333343 4678888886655   775  


Q ss_pred             CCCCCHHHHHHHHHhccCC
Q psy15598        142 FNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       142 ~~~pS~STI~RiLrr~~~~  160 (258)
                          +.+...|.+++.-+.
T Consensus        82 ----~~s~F~r~Fk~~~G~   96 (103)
T 3lsg_A           82 ----DVNYFITKFKKYYQI   96 (103)
T ss_dssp             ----CHHHHHHHHHHHHSS
T ss_pred             ----CHHHHHHHHHHHHCc
Confidence                889999999876543

>2b0l_A GTP-sensing transcriptional pleiotropic repressor; CODY, DNA-binding, nucleotide-binding, transcript regulation, winged HTH motif.; 2.90A {Bacillus subtilis} SCOP: a.4.5.66

Probab=95.57  E-value=0.005  Score=47.55  Aligned_cols=45  Identities=13%  Similarity=0.209  Sum_probs=38.1

Q ss_pred             HHHHHHHHHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         53 RMRIVELAQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        53 R~RIV~L~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      |.+|+..+..|  + +..++|+.||||++||++-+++..+.|.|...+
T Consensus        30 ~~~I~~~l~~g~~lps~~eLa~~lgVSr~tVr~al~~L~~~GlI~~~~   77 (102)
T 2b0l_A           30 IEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS   77 (102)
T ss_dssp             HHHHTTSSBTTEEEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHhhhcCCCcCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            78888555545  4 999999999999999999999999999886544

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=95.57  E-value=0.017  Score=44.80  Aligned_cols=56  Identities=23%  Similarity=0.182  Sum_probs=42.5

Q ss_pred             CCCCCHHHHHHHHHHHHcC-----C---CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         45 GRPLPNSVRMRIVELAQLG-----I---RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G-----~---S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..++...+...|...+..|     .   +.+++|++||||+.||++-+++..+.|-+...+..|
T Consensus         7 ~~~~~~~i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~~~G   70 (113)
T 3tqn_A            7 KKPIYQQLRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRRGLG   70 (113)
T ss_dssp             SSCHHHHHHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             CCCHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCe
Confidence            3445555666666665543     2   889999999999999999999999999886554444

>2pn6_A ST1022, 150AA long hypothetical transcriptional regulator; LRP/ASNC family Gln binding, structural genomics, NPPSFA; HET: GLN; 1.44A {Sulfolobus tokodaii} PDB: 2efn_A* 2e7x_A* 2e7w_A* 2yx4_A* 2efq_A* 2pmh_A* 2yx7_A* 2efp_A* 2efo_A*

Probab=95.53  E-value=0.023  Score=45.29  Aligned_cols=44  Identities=20%  Similarity=0.409  Sum_probs=38.4

Q ss_pred             HHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.+.+|+.+...  ..+.++||+.+|+|++||++.+++..+.|-+.
T Consensus         3 ~~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~   48 (150)
T 2pn6_A            3 EIDLRILKILQYNAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIK   48 (150)
T ss_dssp             HHHHHHHHHHTTCTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSC
T ss_pred             hHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence            467788888753  48999999999999999999999999999763

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

Probab=95.49  E-value=0.022  Score=42.25  Aligned_cols=41  Identities=17%  Similarity=0.404  Sum_probs=35.6

Q ss_pred             HHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|+++++ .| ++..++|+.|+||..||++-+.+..+.|.+.
T Consensus         5 ~~Il~~L~~~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~   47 (78)
T 1xn7_A            5 IQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV   47 (78)
T ss_dssp             HHHHHHHHHSCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            46777765 45 7999999999999999999999999999763

>2w48_A Sorbitol operon regulator; SORC, activator, repressor, DNA-binding, transcription, transcription regulator, transcription regulation; 3.20A {Klebsiella pneumoniae}

Probab=95.47  E-value=0.017  Score=52.10  Aligned_cols=50  Identities=20%  Similarity=0.284  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++-.+|..++. ++++..+||++||||+.||+|-+++-++.|.+.-+-.+|
T Consensus         8 ~~~~~ia~l~~~~~~~~~ela~~l~vS~~tIrRdL~~l~~~G~v~iri~g~   58 (315)
T 2w48_A            8 RLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYD   58 (315)
T ss_dssp             HHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSS
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEEecCC
Confidence            34455666655 689999999999999999999999999999885333343

>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=95.41  E-value=0.0074  Score=42.80  Aligned_cols=23  Identities=4%  Similarity=0.066  Sum_probs=20.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++..++|+.||||++||++|++.
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            46789999999999999999975

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

Probab=95.40  E-value=0.016  Score=42.94  Aligned_cols=45  Identities=24%  Similarity=0.372  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHH-c-----C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQ-L-----G--IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~-~-----G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+.+.+|+++++ .     |  .+++|||+.||||.+||++-++...+.|.|.
T Consensus         3 ~~r~~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~   55 (77)
T 2jt1_A            3 ESIVTKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLE   55 (77)
T ss_dssp             CTHHHHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            345677777764 3     3  4799999999999999999999999999874

>3iuo_A ATP-dependent DNA helicase RECQ; C-terminal, GI PSI, MCSG, structural genomics, midwest center for structur genomics; 1.60A {Porphyromonas gingivalis}

Probab=95.37  E-value=0.077  Score=42.10  Aligned_cols=94  Identities=14%  Similarity=-0.003  Sum_probs=70.7

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC-cccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHH
Q psy15598         50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS-ILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs-l~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~E  128 (258)
                      ......++.++++|++..+||+.-|++.+||..-+.++...|. +.-..-   -+..++++....|.+.+.+.....+..
T Consensus        19 ~~t~~~t~~l~~~G~sleeIA~~R~L~~~TI~~Hl~~~v~~G~~l~i~~~---i~~~l~~~~~~~I~~~~~~~~~~~Lk~   95 (122)
T 3iuo_A           19 SKMKVSIVQQIDRKVALDDIAVSHGLDFPELLSEVETIVYSGTRINIDYF---INEVMDEDHLEDIFEYFKESTTDSLEE   95 (122)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHHHHHHHTTCCCCCHHH---HHHHSCHHHHHHHHHHHHHCSCCCHHH
T ss_pred             CccHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHcCCccCHHHH---cccccCHHHHHHHHHHHHHcCcccHHH
Confidence            3577889999999999999999999999999999999999985 311100   011344777788888888877778888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHH
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRIL  154 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiL  154 (258)
                      +.+.|..   .     +|+-.|+=++
T Consensus        96 i~e~l~~---~-----~sy~eIRlv~  113 (122)
T 3iuo_A           96 AMQELGK---D-----YSEEEIRLVR  113 (122)
T ss_dssp             HHHHHTT---T-----SCHHHHHHHH
T ss_pred             HHHHccC---c-----CCHHHHHHHH
Confidence            8888842   2     3777775443

>3gpv_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, structural genomics; 1.90A {Bacillus thuringiensis serovarkonkukian}

Probab=95.36  E-value=0.061  Score=43.94  Aligned_cols=68  Identities=9%  Similarity=0.059  Sum_probs=49.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      -+++.++|+.+|||.+|++.|-    +.|.+.|..+..+.-|..++++...|..+.. .+-.+++.+|++.|.
T Consensus        16 ~~~I~evA~~~gvs~~tLR~Ye----~~Gll~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sL~eIk~~l~   84 (148)
T 3gpv_A           16 YYTIGQVAKMQHLTISQIRYYD----KQGLFPFLQRNEKGDRIFNEEALKYLEMILCLKNTGMPIQKIKQFID   84 (148)
T ss_dssp             CBCHHHHHHHTTCCHHHHHHHH----HTTCCTTCEECTTCCEEBCHHHHHHHHHHHHHHTTTCCHHHHHHHHH
T ss_pred             ceeHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            4789999999999999998764    4577754433322457788887776655533 445889999998886

>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=95.35  E-value=0.03  Score=39.94  Aligned_cols=43  Identities=16%  Similarity=0.159  Sum_probs=30.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~  119 (258)
                      ++..+||+.+|||++||+++++.-.           + . ...+++...+|.+..+
T Consensus         1 ~T~~diA~~aGVS~sTVSrvLng~~-----------~-~-~~vs~et~~rI~~aa~   43 (65)
T 1uxc_A            1 MKLDEIARLAGVSRTTASYVINGKA-----------K-Q-YRVSDKTVEKVMAVVR   43 (65)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTCT-----------T-T-TTCTTHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCCC-----------C-C-CCCCHHHHHHHHHHHH
Confidence            4688999999999999999986310           0 0 1255666777766654

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=95.32  E-value=0.035  Score=40.63  Aligned_cols=44  Identities=27%  Similarity=0.330  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..+.+|+..+.  .+.+..+||+.++++++||++.+++..+.|-|.
T Consensus        20 ~~~~~il~~l~~~~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~   65 (109)
T 1sfx_A           20 PSDVRIYSLLLERGGMRVSEIARELDLSARFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             HHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            34556666653  568999999999999999999999999999774

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

Probab=95.26  E-value=0.032  Score=45.25  Aligned_cols=43  Identities=14%  Similarity=0.307  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +...+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus        10 ~~~~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   54 (162)
T 2p5v_A           10 KTDIKILQVLQENGRLTNVELSERVALSPSPCLRRLKQLEDAGIV   54 (162)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            34557777765 3 4899999999999999999999999999976

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

Probab=95.25  E-value=0.035  Score=44.23  Aligned_cols=43  Identities=16%  Similarity=0.311  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +...+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|-+
T Consensus         5 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   49 (144)
T 2cfx_A            5 QIDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGII   49 (144)
T ss_dssp             HHHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            34457777765 3 4899999999999999999999999999976

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

Probab=95.24  E-value=0.044  Score=43.74  Aligned_cols=43  Identities=14%  Similarity=0.295  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +...+|+.+.+ + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus         9 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   53 (151)
T 2dbb_A            9 RVDMQLVKILSENSRLTYRELADILNTTRQRIARRIDKLKKLGII   53 (151)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            34457777765 3 4899999999999999999999999999976

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

Probab=95.23  E-value=0.045  Score=43.70  Aligned_cols=43  Identities=12%  Similarity=0.144  Sum_probs=36.6

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+.+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus         7 ~~~~~iL~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   51 (150)
T 2w25_A            7 DIDRILVRELAADGRATLSELATRAGLSVSAVQSRVRRLESRGVV   51 (150)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            34557777764 4 4899999999999999999999999999976

>3hh0_A Transcriptional regulator, MERR family; protein structure initiative II(PSI II), NYSGXRC, 11183J, structural genomics; 2.67A {Bacillus cereus atcc 14579}

Probab=95.23  E-value=0.045  Score=44.71  Aligned_cols=69  Identities=14%  Similarity=0.122  Sum_probs=48.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      ..+++.++|+.+|||.+|++.|-+    .|.+.|..+..+.-|..++++...|..... ..-.+++.+|+..|.
T Consensus         3 ~~~tI~evA~~~Gvs~~tLR~ye~----~GLl~p~~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~~I~~~l~   72 (146)
T 3hh0_A            3 LAWLISEFASVGDVTVRALRYYDK----INLLKPSDYTEGGHRLYTKDDLYVLQQIQSFKHLGFSLGEIQNIIL   72 (146)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHH----TTSSCCSEECTTSCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHT
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCeECCCCCEeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            357899999999999999987654    487766543222457788887766655432 234788888888775

>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=95.22  E-value=0.033  Score=44.63  Aligned_cols=43  Identities=16%  Similarity=0.226  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+.+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus         8 ~~d~~il~~L~~~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i   52 (152)
T 2cg4_A            8 NLDRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGII   52 (152)
T ss_dssp             HHHHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence            44567888765 3 4899999999999999999999999999965

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

Probab=95.21  E-value=0.032  Score=45.61  Aligned_cols=43  Identities=16%  Similarity=0.303  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ++..+|+.+.+ +| .+.++||+.+|+|.+||++-+++..+.|.+
T Consensus         3 ~~d~~il~~L~~~~~~s~~~la~~lg~s~~tv~~rl~~L~~~g~i   47 (162)
T 3i4p_A            3 RLDRKILRILQEDSTLAVADLAKKVGLSTTPCWRRIQKMEEDGVI   47 (162)
T ss_dssp             HHHHHHHHHHTTCSCSCHHHHHHHHTCCHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHHCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            45567888876 33 899999999999999999999999999965

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

Probab=95.20  E-value=0.1  Score=39.23  Aligned_cols=80  Identities=14%  Similarity=0.098  Sum_probs=53.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCC-CHHHHHHHHHHHHhCCC-CCHHHHHHHHHhcCC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVT-TPKVVSYIKELKQKDPG-IFAWEIRDRLLSDGV  138 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrkl-T~e~~~~I~~lv~~nP~-ita~EIr~~L~~~Gv  138 (258)
                      .+..+..+||+.+|+|++++.+..++.-  |.         .|... ...-.+...+++..... ++..||+..+   |.
T Consensus        16 ~~~~~~~~lA~~~~~s~~~l~r~fk~~~--G~---------s~~~~~~~~Rl~~A~~lL~~~~~~~si~~IA~~~---Gf   81 (108)
T 3mn2_A           16 MRPITIEKLTALTGISSRGIFKAFQRSR--GY---------SPMAFAKRVRLQHAHNLLSDGATPTTVTAAALSC---GF   81 (108)
T ss_dssp             TSCCCHHHHHHHHTCCHHHHHHHHHHHT--SS---------CHHHHHHHHHHHHHHHHHHSSSSCCCHHHHHHHT---TC
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHh--Cc---------CHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHh---CC
Confidence            3568999999999999999999999873  21         11111 11122333444444332 7888887655   66


Q ss_pred             CCCCCCCCHHHHHHHHHhccCC
Q psy15598        139 CDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       139 ~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .      +.+...|.+++.-+.
T Consensus        82 ~------~~s~F~r~Fk~~~G~   97 (108)
T 3mn2_A           82 S------NLGHFARDYRDMFGE   97 (108)
T ss_dssp             C------CHHHHHHHHHHHHSS
T ss_pred             C------CHHHHHHHHHHHHCc
Confidence            5      889999999876543

>2k27_A Paired box protein PAX-8; paired domain, solution structure, triple frequency, 3D NMR, induced FIT, alternative splicing, developmental protein; NMR {Homo sapiens}

Probab=95.20  E-value=0.026  Score=45.47  Aligned_cols=48  Identities=13%  Similarity=0.102  Sum_probs=40.9

Q ss_pred             CCCCCHHHHHHHHHHHHc--CCCHHHHHHHh----------CCCHHHHHHHHHHhhhhCC
Q psy15598         45 GRPLPNSVRMRIVELAQL--GIRPCDISRQL----------RVSHGCVSKILARYHETGS   92 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~--G~S~~eIAr~L----------GVSrsTVsRwikRyrEtGs   92 (258)
                      .+.++.+.+..|++++.+  +++..+|+..|          .+|.+||++|++++.+.|.
T Consensus        81 ~~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~~~~~S~sTV~r~L~~~~~~~~  140 (159)
T 2k27_A           81 PKVATPKVVEKIGDYKRQNPTMFAWEIRDRLLAEGVCDNDTVPSVSSINRIIRTKVQQPF  140 (159)
T ss_dssp             CCCCCTTHHHHHHHHHHHCSSSCHHHHHHHHHHHTCSCTTTSCCHHHHHHHHHHHSCCCS
T ss_pred             CCCCCHHHHHHHHHHHHHCccchHHHHHHHHHHhcccccCCccCHHHHHHHHHHHhCCCc
Confidence            345788889999998764  58999999988          4899999999999998884

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

Probab=95.18  E-value=0.024  Score=43.15  Aligned_cols=40  Identities=18%  Similarity=0.417  Sum_probs=35.0

Q ss_pred             HHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         54 MRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        54 ~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+|+++++ .| ++..++|+.|+||..||++-+.+..+.|.+
T Consensus         5 ~~Il~~L~~~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l   46 (87)
T 2k02_A            5 MEVRDMLALQGRMEAKQLSARLQTPQPLIDAMLERMEAMGKV   46 (87)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCS
T ss_pred             HHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            45777765 45 799999999999999999999999999976

>1neq_A DNA-binding protein NER; NMR {Enterobacteria phage MU} SCOP: a.35.1.2 PDB: 1ner_A

Probab=95.16  E-value=0.016  Score=42.24  Aligned_cols=32  Identities=16%  Similarity=0.212  Sum_probs=26.8

Q ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.+|+.+. +.|+|..++|+.+|||++||++|.
T Consensus        11 ~~ri~~~l~~~glT~~~LA~~~Gvs~stls~~~   43 (74)
T 1neq_A           11 RADVIAGLKKRKLSLSALSRQFGYAPTTLANAL   43 (74)
T ss_dssp             HHHHHHHHHTTSCCHHHHHHHHSSCHHHHHHTT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            55666555 579999999999999999999883

>2lfw_A PHYR sigma-like domain; signal transduction, response regulator, sigma factor mimicr sigma factor, general stress response, signaling protein; NMR {Sphingomonas SP}

Probab=95.14  E-value=0.0088  Score=48.20  Aligned_cols=44  Identities=16%  Similarity=0.173  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus        92 ~~Lp~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~rar~  135 (157)
T 2lfw_A           92 ARMTPLSRQALLLTAMEGFSPEDAAYLIEVDTSEVETLVTEALA  135 (157)
T ss_dssp             TTSCTTHHHHHTTTSSSCCCHHHHHHTTTSCHHHHHHHHHHHHH
T ss_pred             HhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            34777788665555679999999999999999999999988764

>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=95.12  E-value=0.033  Score=43.67  Aligned_cols=42  Identities=24%  Similarity=0.268  Sum_probs=36.2

Q ss_pred             HHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+.+|+.+.. + ..+.++||+.||+|++||++.+++..+.|-+
T Consensus         5 ~~~~il~~L~~~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i   48 (141)
T 1i1g_A            5 RDKIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGII   48 (141)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            4556777764 3 4899999999999999999999999999976

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

Probab=95.10  E-value=0.046  Score=41.60  Aligned_cols=86  Identities=20%  Similarity=0.198  Sum_probs=57.2

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~E  128 (258)
                      .++++.++    +..+..+||+.+|||++++.+..++.-  |.         .|.... ..-.....+++. +++.+..|
T Consensus        10 ~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~--G~---------s~~~~~~~~Rl~~A~~lL~-~~~~~i~e   77 (113)
T 3oio_A           10 TEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYL--GT---------VPSKYYLELRLNRARQLLQ-QTSKSIVQ   77 (113)
T ss_dssp             HHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHT--SS---------CHHHHHHHHHHHHHHHHHH-HCCCCHHH
T ss_pred             HHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCCCCHHH
Confidence            45555554    357999999999999999999999873  21         111111 111223333443 46788888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      +.+...|.+++.-+.
T Consensus        78 IA~~~---Gf~------~~s~F~r~Fk~~~G~  100 (113)
T 3oio_A           78 IGLAC---GFS------SGPHFSSTYRNHFNI  100 (113)
T ss_dssp             HHHHT---TCS------CHHHHHHHHHHHHSS
T ss_pred             HHHHH---CCC------CHHHHHHHHHHHHCc
Confidence            87655   675      889999999886554

>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=95.09  E-value=0.038  Score=42.56  Aligned_cols=42  Identities=12%  Similarity=0.037  Sum_probs=33.7

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+-    +|++..+||+.||||++||..++.+-.
T Consensus        19 ~Lp~reR~Vi~Lry~l~~~e~~s~~EIA~~lgiS~~tVr~~~~rAl   64 (99)
T 3t72_q           19 GLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKAL   64 (99)
T ss_pred             cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            467777765555553    689999999999999999999988864

>3u1d_A Uncharacterized protein; GNTR-superfamily, structural genomics, PSI-biology, midwest for structural genomics, MCSG; 1.80A {Halomicrobium mukohataei}

Probab=95.00  E-value=0.057  Score=45.02  Aligned_cols=69  Identities=7%  Similarity=0.126  Sum_probs=52.0

Q ss_pred             CCHHHHHHHHHHHHc---C-CCHHHHHHHhC-CCHHHHHHHHHHhhhhCCccc-----CCCCCCCCC---CCCHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQL---G-IRPCDISRQLR-VSHGCVSKILARYHETGSILP-----GAIGGSKPR---VTTPKVVSYI  114 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~---G-~S~~eIAr~LG-VSrsTVsRwikRyrEtGsl~p-----k~rgG~RPr---klT~e~~~~I  114 (258)
                      +....|.+|+.++..   + .+..+|+..++ ||++|||+-++...+.|.|..     +..++++|+   .+|++-+..+
T Consensus        26 l~~~tR~~IL~~Ll~~p~~~~ta~eL~~~l~~lS~aTVyrhL~~L~eaGLV~~~~~~~~~~~rGrP~k~Y~LT~~Gr~~l  105 (151)
T 3u1d_A           26 VLHETRLDVLHQILAQPDGVLSVEELLYRNPDETEANLRYHVDELVDRGIVEKIPVPRAKSVDDPPTTFYAVTGEGIALL  105 (151)
T ss_dssp             HCCHHHHHHHHHHHHSTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEECCCCTTSSSCCCEEEEECHHHHHHH
T ss_pred             hcchHHHHHHHHHHcCCCCCCCHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEEeecCcCcccCCCCceEEEECHHHHHHH
Confidence            555689999998743   3 68999999999 999999999999999998741     112223565   3788777666


Q ss_pred             HH
Q psy15598        115 KE  116 (258)
Q Consensus       115 ~~  116 (258)
                      .+
T Consensus       106 ~~  107 (151)
T 3u1d_A          106 RA  107 (151)
T ss_dssp             HH
T ss_pred             HH
Confidence            43

>3kz3_A Repressor protein CI; five helix bundle, DNA-binding, transcription, transcription regulation; 1.64A {Enterobacteria phage lambda}

Probab=94.98  E-value=0.035  Score=39.56  Aligned_cols=34  Identities=9%  Similarity=0.253  Sum_probs=27.0

Q ss_pred             HHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +..++-.+. +.|++..++|+.+|||++||++|.+
T Consensus        13 l~~~l~~~r~~~gltq~~lA~~~gvs~~~is~~e~   47 (80)
T 3kz3_A           13 LKAIWEKKKNELGLSYESVADKMGMGQSAVAALFN   47 (80)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            344444444 3699999999999999999999974

>1x57_A Endothelial differentiation-related factor 1; HMBF1alpha, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.35.1.12

Probab=94.98  E-value=0.059  Score=39.20  Aligned_cols=40  Identities=13%  Similarity=0.121  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+...+-.+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         8 ~~~~~~~~~~l~~~r~~~glsq~~lA~~~gis~~~is~~e~   48 (91)
T 1x57_A            8 DRVTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYES   48 (91)
T ss_dssp             SCCCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3455567777777765 699999999999999999999976

>3eet_A Putative GNTR-family transcriptional regulator; structural genomics, PSI-2, protein structure initiative; 1.97A {Streptomyces avermitilis}

Probab=94.92  E-value=0.031  Score=49.75  Aligned_cols=57  Identities=14%  Similarity=0.067  Sum_probs=43.0

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         44 NGRPLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ...++-..+...|...+.+|       + +..++|++||||+.||++-+++..+.|.|...++.|
T Consensus        26 ~~~~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   90 (272)
T 3eet_A           26 GEQPAYLRVAGDLRKKIVDGSLPPHTRLPSQARIREEYGVSDTVALEARKVLMAEGLVEGRSGSG   90 (272)
T ss_dssp             -CCCHHHHHHHHHHHHHHHTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCC--
T ss_pred             CCCCHHHHHHHHHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence            34456666666676666544       2 899999999999999999999999999886555444

>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=94.92  E-value=0.04  Score=42.45  Aligned_cols=38  Identities=13%  Similarity=0.088  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|..|..+++ .|-..+++|+.||||++|+++++++|.
T Consensus        58 ~Er~~I~~aL~~~~gn~~~AA~~LGIsR~TL~rkLkk~g   96 (98)
T 1eto_A           58 VEQPLLDMVMQYTLGNQTRAALMMGINRGTLRKKLKKYG   96 (98)
T ss_dssp             HHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence            34555555554 577899999999999999999999984

>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=94.92  E-value=0.029  Score=38.08  Aligned_cols=32  Identities=13%  Similarity=0.372  Sum_probs=26.1

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus         4 ~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   36 (69)
T 1r69_A            4 SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLEN   36 (69)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3444544 4799999999999999999999964

>2b5a_A C.BCLI; helix-turn-helix motif, gene regulation; 1.54A {Bacillus caldolyticus} SCOP: a.35.1.3

Probab=94.91  E-value=0.014  Score=40.65  Aligned_cols=35  Identities=9%  Similarity=0.173  Sum_probs=27.9

Q ss_pred             HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+..+|..+. +.|++..++|+.+|||++||++|.+
T Consensus        10 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (77)
T 2b5a_A           10 KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            3445555555 3699999999999999999999864

>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=94.89  E-value=0.014  Score=40.66  Aligned_cols=28  Identities=14%  Similarity=0.097  Sum_probs=23.9

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         57 VELAQLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        57 V~L~~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -++.+.+.+..++|+.+|||++||++|.
T Consensus         4 ~~~i~~~~tq~~lA~~lGvs~~~Vs~we   31 (61)
T 1rzs_A            4 KDVIDHFGTQRAVAKALGISDAAVSQWK   31 (61)
T ss_dssp             HHHHHHHSSHHHHHHHHTCCHHHHHHCC
T ss_pred             HHHHHHcCCHHHHHHHhCCCHHHHHHHH
Confidence            3455566799999999999999999996

>3bhq_A Transcriptional regulator; bacterial RE proteins, structural genomics, joint center for structural JCSG, protein structure initiative, PSI-2; HET: MSE; 1.54A {Mesorhizobium loti}

Probab=94.81  E-value=0.028  Score=45.67  Aligned_cols=46  Identities=20%  Similarity=0.244  Sum_probs=33.6

Q ss_pred             CcccCCCCCCHHHHHHHHHHHH-----cC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         40 GVFVNGRPLPNSVRMRIVELAQ-----LG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        40 ~~~~~gR~~S~dlR~RIV~L~~-----~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |+..+++.-+.+.|.+|++...     .|   .|..+||+..|||++|+|+..+
T Consensus         1 ~~~~~~~~r~~~~r~~Il~aA~~lf~~~G~~~ts~~~IA~~aGvsk~tlY~~F~   54 (211)
T 3bhq_A            1 GMKIDGETRSARKDREIIQAATAAFISKGYDGTSMEEIATKAGASKQTVYKHFT   54 (211)
T ss_dssp             ------CCHHHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             CCCcccCCccHhHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            4556777778889999998642     34   6999999999999999998654

>2q0o_A Probable transcriptional activator protein TRAR; helix-turn-helix, two-helix coiled coil; HET: LAE; 2.00A {Rhizobium SP}

Probab=94.80  E-value=0.051  Score=46.51  Aligned_cols=43  Identities=12%  Similarity=0.071  Sum_probs=36.6

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++...|. |+.++.+|++.++||+.||||.+||...+++-++
T Consensus       174 ~~Lt~~e~~-vl~~~~~g~s~~eIa~~l~is~~tV~~~~~~~~~  216 (236)
T 2q0o_A          174 QMLSPREML-CLVWASKGKTASVTANLTGINARTVQHYLDKARA  216 (236)
T ss_dssp             GSCCHHHHH-HHHHHHTTCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHHH-HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            358887775 6677789999999999999999999999988763

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

Probab=94.80  E-value=0.33  Score=37.53  Aligned_cols=49  Identities=16%  Similarity=0.173  Sum_probs=37.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .+.+.++||+.|+|+++||++.+++..+.|-|.-..    +.-.+|++-.+.+
T Consensus        30 ~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~----~~~~Lt~~g~~~~   78 (139)
T 2x4h_A           30 EGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE----DGVWITNNGTRSI   78 (139)
T ss_dssp             SCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET----TEEEECHHHHHHH
T ss_pred             CCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC----CeEEEChhHHHHH
Confidence            457999999999999999999999999999874322    2244666544433

>3b7h_A Prophage LP1 protein 11; structural genomics, PSI2, MCSG, protein structure initiative, midwest center for structural genomics; 2.00A {Lactobacillus plantarum WCFS1}

Probab=94.78  E-value=0.043  Score=38.25  Aligned_cols=36  Identities=11%  Similarity=0.189  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+..+|..+.+ .|++..++|+.+|||++||++|.+
T Consensus         6 ~~~~~~l~~~r~~~g~sq~~lA~~~gis~~~i~~~e~   42 (78)
T 3b7h_A            6 EFVSEHLMELITQQNLTINRVATLAGLNQSTVNAMFE   42 (78)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345666666654 699999999999999999999864

>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=94.77  E-value=0.044  Score=37.41  Aligned_cols=32  Identities=16%  Similarity=0.218  Sum_probs=26.3

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus         6 ~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   38 (71)
T 1zug_A            6 ERLKKRRIALKMTQTELATKAGVKQQSIQLIEA   38 (71)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4455554 4799999999999999999999874

>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=94.74  E-value=0.059  Score=38.49  Aligned_cols=36  Identities=8%  Similarity=0.219  Sum_probs=29.8

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .++-.+|..+.+ .|++..++|+.+|||++||++|.+
T Consensus        11 ~~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   47 (88)
T 2wiu_B           11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN   47 (88)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            355566666654 699999999999999999999986

>3hrs_A Metalloregulator SCAR; DTXR/MNTR family member, transcription; 2.70A {Streptococcus gordonii} PDB: 3hrt_A 3hru_A

Probab=94.74  E-value=0.22  Score=42.49  Aligned_cols=89  Identities=13%  Similarity=0.069  Sum_probs=56.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH----------hCCCCCHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ----------KDPGIFAWEIRDR  132 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~----------~nP~ita~EIr~~  132 (258)
                      +++..+||+.|+||++||++.+++..+.|-+.-.+.   +.-.+|++=++...++.+          +.-.++..++.+.
T Consensus        20 ~~~~~~lA~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~i~LT~~G~~~~~~~~~~h~~~e~~l~~~lg~~~~e~~~~   96 (214)
T 3hrs_A           20 KITNKEIAQLMQVSPPAVTEMMKKLLAEELLIKDKK---AGYLLTDLGLKLVSDLYRKHRLIEVFLVHHLGYTTEEIHEE   96 (214)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT---TEEEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhHHHHHHHHHHHCCCEEEecC---CCeEECHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            589999999999999999999999999998743322   224567664444433332          3334454444332


Q ss_pred             HHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        133 LLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       133 L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      ....-..     +|..++.++-...+.
T Consensus        97 a~~lEh~-----~s~~~~~~l~~~l~~  118 (214)
T 3hrs_A           97 AEVLEHT-----VSDHFVERLDQLLDY  118 (214)
T ss_dssp             HHHHHTT-----SCHHHHHHHHHHTTC
T ss_pred             HHHHhcc-----CCHHHHHHHHHHhCC
Confidence            2221122     488888777665544

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

Probab=94.73  E-value=0.041  Score=41.12  Aligned_cols=44  Identities=7%  Similarity=0.314  Sum_probs=39.9

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHH-HHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHG-CVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrs-TVsRwikRyrEtGsl~   94 (258)
                      +.+.+|+.+.+ . +.+..+||+.|||+.. .|++-+.+-.+.|.|.
T Consensus        11 ~~~~~IL~~Lk~~g~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~   57 (79)
T 1xmk_A           11 EIKEKICDYLFNVSDSSALNLAKNIGLTKARDINAVLIDMERQGDVY   57 (79)
T ss_dssp             HHHHHHHHHHHHTCCEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEE
T ss_pred             hHHHHHHHHHHHcCCcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEE
Confidence            67899999875 3 5899999999999999 9999999999999986

>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=94.73  E-value=0.042  Score=37.05  Aligned_cols=33  Identities=24%  Similarity=0.257  Sum_probs=26.6

Q ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus         7 ~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~   40 (68)
T 2r1j_L            7 GERIRARRKKLKIRQAALGKMVGVSNVAISQWER   40 (68)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            34455554 3699999999999999999999864

>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=94.73  E-value=0.048  Score=39.36  Aligned_cols=35  Identities=17%  Similarity=0.246  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+..+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus        18 ~~~~~l~~~r~~~glsq~elA~~~gis~~~is~~e~   53 (83)
T 2a6c_A           18 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   53 (83)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            45566666655 599999999999999999999875

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

Probab=94.69  E-value=0.094  Score=39.41  Aligned_cols=78  Identities=13%  Similarity=0.124  Sum_probs=52.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v  140 (258)
                      ...+..++|+.+|+|++++.+..++.-  |.         .|.... ..-.....+++. +++.+..+|+..+   |.. 
T Consensus        19 ~~~~~~~lA~~~~~S~~~l~r~fk~~~--G~---------s~~~~~~~~Rl~~A~~lL~-~~~~si~~IA~~~---Gf~-   82 (107)
T 2k9s_A           19 SNFDIASVAQHVCLSPSRLSHLFRQQL--GI---------SVLSWREDQRISQAKLLLS-TTRMPIATVGRNV---GFD-   82 (107)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHHH-HCCCCHHHHHHHT---TCC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCCCCHHHHHHHh---CCC-
Confidence            357999999999999999999999863  21         111111 111222333343 4578888886655   775 


Q ss_pred             CCCCCCHHHHHHHHHhccCC
Q psy15598        141 KFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~~~~  160 (258)
                           +.+...|.+++.-+.
T Consensus        83 -----~~s~F~r~Fk~~~G~   97 (107)
T 2k9s_A           83 -----DQLYFSRVFKKCTGA   97 (107)
T ss_dssp             -----CHHHHHHHHHHHHSS
T ss_pred             -----CHHHHHHHHHHHHCc
Confidence                 889999999876543

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

Probab=94.64  E-value=0.065  Score=41.94  Aligned_cols=42  Identities=14%  Similarity=0.278  Sum_probs=34.9

Q ss_pred             HHHHHHHH-H-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELA-Q-LG--IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~-~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.+|+..+ + .+  ++..+||+.+++|++||+|.+++..+.|-|.
T Consensus        28 e~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~   73 (123)
T 3r0a_A           28 DLNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQ   73 (123)
T ss_dssp             HHHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            44555554 3 35  7999999999999999999999999999774

>1y7y_A C.AHDI; helix-turn-helix, DNA-binding protein, transcriptional regulator, transcription regulator; 1.69A {Aeromonas hydrophila} SCOP: a.35.1.3

Probab=94.59  E-value=0.058  Score=37.06  Aligned_cols=35  Identities=14%  Similarity=0.153  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+-.+|..+.+ .|++..++|+.+|||+++|++|.+
T Consensus        13 ~~~~~l~~~r~~~g~s~~~lA~~~gis~~~i~~~e~   48 (74)
T 1y7y_A           13 KFGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   48 (74)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            34455555553 699999999999999999999864

>1k78_A Paired box protein PAX5; paired domain, ETS domain, transcription factor, transcription/DNA complex; 2.25A {Homo sapiens} SCOP: a.4.1.5 a.4.1.5 PDB: 1mdm_A 6pax_A

Probab=94.55  E-value=0.05  Score=43.12  Aligned_cols=44  Identities=16%  Similarity=0.202  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHHc--CCCHHHHHHHh--------C--CCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQL--GIRPCDISRQL--------R--VSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~--G~S~~eIAr~L--------G--VSrsTVsRwikRyrE   89 (258)
                      +.++.+.+..|++++.+  ..+..+|+..|        |  +|.+||++|++++.+
T Consensus        89 ~~~~~~~~~~I~~~~~~~~~~s~~~i~~~l~~~~~~~~g~~~S~sTV~r~L~~~~~  144 (149)
T 1k78_A           89 KVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTKVQ  144 (149)
T ss_dssp             SSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC--
T ss_pred             CCCCHHHHHHHHHHHHhCcchhHHHHHHHHHHhcccccCCCcCHHHHHHHHHHHhc
Confidence            45888999999998864  58999999998        7  899999999998753

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

Probab=94.53  E-value=0.11  Score=40.00  Aligned_cols=89  Identities=18%  Similarity=0.103  Sum_probs=58.3

Q ss_pred             HHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCC
Q psy15598         50 NSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGI  124 (258)
Q Consensus        50 ~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~i  124 (258)
                      .++-.+|+..++    +..+..+||+.+|+|++++.+..++.   |.         .|.... ..-.+...+++ .+++.
T Consensus         6 ~~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~---G~---------s~~~~~~~~Rl~~A~~lL-~~~~~   72 (120)
T 3mkl_A            6 PNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE---ET---------SYSQLLTECRMQRALQLI-VIHGF   72 (120)
T ss_dssp             CCHHHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHT---TC---------CHHHHHHHHHHHHHHHHH-TSTTC
T ss_pred             HHHHHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHc---CC---------CHHHHHHHHHHHHHHHHH-HcCCC
Confidence            344456666664    35799999999999999999988763   32         111111 11122233333 56788


Q ss_pred             CHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        125 FAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       125 ta~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      +..||+..+   |..      +.+...|.+++.-+.
T Consensus        73 si~eIA~~~---Gf~------~~s~F~r~Fk~~~G~   99 (120)
T 3mkl_A           73 SIKRVAVSC---GYH------SVSYFIYVFRNYYGM   99 (120)
T ss_dssp             CHHHHHHHT---TCS------CHHHHHHHHHHHHSS
T ss_pred             CHHHHHHHH---CCC------CHHHHHHHHHHHHCc
Confidence            888887665   665      788999999876654

>1l3l_A Transcriptional activator protein TRAR; helix-turn-helix DNA binding motif, alpha/beta/alpha sandwich; HET: LAE; 1.66A {Agrobacterium tumefaciens} SCOP: a.4.6.2 d.110.5.1 PDB: 1h0m_A*

Probab=94.51  E-value=0.056  Score=46.22  Aligned_cols=43  Identities=14%  Similarity=-0.001  Sum_probs=36.5

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++...| .|+.++.+|++.++||+.||||.+||...+++-++
T Consensus       172 ~~Lt~~e~-~vl~~~~~g~s~~eIa~~l~is~~tV~~~~~~~~~  214 (234)
T 1l3l_A          172 AWLDPKEA-TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMK  214 (234)
T ss_dssp             CCCCHHHH-HHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            35888877 56666779999999999999999999999988753

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

Probab=94.50  E-value=0.085  Score=43.66  Aligned_cols=43  Identities=19%  Similarity=0.305  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +...+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|.+
T Consensus        17 ~~d~~IL~~L~~~~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I   61 (171)
T 2ia0_A           17 DLDRNILRLLKKDARLTISELSEQLKKPESTIHFRIKKLQERGVI   61 (171)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            34447777765 4 4899999999999999999999999999976

>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=94.48  E-value=0.016  Score=53.23  Aligned_cols=51  Identities=14%  Similarity=0.235  Sum_probs=35.3

Q ss_pred             CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         44 NGRPLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      |++..-...+.+|+.++. ..+|..+||+.+|+|++||++.+++..+.|.+.
T Consensus        13 ~~~~~~~~~~~~il~~l~~~~~sr~~la~~~gls~~tv~~~v~~L~~~gli~   64 (380)
T 2hoe_A           13 MPKSVRAENISRILKRIMKSPVSRVELAEELGLTKTTVGEIAKIFLEKGIVV   64 (380)
T ss_dssp             ---------CCCSHHHHHHSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSEE
T ss_pred             CchhHHHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            444444444555666543 458999999999999999999999999999763

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

Probab=94.45  E-value=0.19  Score=38.90  Aligned_cols=58  Identities=14%  Similarity=0.013  Sum_probs=42.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      ..+.+..+||+.++++++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        43 ~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  103 (145)
T 3g3z_A           43 EGSRTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQEGEQDRRKRLLSLTETGKAYAAPLT  103 (145)
T ss_dssp             HCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECCCSSCGGGSCEEECHHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeccCCCCCceeeeeEChhHHHHHHHHH
Confidence            35799999999999999999999999999998753222  11 122347777666555443

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

Probab=94.43  E-value=0.073  Score=41.55  Aligned_cols=91  Identities=11%  Similarity=0.108  Sum_probs=60.2

Q ss_pred             CHHHHHHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCH-HHHHHHHHHHHhCCC
Q psy15598         49 PNSVRMRIVELAQL----GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTP-KVVSYIKELKQKDPG  123 (258)
Q Consensus        49 S~dlR~RIV~L~~~----G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~-e~~~~I~~lv~~nP~  123 (258)
                      ..+.-.+|++.+++    ..+..+||+.+|+|++++.+..++.-  |.         .|..... .-.....+++. +.+
T Consensus         9 ~~~~i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~--G~---------s~~~~l~~~Rl~~A~~lL~-~~~   76 (129)
T 1bl0_A            9 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKET--GH---------SLGQYIRSRKMTEIAQKLK-ESN   76 (129)
T ss_dssp             CHHHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHHH-HCC
T ss_pred             hHHHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCC
Confidence            44445566666653    57999999999999999999999873  21         1111111 11222333343 357


Q ss_pred             CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        124 IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       124 ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      .+..+|+..+   |..      +.+...|.+++.-+.
T Consensus        77 ~si~~IA~~~---Gf~------~~s~F~r~Fk~~~G~  104 (129)
T 1bl0_A           77 EPILYLAERY---GFE------SQQTLTRTFKNYFDV  104 (129)
T ss_dssp             CCHHHHHHHT---TCS------CHHHHHHHHHHHHSS
T ss_pred             CCHHHHHHHH---CCC------CHHHHHHHHHHHHCc
Confidence            7888886655   775      889999999987665

>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=94.43  E-value=0.061  Score=44.98  Aligned_cols=44  Identities=18%  Similarity=0.255  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHH-c-C-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC-cc
Q psy15598         51 SVRMRIVELAQ-L-G-IRPCDISRQLRVSHGCVSKILARYHETGS-IL   94 (258)
Q Consensus        51 dlR~RIV~L~~-~-G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs-l~   94 (258)
                      +.+.+|+.+.. + + ++.+++|+.||||++||++-+++.++.|. +.
T Consensus        21 ~R~~~Il~~L~~~~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~   68 (187)
T 1j5y_A           21 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIV   68 (187)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCE
T ss_pred             HHHHHHHHHHHHcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence            45677888875 3 4 89999999999999999999999999997 53

>2qq9_A Diphtheria toxin repressor; regulator, DTXR, helix-turn-helix, metal ION, ACT DNA-binding, ferrous iron, transcription; 1.71A {Corynebacterium diphtheriae} PDB: 2tdx_A 1ddn_A 1g3t_A 1g3s_A 1g3w_A 2qqa_A 2qqb_A 2dtr_A 1bi0_A 1bi2_A 1bi3_A 1dpr_A 1bi1_A 1fwz_A 1g3y_A 1c0w_A* 3glx_A 1p92_A 1xcv_A 1f5t_A ...

Probab=94.42  E-value=0.39  Score=41.19  Aligned_cols=92  Identities=17%  Similarity=0.157  Sum_probs=57.0

Q ss_pred             HHcCCCH--HHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH----------hCCCCCHH
Q psy15598         60 AQLGIRP--CDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ----------KDPGIFAW  127 (258)
Q Consensus        60 ~~~G~S~--~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~----------~nP~ita~  127 (258)
                      .++|.+.  .+||+.|+|+++||++.+++..+.|-+.-.+.   +.-.+|++-.+.+.++.+          +.-.++..
T Consensus        19 ~~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~~~~~~~~~e~~l~~~lgl~~e   95 (226)
T 2qq9_A           19 EEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASD---RSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDIN   95 (226)
T ss_dssp             HHHTCCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SBEEECHHHHHHHHHHHHHHHHHHHHHHHTTCCCHH
T ss_pred             hhcCCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC---CCeEECHHHHHHHHHHHHHHHHHHHHHHHHcCCCHH
Confidence            3457766  99999999999999999999999998753322   224566654444433332          21234444


Q ss_pred             HHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        128 EIRDRLLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       128 EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      ++.+.....-..     +|..++.|+....+.
T Consensus        96 e~~~~a~~leh~-----~s~~~~~~l~~~l~~  122 (226)
T 2qq9_A           96 KVHDEADRWEHV-----MSDEVERRLVKVLKD  122 (226)
T ss_dssp             HHHHHHHHHTTT-----CCHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHhh-----CCHHHHHHHHHHhCC
Confidence            443333221111     477888777665543

>2kpj_A SOS-response transcriptional repressor, LEXA; NESG, GFT, structural genomics, PSI-2, protein structure initiative; NMR {Eubacterium rectale atcc 33656}

Probab=94.42  E-value=0.047  Score=40.18  Aligned_cols=35  Identities=9%  Similarity=0.023  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+..+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         9 ~~~~~lk~~r~~~glsq~~lA~~~gis~~~is~~e~   44 (94)
T 2kpj_A            9 IFSENLNSYIAKSEKTQLEIAKSIGVSPQTFNTWCK   44 (94)
T ss_dssp             HHHHHHHHHHTTSSSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            45556666654 699999999999999999999864

>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=94.41  E-value=0.034  Score=39.54  Aligned_cols=38  Identities=18%  Similarity=0.228  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +...+-.+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         8 ~~~~~g~~lk~~R~~~glsq~~lA~~~gis~~~i~~~e~   46 (82)
T 3s8q_A            8 LLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   46 (82)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            33455566666654 699999999999999999999854

>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=94.40  E-value=0.038  Score=40.98  Aligned_cols=54  Identities=19%  Similarity=0.194  Sum_probs=39.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-CCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      ++..+||+.++++++||++.+++..+.|-|. .+..++ +--.+|++-.+.+.++.
T Consensus        31 ~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~-~~~d~R~~~v~LT~~G~~~~~~~~   85 (95)
T 2qvo_A           31 VYIQYIASKVNSPHSYVWLIIKKFEEAKMVE-CELEGRTKIIRLTDKGQKIAQQIK   85 (95)
T ss_dssp             EEHHHHHHHSSSCHHHHHHHHHHHHHTTSEE-EEEETTEEEEEECHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCcc-CCCCCCeEEEEEChhHHHHHHHHH
Confidence            8999999999999999999999999999882 222221 22357776665555443

>1jgs_A Multiple antibiotic resistance protein MARR; transcription regulation, DNA-binding, repressor, transcription; HET: SAL; 2.30A {Escherichia coli} SCOP: a.4.5.28

Probab=94.40  E-value=0.17  Score=38.60  Aligned_cols=56  Identities=16%  Similarity=0.183  Sum_probs=42.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCCCC--CCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGSKP--RVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~RP--rklT~e~~~~I~~lv  118 (258)
                      .+.+..+||+.++++++||++.+++..+.|-+.-.  +..+ |.  -.+|++-.+.+.+..
T Consensus        47 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~-R~~~~~lT~~G~~~~~~~~  106 (138)
T 1jgs_A           47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDK-RGVLVKLTTGGAAICEQCH  106 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCS-SCEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCcccC-ceeEeEEChhHHHHHHHHH
Confidence            57899999999999999999999999999987422  2222 22  347777666665554

>1adr_A P22 C2 repressor; transcription regulation; NMR {Enterobacteria phage P22} SCOP: a.35.1.2

Probab=94.39  E-value=0.054  Score=37.41  Aligned_cols=33  Identities=24%  Similarity=0.257  Sum_probs=26.5

Q ss_pred             HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+|-.+. +.|++..++|+.+|||+++|++|.+
T Consensus         7 ~~~l~~~r~~~gls~~~lA~~~gis~~~i~~~e~   40 (76)
T 1adr_A            7 GERIRARRKKLKIRQAALGKMVGVSNVAISQWER   40 (76)
T ss_dssp             HHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34444544 3699999999999999999999864

>2hin_A GP39, repressor protein; transcription factor, dimer interface, helix-turn-helix; 1.05A {Enterobacteria phage N15} PDB: 3qws_A

Probab=94.39  E-value=0.031  Score=40.90  Aligned_cols=22  Identities=18%  Similarity=0.135  Sum_probs=20.4

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q psy15598         65 RPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +..++|+.||||++||++|++.
T Consensus        12 ~~~~lA~~lGVs~~aVs~W~~g   33 (71)
T 2hin_A           12 DVEKAAVGVGVTPGAVYQWLQA   33 (71)
T ss_dssp             SHHHHHHHHTSCHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHhC
Confidence            5899999999999999999975

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

Probab=94.37  E-value=0.052  Score=46.12  Aligned_cols=45  Identities=16%  Similarity=0.251  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+.+.+|+.+..+ .++.++||+.+|+|.+||++-+++..+.|-+.
T Consensus        19 d~~~~~IL~~L~~~~~s~~eLA~~lglS~stv~~~l~~Le~~GlI~   64 (192)
T 1uly_A           19 EDTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVE   64 (192)
T ss_dssp             SHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            4677888888765 48999999999999999999999999999764

>2ewt_A BLDD, putative DNA-binding protein; the DNA-binding domain of BLDD; 1.81A {Streptomyces coelicolor}

Probab=94.33  E-value=0.039  Score=37.87  Aligned_cols=35  Identities=6%  Similarity=0.078  Sum_probs=28.1

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhC--CCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLR--VSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LG--VSrsTVsRwik   85 (258)
                      .+-.+|-.+.+ .|++..++|+.+|  ||+++|++|.+
T Consensus         8 ~~g~~l~~~r~~~glsq~~lA~~~g~~is~~~i~~~e~   45 (71)
T 2ewt_A            8 QLGAKLRAIRTQQGLSLHGVEEKSQGRWKAVVVGSYER   45 (71)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHTTTSSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCcCCHHHHHHHHC
Confidence            34455555554 6999999999999  99999999875

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

Probab=94.32  E-value=0.066  Score=41.02  Aligned_cols=44  Identities=14%  Similarity=0.240  Sum_probs=37.0

Q ss_pred             HHHHHHHHHH-HcCCCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELA-QLGIRPCDISRQL-RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~-~~G~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..+..|+... +.+++..+||+.+ +|+++||++.+++..+.|-|.
T Consensus        22 ~~~~~IL~~L~~~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~   67 (112)
T 1z7u_A           22 KWKLSLMDELFQGTKRNGELMRALDGITQRVLTDRLREMEKDGLVH   67 (112)
T ss_dssp             TTHHHHHHHHHHSCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             ccHHHHHHHHHhCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEE
Confidence            3455666654 4568999999999 999999999999999999874

>2cob_A LCOR protein; MLR2, KIAA1795, helix-turn-helix, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.15

Probab=94.30  E-value=0.11  Score=38.16  Aligned_cols=44  Identities=7%  Similarity=0.099  Sum_probs=38.7

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         44 NGRPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ..+.|+.|.-+..|+++.+| +|+..+|+.|||.++|+..=++.-
T Consensus        10 ryr~Yte~~L~~Ai~aVr~g~mS~~~Aak~yGVP~sTL~~RVk~~   54 (70)
T 2cob_A           10 RYRQYNSEILEEAISVVMSGKMSVSKAQSIYGIPHSTLEYKVKER   54 (70)
T ss_dssp             CSCCCCHHHHHHHHHHHHTTSSCHHHHHHHHTCCHHHHHHHHHHH
T ss_pred             cccccCHHHHHHHHHHHHcCCccHHHHHHHhCCChHHHHHHHHhh
Confidence            45679999999999999999 999999999999999998766654

>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=94.30  E-value=0.042  Score=36.83  Aligned_cols=25  Identities=20%  Similarity=0.258  Sum_probs=22.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|++..++|+.+|||++||++|.+
T Consensus        12 ~~g~s~~~lA~~~gis~~~i~~~e~   36 (66)
T 2xi8_A           12 KKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999864

>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=94.25  E-value=0.067  Score=37.95  Aligned_cols=34  Identities=21%  Similarity=0.217  Sum_probs=27.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +..+|..+.+ .|++..++|+.+|||+++|++|.+
T Consensus        15 ~~~~l~~~R~~~gltq~elA~~~gis~~~is~~e~   49 (83)
T 3f6w_A           15 LLDLLLEARSAAGITQKELAARLGRPQSFVSKTEN   49 (83)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3445555543 699999999999999999999864

>3sxy_A Transcriptional regulator, GNTR family; transcription factor, metal-binding, structur genomics, PSI-2, protein structure initiative; 1.65A {Thermotoga maritima} PDB: 3dbw_A 3fms_A*

Probab=94.14  E-value=0.13  Score=43.50  Aligned_cols=68  Identities=16%  Similarity=0.084  Sum_probs=45.3

Q ss_pred             CCCCCHHHHHHHHHHHHc-----C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQL-----G--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~-----G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      ..+++..+-..|...+..     |  ++..++|++||||+++|+.-+++....|-|...++.|..=..++.+...
T Consensus        10 ~~~l~~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~   84 (218)
T 3sxy_A           10 VDLVRTKVYNLLKEMILNHELKLGEKLNVRELSEKLGISFTPVRDALLQLATEGLVKVVPRVGFFVTDVDEKFIR   84 (218)
T ss_dssp             ----CHHHHHHHHHHHHTTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEETTTEEEECCCCHHHHH
T ss_pred             cccHHHHHHHHHHHHHHhCCCCCCCEeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCceEEcCCCHHHHH
Confidence            345666555555555543     3  4889999999999999999999999999887666555322334444333

>2k9q_A Uncharacterized protein; all helix, helix-turn-helix, plasmid, structural genomics, PSI-2, protein structure initiative; NMR {Bacteroides thetaiotaomicron}

Probab=94.14  E-value=0.064  Score=37.77  Aligned_cols=32  Identities=9%  Similarity=0.156  Sum_probs=25.8

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus         5 ~~lk~~r~~~glsq~~lA~~~gis~~~i~~~e~   37 (77)
T 2k9q_A            5 NELKVERIRLSLTAKSVAEEMGISRQQLCNIEQ   37 (77)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            3444444 4699999999999999999998863

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=94.14  E-value=0.15  Score=40.50  Aligned_cols=63  Identities=24%  Similarity=0.159  Sum_probs=43.7

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598         52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l  117 (258)
                      +-..|+.+..  .+.+.++||+.|+||++||++.+++..+.|-|.-.+  + +.-.+|+.-...+...
T Consensus        41 ~~~~i~~~l~~~~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~--~-~~~~lT~~g~~~~~~~  105 (155)
T 2h09_A           41 YVELISDLIREVGEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIP--W-RGVFLTAEGEKLAQES  105 (155)
T ss_dssp             HHHHHHHHHHHHSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEET--T-TEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEec--C-CceEEChhHHHHHHHH
Confidence            3334444543  468999999999999999999999999999774332  1 2345666555444443

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=94.13  E-value=0.15  Score=39.72  Aligned_cols=51  Identities=22%  Similarity=0.161  Sum_probs=38.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      .+.+.++||+.|+||++||++.+++..+.|-|.-.+.   +.-.+|+.-...+.
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~~---~~~~LT~~g~~~~~   71 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKY---RGLVLTSKGKKIGK   71 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT---TEEEECHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeeC---ceEEEchhHHHHHH
Confidence            5799999999999999999999999999998743221   22445655444433

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

Probab=94.12  E-value=0.17  Score=39.07  Aligned_cols=57  Identities=16%  Similarity=0.020  Sum_probs=41.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-..  ..++ .--.+|++-.+.+.+..
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  109 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVREISTEDRRISLLSLTDKGRKETTELR  109 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC----CCSCEEEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeeccCCCccCceeeeeECHHHHHHHHHHH
Confidence            678999999999999999999999999999874222  2221 12237777666655543

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

Probab=94.12  E-value=0.2  Score=39.36  Aligned_cols=63  Identities=13%  Similarity=0.135  Sum_probs=44.1

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCCCC--CCCCHHHHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGSKP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~RP--rklT~e~~~~I~~l  117 (258)
                      ..|+..+ + .+.+..+||+.++++++||++.+++..+.|-|.-..  ..+ |.  -.+|++-.+.+..+
T Consensus        47 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~-R~~~~~lT~~G~~~~~~~  115 (154)
T 2eth_A           47 LYAFLYVALFGPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDR-RTYRVVLTEKGKEIFGEI  115 (154)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTS-SCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCc-ceeEEEECHHHHHHHHHH
Confidence            3444443 3 578999999999999999999999999999774222  122 22  34677766655554

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

Probab=94.12  E-value=0.11  Score=40.98  Aligned_cols=62  Identities=23%  Similarity=0.299  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHHH-cC-CCHHHHHHHh--CCCHHHHHHHHHHhhhhCCcccCCCCCCCC-CCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-LG-IRPCDISRQL--RVSHGCVSKILARYHETGSILPGAIGGSKP-RVTTPKVVSYIK  115 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G-~S~~eIAr~L--GVSrsTVsRwikRyrEtGsl~pk~rgG~RP-rklT~e~~~~I~  115 (258)
                      ...+.+|+.++. +| .+..+||+.+  ++|+++|++-+++-.+.|.|...   | ++ -.+|++-.+++.
T Consensus        12 d~~d~~IL~~L~~~g~~s~~eLA~~l~~giS~~aVs~rL~~Le~~GLV~~~---~-rg~Y~LT~~G~~~l~   78 (111)
T 3b73_A           12 TIWDDRILEIIHEEGNGSPKELEDRDEIRISKSSVSRRLKKLADHDLLQPL---A-NGVYVITEEGEAYLN   78 (111)
T ss_dssp             CHHHHHHHHHHHHHSCBCHHHHHTSTTCCSCHHHHHHHHHHHHHTTSEEEC---S-TTCEEECHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEec---C-CceEEECchHHHHHH
Confidence            355678888875 34 8999999999  99999999999999999988643   2 22 457777666554

>2ef8_A C.ECOT38IS, putative transcription factor; helix-turn-helix, DNA binding protein, transcription regulator; HET: CME; 1.95A {Enterobacteria phage P2}

Probab=94.11  E-value=0.081  Score=37.31  Aligned_cols=34  Identities=18%  Similarity=0.247  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +-.+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus        11 ~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   45 (84)
T 2ef8_A           11 LVQLLTKLRKEASLSQSELAIFLGLSQSDISKIES   45 (84)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            4455555553 699999999999999999998864

>3clo_A Transcriptional regulator; NP_811094.1, bacterial regulatory proteins, LUXR family, structural genomics; 2.04A {Bacteroides thetaiotaomicron vpi-5482}

Probab=94.10  E-value=0.09  Score=45.73  Aligned_cols=43  Identities=16%  Similarity=0.175  Sum_probs=36.7

Q ss_pred             CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..++...|.-++.. .+|++.++||+.||||.+||...+.|-++
T Consensus       196 ~~L~~~erevl~L~-~~G~s~~EIA~~L~iS~~TVk~~l~ra~~  238 (258)
T 3clo_A          196 NILSEREKEILRCI-RKGLSSKEIAATLYISVNTVNRHRQNILE  238 (258)
T ss_dssp             TSSCHHHHHHHHHH-HTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            46888888655554 69999999999999999999999998763

>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=94.08  E-value=0.14  Score=39.50  Aligned_cols=57  Identities=11%  Similarity=0.064  Sum_probs=37.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        50 ~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~  109 (142)
T 3ech_A           50 RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHLHAE  109 (142)
T ss_dssp             TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC----------CCEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeeccCCCCCCeeeeEECHHHHHHHHHHH
Confidence            5799999999999999999999999999998743221  12 122347777666665553

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

Probab=94.06  E-value=0.18  Score=39.02  Aligned_cols=70  Identities=14%  Similarity=0.063  Sum_probs=46.4

Q ss_pred             CCHHHHHHHHHH-HH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVEL-AQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L-~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ++...- .|+.. .. .+.+.++||+.++++++||++.+++..+.|-|.-..  ..+ .+.-.+|++-.+.+....
T Consensus        38 l~~~~~-~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~lT~~G~~~~~~~~  112 (148)
T 3nrv_A           38 IGMTEW-RIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS  112 (148)
T ss_dssp             CCHHHH-HHHHHHHHSSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCBEECHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCcceeEeEECHhHHHHHHHHH
Confidence            444433 34443 34 468999999999999999999999999999774222  112 133457777666665554

>3edp_A LIN2111 protein; APC88337, listeria innocua CLIP11262, structural GE PSI-2, protein structure initiative, midwest center for STR genomics, MCSG; 2.09A {Listeria innocua}

Probab=94.05  E-value=0.055  Score=47.04  Aligned_cols=57  Identities=12%  Similarity=0.166  Sum_probs=43.9

Q ss_pred             CCCCCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         44 NGRPLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ...++-..+...|.+...+|       + +..++|++||||+.||++-++...+.|.+...++.|
T Consensus         6 ~~~~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   70 (236)
T 3edp_A            6 AKKPLFEVIASKIKDSINRDEYKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVG   70 (236)
T ss_dssp             -CCCHHHHHHHHHHHHHHTTSSCCCC--CCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             cCCCHHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEECCce
Confidence            34455566777777777654       2 789999999999999999999999999986555444

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=94.05  E-value=0.026  Score=42.53  Aligned_cols=51  Identities=25%  Similarity=0.259  Sum_probs=38.1

Q ss_pred             HHHHHHHHH-HHHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         50 NSVRMRIVE-LAQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        50 ~dlR~RIV~-L~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..+|.+|+. .+..|  + +.+++|+.||||++||++-+++..+.|.+...+..|
T Consensus        18 ~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~g~G   72 (102)
T 1v4r_A           18 THFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGALG   72 (102)
T ss_dssp             HHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETTTE
T ss_pred             HHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            345555555 23333  3 899999999999999999999999999886444333

>2zhg_A Redox-sensitive transcriptional activator SOXR; oxidative stress, MERR family, activator; HET: DNA; 2.80A {Escherichia coli} PDB: 2zhh_A

Probab=94.02  E-value=0.061  Score=44.31  Aligned_cols=66  Identities=20%  Similarity=0.201  Sum_probs=45.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHH---HHHHHHhCCCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSY---IKELKQKDPGIFAWEIRDRLL  134 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~---I~~lv~~nP~ita~EIr~~L~  134 (258)
                      .-+++.++|+.+|||.+|++.|-+    .|.+.|....+ .-|..++++...   |..+...  .+++.+|++.|.
T Consensus        10 ~~~~i~e~A~~~gvs~~TLR~ye~----~Gll~p~r~~~-g~R~Y~~~dl~~l~~I~~lr~~--G~sl~eI~~~l~   78 (154)
T 2zhg_A           10 ALLTPGEVAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQRI--GIPLATIGEAFG   78 (154)
T ss_dssp             CCBCHHHHHHHHTSCHHHHHHHHH----TTSSCCEECTT-SCEEBCTTHHHHHHHHHHHHHH--TCCHHHHHHHHC
T ss_pred             cCCCHHHHHHHHCcCHHHHHHHHH----cCCCCcccCCC-CCEEeCHHHHHHHHHHHHHHHC--CCCHHHHHHHHH
Confidence            458999999999999999987754    47676543222 345666665554   4444333  788999988774

>3bd1_A CRO protein; transcription factor, helix-turn-helix, prophage, structural evolution, transcription; 1.40A {Xylella fastidiosa}

Probab=94.01  E-value=0.062  Score=38.21  Aligned_cols=25  Identities=28%  Similarity=0.413  Sum_probs=22.8

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.| +..++|+.+|||++||++|.+.
T Consensus        10 ~~g-sq~~lA~~lgvs~~~is~~e~g   34 (79)
T 3bd1_A           10 KLG-SVSALAASLGVRQSAISNWRAR   34 (79)
T ss_dssp             HHS-SHHHHHHHHTCCHHHHHHHHHH
T ss_pred             HhC-CHHHHHHHHCCCHHHHHHHHHC
Confidence            358 9999999999999999999875

>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=93.99  E-value=0.077  Score=37.99  Aligned_cols=41  Identities=15%  Similarity=0.177  Sum_probs=31.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+..+||+.+|||++||+++++.               ++ ..+++..+.|.+.+++
T Consensus        10 ~t~~diA~~aGVS~sTVSr~ln~---------------~~-~vs~~t~~rV~~~a~~   50 (67)
T 2l8n_A           10 ATMKDVALKAKVSTATVSRALMN---------------PD-KVSQATRNRVEKAARE   50 (67)
T ss_dssp             CCHHHHHHHTTCCHHHHHHTTTC---------------CC-CSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence            68999999999999999998732               12 2567777877777654

>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=93.93  E-value=0.19  Score=38.76  Aligned_cols=65  Identities=11%  Similarity=0.170  Sum_probs=44.2

Q ss_pred             HHHHHHH-H--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         54 MRIVELA-Q--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        54 ~RIV~L~-~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ..|+..+ .  .+.+.++||+.++|+++||++.+++..+.|-|.-..  ..+ ..--.+|++-...+....
T Consensus        38 ~~iL~~l~~~~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~  108 (147)
T 2hr3_A           38 LVVLGAIDRLGGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNR  108 (147)
T ss_dssp             HHHHHHHHHTTSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeCCCCCCCCceeeEECHHHHHHHHHHH
Confidence            3444443 3  468999999999999999999999999999874222  122 112347777666655553

>3v4g_A Arginine repressor; vibrio vulnificus CMCP6, virulence, type secretion system, center for structural genomics of infecti diseases, csgid; 1.60A {Vibrio vulnificus} PDB: 1aoy_A

Probab=93.88  E-value=0.11  Score=44.57  Aligned_cols=54  Identities=20%  Similarity=0.127  Sum_probs=47.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      +.-.+.|++++.++.--+..||.+.|++.|+.+    ++.+||+|-|+..+..|....
T Consensus        32 ~~r~~~I~eiI~~~~I~TQeEL~~~L~~~Gi~v----iTQATvSRDIkELglvKv~~~   85 (180)
T 3v4g_A           32 DNLVRAFKALLKEERFGSQGEIVEALKQEGFEN----INQSKVSRMLTKFGAVRTRNA   85 (180)
T ss_dssp             HHHHHHHHHHHHHTCCCSHHHHHHHHHHTTCTT----CCHHHHHHHHHHTTCEEEECT
T ss_pred             HHHHHHHHHHHhhCCcCCHHHHHHHHHHCCCcc----cCHHHHHHHHHHcCCEEeeCC
Confidence            456789999999999999999999999999984    599999999999999987643

>2frh_A SARA, staphylococcal accessory regulator A; winged-helix protein, divalent metal binding, transcription; 2.50A {Staphylococcus aureus} SCOP: a.4.5.28 PDB: 2fnp_A 1fzp_D

Probab=93.88  E-value=0.14  Score=39.62  Aligned_cols=58  Identities=12%  Similarity=-0.037  Sum_probs=41.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~lv~  119 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-.+  ..++ .--.+|++-.+.+.++..
T Consensus        52 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~i~LT~~G~~~~~~~~~  112 (127)
T 2frh_A           52 KEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLLS  112 (127)
T ss_dssp             SEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHH
Confidence            458999999999999999999999999999874322  2221 112477776666655543

>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=93.87  E-value=0.21  Score=38.86  Aligned_cols=57  Identities=18%  Similarity=0.229  Sum_probs=35.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+.+.++||+.++++++||++.+++-.+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        56 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~  115 (148)
T 3jw4_A           56 SGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERRIPENNARQKNIYVLPKGAALVEEFN  115 (148)
T ss_dssp             TCCCHHHHHHC------CHHHHHHHHHHTTSBCCC--------CCCCBCHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeeCCCCCchhheeeECHHHHHHHHHHH
Confidence            5799999999999999999999999999998743321  12 123347777666655543

>2cw1_A SN4M; lambda CRO fold, de novo protein; NMR {Synthetic} SCOP: k.46.1.1

Probab=93.85  E-value=0.058  Score=38.70  Aligned_cols=23  Identities=22%  Similarity=0.270  Sum_probs=21.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.+++|+.||||+++|++|++.
T Consensus        14 ~sq~~~A~~Lgvsq~aVS~~~~~   36 (65)
T 2cw1_A           14 KNQEYAARALGLSQKLIEEVLKR   36 (65)
T ss_dssp             SCHHHHHHHSSSCHHHHHHHHHT
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHh
Confidence            39999999999999999999964

>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=93.82  E-value=0.078  Score=38.76  Aligned_cols=31  Identities=19%  Similarity=0.354  Sum_probs=25.6

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +|-.+. +.|++..++|+.+|||++||++|.+
T Consensus        12 ~l~~~r~~~gltq~~lA~~~gis~~~is~~e~   43 (94)
T 2ict_A           12 IIQESLDELNVSLREFARAMEIAPSTASRLLT   43 (94)
T ss_dssp             HHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            333433 4699999999999999999999986

>3omt_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.65A {Cytophaga hutchinsonii}

Probab=93.77  E-value=0.053  Score=37.75  Aligned_cols=25  Identities=20%  Similarity=0.122  Sum_probs=23.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|++..++|+.+|||++||++|.+
T Consensus        19 ~~glsq~~lA~~~gis~~~is~~e~   43 (73)
T 3omt_A           19 EKGKTNLWLTETLDKNKTTVSKWCT   43 (73)
T ss_dssp             HHTCCHHHHHHHTTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999875

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

Probab=93.75  E-value=0.22  Score=39.48  Aligned_cols=57  Identities=11%  Similarity=0.054  Sum_probs=41.7

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~lv  118 (258)
                      .+.+..+||+.++|+++||++.+++..+.|-|.-...  .++ .--.+|++-.+.+.+..
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~DrR~~~~~LT~~G~~~~~~~~  125 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSISDADQRKRTVVLTRKGKKKLAEIS  125 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC---CCCSCEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCcccCCeeEeeECHHHHHHHHHHH
Confidence            5799999999999999999999999999998743322  221 12247777666655553

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

Probab=93.75  E-value=0.22  Score=38.39  Aligned_cols=70  Identities=19%  Similarity=0.185  Sum_probs=45.3

Q ss_pred             CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      ++... ..|+... ..|.+.++||+.+++|++||++.+++-.+.|-|.-.+.  .+ ..--.+|++-...+....
T Consensus        36 lt~~~-~~iL~~l~~~~~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~~~~d~R~~~~~lT~~g~~~~~~~~  109 (146)
T 3tgn_A           36 LTNTQ-EHILMLLSEESLTNSELARRLNVSQAAVTKAIKSLVKEGMLETSKDSKDARVIFYQLTDLARPIAEEHH  109 (146)
T ss_dssp             CCHHH-HHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----------CCEECGGGHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeccCCCCCceeEEEECHhHHHHHHHHH
Confidence            45443 4455554 45699999999999999999999999999998743221  22 123346665555544443

>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=93.74  E-value=0.065  Score=39.52  Aligned_cols=56  Identities=16%  Similarity=0.061  Sum_probs=41.1

Q ss_pred             CCCHHHHHHHhCCCHHH-HHHHHHHhhhhCCcccCCCCCC-CCCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGC-VSKILARYHETGSILPGAIGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsT-VsRwikRyrEtGsl~pk~rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      +.+.++||+.++++++| |++.+++..+.|-|...+..++ .--.+|++-.+.+.+..
T Consensus        30 ~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~~~~drR~~~~~LT~~G~~~~~~~~   87 (95)
T 2pg4_A           30 EPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKEETLSYRVKTLKLTEKGRRLAECLE   87 (95)
T ss_dssp             CCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeecCCCCCCeEEEEECHhHHHHHHHHH
Confidence            58999999999999999 9999999999998862222221 12347777666555543

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

Probab=93.73  E-value=0.031  Score=42.58  Aligned_cols=44  Identities=14%  Similarity=0.215  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQL-GIRPCDISRQL-RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~-G~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|..|+....+ +.+.++||+.+ +||.+||++.+++..+.|-|.
T Consensus        14 ~~~~~IL~~L~~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~   59 (107)
T 2hzt_A           14 KWKXVILXHLTHGKKRTSELKRLMPNITQKMLTQQLRELEADGVIN   59 (107)
T ss_dssp             TTHHHHHHHHTTCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             ccHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence            346667766544 58999999999 999999999999999999874

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

Probab=93.73  E-value=0.23  Score=38.37  Aligned_cols=69  Identities=9%  Similarity=0.086  Sum_probs=45.5

Q ss_pred             CCHHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ++... ..|+..+ . .+.+.++||+.++++++||++.+++..+.|-|.-.  +..+ ...-.+|++-.+.+.+.
T Consensus        40 l~~~~-~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  113 (150)
T 2rdp_A           40 ITPPQ-FVALQWLLEEGDLTVGELSNKMYLACSTTTDLVDRMERNGLVARVRDEHDRRVVRIRLLEKGERIIEEV  113 (150)
T ss_dssp             SCHHH-HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC---CEEEEECHHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCcceeEeEECHhHHHHHHHH
Confidence            45432 3344443 3 57899999999999999999999999999977422  1122 12234777766655544

>1rr7_A Middle operon regulator; MOR, transcription; 2.20A {Enterobacteria phage MU} SCOP: a.4.1.14

Probab=93.73  E-value=0.045  Score=44.18  Aligned_cols=47  Identities=17%  Similarity=0.186  Sum_probs=37.0

Q ss_pred             CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      ++.......|.+.|..--.|.+..++|+.+|+|..+|++++++.+..
T Consensus        73 k~~~~~~~~Rn~~I~~~f~G~n~~eLArkYgLSer~I~~Ii~~~r~~  119 (129)
T 1rr7_A           73 RGQALDSLIRDLRIWNDFNGRNVSELTTRYGVTFNTVYKAIRRMRRL  119 (129)
T ss_dssp             CSHHHHHHHHHHHHHHHCCSSCHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCchHHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence            33333445777777665579999999999999999999999988743

>2pij_A Prophage PFL 6 CRO; transcription factor, helix-turn-helix, structural evolution, transcription; 1.70A {Pseudomonas fluorescens}

Probab=93.73  E-value=0.079  Score=36.27  Aligned_cols=25  Identities=16%  Similarity=0.385  Sum_probs=22.7

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.| +..++|+.+|||.++|++|++
T Consensus        11 ~~~g-s~~~~A~~lgis~~~vs~~~~   35 (67)
T 2pij_A           11 EEHG-TQSALAAALGVNQSAISQMVR   35 (67)
T ss_dssp             HHTC-CHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHcC-CHHHHHHHHCcCHHHHHHHHc
Confidence            3568 999999999999999999995

>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=93.72  E-value=0.15  Score=34.52  Aligned_cols=36  Identities=14%  Similarity=0.124  Sum_probs=28.3

Q ss_pred             HHHHHHHHH-HHH-c-CCCHHHHHHHh-----CCCHHHHHHHHH
Q psy15598         50 NSVRMRIVE-LAQ-L-GIRPCDISRQL-----RVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~-L~~-~-G~S~~eIAr~L-----GVSrsTVsRwik   85 (258)
                      ...|..+|. +.. . ..+..+|++.|     +||.+||+|.++
T Consensus         3 ~~~R~~~i~~ll~~~~~~t~~el~~~l~~~~~~vs~~Tv~R~L~   46 (64)
T 2p5k_A            3 KGQRHIKIREIITSNEIETQDELVDMLKQDGYKVTQATVSRDIK   46 (64)
T ss_dssp             HHHHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCcCHHHHHHHHH
Confidence            345665544 444 3 47999999999     999999999999

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

Probab=93.69  E-value=0.14  Score=39.32  Aligned_cols=40  Identities=8%  Similarity=0.134  Sum_probs=33.8

Q ss_pred             HHHHHH-H--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         55 RIVELA-Q--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        55 RIV~L~-~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|+..+ .  .+.+..+||+.++++++||++.+++..+.|-|.
T Consensus        41 ~iL~~l~~~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~   83 (146)
T 2fbh_A           41 LVLLHLARHRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVR   83 (146)
T ss_dssp             HHHHHHHHCSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCee
Confidence            344444 3  468999999999999999999999999999774

>3lap_A Arginine repressor; arginine repressor, DNA binding, DNA-canavanine ternary complex; HET: GGB; 2.15A {Mycobacterium tuberculosis} PDB: 3fhz_A* 3ere_D* 3laj_A*

Probab=93.68  E-value=0.13  Score=43.55  Aligned_cols=52  Identities=13%  Similarity=0.033  Sum_probs=46.6

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      +-...|++++.++.--+..||.+.|++.|+.+     +.+||+|-|+.++..|....
T Consensus        20 ~R~~~I~~iI~~~~I~tQeEL~~~L~~~Gi~v-----TQATlSRDikEL~lvKv~~~   71 (170)
T 3lap_A           20 GRQARIVAILSSAQVRSQNELAALLAAEGIEV-----TQATLSRDLEELGAVKLRGA   71 (170)
T ss_dssp             HHHHHHHHHHHHSCCCSHHHHHHHHHHTTCCC-----CHHHHHHHHHHHTCEEECCT
T ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCc-----CchhHHHHHHHcCcEEeecC
Confidence            34678999999999999999999999999986     99999999999999987643

>3szt_A QCSR, quorum-sensing control repressor; quorum sensing acyl-homoserine lactone, helix-turn-helix, transcription factor, 3-OXO-C12 HSL; HET: OHN; 2.55A {Pseudomonas aeruginosa}

Probab=93.67  E-value=0.11  Score=44.88  Aligned_cols=44  Identities=11%  Similarity=0.107  Sum_probs=37.0

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ...++...+ +|+.+..+|++.++||+.|+||.+||...+++-.+
T Consensus       173 ~~~Lt~re~-~vl~~~~~G~s~~eIa~~l~is~~tV~~~~~~~~~  216 (237)
T 3szt_A          173 NVRLTARET-EMLKWTAVGKTYGEIGLILSIDQRTVKFHIVNAMR  216 (237)
T ss_dssp             GCCCCHHHH-HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            345777666 57777789999999999999999999999998763

>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=93.66  E-value=0.23  Score=38.04  Aligned_cols=56  Identities=20%  Similarity=0.206  Sum_probs=40.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCC-CCCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      +.+.++||+.++++++||++.+++..+.|-|.-.  +..++ .--.+|++-.+.+.+..
T Consensus        47 ~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~~~~~D~R~~~~~LT~~G~~~~~~~~  105 (139)
T 3eco_A           47 GLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRYVDAQDTRRKNIGLTTSGIKLVEAFT  105 (139)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECCC--CCEEEEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecCCCCCCCeeeeEECHHHHHHHHHHH
Confidence            7899999999999999999999999999987422  22221 12347777666655543

>1l0o_C Sigma factor; bergerat fold, helix-turn-helix, protein binding; HET: ADP; 2.90A {Geobacillus stearothermophilus} SCOP: a.4.13.2

Probab=93.64  E-value=0.012  Score=48.84  Aligned_cols=42  Identities=12%  Similarity=0.112  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||++++.|-+
T Consensus       198 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~  239 (243)
T 1l0o_C          198 ELDERERLIVYLRYYKDQTQSEVASRLGISQVQMSRLEKKIL  239 (243)
T ss_dssp             ------------------------------------------
T ss_pred             hCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            467777765555567999999999999999999999998865

>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=93.64  E-value=0.21  Score=38.76  Aligned_cols=64  Identities=19%  Similarity=0.194  Sum_probs=43.6

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~l  117 (258)
                      ..|+..+ . .+.+.++||+.++++++||++.+++..+.|-|.-..  ..++ .--.+|++-.+.+...
T Consensus        43 ~~iL~~l~~~~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  111 (152)
T 3bj6_A           43 RAILEGLSLTPGATAPQLGAALQMKRQYISRILQEVQRAGLIERRTNPEHARSHRYWLTPRGEAIITAI  111 (152)
T ss_dssp             HHHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCSSSTTSCEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCcccccceeeEEChhhHHHHHHH
Confidence            3444443 3 468999999999999999999999999999874222  1221 1224677655555444

>4g6q_A Putative uncharacterized protein; structural genomics, PSI-biology, protein structure initiati midwest center for structural genomics, MCSG; 2.08A {Kribbella flavida}

Probab=93.63  E-value=0.044  Score=46.00  Aligned_cols=49  Identities=16%  Similarity=0.259  Sum_probs=43.2

Q ss_pred             CCCCHHHHHHHHHHHHc-CCCHHHHHHHhC-CCHHHHHHHHHHhhhhCCcc
Q psy15598         46 RPLPNSVRMRIVELAQL-GIRPCDISRQLR-VSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~-G~S~~eIAr~LG-VSrsTVsRwikRyrEtGsl~   94 (258)
                      +-++.-.|.+|+.+..+ +++.++||+.|+ ++.+||++-++..++.|-|+
T Consensus        18 ~~La~P~Rl~il~~L~~~~~~~~~l~~~l~~~~~~~~s~Hl~~L~~aglv~   68 (182)
T 4g6q_A           18 DLLHHPLRWRITQLLIGRSLTTRELAELLPDVATTTLYRQVGILVKAGVLM   68 (182)
T ss_dssp             HHTTSHHHHHHHHHTTTSCEEHHHHHHHCTTBCHHHHHHHHHHHHHHTSEE
T ss_pred             HHhCCHHHHHHHHHHHhCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCeE
Confidence            34778899999999864 589999999996 99999999999999999764

>3qao_A LMO0526 protein, MERR-like transcriptional regulator; structural genomics, the center for structural genomics of I diseases, csgid; 1.87A {Listeria monocytogenes}

Probab=93.62  E-value=0.17  Score=44.69  Aligned_cols=69  Identities=14%  Similarity=0.082  Sum_probs=49.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      +.+++.++|+.+|||..|++.|-+    .|.+.|..+..+.-|..++++...|..++. ..-.+++.+|+..|.
T Consensus         2 ~~~tI~evA~~~gvs~~TLRyYe~----~GLL~p~~~~~~GyR~Y~~~dl~~L~~I~~lr~~G~sL~eIk~~l~   71 (249)
T 3qao_A            2 NAMQIKELAELTGVSVRTLHHYDK----IGLLVPQKDDWNGYRIYSEKDVDKLQQILFFKELDFPLKKIQQILD   71 (249)
T ss_dssp             CCBCHHHHHHHHCCCHHHHHHHHH----TTSSCCEECTTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHH----CCCCCCceECCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHhc
Confidence            357899999999999999976654    688877653322457788877766655433 334788888888775

>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=93.61  E-value=0.09  Score=48.42  Aligned_cols=45  Identities=16%  Similarity=0.211  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         50 NSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        50 ~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..-+.+|+.++..  .+|..+||+.+|+|++||++++++..+.|.+.
T Consensus        15 ~~n~~~il~~l~~~~~~sr~~la~~~~ls~~tv~~~v~~L~~~g~i~   61 (406)
T 1z6r_A           15 QTNAGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQ   61 (406)
T ss_dssp             HHHHHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HhHHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            3455678888763  48999999999999999999999999999763

>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=93.59  E-value=0.19  Score=38.63  Aligned_cols=57  Identities=9%  Similarity=0.001  Sum_probs=41.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ..+.+.++||+.++++++||++.+++..+.|-|.-..  ..+ ...-.+|++-...+...
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~~  107 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRVRDREDRRKILIEITEKGLETFNKG  107 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHH
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeecCCCCCceEEEEECHHHHHHHHHH
Confidence            4568999999999999999999999999999874221  122 11234677666555444

>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=93.55  E-value=0.077  Score=37.54  Aligned_cols=25  Identities=12%  Similarity=0.085  Sum_probs=22.8

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|+|..++|+.+|||++||++|-+
T Consensus        22 ~~gltq~elA~~~gvs~~tis~~E~   46 (73)
T 3fmy_A           22 KLSLTQKEASEIFGGGVNAFSRYEK   46 (73)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHT
T ss_pred             HcCCCHHHHHHHhCcCHHHHHHHHc
Confidence            4799999999999999999999864

>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=93.52  E-value=0.21  Score=39.69  Aligned_cols=64  Identities=13%  Similarity=0.151  Sum_probs=44.3

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      .|+..+ . .+.+..+||+.++|+++||++.+++..+.|-|.-..  ..++ .--.+|++-.+.+.+..
T Consensus        50 ~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~  118 (162)
T 3k0l_A           50 TALSVLAAKPNLSNAKLAERSFIKPQSANKILQDLLANGWIEKAPDPTHGRRILVTVTPSGLDKLNQCN  118 (162)
T ss_dssp             HHHHHHHHCTTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEEECCSSSCCEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEecCCCCcCCeeEeEECHhHHHHHHHHH
Confidence            344443 3 579999999999999999999999999999874222  2221 12347777666655543

>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=93.51  E-value=0.24  Score=37.84  Aligned_cols=32  Identities=9%  Similarity=0.210  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.+..+||+.++++++||++.+++..+.|-|.
T Consensus        50 ~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~   81 (141)
T 3bro_A           50 EVLQRDLESEFSIKSSTATVLLQRMEIKKLLY   81 (141)
T ss_dssp             CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHHCCCcchHHHHHHHHHHCCCEE
Confidence            58999999999999999999999999999774

>3ihu_A Transcriptional regulator, GNTR family; YP_298823.1, DNA binding protein, structural genomics, joint for structural genomics, JCSG; HET: MSE; 1.92A {Ralstonia eutropha}

Probab=93.50  E-value=0.18  Score=42.73  Aligned_cols=49  Identities=16%  Similarity=0.154  Sum_probs=38.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      ++..++|++||||+++|+.-+++....|-|...++.|..=+.++.+...
T Consensus        40 L~E~~La~~lgVSRtpVREAl~~L~~eGlv~~~~~~G~~V~~~~~~~~~   88 (222)
T 3ihu_A           40 LVETDLVAHFGVGRNSVREALQRLAAEGIVDLQRHRGAVIRRLSLQETL   88 (222)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECSTTCEEECCCCHHHHH
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHHHH
Confidence            4789999999999999999999999999987666656332334544333

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

Probab=93.50  E-value=0.21  Score=40.04  Aligned_cols=57  Identities=11%  Similarity=0.047  Sum_probs=41.5

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-..  ..+ ..--.+|++-.+.+.+..
T Consensus        58 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~  117 (168)
T 2nyx_A           58 GPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVT  117 (168)
T ss_dssp             CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHHHH
Confidence            578999999999999999999999999999874221  122 112347777666655543

>1hw1_A FADR, fatty acid metabolism regulator protein; helix-turn-helix, helix bundle, transcription; 1.50A {Escherichia coli} SCOP: a.4.5.6 a.78.1.1 PDB: 1hw2_A 1e2x_A 1h9g_A* 1h9t_A

Probab=93.47  E-value=0.071  Score=45.34  Aligned_cols=54  Identities=13%  Similarity=0.089  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         47 PLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++...+-..|.+.+..|       + +-.++|++||||+.||+.-+++-...|-|...++.|
T Consensus         7 ~~~~~v~~~l~~~I~~g~l~pG~~LPsE~eLa~~~gVSR~tVReAL~~L~~eGlv~~~~g~G   68 (239)
T 1hw1_A            7 SPAGFAEEYIIESIWNNRFPPGTILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   68 (239)
T ss_dssp             SHHHHHHHHHHHHHHTTSSCTTSBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTEE
T ss_pred             cHHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCCC
Confidence            34444555555555443       3 789999999999999999999999999886555444

>3g5g_A Regulatory protein; transcriptional regulator, helix-turn-helix, restriction- modification, transcription regulator; 2.80A {Enterobacter SP} PDB: 3fya_A

Probab=93.46  E-value=0.061  Score=40.60  Aligned_cols=42  Identities=17%  Similarity=0.151  Sum_probs=31.9

Q ss_pred             CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |...+...+-.+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus        21 M~~~~~~~ig~~lr~~R~~~gltq~elA~~~gis~~~is~iE~   63 (99)
T 3g5g_A           21 MESFLLSKVSFVIKKIRLEKGMTQEDLAYKSNLDRTYISGIER   63 (99)
T ss_dssp             -CCHHHHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            333444556666666654 699999999999999999999854

>3vib_A MTRR; helix-turn-helix motif, DNA binding, DNA binding protein; HET: CXS; 2.40A {Neisseria gonorrhoeae}

Probab=93.42  E-value=0.11  Score=41.87  Aligned_cols=41  Identities=10%  Similarity=0.086  Sum_probs=30.3

Q ss_pred             CCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.-..+.|++|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         4 ~~~~~~~tR~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~t~Y~~F~   52 (210)
T 3vib_A            4 TKTEALKTKEHLMLAALETFYRKGIARTSLNEIAQAAGVTRDALYWHFK   52 (210)
T ss_dssp             ----CHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             CchhHHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCC
Confidence            3445677899999864     344   6999999999999999998643

>2dg7_A Putative transcriptional regulator; helix-turn-helix motif, TETR family, gene regulation; 2.30A {Streptomyces coelicolor}

Probab=93.41  E-value=0.085  Score=42.01  Aligned_cols=42  Identities=14%  Similarity=0.187  Sum_probs=32.1

Q ss_pred             CCCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      |+|+ ..+.|.+|++..     +.|   .|.++||+..|||++|+|+....
T Consensus         1 M~R~-~~~~r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   50 (195)
T 2dg7_A            1 MARW-DPGAEQRLKRAALELYSEHGYDNVTVTDIAERAGLTRRSYFRYFPD   50 (195)
T ss_dssp             CCSS-CTTHHHHHHHHHHHHHHHSCGGGCCHHHHHHHTTCCHHHHHHHCSS
T ss_pred             CCCC-cHHHHHHHHHHHHHHHHhcCccccCHHHHHHHhCCCHHHHHHHcCC
Confidence            4554 456777888754     334   79999999999999999987654

>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=93.40  E-value=0.12  Score=37.42  Aligned_cols=50  Identities=8%  Similarity=0.204  Sum_probs=34.6

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA  126 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita  126 (258)
                      +.|++..++|+.+|||++||++|.+-     .           +..+.+....|.+.+.-++....
T Consensus        28 ~~glsq~~lA~~~gis~~~is~~e~g-----~-----------~~~~~~~l~~ia~~l~v~~~~l~   77 (92)
T 1lmb_3           28 ELGLSQESVADKMGMGQSGVGALFNG-----I-----------NALNAYNAALLAKILKVSVEEFS   77 (92)
T ss_dssp             HHTCCHHHHHHHHTSCHHHHHHHHTT-----S-----------SCCCHHHHHHHHHHHTSCGGGTC
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHcC-----C-----------CCCCHHHHHHHHHHHCCCHHHHh
Confidence            46999999999999999999999752     1           11234455666666655554433

>3c7j_A Transcriptional regulator, GNTR family; structural genomics, PSI-2, protein structure initiative, midwest center for STR genomics; HET: MSE; 2.10A {Pseudomonas syringae PV}

Probab=93.32  E-value=0.059  Score=46.71  Aligned_cols=52  Identities=17%  Similarity=0.208  Sum_probs=41.1

Q ss_pred             CHHHHHHHHHH-HHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         49 PNSVRMRIVEL-AQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        49 S~dlR~RIV~L-~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      -..+|..|+.. +..|  ++..++|++||||++||+.-+++....|.|...+++|
T Consensus        32 ~~~L~~~I~~g~l~pG~~L~e~~La~~lgVSr~~VReAL~~L~~~Glv~~~~~~G   86 (237)
T 3c7j_A           32 EEKLRNAIIDGSLPSGTALRQQELATLFGVSRMPVREALRQLEAQSLLRVETHKG   86 (237)
T ss_dssp             HHHHHHHHHTSSSCTTCBCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHHhCCCCCcCeeCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence            34566667653 3334  6999999999999999999999999999987665555

>3bs3_A Putative DNA-binding protein; XRE-family, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.65A {Bacteroides fragilis}

Probab=93.30  E-value=0.078  Score=36.68  Aligned_cols=25  Identities=12%  Similarity=0.044  Sum_probs=22.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|++..++|+.+|||++||++|.+
T Consensus        21 ~~g~s~~~lA~~~gis~~~i~~~e~   45 (76)
T 3bs3_A           21 EKQRTNRWLAEQMGKSENTISRWCS   45 (76)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999874

>3rkx_A Biotin-[acetyl-COA-carboxylase] ligase; biotin protein ligase, 3 domains, enzyme DNA binding, biotin coupling domains; 2.10A {Staphylococcus aureus} PDB: 3rir_A* 3rkw_A 3rky_A* 3v7c_A* 3v7s_A* 3v8j_A 3v7r_A 3v8k_A* 3v8l_A* 4dq2_A*

Probab=93.27  E-value=0.09  Score=48.16  Aligned_cols=42  Identities=19%  Similarity=0.282  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHH--cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         51 SVRMRIVELAQ--LG--IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        51 dlR~RIV~L~~--~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +.|.+|+++..  .|  +|..+||++||||+++|++-+++.++.|.
T Consensus         3 ~~~~~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~   48 (323)
T 3rkx_A            3 KYSQDVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLEGC   48 (323)
T ss_dssp             CHHHHHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTC
T ss_pred             hHHHHHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCC
Confidence            36788998873  35  79999999999999999999999999996

>2fq4_A Transcriptional regulator, TETR family; DNA-binding protein, bacillu structural genomics, PSI, protein structure initiative; 1.79A {Bacillus cereus} SCOP: a.4.1.9 a.121.1.1

Probab=93.27  E-value=0.13  Score=41.07  Aligned_cols=42  Identities=21%  Similarity=0.322  Sum_probs=31.7

Q ss_pred             CCCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+++-..+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         5 ~~r~r~~~~r~~Il~aA~~lf~e~G~~~~t~~~IA~~agvsk~tlY~~F~   54 (192)
T 2fq4_A            5 RGRPRNIETQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   54 (192)
T ss_dssp             ----CCHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             CCCCCChHHHHHHHHHHHHHHHHcCcccccHHHHHHHcCCCHHHHHHHCC
Confidence            35556778899998864     234   6999999999999999999764

>3qq6_A HTH-type transcriptional regulator SINR; helix-turn-helix motif, biofilm, repressor, SINI; 1.90A {Bacillus subtilis}

Probab=93.25  E-value=0.096  Score=37.44  Aligned_cols=34  Identities=18%  Similarity=0.277  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +=.+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus        11 ~~~~ik~~R~~~gltq~elA~~~gis~~~is~~E~   45 (78)
T 3qq6_A           11 IGQRIKQYRKEKGYSLSELAEKAGVAKSYLSSIER   45 (78)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             ccHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3445555554 799999999999999999999864

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

Probab=93.22  E-value=0.35  Score=37.94  Aligned_cols=63  Identities=17%  Similarity=0.199  Sum_probs=42.8

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~l  117 (258)
                      .|+..+ . .+.+..+||+.++|+++||++.+++..+.|-|.-..  ..+ ..--.+|++-.+.+.+.
T Consensus        53 ~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  120 (162)
T 2fa5_A           53 RVITILALYPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRETHGDDRRRSMLALSPAGRQVYETV  120 (162)
T ss_dssp             HHHHHHHHSTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC---------CCCEECHHHHHHHHHH
T ss_pred             HHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeecCCCCCCeeEEEECHHHHHHHHHH
Confidence            344443 3 469999999999999999999999999999874322  122 12234677766655544

>1mkm_A ICLR transcriptional regulator; structural genomics, winged helix-turn-helix, PSI, protein structure initiative; 2.20A {Thermotoga maritima} SCOP: a.4.5.33 d.110.2.2

Probab=93.21  E-value=0.13  Score=44.56  Aligned_cols=69  Identities=14%  Similarity=0.174  Sum_probs=47.2

Q ss_pred             CHHHHHHHHHHHH-c--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         49 PNSVRMRIVELAQ-L--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        49 S~dlR~RIV~L~~-~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.+.-.+|++++. .  +++.++||+.+|++++||+|.++...+.|-+.-. ..+  .-.+++...+.-......
T Consensus         6 sl~r~l~iL~~l~~~~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~-~~~--~Y~lg~~~~~l~~~~~~~   77 (249)
T 1mkm_A            6 TLKKAFEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRK-KDK--RYVPGYKLIEYGSFVLRR   77 (249)
T ss_dssp             THHHHHHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC-TTS--CEEECTHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEC-CCC--cEEECHHHHHHHHHHHhc
Confidence            3444567787764 2  5899999999999999999999999999987533 222  233555544443333333

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

Probab=93.21  E-value=0.27  Score=38.26  Aligned_cols=64  Identities=13%  Similarity=0.168  Sum_probs=44.3

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc--CCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILP--GAIGGS-K--PRVTTPKVVSYIKELK  118 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p--k~rgG~-R--PrklT~e~~~~I~~lv  118 (258)
                      .|+..+ . .+.+.++||+.++++++||++.+++..+.|-|.-  ...... |  --.+|++-.+.+.+..
T Consensus        45 ~iL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~~~d~R~~~~~LT~~G~~~~~~~~  115 (154)
T 2qww_A           45 AMINVIYSTPGISVADLTKRLIITGSSAAANVDGLISLGLVVKLNKTIPNDSMDLTLKLSKKGEDLSKRST  115 (154)
T ss_dssp             HHHHHHHHSTTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEESCC--CTTCTTCEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCcCCCCCCceeEeEECHHHHHHHHHHH
Confidence            444443 3 4689999999999999999999999999998754  322211 2  2347777666655543

>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=93.16  E-value=0.091  Score=39.78  Aligned_cols=35  Identities=17%  Similarity=0.285  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+-.+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         9 ~~~~~l~~~r~~~glsq~~lA~~~gis~~~i~~~e~   44 (114)
T 3op9_A            9 QFAENLSRLKKEHGLKNHQIAELLNVQTRTVAYYMS   44 (114)
T ss_dssp             CHHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            35556666654 699999999999999999999976

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

Probab=93.15  E-value=0.17  Score=40.78  Aligned_cols=44  Identities=25%  Similarity=0.236  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHHc---CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQL---GIRPCDISRQL-----RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~---G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|..|++++.+   .+|..+|.+.|     +||.+||||-++.+.+.|.+.
T Consensus        22 ~qR~~Il~~L~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   73 (145)
T 2fe3_A           22 PQRHAILEYLVNSMAHPTADDIYKALEGKFPNMSVATVYNNLRVFRESGLVK   73 (145)
T ss_dssp             HHHHHHHHHHHHCSSCCCHHHHHHHHGGGCTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCChhhHHHHHHHHHHCCCEE
Confidence            467788888742   47999999999     899999999999999999763

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

Probab=93.13  E-value=0.19  Score=39.67  Aligned_cols=64  Identities=17%  Similarity=0.135  Sum_probs=43.4

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ..|+..+ . .+.+.++||+.++|+++||++.+++..+.|-|.-..  ..+ .+--.+|++-.+.+...
T Consensus        55 ~~iL~~l~~~~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~  123 (162)
T 3cjn_A           55 MRALAILSAKDGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRREVDSDDQRSSRVYLTPAGRAVYDRL  123 (162)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEC--CCSSEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHH
Confidence            3444443 3 468999999999999999999999999999874221  122 11234677655555444

>2di3_A Bacterial regulatory proteins, GNTR family; helix-turn-helix, transcription; 2.05A {Corynebacterium glutamicum}

Probab=93.13  E-value=0.19  Score=42.98  Aligned_cols=50  Identities=22%  Similarity=0.282  Sum_probs=38.2

Q ss_pred             HHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCccc--CCC--CC
Q psy15598         51 SVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILP--GAI--GG  100 (258)
Q Consensus        51 dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p--k~r--gG  100 (258)
                      .+|..|+.. +.-|  + +-.++|++||||+++|+.-+++-...|-|+.  .++  +|
T Consensus        12 ~L~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~L~~~GlV~~~~~~~~~~G   69 (239)
T 2di3_A           12 WVTEELRSGRLKIGDHLPSERALSETLGVSRSSLREALRVLEALGTISTATGSGPRSG   69 (239)
T ss_dssp             HHHHHHHHTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHHTSEECCSTTSGGGC
T ss_pred             HHHHHHHhCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEeecccCCCCC
Confidence            344555543 2234  4 5789999999999999999999999999877  666  55

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

Probab=93.07  E-value=0.18  Score=39.42  Aligned_cols=63  Identities=13%  Similarity=0.106  Sum_probs=41.4

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-CC--CCCCHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-KP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-RP--rklT~e~~~~I~~l  117 (258)
                      .|+..+ . .+.+.++||+.++++++||++.+++..+.|-|.-.+.... |.  -.+|++-.+.+.+.
T Consensus        45 ~iL~~l~~~~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~  112 (149)
T 4hbl_A           45 LVMLTLWEENPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRERQQSDKRQLIITLTDNGQQQQEAV  112 (149)
T ss_dssp             HHHHHHHHSSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC---------CEEEECSHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeCCCCCCcceeeeeECHHHHHHHHHH
Confidence            344443 3 5789999999999999999999999999998743322111 21  23666655555444

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

Probab=93.06  E-value=0.16  Score=36.42  Aligned_cols=50  Identities=20%  Similarity=0.149  Sum_probs=37.0

Q ss_pred             CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        106 TTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       106 lT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +++. +..|.+++.+.  ...++.||.+.|.+.+..+     |.+||+|.|+.+....
T Consensus        15 ~t~~-r~~IL~~l~~~~~~~~s~~el~~~l~~~~~~i-----s~~TVyR~L~~L~~~G   66 (83)
T 2fu4_A           15 VTLP-RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI-----GLATVYRVLNQFDDAG   66 (83)
T ss_dssp             CCHH-HHHHHHHHTSGGGSSBCHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHHHT
T ss_pred             cCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCC-----CHhhHHHHHHHHHHCC
Confidence            4554 45566666554  4689999999998776654     9999999998765443

>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=93.02  E-value=0.31  Score=38.01  Aligned_cols=58  Identities=17%  Similarity=0.115  Sum_probs=41.0

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc----CCCCC-CCCCCCCHHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILARYHETGSILP----GAIGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p----k~rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ...+.+.++||+.++++++||++.+++..+.|-|.-    .+..+ ..--.+|++-.+.+.+.
T Consensus        48 ~~~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~~~~~~D~R~~~~~lT~~G~~~~~~~  110 (151)
T 3kp7_A           48 SIEALTVGQITEKQGVNKAAVSRRVKKLLNAELVKLEKPDSNTDQRLKIIKLSNKGKKYIKER  110 (151)
T ss_dssp             HHSCBCHHHHHHHHCSCSSHHHHHHHHHHHTTSEEC-----------CCBEECHHHHHHHHHH
T ss_pred             HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCCCeeEEEECHhHHHHHHHH
Confidence            446799999999999999999999999999998753    22222 12234777655555544

>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=93.00  E-value=0.17  Score=39.48  Aligned_cols=56  Identities=11%  Similarity=0.144  Sum_probs=39.5

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      +++.++||+.++++++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        54 ~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  112 (150)
T 3fm5_A           54 GVNQRGVAATMGLDPSQIVGLVDELEERGLVVRTLDPSDRRNKLIAATEEGRRLRDDAK  112 (150)
T ss_dssp             CCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-----------CEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeeCCccccchheeeECHHHHHHHHHHH
Confidence            579999999999999999999999999998743222  12 112347777666665554

>1sfu_A 34L protein; protein/Z-DNA complex, DNA binding protein/DNA complex; 2.00A {Yaba-like disease virus} SCOP: a.4.5.19

Probab=92.94  E-value=0.065  Score=39.94  Aligned_cols=30  Identities=10%  Similarity=0.315  Sum_probs=28.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+..+||++||++++.|.|.+-+..+.|.+
T Consensus        30 ~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V   59 (75)
T 1sfu_A           30 TTAISLSNRLKINKKKINQQLYKLQKEDTV   59 (75)
T ss_dssp             ECHHHHHHHTTCCHHHHHHHHHHHHHTTSE
T ss_pred             hHHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence            689999999999999999999999999987

>3eus_A DNA-binding protein; structural genomics, PSI2,MCSG, protein structure initiative, midwest center for structural genomic binding; 1.80A {Silicibacter pomeroyi}

Probab=92.93  E-value=0.093  Score=38.12  Aligned_cols=33  Identities=18%  Similarity=0.329  Sum_probs=27.3

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +-.+|-.+.+ .|+|..++|+.+|||+++|++|.
T Consensus        15 ~g~~l~~~R~~~gltq~elA~~~gis~~~is~~E   48 (86)
T 3eus_A           15 LCQRLRQARLDAGLTQADLAERLDKPQSFVAKVE   48 (86)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHTTCCHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence            4556666554 79999999999999999999885

>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=92.93  E-value=0.27  Score=38.24  Aligned_cols=63  Identities=11%  Similarity=0.084  Sum_probs=42.8

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I~~l  117 (258)
                      .|+..+ . .+.+.++||+.++++++||++.+++..+.|-|.-.  +..+ ...-.+|++-...+...
T Consensus        41 ~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  108 (155)
T 1s3j_A           41 FVLASLKKHGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEV  108 (155)
T ss_dssp             HHHHHHHHHSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCceEEEEECHHHHHHHHHH
Confidence            344443 3 46899999999999999999999999999977422  1122 11234677655554443

>1tbx_A ORF F-93, hypothetical 11.0 kDa protein; sulfolobus spindle virus, winged helix, fusellovirus; 2.70A {Sulfolobus virus 1} SCOP: a.4.5.48

Probab=92.92  E-value=0.069  Score=39.44  Aligned_cols=64  Identities=17%  Similarity=0.139  Sum_probs=44.0

Q ss_pred             HHHHHH-H-cCCCHHHH----HHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDI----SRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eI----Ar~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      .|+..+ + .+.+..+|    |+.++++++||++.+++..+.|-+.-...++.+--.+|++-.+.+..+.
T Consensus        12 ~iL~~l~~~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~~~~r~~~~~LT~~G~~~~~~~~   81 (99)
T 1tbx_A           12 IVLAYLYDNEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKERQERGEKRLYLTEKGKLFAISLK   81 (99)
T ss_dssp             HHHHHHTTCTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEEecCCceEEEECHHHHHHHHHHH
Confidence            344444 3 46899999    8999999999999999999999874322112123447776666555443

>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=92.90  E-value=0.24  Score=38.08  Aligned_cols=55  Identities=20%  Similarity=0.181  Sum_probs=39.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCCCC--CCCCHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGSKP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~RP--rklT~e~~~~I~~l  117 (258)
                      .+.+.++||+.+++|++||++.+++..+.|-|.-..  ..+ |.  -.+|++-...+...
T Consensus        42 ~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~~~~~d~-R~~~~~lT~~G~~~~~~~  100 (144)
T 1lj9_A           42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNK-KIKRIYATEKGKNVYPII  100 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCT-TCEEEEECHHHHHHHHHH
T ss_pred             cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCC-ceeeeEEChhHHHHHHHH
Confidence            468999999999999999999999999999774221  122 22  34677655555444

>1fx7_A Iron-dependent repressor IDER; DTXR, iron-dependent regulator, signaling protein; 2.00A {Mycobacterium tuberculosis} SCOP: a.4.5.24 a.76.1.1 b.34.1.2 PDB: 1u8r_A

Probab=92.89  E-value=1.1  Score=38.31  Aligned_cols=62  Identities=19%  Similarity=0.196  Sum_probs=45.0

Q ss_pred             HHHHHHH-HcCCCH--HHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRP--CDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        54 ~RIV~L~-~~G~S~--~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      .+++... +.|.+.  .+||+.|++|++||++.+++..+.|-+.-.+.   +.-.+|+.-.+.+.+..
T Consensus        12 L~~L~~l~~~~~~~~~~~La~~l~vs~~tvs~~l~~Le~~GlV~r~~~---~~v~LT~~G~~~~~~~~   76 (230)
T 1fx7_A           12 LRTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAGD---RHLELTEKGRALAIAVM   76 (230)
T ss_dssp             HHHHHHHHHHTSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTT---SCEEECHHHHHHHHHHH
T ss_pred             HHHHHHHhhcCCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC---ccEEECHHHHHHHHHHH
Confidence            3444433 468877  99999999999999999999999998754332   33457777666555444

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

Probab=92.86  E-value=0.14  Score=40.45  Aligned_cols=43  Identities=19%  Similarity=0.232  Sum_probs=37.6

Q ss_pred             HHHHHHHHHHH-c--CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ-L--GIRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~-~--G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      ..|..|++++. .  .+|..+|.+.|     +||.+||||.++.+.+.|.+
T Consensus        11 ~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv   61 (131)
T 2o03_A           11 RQRAAISTLLETLDDFRSAQELHDELRRRGENIGLTTVYRTLQSMASSGLV   61 (131)
T ss_dssp             HHHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHTTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCE
Confidence            46888888875 2  37999999999     89999999999999999975

>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=92.86  E-value=0.14  Score=38.13  Aligned_cols=46  Identities=13%  Similarity=0.075  Sum_probs=37.6

Q ss_pred             CHHHHHHHHHHHHhCC---CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        107 TPKVVSYIKELKQKDP---GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       107 T~e~~~~I~~lv~~nP---~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ..+.+..|++++++++   .+++.||++.|.          +|.+||++.|.++..+..
T Consensus         8 ~~~~~~~IL~~L~~~~pg~~~t~~eLA~~Lg----------vsr~tV~~~L~~Le~~G~   56 (81)
T 1qbj_A            8 YQDQEQRILKFLEELGEGKATTAHDLSGKLG----------TPKKEINRVLYSLAKKGK   56 (81)
T ss_dssp             HHHHHHHHHHHHHHHCTTCCBCHHHHHHHHT----------CCHHHHHHHHHHHHHTTS
T ss_pred             chHHHHHHHHHHHHcCCCCCcCHHHHHHHHC----------cCHHHHHHHHHHHHHCCC
Confidence            3556778889999988   899999999884          499999999998765543

>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=92.85  E-value=0.068  Score=49.85  Aligned_cols=44  Identities=18%  Similarity=0.197  Sum_probs=37.2

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      -+.+|+.++.  ..+|..+||+.+|+|++||++++++..+.|.+..
T Consensus        40 n~~~il~~l~~~~~~sr~ela~~~gls~~tv~~~v~~L~~~gli~~   85 (429)
T 1z05_A           40 NAGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIHE   85 (429)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            4556887764  3589999999999999999999999999997643

>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=92.83  E-value=0.08  Score=40.64  Aligned_cols=33  Identities=30%  Similarity=0.398  Sum_probs=30.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+++.++||+.+|++++||++.+++..+.|-|.
T Consensus        40 ~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~   72 (152)
T 1ku9_A           40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVR   72 (152)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            568999999999999999999999999999874

>2wv0_A YVOA, HTH-type transcriptional repressor YVOA; DNA-binding, transcription regulation, transcriptional regulator, GNTR/HUTC family; 2.40A {Bacillus subtilis}

Probab=92.80  E-value=0.17  Score=44.09  Aligned_cols=54  Identities=15%  Similarity=0.190  Sum_probs=40.2

Q ss_pred             CCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         47 PLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++...+...|......|       + +.+++|++||||+.||++-++...+.|.+.-.+..|
T Consensus        10 ~~~~~i~~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   71 (243)
T 2wv0_A           10 PIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRG   71 (243)
T ss_dssp             CHHHHHHHHHHHHHHHTSSCTTCBCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTTSC
T ss_pred             CHHHHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEeCCCe
Confidence            33444555555555433       2 789999999999999999999999999886555444

>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=92.80  E-value=0.18  Score=41.98  Aligned_cols=43  Identities=19%  Similarity=0.209  Sum_probs=34.3

Q ss_pred             HHHHHHHHHH-cCC--CHHHHHHHhCCC-HHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQ-LGI--RPCDISRQLRVS-HGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~-~G~--S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~   94 (258)
                      +..+|.++.+ .|+  +.+++|+.+||+ ++||++|+++..+.|.+.
T Consensus        11 i~~~i~~~~~~~g~~ps~~elA~~lgiss~~tv~~~~~~l~~~~~l~   57 (202)
T 1jhf_A           11 VFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIE   57 (202)
T ss_dssp             HHHHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCccHHHHHHHhCCCChHHHHHHHHHHHHCCCce
Confidence            4455666554 588  999999999999 999999999887766553

>3qp6_A CVIR transcriptional regulator; quorum sensing, agonist, antagonist, LUXR, acylated homoseri lactone, transcription factor; HET: HL6; 2.00A {Chromobacterium violaceum} PDB: 3qp5_A*

Probab=92.79  E-value=0.17  Score=44.62  Aligned_cols=42  Identities=21%  Similarity=0.207  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...+ +|+.+..+|++..+||+.|+||.+||...+++-++
T Consensus       197 ~Lt~re~-~vl~~~~~G~s~~eIA~~l~is~~TV~~~~~~~~~  238 (265)
T 3qp6_A          197 PLSQREY-DIFHWMSRGKTNWEIATILNISERTVKFHVANVIR  238 (265)
T ss_dssp             CCCHHHH-HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            5776665 46666679999999999999999999999998763

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

Probab=92.77  E-value=0.17  Score=40.00  Aligned_cols=55  Identities=15%  Similarity=0.243  Sum_probs=40.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCCCC--CCCCHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGSKP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~RP--rklT~e~~~~I~~l  117 (258)
                      .+.+..+||+.++++++||++.+++..+.|-|.-..  ..+ |-  -.+|++-.+.+.+.
T Consensus        63 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~Dr-R~~~l~LT~~G~~~~~~~  121 (159)
T 3s2w_A           63 DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQRDEKDR-RSYRVFLTEKGKKLEPDM  121 (159)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC----CCEEEEECHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCC-CeeEEEECHHHHHHHHHH
Confidence            568999999999999999999999999999874222  222 22  23677655555544

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

Probab=92.75  E-value=0.23  Score=38.76  Aligned_cols=65  Identities=9%  Similarity=0.031  Sum_probs=44.8

Q ss_pred             HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      ..|+..+.  .+.+.++||+.++++++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        46 ~~iL~~l~~~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~  115 (155)
T 3cdh_A           46 WRVLACLVDNDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRVADAKDKRRVRVRLTDDGRALAESLV  115 (155)
T ss_dssp             HHHHHHHSSCSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC------CCCEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCcCCeeEeEECHHHHHHHHHHH
Confidence            34555543  4689999999999999999999999999998743221  22 122347777666665543

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

Probab=92.66  E-value=0.23  Score=37.77  Aligned_cols=70  Identities=11%  Similarity=0.056  Sum_probs=46.5

Q ss_pred             CCCHHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        47 ~~S~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~l  117 (258)
                      .++... ..|+..+ . .+.+.++||+.++++++||++.+++..+.|-+.-...  .+ ..--.+|++-.+.+.+.
T Consensus        35 ~l~~~~-~~iL~~l~~~~~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~  109 (140)
T 2nnn_A           35 GLTPTQ-WAALVRLGETGPCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRSADPDDGRRLLVSLSPAGRAELEAG  109 (140)
T ss_dssp             CCCHHH-HHHHHHHHHHSSBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             CCCHHH-HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeCCCCCCCeeeeEECHhHHHHHHHH
Confidence            355432 3444443 3 5789999999999999999999999999997742211  11 11234677766655544

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

Probab=92.64  E-value=0.21  Score=39.66  Aligned_cols=44  Identities=18%  Similarity=0.411  Sum_probs=37.8

Q ss_pred             HHHHHHHHHHHc----CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQL----GIRPCDISRQL-----RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~----G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..|..|++++.+    ..+..+|.+.|     +||.+||||-++.+.+.|.+.
T Consensus        18 ~qR~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv~   70 (136)
T 1mzb_A           18 LPRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLVV   70 (136)
T ss_dssp             HHHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCcEE
Confidence            467788888753    37999999999     899999999999999999763

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=92.64  E-value=0.066  Score=39.23  Aligned_cols=45  Identities=13%  Similarity=0.085  Sum_probs=37.2

Q ss_pred             CCHHHHHHHHHHHHhCC---CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        106 TTPKVVSYIKELKQKDP---GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       106 lT~e~~~~I~~lv~~nP---~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      ++++.+..|..++++++   .+++.||++.|.          +|.+||+|.|.++..+
T Consensus        11 ~~~~~~~~IL~~L~~~~~~~~~t~~eLA~~Lg----------vs~~tV~~~L~~L~~~   58 (77)
T 1qgp_A           11 IYQDQEQRILKFLEELGEGKATTAHDLSGKLG----------TPKKEINRVLYSLAKK   58 (77)
T ss_dssp             HHHHHHHHHHHHHHHHCSSSCEEHHHHHHHHC----------CCHHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHC----------cCHHHHHHHHHHHHHC
Confidence            45666788889999998   899999999883          4999999999987544

>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=92.62  E-value=0.1  Score=37.38  Aligned_cols=28  Identities=11%  Similarity=0.116  Sum_probs=23.8

Q ss_pred             HHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         58 ELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        58 ~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++.+.+ +..++|+.||||.++|++|++.
T Consensus         9 ~~~~~~-s~t~aA~~L~vtQ~AVS~~ir~   36 (66)
T 2ovg_A            9 DYAMRF-GQTKTAKDLGVYPSSINQAIHA   36 (66)
T ss_dssp             HHHHHH-CHHHHHHHHTSCHHHHHHHHHH
T ss_pred             HHHHHC-CHHHHHHHhCCCHHHHHHHHHh
Confidence            345555 9999999999999999999974

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

Probab=92.60  E-value=0.29  Score=39.28  Aligned_cols=52  Identities=23%  Similarity=0.022  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        105 VTTPKVVSYIKELKQK-DPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       105 klT~e~~~~I~~lv~~-nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ++|+. +..|.+++.+ +..+++.||.+.|++.+..+     |.+||+|.|+.+....+
T Consensus        19 r~T~q-R~~Il~~L~~~~~~~sa~ei~~~l~~~~~~i-----s~aTVYR~L~~L~e~Gl   71 (145)
T 2fe3_A           19 RITPQ-RHAILEYLVNSMAHPTADDIYKALEGKFPNM-----SVATVYNNLRVFRESGL   71 (145)
T ss_dssp             CCCHH-HHHHHHHHHHCSSCCCHHHHHHHHGGGCTTC-----CHHHHHHHHHHHHHTTS
T ss_pred             CCCHH-HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC-----ChhhHHHHHHHHHHCCC
Confidence            35555 5555555554 45689999999998777664     99999999998776654

>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=92.59  E-value=0.14  Score=38.86  Aligned_cols=34  Identities=18%  Similarity=0.390  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.++..+.. |++..++|+..|||++|++.+.+
T Consensus        21 ~~~~kLK~il~-GikQ~eLAK~iGIsqsTLSaIen   54 (83)
T 2l1p_A           21 TVRNALKDLLK-DMNQSSLAKECPLSQSMISSIVN   54 (83)
T ss_dssp             HHHHHHHHHHT-TSCHHHHHHHSSSCHHHHHHHHT
T ss_pred             HHHHHHHHHHH-hcCHHHHHHHcCCCHHHHHHHHc
Confidence            35566666655 99999999999999999998864

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

Probab=92.59  E-value=0.18  Score=38.25  Aligned_cols=63  Identities=8%  Similarity=0.148  Sum_probs=43.9

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCCCC--CCCCHHHHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGSKP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~RP--rklT~e~~~~I~~l  117 (258)
                      ..|+..+ . .+.+.++||+.++++++||++.+++..+.|-+.-.  +..+ |.  -.+|+.-.+.+...
T Consensus        36 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~-r~~~~~lT~~G~~~~~~~  104 (139)
T 3bja_A           36 FGVIQVLAKSGKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTEKNPNDQ-RETLVYLTKKGEETKKQV  104 (139)
T ss_dssp             HHHHHHHHHSCSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEEECSSCT-TCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeeccCCCCC-ceeEEEECHHHHHHHHHH
Confidence            3444444 3 45899999999999999999999999999977422  1122 22  34677766655544

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

Probab=92.57  E-value=0.072  Score=45.69  Aligned_cols=47  Identities=32%  Similarity=0.303  Sum_probs=41.0

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++...|.+|+.+.. .+++..+||+.+|+|.+||++-+++..+.|-|.
T Consensus        12 L~~~~rl~IL~~L~~~~~s~~eLa~~l~is~stvs~hLk~Le~~GLV~   59 (202)
T 2p4w_A           12 LGNETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEAGLIE   59 (202)
T ss_dssp             HHSHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCceE
Confidence            45578888998875 468999999999999999999999999999763

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=92.41  E-value=0.36  Score=38.89  Aligned_cols=53  Identities=13%  Similarity=0.014  Sum_probs=38.4

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      -++|+. +..|.+.+.+....++.||.+.|.+.+..+     |.+||+|.|..+....+
T Consensus        15 ~r~T~q-R~~Il~~l~~~~h~ta~ei~~~l~~~~~~i-----s~~TVYR~L~~L~e~Gl   67 (145)
T 3eyy_A           15 YRLTPQ-RQLVLEAVDTLEHATPDDILGEVRKTASGI-----NISTVYRTLELLEELGL   67 (145)
T ss_dssp             CCCCHH-HHHHHHHHHHHSSBCHHHHHHHHHTTCTTC-----CHHHHHHHHHHHHHHTS
T ss_pred             CCcCHH-HHHHHHHHHhcCCCCHHHHHHHHHhhCCCC-----CHhHHHHHHHHHHHCCc
Confidence            335665 445555544434789999999999877664     99999999987665544

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

Probab=92.35  E-value=0.2  Score=44.23  Aligned_cols=60  Identities=10%  Similarity=0.131  Sum_probs=43.8

Q ss_pred             HHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHH
Q psy15598         52 VRMRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSY  113 (258)
Q Consensus        52 lR~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~  113 (258)
                      ...+|+.+.  +.+++.++||+.+|++++||+|.+++..+.|-+.-..+.  +.-.+|+.-...
T Consensus       153 ~~~~IL~~L~~~~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~~r~--~~~~LT~~G~~l  214 (244)
T 2wte_A          153 EEMKLLNVLYETKGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGKD--RKVELNELGLNV  214 (244)
T ss_dssp             HHHHHHHHHHHHTCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTT--TEEEECHHHHHH
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCc--cEEEECHHHHHH
Confidence            445666664  357999999999999999999999999999987533211  223466665443

>3f52_A CLP gene regulator (CLGR); helix-turn-helix motif, transcriptional ACTI human pathogen, transcription activator; 1.75A {Corynebacterium glutamicum} PDB: 3f51_A

Probab=92.32  E-value=0.13  Score=38.98  Aligned_cols=37  Identities=16%  Similarity=0.275  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...+-.+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus        26 ~~~~g~~l~~~R~~~glsq~~lA~~~gis~~~is~~E~   63 (117)
T 3f52_A           26 REALGAALRSFRADKGVTLRELAEASRVSPGYLSELER   63 (117)
T ss_dssp             HHHHHHHHHHHHHHHTCCHHHHHHHTTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            3455566666654 699999999999999999999863

>2jvl_A TRMBF1; coactivator, helix-turn-helix, Pro binding, transcription; NMR {Trichoderma reesei}

Probab=92.25  E-value=0.26  Score=37.42  Aligned_cols=41  Identities=10%  Similarity=0.123  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...+...+..+|-.+.+   .|++..++|+.+|||++||++|.+
T Consensus        28 ~~~~~~~~g~~lk~~R~~~~~glsq~elA~~~gis~~~is~~E~   71 (107)
T 2jvl_A           28 PKTVGKEVGKAIEQGRQKFEPTMTQAELGKEIGETAATVASYER   71 (107)
T ss_dssp             CCCCCHHHHHHHHHHHTTSSSCCCHHHHHHHHTCCHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            44566778777777765   489999999999999999998854

>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=92.25  E-value=0.15  Score=37.90  Aligned_cols=31  Identities=16%  Similarity=0.204  Sum_probs=25.5

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+|..+. +.|++..++|+.+|||++||++|.
T Consensus        33 ~~lk~~R~~~glsq~elA~~lgvs~~~is~~E   64 (99)
T 2ppx_A           33 PRIKIIRRALKLTQEEFSARYHIPLGTLRDWE   64 (99)
T ss_dssp             CHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence            3455554 379999999999999999999994

>2f2e_A PA1607; transcription factor, helix-TRUN-helix, APC5613, structural genomics, PSI, protein structure initiative; HET: GLC; 1.85A {Pseudomonas aeruginosa} SCOP: a.4.5.69

Probab=92.25  E-value=0.23  Score=39.96  Aligned_cols=42  Identities=21%  Similarity=0.194  Sum_probs=36.2

Q ss_pred             HHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +..|+..+.. .++..+|++.+|||++||++-+++..+.|-|.
T Consensus        26 ~l~IL~~L~~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~   68 (146)
T 2f2e_A           26 SMLIVRDAFEGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMV   68 (146)
T ss_dssp             HHHHHHHHHTTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            5566666554 48999999999999999999999999999875

>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=92.24  E-value=0.073  Score=39.97  Aligned_cols=42  Identities=21%  Similarity=0.289  Sum_probs=32.9

Q ss_pred             CCCCHHHHHHHHHHHHc--CCCHHHHHHHh---C-------CCHHHHHHHHHHh
Q psy15598         46 RPLPNSVRMRIVELAQL--GIRPCDISRQL---R-------VSHGCVSKILARY   87 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~--G~S~~eIAr~L---G-------VSrsTVsRwikRy   87 (258)
                      +.++.+.+..|++++.+  ..+..+|+..|   |       +|.+||++|+++.
T Consensus        74 ~~l~~~~~~~i~~~~~~~~~~s~~~i~~~l~~~g~~~~~~~~s~~tv~r~l~~~  127 (128)
T 1pdn_C           74 RIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLVRGR  127 (128)
T ss_dssp             CSSCSTHHHHHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC---
T ss_pred             CcCCHHHHHHHHHHHHhCcchHHHHHHHHHHHcCCccccCCcCHHHHHHHHHhc
Confidence            45777788888888753  58999999999   7       5999999999864

>2hs5_A Putative transcriptional regulator GNTR; APC6050, rhodococcus SP. RH structural genomics, PSI-2, protein structure initiative; 2.20A {Rhodococcus SP} SCOP: a.4.5.6 a.78.1.1

Probab=92.24  E-value=0.18  Score=43.56  Aligned_cols=37  Identities=22%  Similarity=0.179  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ++..++|++||||+++|+.-+++....|-|...++.|
T Consensus        52 L~e~~La~~lgVSRtpVREAL~~L~~eGlv~~~~~~G   88 (239)
T 2hs5_A           52 LSEPDICAALDVSRNTVREAFQILIEDRLVAHELNRG   88 (239)
T ss_dssp             ECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             eCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence            4899999999999999999999999999887665555

>3bwg_A Uncharacterized HTH-type transcriptional regulato; APC85486, YYDK, transcriptional regulator, structural genomi 2; 2.09A {Bacillus subtilis subsp} SCOP: a.4.5.6 d.190.1.2

Probab=92.23  E-value=0.14  Score=44.33  Aligned_cols=51  Identities=24%  Similarity=0.274  Sum_probs=37.0

Q ss_pred             HHHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         50 NSVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        50 ~dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..++.+|..- +..|  + +..++|++||||+.||++-++...+.|.+.-.+..|
T Consensus        12 ~~l~~~I~~g~~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~g~G   66 (239)
T 3bwg_A           12 TEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSG   66 (239)
T ss_dssp             HHHHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHhCCCCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEeCCce
Confidence            3444454442 2233  3 889999999999999999999999999875444333

>4ghj_A Probable transcriptional regulator; structural genomics, niaid, national institute of allergy AN infectious diseases; HET: MSE; 1.75A {Vibrio vulnificus}

Probab=92.20  E-value=0.23  Score=38.14  Aligned_cols=37  Identities=8%  Similarity=0.127  Sum_probs=30.3

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +..++=.+|-.+.+ .|+|..++|+.+|||++||++|-
T Consensus        33 l~~~lG~~ir~~R~~~glTQ~eLA~~~gvs~~~is~~E   70 (101)
T 4ghj_A           33 LAEEIGDRLKQARLNRDLTQSEVAEIAGIARKTVLNAE   70 (101)
T ss_dssp             HHHHHHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHH
Confidence            34456667777764 79999999999999999999884

>3nqo_A MARR-family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; HET: MSE PG4; 2.20A {Clostridium difficile}

Probab=92.18  E-value=0.49  Score=38.91  Aligned_cols=71  Identities=13%  Similarity=0.093  Sum_probs=47.4

Q ss_pred             CCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ++...-.-+..+..   .+++.++||+.++++++||++.+++..+.|-|.-..  ..+ ..--.+|++-.+.+.+..
T Consensus        39 lt~~q~~vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~  115 (189)
T 3nqo_A           39 LTSRQYMTILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVIPSPHDKRAINVKVTDLGKKVMVTCS  115 (189)
T ss_dssp             SCHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCSSCEEEEECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHHHHHHHHHHH
Confidence            55544333333443   479999999999999999999999999999874222  122 122347777666655554

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

Probab=92.16  E-value=0.15  Score=40.35  Aligned_cols=49  Identities=22%  Similarity=0.166  Sum_probs=38.0

Q ss_pred             HHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        110 VVSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       110 ~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      ++..|.+++.+. ..+++.||.+.|++.+..+     |.+||+|.|+.+.....-
T Consensus        12 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i-----s~~TVYR~L~~L~e~Glv   61 (131)
T 2o03_A           12 QRAAISTLLETLDDFRSAQELHDELRRRGENI-----GLTTVYRTLQSMASSGLV   61 (131)
T ss_dssp             HHHHHHHHHHHCCSCEEHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHTTTSE
T ss_pred             HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC-----CHhhHHHHHHHHHHCCCE
Confidence            355666666544 4689999999999877664     999999999988777653

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=92.11  E-value=0.25  Score=38.04  Aligned_cols=34  Identities=21%  Similarity=0.322  Sum_probs=31.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-
T Consensus        53 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r   86 (147)
T 1z91_A           53 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITR   86 (147)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEEC
T ss_pred             CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEe
Confidence            5689999999999999999999999999998753

>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=92.11  E-value=0.3  Score=37.41  Aligned_cols=64  Identities=20%  Similarity=0.197  Sum_probs=44.0

Q ss_pred             HHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHH
Q psy15598         54 MRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~l  117 (258)
                      ..|+..+  ..+.+..+||+.++++++||++.+++..+.|-|.-...  .+ ...-.+|++-...+...
T Consensus        36 ~~iL~~l~~~~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~~~~~d~r~~~~~lT~~G~~~~~~~  104 (145)
T 2a61_A           36 FDILQKIYFEGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKV  104 (145)
T ss_dssp             HHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeecCCCCCCceEEEEECHHHHHHHHHH
Confidence            3344443  35789999999999999999999999999997743211  11 11234677766655544

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

Probab=92.10  E-value=0.23  Score=37.76  Aligned_cols=63  Identities=17%  Similarity=0.177  Sum_probs=42.6

Q ss_pred             HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHH
Q psy15598         55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~l  117 (258)
                      .|+... . .+.+.++||+.++++++||++.+++..+.|-+.-..  ..+ ...-.+|++-...+...
T Consensus        33 ~iL~~l~~~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~~~~~d~R~~~~~lT~~G~~~~~~~  100 (138)
T 3bpv_A           33 ACLLRIHREPGIKQDELATFFHVDKGTIARTLRRLEESGFIEREQDPENRRRYILEVTRRGEEIIPLI  100 (138)
T ss_dssp             HHHHHHHHSTTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHTHHHH
T ss_pred             HHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeecCCCCceeEEeeECHhHHHHHHHH
Confidence            344443 3 468999999999999999999999999999874321  111 01234666655544443

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

Probab=92.07  E-value=0.31  Score=37.06  Aligned_cols=61  Identities=13%  Similarity=0.177  Sum_probs=41.9

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYI  114 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I  114 (258)
                      ..|+..+ . .+.+.++||+.+++|++||++.+++..+.|-+.-.  +..+ .+.-.+|++-.+.+
T Consensus        34 ~~iL~~l~~~~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~~~~d~r~~~~~lT~~G~~~~   99 (142)
T 3bdd_A           34 YSILQTLLKDAPLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKRNPDNQREVLVWPTEQAREAL   99 (142)
T ss_dssp             HHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSSTTCEEEEECHHHHHHH
T ss_pred             HHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence            3455444 3 56899999999999999999999999999976422  1122 11234666655544

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=92.04  E-value=0.22  Score=39.57  Aligned_cols=64  Identities=17%  Similarity=0.081  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcccCCCCCCCC---CCCCHHHHHHH
Q psy15598         51 SVRMRIVELAQL-GIRPCDISRQL-RVSHGCVSKILARYHETGSILPGAIGGSKP---RVTTPKVVSYI  114 (258)
Q Consensus        51 dlR~RIV~L~~~-G~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~pk~rgG~RP---rklT~e~~~~I  114 (258)
                      ..|..|+..+.. +++..+|++.+ |||.+||++.+++..+.|-|.-......++   -.+|+.-.+.+
T Consensus        35 ~w~l~IL~~L~~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~~~~d~r~~~y~LT~~G~~l~  103 (131)
T 1yyv_A           35 RWGVLILVALRDGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVSYPVVPPHVEYSLTPLGEQVS  103 (131)
T ss_dssp             HHHHHHHHHGGGCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEEECSSSCEEEEEECHHHHHHH
T ss_pred             CcHHHHHHHHHcCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEecCCCCCeEEEEECccHHHHH
Confidence            456667666544 58999999999 799999999999999999875322222122   24777654433

>3cwr_A Transcriptional regulator, TETR family; YP_425770.1, transcriptional regulator of TETR family, bacterial regulatory proteins; 1.50A {Rhodospirillum rubrum atcc 11170}

Probab=92.02  E-value=0.24  Score=39.08  Aligned_cols=42  Identities=24%  Similarity=0.340  Sum_probs=32.3

Q ss_pred             CCCC-C-HHHHHHHHHHHH-----c---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         45 GRPL-P-NSVRMRIVELAQ-----L---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        45 gR~~-S-~dlR~RIV~L~~-----~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +++- + .+.|.+|++...     .   +.|.++||+..|||++|+|+..+.
T Consensus         9 ~r~r~~~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   60 (208)
T 3cwr_A            9 GRPAVPDAVVRESIVGAAQRLLSSGGAAAMTMEGVASEAGIAKKTLYRFASG   60 (208)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             CCCCcccHHHHHHHHHHHHHHHHHcCHHhccHHHHHHHhCCCHHHHHHHcCC
Confidence            4444 6 888999988642     3   479999999999999999987543

>2xrn_A HTH-type transcriptional regulator TTGV; DNA-binding protein, tetramer gene regulator, cooperative DN binding, multidrug binding protein; 2.90A {Pseudomonas putida} PDB: 2xro_A

Probab=92.02  E-value=0.14  Score=44.33  Aligned_cols=42  Identities=14%  Similarity=0.197  Sum_probs=35.9

Q ss_pred             HHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         54 MRIVELAQL---GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        54 ~RIV~L~~~---G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+|++++.+   +++.++||+.+|++++||+|+++...+.|-+.-
T Consensus         9 l~iL~~l~~~~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~   53 (241)
T 2xrn_A            9 ASIMRALGSHPHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEA   53 (241)
T ss_dssp             HHHHHHHHTCTTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            467776642   589999999999999999999999999998753

>1qpz_A PURA, protein (purine nucleotide synthesis repressor); transcription regulation, DNA-binding, purine biosynthesis; HET: DNA HPA; 2.50A {Escherichia coli} SCOP: a.35.1.5 c.93.1.1 PDB: 1bdi_A* 1qp0_A* 1qp4_A* 1pnr_A* 1wet_A* 1zay_A* 1vpw_A* 2pue_A* 2puf_A* 2pug_A* 1bdh_A* 1qp7_A* 1qqa_A* 1qqb_A* 2puc_A* 2pua_A* 2pub_A* 2pud_A* 1jfs_A* 1jh9_A* ...

Probab=91.99  E-value=0.23  Score=43.64  Aligned_cols=40  Identities=13%  Similarity=0.117  Sum_probs=30.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~  119 (258)
                      .+.++||+..|||++||+|.++.-               +. .+++.+++|.+..+
T Consensus         1 ~ti~diA~~agVS~~TVSrvLn~~---------------~~-vs~~tr~rV~~~a~   40 (340)
T 1qpz_A            1 ATIKDVAKRANVSTTTVSHVINKT---------------RF-VAEETRNAVWAAIK   40 (340)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHTC---------------SC-CCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcCc---------------CC-CCHHHHHHHHHHHH
Confidence            368999999999999999999831               11 45666777666544

>2zb9_A Putative transcriptional regulator; transcription regulator, TETR family, helix-turn-helix, DNA- binding, transcription regulation; 2.25A {Streptomyces coelicolor}

Probab=91.96  E-value=0.15  Score=41.19  Aligned_cols=42  Identities=21%  Similarity=0.247  Sum_probs=32.7

Q ss_pred             CCCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++|+-..+.|.+|++..     +.|   .|..+||+..|||++|+|+...
T Consensus        16 ~~r~r~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   65 (214)
T 2zb9_A           16 RGRRPAEEVRAEVLHAVGELLLTEGTAQLTFERVARVSGVSKTTLYKWWP   65 (214)
T ss_dssp             -CCSHHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             CCCCccHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCHHHHHHHCC
Confidence            55566677888888854     234   7999999999999999998743

>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB: 1bib_A* 1hxd_A* 2ewn_A*

Probab=91.95  E-value=0.2  Score=45.43  Aligned_cols=44  Identities=16%  Similarity=0.292  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.+.+|+.+..++  ++..++|++|+||++||+|-++..++.|.+.
T Consensus         5 ~r~~~Il~~L~~~~~~s~~eLa~~l~vS~~ti~r~l~~L~~~G~~i   50 (321)
T 1bia_A            5 TVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGVDV   50 (321)
T ss_dssp             HHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCCC
T ss_pred             hHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCcE
Confidence            5677888888653  7999999999999999999999999999653

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

Probab=91.93  E-value=0.73  Score=36.67  Aligned_cols=33  Identities=12%  Similarity=0.254  Sum_probs=30.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+.+.++||+.++|+++||++.+++..+.|-|.
T Consensus        45 ~~~~~~eLa~~l~~~~~tvs~~v~~Le~~GlV~   77 (151)
T 4aik_A           45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLIT   77 (151)
T ss_dssp             TTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCCcHHHHHHHHCcCHHHHHHHHHHHHhCCCeE
Confidence            357889999999999999999999999999874

>2fsw_A PG_0823 protein; alpha-beta structure, helix-turn-helix, winged-helix-turn-HE structural genomics, PSI, protein structure initiative; HET: MSE; 2.16A {Porphyromonas gingivalis} SCOP: a.4.5.69

Probab=91.92  E-value=0.16  Score=38.41  Aligned_cols=43  Identities=19%  Similarity=0.114  Sum_probs=35.8

Q ss_pred             HHHHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQL-GIRPCDISRQL-RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~~-G~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|..|+....+ +++..+|++.+ |||.+||++.+++..+.|-|.
T Consensus        26 ~~~~IL~~L~~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~   70 (107)
T 2fsw_A           26 WTLLIIFQINRRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIK   70 (107)
T ss_dssp             SHHHHHHHHTTSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cHHHHHHHHHhCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEE
Confidence            35566665544 58999999999 599999999999999999875

>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=91.91  E-value=0.18  Score=37.41  Aligned_cols=30  Identities=17%  Similarity=0.252  Sum_probs=25.1

Q ss_pred             HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         56 IVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |-.+. ..|++..++|+.+|||++||++|.+
T Consensus         6 l~~~r~~~gltq~~lA~~~gis~~~i~~~e~   36 (111)
T 1b0n_A            6 IKQYRKEKGYSLSELAEKAGVAKSYLSSIER   36 (111)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            33443 4799999999999999999999975

>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=91.90  E-value=0.42  Score=36.71  Aligned_cols=36  Identities=11%  Similarity=0.240  Sum_probs=30.5

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+-.+|-.+.+ .|+|..++|+.+|||++||++|.+
T Consensus        11 ~~~g~~lk~~R~~~glsq~~lA~~~gis~~~is~~E~   47 (126)
T 3ivp_A           11 RALGLAIKEARKKQGLTREQVGAMIEIDPRYLTNIEN   47 (126)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHC
Confidence            456677777764 799999999999999999999975

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

Probab=91.90  E-value=0.31  Score=38.63  Aligned_cols=52  Identities=13%  Similarity=0.128  Sum_probs=39.1

Q ss_pred             CCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        105 VTTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       105 klT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ++|+. +..|.+++.+.  ...++.||.+.|++.+..+     |.+||+|.|+.+.....
T Consensus        15 r~T~q-R~~Il~~L~~~~~~~~sa~ei~~~l~~~~~~i-----s~aTVYR~L~~L~e~Gl   68 (136)
T 1mzb_A           15 KVTLP-RVKILQMLDSAEQRHMSAEDVYKALMEAGEDV-----GLATVYRVLTQFEAAGL   68 (136)
T ss_dssp             CCCHH-HHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHHHTS
T ss_pred             CCCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHCCc
Confidence            35554 66666666654  3689999999999877664     99999999988766544

>3deu_A Transcriptional regulator SLYA; MARR, WING-helix, transcription regulator, activator, DNA-binding, repressor; HET: SAL; 2.30A {Salmonella typhimurium} SCOP: a.4.5.28

Probab=91.85  E-value=0.36  Score=38.80  Aligned_cols=46  Identities=11%  Similarity=0.190  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHH-HH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVEL-AQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L-~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++... ..|+.. ..  .+++.++||+.++|+++||++.+++..+.|-|.
T Consensus        51 lt~~q-~~vL~~L~~~~~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~   99 (166)
T 3deu_A           51 LTQTH-WVTLHNIHQLPPDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLIS   99 (166)
T ss_dssp             CCHHH-HHHHHHHHHSCSSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHH-HHHHHHHHHcCCCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEE
Confidence            55443 334443 34  358999999999999999999999999999874

>2p8t_A Hypothetical protein PH0730; pyrococcus horikoshii OT3, STR genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: a.4.5.72 d.74.4.2

Probab=91.72  E-value=0.41  Score=41.54  Aligned_cols=88  Identities=18%  Similarity=0.160  Sum_probs=62.8

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC------
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD------  121 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n------  121 (258)
                      .+.+.=.++|....+..+.++||+.|+||.+||+.-+++.++.|.+.-.+ +|   -.+|++=.+...++.+..      
T Consensus        15 ~s~EdYLk~I~~L~~~V~~~~LA~~LgvS~~SV~~~lkkL~e~GLV~~~~-~G---v~LTe~G~~~A~~i~~rhr~~~~l   90 (200)
T 2p8t_A           15 YTVEDVLAVIFLLKEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ-RG---HFLTLKGKEIRDKLLSMFSEPIGV   90 (200)
T ss_dssp             CCHHHHHHHHHHTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---C---EEECHHHHHHHHHHHTTBCCCEEE
T ss_pred             CCHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC-CC---eEECHHHHHHHHHHHHHHHHhcCc
Confidence            44444445555555678999999999999999999999999999886554 33   678888777776665533      


Q ss_pred             ---------------CCCCHHHHHHHHHhcCCC
Q psy15598        122 ---------------PGIFAWEIRDRLLSDGVC  139 (258)
Q Consensus       122 ---------------P~ita~EIr~~L~~~Gv~  139 (258)
                                     |....-++||.+...|.+
T Consensus        91 ~~~~~~~~~~vv~~~~~~~~i~lRD~~Ir~Ga~  123 (200)
T 2p8t_A           91 SVDGYPGIAIVVKNPPEFKSIELRDEAIKFDAK  123 (200)
T ss_dssp             EETTEEEEEEEESSCCCCCHHHHHHHHHHTTCS
T ss_pred             cccCCceEEEEecCCcccchHHHhHHHHHcCCc
Confidence                           233455777777765543

>4fe7_A Xylose operon regulatory protein; HTH_ARAC, helix-turn-helix, PBP, periplasmic binding protein binding transcription regulator, DNA xylose; HET: XYS; 2.90A {Escherichia coli} PDB: 4fe4_A

Probab=91.70  E-value=0.58  Score=42.65  Aligned_cols=79  Identities=13%  Similarity=0.124  Sum_probs=53.9

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVC  139 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~  139 (258)
                      .+..+..++|+.+|+|+++++|..+++-  |.         .+.... ..-.+...+++ .++..+..+|+..+   |..
T Consensus       319 ~~~~~~~~~a~~~~~s~~~l~r~f~~~~--g~---------s~~~~~~~~r~~~a~~~L-~~~~~~i~~ia~~~---Gf~  383 (412)
T 4fe7_A          319 CKGIKVDQVLDAVGISRSNLEKRFKEEV--GE---------TIHAMIHAEKLEKARSLL-ISTTLSINEISQMC---GYP  383 (412)
T ss_dssp             GGTCCHHHHHHHTTCCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHT---TCS
T ss_pred             cCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-hcCCCCHHHHHHHc---CCC
Confidence            3578999999999999999999999873  21         111111 11122223333 34577888887766   665


Q ss_pred             CCCCCCCHHHHHHHHHhccCC
Q psy15598        140 DKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       140 v~~~~pS~STI~RiLrr~~~~  160 (258)
                            +.+...|.+|+.-+.
T Consensus       384 ------~~~~f~~~Fk~~~g~  398 (412)
T 4fe7_A          384 ------SLQYFYSVFKKAYDT  398 (412)
T ss_dssp             ------CHHHHHHHHHHHSSS
T ss_pred             ------CHHHHHHHHHHHHCc
Confidence                  899999999987654

>3lwj_A Putative TETR-family transcriptional regulator; structural G joint center for structural genomics, JCSG, protein structu initiative; 2.07A {Syntrophomonas wolfei subsp}

Probab=91.70  E-value=0.22  Score=39.46  Aligned_cols=37  Identities=19%  Similarity=0.197  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus         9 ~~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   53 (202)
T 3lwj_A            9 QNKERRQKILTCSLDLFIEKGYYNTSIRDIIALSEVGTGTFYNYF   53 (202)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCSCHHHHHHHC
T ss_pred             ccHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchhHHHHc
Confidence            3567788888754     234   699999999999999999854

>2l49_A C protein; P2 bacteriophage, P2 C, direct repeats, DNA-binding protein, binding protein; NMR {Enterobacteria phage P2} PDB: 2xcj_A

Probab=91.63  E-value=0.23  Score=36.27  Aligned_cols=31  Identities=16%  Similarity=0.110  Sum_probs=24.9

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +|-.+. ..|++..++|+.+|||++||++|.+
T Consensus         8 ~l~~~r~~~gltq~~lA~~~gis~~~is~~e~   39 (99)
T 2l49_A            8 KIVLMRKSEYLSRQQLADLTGVPYGTLSYYES   39 (99)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHCCCHHHHHHHTT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            333443 4699999999999999999998854

>3f8m_A GNTR-family protein transcriptional regulator; PHNF, HUTC, winged helix-TUR UTRA, DNA-binding, transcription regulation; 1.80A {Mycobacterium smegmatis}

Probab=91.59  E-value=0.14  Score=44.74  Aligned_cols=50  Identities=14%  Similarity=0.155  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         49 PNSVRMRIVELAQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        49 S~dlR~RIV~L~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      -.+++.+|.. +..|  + +..++|++||||+.||++-+++-.+.|.+.- +..|
T Consensus        20 ~~~l~~~I~~-~~~g~~lPse~~La~~~~vSr~tvr~Al~~L~~~G~i~~-~g~G   72 (248)
T 3f8m_A           20 RAELDRMLDG-MRIGDPFPAEREIAEQFEVARETVRQALRELLIDGRVER-RGRT   72 (248)
T ss_dssp             HHHHHHHHHH-CCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE-ETTE
T ss_pred             HHHHHHHHhC-CCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe-CCCE
Confidence            3456666664 5445  3 8899999999999999999999999998866 5444

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

Probab=91.57  E-value=0.28  Score=37.34  Aligned_cols=57  Identities=12%  Similarity=0.052  Sum_probs=41.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+.+.++||+.++++++||++.+++..+.|-|.-..  ..+ ..--.+|++-.+.+....
T Consensus        49 ~~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~~~~~d~R~~~~~lT~~G~~~~~~~~  108 (142)
T 2fbi_A           49 GEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVSMS  108 (142)
T ss_dssp             CSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEeecCCCCCCeeEEEECHHHHHHHHHHH
Confidence            568999999999999999999999999999774221  111 112347777666655543

>3vk0_A NHTF, transcriptional regulator; HTH motif, XRE transcription factor, DNA binding protein; 1.88A {Neisseria meningitidis}

Probab=91.55  E-value=0.29  Score=37.22  Aligned_cols=36  Identities=14%  Similarity=0.135  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ...+-.+|-.+.+ .|++..++|+.+|||+++|++|.
T Consensus        19 ~~~~g~~lr~~R~~~gltq~elA~~~gis~~~is~~E   55 (114)
T 3vk0_A           19 RAVLAYNMRLFRVNKGWSQEELARQCGLDRTYVSAVE   55 (114)
T ss_dssp             HHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence            3455666666654 79999999999999999999885

>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=91.55  E-value=0.23  Score=43.36  Aligned_cols=23  Identities=26%  Similarity=0.434  Sum_probs=21.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.++||+..|||++||+|.++.
T Consensus         3 ~ti~dvA~~agVS~~TVSrvln~   25 (332)
T 2hsg_A            3 VTIYDVAREASVSMATVSRVVNG   25 (332)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTT
T ss_pred             CCHHHHHHHhCCCHHHHHHHHcC
Confidence            57899999999999999999875

>3hta_A EBRA repressor; TETR family, DNA binding protein, multidrug resistance, MULT binding protein, DNA-binding, transcription; 2.30A {Streptomyces lividans} PDB: 3hth_A* 3hti_A* 3htj_A* 3iuv_A

Probab=91.55  E-value=0.22  Score=40.82  Aligned_cols=42  Identities=24%  Similarity=0.276  Sum_probs=34.3

Q ss_pred             CCCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |++.-..+.|.+|++..     +.|   .|.++||+..|||++|||+...
T Consensus        21 M~r~~~~~~r~~Il~AA~~lf~~~G~~~~t~~~IA~~aGvs~~tlY~~F~   70 (217)
T 3hta_A           21 MPRRHDPERRQRIIDAAIRVVGQKGIAGLSHRTVAAEADVPLGSTTYHFA   70 (217)
T ss_dssp             SCGGGSHHHHHHHHHHHHHHHHHHTGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccCCCchhHHHHHHHHHHHHHHHcCcccCCHHHHHHHcCCCcchhhhcCC
Confidence            56777788899998864     234   6999999999999999998643

>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=91.55  E-value=0.2  Score=39.02  Aligned_cols=25  Identities=12%  Similarity=0.085  Sum_probs=23.0

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|+|..++|+.+|||++||++|-+
T Consensus        82 ~~glsq~~la~~~g~s~~~i~~~E~  106 (133)
T 3o9x_A           82 KLSLTQKEASEIFGGGVNAFSRYEK  106 (133)
T ss_dssp             HTTCCHHHHHHHHCSCTTHHHHHHH
T ss_pred             HcCCCHHHHHHHHCCCHHHHHHHHC
Confidence            4799999999999999999999865

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=91.51  E-value=0.14  Score=39.76  Aligned_cols=64  Identities=6%  Similarity=0.053  Sum_probs=42.8

Q ss_pred             HHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHH
Q psy15598         54 MRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~l  117 (258)
                      ..|+...  ..+.+.++||+.++++++||++.+++..+.|-|.-.+  ..++ .--.+|++-.+.+.+.
T Consensus        39 ~~vL~~l~~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~  107 (140)
T 3hsr_A           39 YIVLMAIENDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRTREEKDERNLQISLTEQGKAIKSPL  107 (140)
T ss_dssp             HHHHHHSCTTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC-------CEEEECHHHHHTHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEecCCCCCcceeeeeEChHHHHHHHHH
Confidence            3444443  2468999999999999999999999999999874222  2221 1123677655555444

>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=91.46  E-value=0.13  Score=42.27  Aligned_cols=36  Identities=6%  Similarity=0.025  Sum_probs=29.2

Q ss_pred             HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+-.+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus         9 ~~~g~~l~~~r~~~g~s~~~la~~~gis~~~ls~~e~   45 (198)
T 2bnm_A            9 TGFAELLKDRREQVKMDHAALASLLGETPETVAAWEN   45 (198)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            345566666654 699999999999999999999865

>3dv8_A Transcriptional regulator, CRP/FNR family; cyclic nucleotide-binding domain, structural genomics, joint for structural genomics; 2.55A {Eubacterium rectale atcc 33656}

Probab=91.45  E-value=0.36  Score=39.27  Aligned_cols=32  Identities=16%  Similarity=0.293  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .++..+||..+|+|+.||+|.++++++.|-+.
T Consensus       169 ~~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  200 (220)
T 3dv8_A          169 KITHETIANHLGSHREVITRMLRYFQVEGLVK  200 (220)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            57999999999999999999999999999884

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

Probab=91.38  E-value=0.3  Score=37.64  Aligned_cols=64  Identities=11%  Similarity=0.082  Sum_probs=43.6

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK  118 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv  118 (258)
                      .|+..+ +.+.+.++||+.++++++||++.+++..+.|-|.-...... |  --.+|++-.+.+.+..
T Consensus        41 ~iL~~l~~~~~~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~D~R~~~~~LT~~G~~~~~~~~  108 (144)
T 3f3x_A           41 SILKATSEEPRSMVYLANRYFVTQSAITAAVDKLEAKGLVRRIRDSKDRRIVIVEITPKGRQVLLEAN  108 (144)
T ss_dssp             HHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCceEEEEECHHHHHHHHHHH
Confidence            444444 33339999999999999999999999999998742221111 1  2347777666655543

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

Probab=91.37  E-value=0.35  Score=39.18  Aligned_cols=55  Identities=24%  Similarity=0.239  Sum_probs=40.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+.++||+.++|+++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+..
T Consensus        87 ~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~~~~~DrR~~~~~LT~~G~~~~~~~~  144 (181)
T 2fbk_A           87 LRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLL  144 (181)
T ss_dssp             BCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence            89999999999999999999999999998743221  12 122347777666665543

>3vp5_A Transcriptional regulator; heme, sensor protein, TETR superf transcription; HET: HEM; 1.90A {Lactococcus lactis} PDB: 3vox_A 3vok_A*

Probab=91.35  E-value=0.33  Score=38.93  Aligned_cols=38  Identities=16%  Similarity=0.308  Sum_probs=30.9

Q ss_pred             CCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        47 ~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus         8 ~~~~~tr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   53 (189)
T 3vp5_A            8 SLSDEKRNRVYDACLNEFQTHSFHEAKIMHIVKALDIPRGSFYQYF   53 (189)
T ss_dssp             TSCHHHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHHHHHHHC
T ss_pred             hCCHHHHHHHHHHHHHHHHHCCcccccHHHHHHHhCCChHHHHHHC
Confidence            36778899988864     234   699999999999999999753

>2bv6_A MGRA, HTH-type transcriptional regulator MGRA; multidrug resistance regulator, virulence determinant, transcriptional factors; 2.8A {Staphylococcus aureus} SCOP: a.4.5.28

Probab=91.29  E-value=0.24  Score=38.00  Aligned_cols=63  Identities=17%  Similarity=0.209  Sum_probs=43.5

Q ss_pred             HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCCCC--CCCCHHHHHHHHHH
Q psy15598         54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGSKP--RVTTPKVVSYIKEL  117 (258)
Q Consensus        54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~RP--rklT~e~~~~I~~l  117 (258)
                      ..|+..+ . .+.+..+||+.++++++||++.+++..+.|-|.-..  ..+ |.  -.+|++-...+...
T Consensus        40 ~~iL~~l~~~~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~~~~d~-R~~~~~lT~~G~~~~~~~  108 (142)
T 2bv6_A           40 FLVLTILWDESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQ-REVFIHLTDKSETIRPEL  108 (142)
T ss_dssp             HHHHHHHHHSSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSST-TCEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHHcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCc-ceEEEEEChHHHHHHHHH
Confidence            3444444 3 358999999999999999999999999999874322  122 22  23677655555443

>2eby_A Putative HTH-type transcriptional regulator YBAQ; hypothetical protein, JW0472, structural genomics, NPPSFA; 2.25A {Escherichia coli}

Probab=91.23  E-value=0.1  Score=39.45  Aligned_cols=33  Identities=15%  Similarity=0.245  Sum_probs=26.4

Q ss_pred             HHHHHH-HH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         53 RMRIVE-LA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        53 R~RIV~-L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+|.. +. ..|++..++|+.+|||++||++|.+
T Consensus        12 g~~l~~~~r~~~glsq~~lA~~~gis~~~is~~e~   46 (113)
T 2eby_A           12 GDILLYEYLEPLDLKINELAELLHVHRNSVSALIN   46 (113)
T ss_dssp             HHHHHHHTTTTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            344444 33 4699999999999999999999975

>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=91.19  E-value=0.19  Score=37.38  Aligned_cols=32  Identities=19%  Similarity=0.371  Sum_probs=25.8

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus        21 ~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~   53 (104)
T 3cec_A           21 EVIADILDDLDINTANFAEILGVSNQTIQEVIN   53 (104)
T ss_dssp             HHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3344443 4699999999999999999999975

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

Probab=91.19  E-value=0.33  Score=39.29  Aligned_cols=51  Identities=16%  Similarity=0.122  Sum_probs=38.5

Q ss_pred             CCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        106 TTPKVVSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       106 lT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      +|+. +..|.+++.+. ...++.||.+.|++.+..+     |.+||+|.|+.+.....
T Consensus        25 ~T~q-R~~IL~~l~~~~~~~sa~ei~~~l~~~~~~i-----s~aTVYR~L~~L~e~Gl   76 (150)
T 2xig_A           25 NSKQ-REEVVSVLYRSGTHLSPEEITHSIRQKDKNT-----SISSVYRILNFLEKENF   76 (150)
T ss_dssp             CHHH-HHHHHHHHHHCSSCBCHHHHHHHHHHHSTTC-----CHHHHHHHHHHHHHTTS
T ss_pred             CCHH-HHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC-----CHhhHHHHHHHHHHCCc
Confidence            4444 56666666554 4689999999998776664     99999999998776654

>3cjd_A Transcriptional regulator, TETR family; YP_510936.1, putative TETR transcriptional regulator, struct genomics; HET: STE; 1.79A {Jannaschia SP}

Probab=91.13  E-value=0.29  Score=39.52  Aligned_cols=39  Identities=18%  Similarity=0.386  Sum_probs=30.4

Q ss_pred             CCCHHHHHHHHHHHH-----c---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQ-----L---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~-----~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .-..+.|.+|++...     .   +.|.++||+..|||++|+|+..+
T Consensus         8 ~~~~~tr~~Il~aA~~l~~e~G~~~~s~~~IA~~agvs~~t~Y~hF~   54 (198)
T 3cjd_A            8 ARKAALREKLIDLAEAQIEAEGLASLRARELARQADCAVGAIYTHFQ   54 (198)
T ss_dssp             --CHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hhHHHHHHHHHHHHHHHHHhCChhhcCHHHHHHHhCCCccHHHHHhC
Confidence            345678888888642     3   47999999999999999998654

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

Probab=91.12  E-value=0.36  Score=39.09  Aligned_cols=45  Identities=20%  Similarity=0.263  Sum_probs=38.6

Q ss_pred             CHHHHHHHHHHHHc---CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         49 PNSVRMRIVELAQL---GIRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        49 S~dlR~RIV~L~~~---G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      ....|..|++++.+   ..|..+|.+.|     +||.+||||-++.+.+.|.+
T Consensus        25 ~T~qR~~IL~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv   77 (150)
T 2xig_A           25 NSKQREEVVSVLYRSGTHLSPEEITHSIRQKDKNTSISSVYRILNFLEKENFI   77 (150)
T ss_dssp             CHHHHHHHHHHHHHCSSCBCHHHHHHHHHHHSTTCCHHHHHHHHHHHHHTTSE
T ss_pred             CCHHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCcE
Confidence            34678888888752   47999999999     89999999999999999976

>2hku_A A putative transcriptional regulator; structural genomics, APC6040, TET rhodococcus SP. RHA1, PSI-2, protein structure initiative; HET: PG4; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=91.11  E-value=0.21  Score=40.45  Aligned_cols=41  Identities=15%  Similarity=0.085  Sum_probs=29.1

Q ss_pred             CCCCCHHHHHHHHHHHH-----c--CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQ-----L--GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~-----~--G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.-..+.|.+|++...     .  +.|.++||+..|||++|||+...
T Consensus        14 ~~~~~~~~r~~Il~aA~~lf~~~G~~~s~~~IA~~aGvs~~tlY~~F~   61 (215)
T 2hku_A           14 TRESGRQTRDALFTAATELFLEHGEGVPITQICAAAGAHPNQVTYYYG   61 (215)
T ss_dssp             ------CHHHHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             CccchHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHhCCCHHHHHHHcC
Confidence            34455678888888642     3  48999999999999999998754

>2dg8_A Putative TETR-family transcriptional regulatory P; helix-turn-helix motif, gene regulation; 2.21A {Streptomyces coelicolor}

Probab=91.09  E-value=0.19  Score=40.11  Aligned_cols=40  Identities=18%  Similarity=0.223  Sum_probs=28.9

Q ss_pred             CCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        46 R~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.-..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus         4 r~~~~~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~   51 (193)
T 2dg8_A            4 GHTDPQRRERILAATLDLIAEEGIARVSHRRIAQRAGVPLGSMTYHFT   51 (193)
T ss_dssp             ---CTTHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCTHHHHHHCS
T ss_pred             CCCChhHHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCchhhheeCC
Confidence            333446777777754     234   7999999999999999997643

>3kz9_A SMCR; transcriptional regulator, quorum S DNA-binding, transcription regulation, transcription regula; HET: MSE; 2.10A {Vibrio vulnificus} PDB: 2pbx_A

Probab=91.05  E-value=0.4  Score=37.66  Aligned_cols=40  Identities=25%  Similarity=0.288  Sum_probs=31.5

Q ss_pred             CCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         46 RPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        46 R~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.-..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        12 ~~~~~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F~   59 (206)
T 3kz9_A           12 RLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFP   59 (206)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHSCCSSCCHHHHHHHHTSCHHHHHHHCC
T ss_pred             cCCHHHHHHHHHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHcC
Confidence            344667888888864     245   6999999999999999998643

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

Probab=91.02  E-value=0.27  Score=37.69  Aligned_cols=61  Identities=18%  Similarity=0.165  Sum_probs=44.2

Q ss_pred             HHHHHHHHHHHcC-CC--HHHHHHHh-CCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         51 SVRMRIVELAQLG-IR--PCDISRQL-RVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        51 dlR~RIV~L~~~G-~S--~~eIAr~L-GVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      ..|..|+.....| .+  ..+|++.+ |||.+++++-+++-.+.|-|.-... ...--.+|+.-.+
T Consensus        27 ~wrl~IL~~L~~g~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~~-r~~~y~LT~~G~~   91 (111)
T 3df8_A           27 KYTMLIISVLGNGSTRQNFNDIRSSIPGISSTILSRRIKDLIDSGLVERRSG-QITTYALTEKGMN   91 (111)
T ss_dssp             TTHHHHHHHHTSSSSCBCHHHHHHTSTTCCHHHHHHHHHHHHHTTSEEEEES-SSEEEEECHHHHH
T ss_pred             ccHHHHHHHHhcCCCCCCHHHHHHHccCCCHHHHHHHHHHHHHCCCEEEeec-CcEEEEECccHHH
Confidence            3477788777665 56  99999999 9999999999999999998753322 1112346665433

>2fxa_A Protease production regulatory protein HPR; protease porduction, regulation, STR genomics, PSI, protein structure initiative; HET: PGE P6G 1PE; 2.40A {Bacillus subtilis} SCOP: a.4.5.28

Probab=90.96  E-value=0.57  Score=39.46  Aligned_cols=61  Identities=10%  Similarity=-0.055  Sum_probs=45.1

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHHHHHhC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKELKQKD  121 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~lv~~n  121 (258)
                      ..+++..+||+.++|+++||++.+++..+.|-|.-...  .++ .--.+|++-.+.+.......
T Consensus        60 ~~~~t~~eLa~~l~i~~stvs~~l~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~  123 (207)
T 2fxa_A           60 LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  123 (207)
T ss_dssp             HTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCCCCceEEEEECHHHHHHHHHHHHHH
Confidence            36799999999999999999999999999998743221  221 22347888777777776543

>2oz6_A Virulence factor regulator; winged helix, helix-turn-helix, transcription factor, CAMP-B proteins, CAMP receptor protein; HET: CMP; 2.80A {Pseudomonas aeruginosa} SCOP: a.4.5.4 b.82.3.2

Probab=90.89  E-value=0.2  Score=40.34  Aligned_cols=31  Identities=26%  Similarity=0.378  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       165 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  195 (207)
T 2oz6_A          165 ITRQEIGRIVGCSREMVGRVLKSLEEQGLVH  195 (207)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            5889999999999999999999999999874

>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=90.84  E-value=0.27  Score=37.18  Aligned_cols=32  Identities=22%  Similarity=0.245  Sum_probs=30.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      |++.++||+.++++.+||.+++++..+.|-|.
T Consensus        36 gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIk   67 (91)
T 2dk5_A           36 GIWSRDVRYKSNLPLTEINKILKNLESKKLIK   67 (91)
T ss_dssp             CEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            89999999999999999999999999999774

>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=90.81  E-value=0.21  Score=40.40  Aligned_cols=31  Identities=23%  Similarity=0.273  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.
T Consensus       168 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~  198 (210)
T 3ryp_A          168 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS  198 (210)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHhCCcHHHHHHHHHHHHHCCcEE
Confidence            5889999999999999999999999999874

>2wui_A MEXZ, transcriptional regulator; gene regulation, transcription regulation, TETR, DNA-binding transcription; 2.90A {Pseudomonas aeruginosa}

Probab=90.72  E-value=0.3  Score=39.48  Aligned_cols=38  Identities=24%  Similarity=0.255  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -+.+.|.+|++..     +.|   .|..+||+..|||++|||+..+
T Consensus         8 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2wui_A            8 ESQKTRDGILDAAERVFLEKGVGTTAMADLADAAGVSRGAVYGHYK   53 (210)
T ss_dssp             -CTHHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hhHHHHHHHHHHHHHHHHHcCccccCHHHHHHHhCCCHHHHHHHcC
Confidence            3557788888864     344   6999999999999999999754

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

Probab=90.70  E-value=0.16  Score=44.38  Aligned_cols=44  Identities=11%  Similarity=0.160  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         51 SVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        51 dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +.-.+|++++.   .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus        14 ~r~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~   60 (257)
T 2g7u_A           14 ERGFAVLLAFDAQRPNPTLAELATEAGLSRPAVRRILLTLQKLGYVA   60 (257)
T ss_dssp             HHHHHHHHTCSSSCSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            34456777664   368999999999999999999999999999774

>3gbg_A TCP pilus virulence regulatory protein; cupin, helix-turn-helix, ARAC family, activator, DNA-binding transcription, transcription regulation; HET: PAM; 1.90A {Vibrio cholerae}

Probab=90.67  E-value=0.52  Score=40.44  Aligned_cols=85  Identities=25%  Similarity=0.241  Sum_probs=55.9

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~E  128 (258)
                      .++++.++    +..+..++|+.+|+|++++.+..+  . +|.         .|.. +...-.....+++. +.+.+..|
T Consensus       172 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk--~-~G~---------t~~~~l~~~Rl~~A~~lL~-~~~~si~e  238 (276)
T 3gbg_A          172 EKISCLVKSDITRNWRWADICGELRTNRMILKKELE--S-RGV---------KFRELINSIRISYSISLMK-TGEFKIKQ  238 (276)
T ss_dssp             HHHHHHHHHTTTSCCCHHHHHHHHTCCHHHHHHHHH--T-TTC---------CHHHHHHHHHHHHHHHHHH-HTCCCHHH
T ss_pred             HHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHH--H-cCC---------CHHHHHHHHHHHHHHHHHh-CCCCCHHH
Confidence            34555543    458999999999999999999995  2 543         1111 11222333333443 45788888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      +.+...|+.|+.-+.
T Consensus       239 IA~~~---Gf~------~~s~F~r~Fkk~~G~  261 (276)
T 3gbg_A          239 IAYQS---GFA------SVSYFSTVFKSTMNV  261 (276)
T ss_dssp             HHHHT---TCS------CHHHHHHHHHHHHSS
T ss_pred             HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence            87766   665      888999999886554

>2v7f_A RPS19, RPS19E SSU ribosomal protein S19E; diamond blackfan anemia small ribosomal subunit; 1.15A {Pyrococcus abyssi} SCOP: a.4.5.84

Probab=90.61  E-value=0.28  Score=40.60  Aligned_cols=51  Identities=20%  Similarity=0.247  Sum_probs=39.0

Q ss_pred             CCHHHHHHHhC--------------CCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLR--------------VSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        64 ~S~~eIAr~LG--------------VSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l  117 (258)
                      ....++|+.||              ||++||++.+++..+.|.|+..+.+|   +.+++...+.|.++
T Consensus        68 ~G~~~La~~~gg~k~~g~~p~~~~~vSr~tVR~AL~~Le~~GlV~~~~~~G---~~Vt~~~~~~l~~i  132 (150)
T 2v7f_A           68 VGIERLRTYYGGRKNRGHAPERFYKAGGSIIRKALQQLEAAGFVEKVPGKG---RVITPKGRSFLDKI  132 (150)
T ss_dssp             BCHHHHHHHHCC----CCCTTSCCCHHHHHHHHHHHHHHHTTSEEEETTTE---EEECHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCccCCcCCccccccchHHHHHHHHHHHHCCCEEEeCCCc---eEECCCCHHHHHHH
Confidence            56699999999              99999999999999999987554444   45555555545444

>2d6y_A Putative TETR family regulatory protein; helix-turn-helix, gene regulation; HET: TLA; 2.30A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=90.60  E-value=0.21  Score=40.38  Aligned_cols=37  Identities=22%  Similarity=0.284  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|+|+..+.
T Consensus         7 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tiY~~F~s   51 (202)
T 2d6y_A            7 EATKARIFEAAVAEFARHGIAGARIDRIAAEARANKQLIYAYYGN   51 (202)
T ss_dssp             CCHHHHHHHHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            34677777653     234   69999999999999999987653

>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=90.59  E-value=0.33  Score=39.80  Aligned_cols=35  Identities=14%  Similarity=0.176  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+..+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus        11 ~~~~~l~~~r~~~gltq~~lA~~~gis~~~is~~e~   46 (192)
T 1y9q_A           11 QIANQLKNLRKSRGLSLDATAQLTGVSKAMLGQIER   46 (192)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            44556666654 699999999999999999999864

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

Probab=90.58  E-value=0.28  Score=38.19  Aligned_cols=46  Identities=13%  Similarity=0.237  Sum_probs=36.1

Q ss_pred             CCHHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++.. ...|+..+ . .+.+.++||+.++|+++||++.+++..+.|-|.
T Consensus        45 l~~~-~~~iL~~l~~~~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~   92 (153)
T 2pex_A           45 LTYP-QYLVMLVLWETDERSVSEIGERLYLDSATLTPLLKRLQAAGLVT   92 (153)
T ss_dssp             CCHH-HHHHHHHHHHSCSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHH-HHHHHHHHHhCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEe
Confidence            4443 33344443 3 468999999999999999999999999999874

>1d5y_A ROB transcription factor; protein-DNA complex, DNA, transcription/DNA complex; HET: DNA; 2.70A {Escherichia coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2

Probab=90.54  E-value=0.27  Score=42.47  Aligned_cols=86  Identities=7%  Similarity=0.011  Sum_probs=56.6

Q ss_pred             HHHHHHHHc----CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHH
Q psy15598         54 MRIVELAQL----GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWE  128 (258)
Q Consensus        54 ~RIV~L~~~----G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~E  128 (258)
                      .++++.+++    ..+..++|+.+|+|+++++|..++.-  |.         .+.... ..-......+++ +.+.+..+
T Consensus         6 ~~~~~~i~~~~~~~~~~~~la~~~~~s~~~l~r~f~~~~--g~---------s~~~~~~~~Rl~~a~~~L~-~~~~~i~~   73 (292)
T 1d5y_A            6 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVT--GH---------AIGAYIRARRLSKSAVALR-LTARPILD   73 (292)
T ss_dssp             HHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHHHH--SS---------CHHHHHHHHHHHHHHHHHH-HCCCCHHH
T ss_pred             HHHHHHHHhCCCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHh-cCCCCHHH
Confidence            455555543    47999999999999999999988763  32         111111 111223333343 45788888


Q ss_pred             HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      |+..+   |..      |.+...|.+++.-+.
T Consensus        74 ia~~~---Gf~------~~~~f~r~fk~~~g~   96 (292)
T 1d5y_A           74 IALQY---RFD------SQQTFTRAFKKQFAQ   96 (292)
T ss_dssp             HHHHT---TCS------CHHHHHHHHHHHHSS
T ss_pred             HHHHc---CCC------CHHHHHHHHHHHHCc
Confidence            87766   665      888999999886655

>3geu_A Intercellular adhesion protein R; TETR family, intercellular adhesion regulator, IDP00851, DNA repressor, transcription; HET: MSE; 1.90A {Staphylococcus aureus}

Probab=90.52  E-value=0.16  Score=40.08  Aligned_cols=36  Identities=17%  Similarity=0.294  Sum_probs=28.5

Q ss_pred             CHHHHHHHHHHHH-----c---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELAQ-----L---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~~-----~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.+.|.+|++...     .   +.|.++||+..|||++|+|++.
T Consensus         1 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F   44 (189)
T 3geu_A            1 SNAMKDKIIDNAITLFSEKGYDGTTLDDIAKSVNIKKASLYYHF   44 (189)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHTTCCHHHHTTTC
T ss_pred             CchHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHh
Confidence            3567888887642     3   4799999999999999998754

>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=90.50  E-value=0.38  Score=37.73  Aligned_cols=32  Identities=9%  Similarity=0.140  Sum_probs=25.7

Q ss_pred             HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|..+. +.|++..++|+.+|||+++|++|.+
T Consensus        43 ~~L~~~R~~~glTQ~eLA~~lGis~~~Is~iE~   75 (120)
T 2o38_A           43 YALNAVIDRARLSQAAAAARLGINQPKVSALRN   75 (120)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            3444444 3699999999999999999999864

>2i10_A Putative TETR transcriptional regulator; structural genomics, APC5890, TETR family, PSI-2, protein ST initiative; HET: MSE NPO PGE; 2.05A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=90.47  E-value=0.2  Score=40.59  Aligned_cols=41  Identities=15%  Similarity=0.193  Sum_probs=26.6

Q ss_pred             CCCCCCHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |+|+- ...|.+|++..     +.   +.|..+||+..|||++|+|+..+
T Consensus         5 ~~r~~-~~~r~~Il~aA~~lF~~~Gy~~ts~~~IA~~aGvsk~tlY~~F~   53 (202)
T 2i10_A            5 GGRRR-GFDDQVALQTAMELFWRQGYEGTSITDLTKALGINPPSLYAAFG   53 (202)
T ss_dssp             --------CCHHHHHHHHHHHHHHTTTTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             CCCCC-CCCHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCChHHHHHHhC
Confidence            45432 23456666643     33   46999999999999999998764

>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=90.44  E-value=0.32  Score=39.05  Aligned_cols=48  Identities=25%  Similarity=0.352  Sum_probs=35.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598         98 IGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus        98 rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      ..| ||.+++++..+.|..++..  ..++.+|+.   ..|+      ||.+||++.|++.
T Consensus         6 k~G-RPtk~t~e~~e~I~~~i~~--G~sl~~i~~---~~~~------ps~~T~~~W~~~~   53 (140)
T 4dyq_A            6 KAG-RPSDYMPEVADDICSLLSS--GESLLKVCK---RPGM------PDKSTVFRWLAKH   53 (140)
T ss_dssp             -----CCSCCTTHHHHHHHHHHT--TCCHHHHHT---STTC------CCHHHHHHHHHHC
T ss_pred             CCC-CCCCCCHHHHHHHHHHHHC--CCcHHHHHh---cCCC------CCHHHHHHHHHcC
Confidence            445 9999999999999999876  577777754   3344      5999999999875

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

Probab=90.36  E-value=0.31  Score=38.18  Aligned_cols=63  Identities=17%  Similarity=0.206  Sum_probs=42.9

Q ss_pred             HHHHHH-H--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHHH
Q psy15598         55 RIVELA-Q--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~-~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~l  117 (258)
                      .|+..+ .  .+.+.++||+.++++++||++.+++..+.|-|.-...  .++ .--.+|++-.+.+...
T Consensus        51 ~iL~~L~~~~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~~~~~d~R~~~~~lT~~G~~~~~~~  119 (160)
T 3boq_A           51 DAMAQLARNPDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKAMSADDRRSFSAKLTDAGLTTFKQA  119 (160)
T ss_dssp             HHHHHHHHCTTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC--------CEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeecCCCCCCeEEEEEChhHHHHHHHH
Confidence            344444 3  4689999999999999999999999999998743221  121 1234777766655444

>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=90.32  E-value=1.3  Score=37.97  Aligned_cols=109  Identities=12%  Similarity=0.065  Sum_probs=62.6

Q ss_pred             HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHH---------------hh-----------hh--C--Cc-----
Q psy15598         50 NSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILAR---------------YH-----------ET--G--SI-----   93 (258)
Q Consensus        50 ~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikR---------------yr-----------Et--G--sl-----   93 (258)
                      .++-.+|..+. +.|++..++|+.+|||.++|++|++.               |.           ..  |  ..     
T Consensus        29 ~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~~~~~~~kraaly~W~~~~~~~i~~~~~~~~~~~~~~~~~~~  108 (194)
T 1ic8_A           29 WRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKGTPMKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGD  108 (194)
T ss_dssp             HHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSBCCCCHHHHHHHHHHHHHHTTTTHHHHCCC------------
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcCccccccccccchhhHHHhhhhhhccccCCCCCCCCCCCccc
Confidence            34445666665 47999999999999999999999752               00           00  0  00     


Q ss_pred             ccCCCCCCCC-CCCCHHHHHHHHHHHHhCCCC--C-HHHHHHHHH-----hcCCCCC------CCCCCHHHHHHHHHhcc
Q psy15598         94 LPGAIGGSKP-RVTTPKVVSYIKELKQKDPGI--F-AWEIRDRLL-----SDGVCDK------FNVPSVSSISRILRNKI  158 (258)
Q Consensus        94 ~pk~rgG~RP-rklT~e~~~~I~~lv~~nP~i--t-a~EIr~~L~-----~~Gv~v~------~~~pS~STI~RiLrr~~  158 (258)
                      .+.....+|. ...+..+...+......++..  . -.+|+..|.     +.|+...      .+.++...|...+++..
T Consensus       109 ~~~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR  188 (194)
T 1ic8_A          109 ELPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRR  188 (194)
T ss_dssp             --------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHH
T ss_pred             ccccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhh
Confidence            1111111122 346788888888887766533  2 345555554     2233211      12268888888886643

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

Probab=90.28  E-value=0.14  Score=44.89  Aligned_cols=42  Identities=10%  Similarity=0.160  Sum_probs=35.7

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+|++++.   .+++.++||+.+|++++||+|+++...+.|-+.-
T Consensus        26 l~iL~~l~~~~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~   70 (260)
T 2o0y_A           26 IDLLELFDAAHPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTS   70 (260)
T ss_dssp             HHHHTTCBTTBSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHhhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            45666653   3689999999999999999999999999998743

>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=90.27  E-value=0.24  Score=40.59  Aligned_cols=31  Identities=13%  Similarity=0.328  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       188 lt~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  218 (230)
T 3iwz_A          188 VSRQELARLVGCSREMAGRVLKKLQADGLLH  218 (230)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999999874

>3qkx_A Uncharacterized HTH-type transcriptional regulato; structural genomics, joint center for structural genomics; HET: MSE; 2.35A {Haemophilus influenzae}

Probab=90.27  E-value=0.4  Score=37.24  Aligned_cols=37  Identities=11%  Similarity=0.240  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus         6 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   50 (188)
T 3qkx_A            6 KTDLAEQIFSATDRLMAREGLNQLSMLKLAKEANVAAGTIYLYFK   50 (188)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCSTTCCHHHHHHHHTCCHHHHHHHSS
T ss_pred             chHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHHcC
Confidence            456778888764     234   7999999999999999997643

>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=90.27  E-value=0.31  Score=40.10  Aligned_cols=32  Identities=19%  Similarity=0.150  Sum_probs=29.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.-
T Consensus       164 ~t~~~lA~~lG~sr~tvsR~l~~L~~~g~I~~  195 (222)
T 1ft9_A          164 FTVEEIANLIGSSRQTTSTALNSLIKEGYISR  195 (222)
T ss_dssp             CCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEE
Confidence            68999999999999999999999999998753

>3k69_A Putative transcription regulator; putative transcriptional regulator, structural genomics, JOI for structural genomics, JCSG; HET: MSE; 1.95A {Lactobacillus plantarum} SCOP: a.4.5.0

Probab=90.25  E-value=0.14  Score=42.32  Aligned_cols=52  Identities=13%  Similarity=0.162  Sum_probs=38.8

Q ss_pred             CCCCCCHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         44 NGRPLPNSVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      +.......+|..+......|  ++..+||+.++||+..|.+++++-++.|-+..
T Consensus         7 is~k~~yAlr~l~~La~~~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s   60 (162)
T 3k69_A            7 MKLDFSVAVHSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTG   60 (162)
T ss_dssp             CTHHHHHHHHHHHHHHTTTTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEE
T ss_pred             ccHHHHHHHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence            33445555665444433333  69999999999999999999999999998753

>3lhq_A Acrab operon repressor (TETR/ACRR family); structural genomics, IDP02616, csgid, DNA-binding, transcription, transcription regulation; 1.56A {Salmonella enterica subsp} PDB: 3bcg_A 2qop_A

Probab=90.21  E-value=0.44  Score=37.75  Aligned_cols=37  Identities=22%  Similarity=0.317  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        12 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   56 (220)
T 3lhq_A           12 ALETRQHILDVALRLFSQQGVSATSLAEIANAAGVTRGAIYWHFK   56 (220)
T ss_dssp             SHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCceeehhhcC
Confidence            456788888754     344   6999999999999999998643

>4ev0_A Transcription regulator, CRP family; CAMP binding, winged helix-turn-helix motif, DNA binding, transcription activator; HET: CMP; 2.40A {Thermus thermophilus}

Probab=90.21  E-value=0.25  Score=40.06  Aligned_cols=31  Identities=26%  Similarity=0.358  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.
T Consensus       164 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  194 (216)
T 4ev0_A          164 IRHHELAALAGTSRETVSRVLHALAEEGVVR  194 (216)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999999885

>2zcw_A TTHA1359, transcriptional regulator, FNR/CRP family; stationary phase, DNA-binding, transcription regulation; 1.50A {Thermus thermophilus}

Probab=90.21  E-value=0.25  Score=40.05  Aligned_cols=31  Identities=13%  Similarity=0.212  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       147 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  177 (202)
T 2zcw_A          147 ATHDELAAAVGSVRETVTKVIGELAREGYIR  177 (202)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999885

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

Probab=90.19  E-value=0.18  Score=44.71  Aligned_cols=41  Identities=20%  Similarity=0.355  Sum_probs=33.6

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|++++.   .+++.+|||+.+|++++||+|+++...+.|-+.
T Consensus        33 l~IL~~l~~~~~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~   76 (275)
T 3mq0_A           33 VRILDLVAGSPRDLTAAELTRFLDLPKSSAHGLLAVMTELDLLA   76 (275)
T ss_dssp             HHHHHHHHHCSSCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            55777764   258999999999999999999999999999875

>3dkw_A DNR protein; CRP-FNR, HTH, beta barrel, dimerization helix, homodimer, transcription regulator; 3.60A {Pseudomonas aeruginosa}

Probab=90.14  E-value=0.23  Score=40.64  Aligned_cols=32  Identities=19%  Similarity=0.273  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.-
T Consensus       179 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  210 (227)
T 3dkw_A          179 VAKQLVAGHLSIQPETFSRIMHRLGDEGIIHL  210 (227)
T ss_dssp             SCTHHHHHHTTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCcEEe
Confidence            47899999999999999999999999998743

>4ets_A Ferric uptake regulation protein; metal binding protein, transcription factor; 2.10A {Campylobacter jejuni subsp}

Probab=90.11  E-value=0.38  Score=39.67  Aligned_cols=52  Identities=8%  Similarity=-0.004  Sum_probs=39.4

Q ss_pred             CCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhc--CCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        106 TTPKVVSYIKELKQKD-PGIFAWEIRDRLLSD--GVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       106 lT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~--Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      +|+. +..|.+.+.+. ...++.||.+.|.+.  +..+     |.+||+|.|..+.....-
T Consensus        31 ~T~q-R~~IL~~L~~~~~h~sA~eI~~~l~~~~~~~~i-----s~aTVYRtL~~L~e~Glv   85 (162)
T 4ets_A           31 YTKQ-REVLLKTLYHSDTHYTPESLYMEIKQAEPDLNV-----GIATVYRTLNLLEEAEMV   85 (162)
T ss_dssp             CCHH-HHHHHHHHHSCCSCBCHHHHHHHHHHHCGGGCC-----CHHHHHHHHHHHHHTTSE
T ss_pred             CCHH-HHHHHHHHHhCCCCCCHHHHHHHHHhhcCCCCC-----CHHHHHHHHHHHHHCCCE
Confidence            4554 56666666654 468999999999876  6664     999999999987766553

>3egq_A TETR family transcriptional regulator; DNA-binding, transcription regulation, bacterial regulatory DNA/RNA-binding 3-helical bundle fold; HET: MSE PE8; 2.55A {Archaeoglobus fulgidus}

Probab=90.08  E-value=0.39  Score=37.19  Aligned_cols=35  Identities=23%  Similarity=0.266  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHH-----cC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-----LG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-----~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++...     .|   .|.++||+..|||++|+|+...
T Consensus         4 ~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   46 (170)
T 3egq_A            4 DQSVRIIEAALRLYMKKPPHEVSIEEIAREAKVSKSLIFYHFE   46 (170)
T ss_dssp             HHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHhcCCccCcHHHHHHHhCCCchhHHHHcC
Confidence            56777777642     34   6999999999999999998743

>2f07_A YVDT; helix-turn-helix, transcription; HET: BTB; 2.30A {Bacillus subtilis subsp}

Probab=90.07  E-value=0.35  Score=38.82  Aligned_cols=37  Identities=16%  Similarity=0.241  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         8 ~~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~Agvskgt~Y~yF~   52 (197)
T 2f07_A            8 TSGKYEKILQAAIEVISEKGLDKASISDIVKKAGTAQGTFYLYFS   52 (197)
T ss_dssp             CCSHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hhHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCchHHHHhCC
Confidence            346677787754     234   6999999999999999998753

>3h5t_A Transcriptional regulator, LACI family; DNA-dependent, protein structure initiative II(PSI II), NYSGXRC, 11232D), structural genomics; 2.53A {Corynebacterium glutamicum}

Probab=90.05  E-value=0.28  Score=43.52  Aligned_cols=41  Identities=17%  Similarity=0.142  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+.++||+.+|||++||+|.++..               + ..+++.+++|.+..++
T Consensus        10 ~Ti~diA~~aGVS~~TVSrvLn~~---------------~-~Vs~~tr~rV~~~a~~   50 (366)
T 3h5t_A           10 GTLASIAAKLGISRTTVSNAYNRP---------------E-QLSAELRQRILDTAED   50 (366)
T ss_dssp             THHHHHHHHHTSCHHHHHHHHHCG---------------G-GSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHhCCCHHHHHHHHCCC---------------C-CCCHHHHHHHHHHHHH
Confidence            578999999999999999999742               1 2567788888888775

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

Probab=90.04  E-value=0.37  Score=39.05  Aligned_cols=52  Identities=23%  Similarity=0.158  Sum_probs=39.0

Q ss_pred             CCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        105 VTTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       105 klT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ++|+. +..|.+++.+.  ..+++.||.+.|.+.+..+     |.+||+|.|+.+.....
T Consensus        14 r~T~q-R~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i-----s~aTVYR~L~~L~e~Gl   67 (150)
T 2w57_A           14 KVTLP-RLKILEVLQQPECQHISAEELYKKLIDLGEEI-----GLATVYRVLNQFDDAGI   67 (150)
T ss_dssp             CCCHH-HHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHHTTS
T ss_pred             CCCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCC-----CHHHHHHHHHHHHHCCc
Confidence            35554 55666666543  3689999999999877664     99999999998766654

>3kjx_A Transcriptional regulator, LACI family; LACL family, protein structure initiative II(PSI II), NYSGXRC, structural genomics; 2.33A {Silicibacter pomeroyi}

Probab=90.02  E-value=0.3  Score=42.97  Aligned_cols=23  Identities=30%  Similarity=0.325  Sum_probs=21.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.++||+.+|||++||+|.++.
T Consensus        11 ~ti~diA~~agVS~~TVSr~Ln~   33 (344)
T 3kjx_A           11 LTLRDVSEASGVSEMTVSRVLRN   33 (344)
T ss_dssp             CCHHHHHHHHCCCSHHHHHHHTT
T ss_pred             CCHHHHHHHHCCCHHHHHHHHcC
Confidence            68999999999999999998864

>3e97_A Transcriptional regulator, CRP/FNR family; YP_604437.1, structural genomics, joint center for structural genomics, JCSG; HET: MSE; 1.86A {Deinococcus geothermalis dsm 11300}

Probab=89.99  E-value=0.31  Score=40.19  Aligned_cols=32  Identities=22%  Similarity=0.244  Sum_probs=29.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.-
T Consensus       176 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g~I~~  207 (231)
T 3e97_A          176 LGTQDIMARTSSSRETVSRVLKRLEAHNILEV  207 (231)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCcEEe
Confidence            58999999999999999999999999998853

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

Probab=89.99  E-value=0.34  Score=38.76  Aligned_cols=43  Identities=16%  Similarity=0.147  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHc---CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQL---GIRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~~---G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      ..|..|++.+.+   .+|..+|.+.|     +||.+||||-++.+.+.|.+
T Consensus        14 ~qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~is~aTVYR~L~~L~e~Glv   64 (139)
T 3mwm_A           14 RQRAAVSAALQEVEEFRSAQELHDMLKHKGDAVGLTTVYRTLQSLADAGEV   64 (139)
T ss_dssp             HHHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSS
T ss_pred             HHHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCCE
Confidence            468888888753   37999999998     79999999999999999976

>3b81_A Transcriptional regulator, ACRR family; NP_350189.1, predicted DNA-binding transcriptional regulator TETR/ACRR family; 2.10A {Clostridium acetobutylicum atcc 824}

Probab=89.97  E-value=0.31  Score=38.44  Aligned_cols=37  Identities=19%  Similarity=0.179  Sum_probs=29.4

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus         8 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~agvs~~t~Y~~F   52 (203)
T 3b81_A            8 NFNNKRTELANKIWDIFIANGYENTTLAFIINKLGISKGALYHYF   52 (203)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHTTC
T ss_pred             ChHHHHHHHHHHHHHHHHHcCcccCcHHHHHHHhCCCchhHHHHc
Confidence            3467888888864     234   799999999999999998743

>2eh3_A Transcriptional regulator; all alpha proteins, tetracyclin repressor-like, C-terminal D homeodomain-like, DNA/RNA-binding 3-helical bundle; 1.55A {Aquifex aeolicus}

Probab=89.91  E-value=0.33  Score=38.17  Aligned_cols=35  Identities=20%  Similarity=0.322  Sum_probs=26.9

Q ss_pred             HHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         2 ~tr~~Il~aA~~lf~~~Gy~~~s~~~Ia~~agvskgtlY~~F~   44 (179)
T 2eh3_A            2 GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFK   44 (179)
T ss_dssp             CHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cHHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCCcHHHHHHcC
Confidence            3566776653     334   6999999999999999998643

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

Probab=89.87  E-value=0.35  Score=39.15  Aligned_cols=43  Identities=21%  Similarity=0.467  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHc----CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQL----GIRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~~----G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      ..|..|++.+.+    .+|..+|.+.|     +||.+||||-++.+.+.|.|
T Consensus        17 ~qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Glv   68 (150)
T 2w57_A           17 LPRLKILEVLQQPECQHISAEELYKKLIDLGEEIGLATVYRVLNQFDDAGIV   68 (150)
T ss_dssp             HHHHHHHHHHTSGGGSSEEHHHHHHHHHHTTCCCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHCCcE
Confidence            467788888742    37999999999     89999999999999999976

>2fmy_A COOA, carbon monoxide oxidation system transcription RE COOA-1; DNA transcription regulator, DNA binding protein; HET: HEM; 2.20A {Carboxydothermus hydrogenoformans} PDB: 2hkx_A*

Probab=89.86  E-value=0.27  Score=40.31  Aligned_cols=31  Identities=19%  Similarity=0.320  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       168 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  198 (220)
T 2fmy_A          168 LNTEEIALMLGTTRQTVSVLLNDFKKMGILE  198 (220)
T ss_dssp             SCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999874

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=89.84  E-value=0.46  Score=37.53  Aligned_cols=55  Identities=16%  Similarity=0.169  Sum_probs=38.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCC-CCCCCCHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~-RPrklT~e~~~~I~~l  117 (258)
                      +++.++||+.++|+++||.+.+++..+.|-|.-.  +..++ .--.+|++=.+.+.+.
T Consensus        51 ~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~  108 (147)
T 4b8x_A           51 ELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKRPNPNDGRGTLATITDKGREVVEAA  108 (147)
T ss_dssp             EEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECC----CEEEEECHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEeecCCcCceeEEEECHHHHHHHHHH
Confidence            4899999999999999999999999999987422  22221 1233677655555443

>3b02_A Transcriptional regulator, CRP family; structural genomics, riken structural genomics/proteomics in RSGI; 1.92A {Thermus thermophilus} PDB: 2zdb_A

Probab=89.82  E-value=0.24  Score=39.98  Aligned_cols=31  Identities=26%  Similarity=0.297  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       140 ~t~~~lA~~lg~sr~tvsR~l~~L~~~g~I~  170 (195)
T 3b02_A          140 VSHEEIADATASIRESVSKVLADLRREGLIA  170 (195)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHHHHHHHTSEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999999874

>2xdn_A HTH-type transcriptional regulator TTGR; transcription regulation, TETR family; 2.20A {Pseudomonas putida} PDB: 2uxu_A* 2uxi_A* 2uxo_A* 2uxp_A* 2uxh_A*

Probab=89.79  E-value=0.22  Score=40.17  Aligned_cols=36  Identities=25%  Similarity=0.351  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F~   53 (210)
T 2xdn_A           10 QETRAQIIEAAERAFYKRGVARTTLADIAELAGVTRGAIYWHFN   53 (210)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCTTHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCcHHHHHHHHCCChHHHHHHhC
Confidence            46788888764     234   6999999999999999998754

>2gqq_A Leucine-responsive regulatory protein; helix-turn-helix, transcription; 3.20A {Escherichia coli} PDB: 2l4a_A

Probab=89.78  E-value=0.027  Score=45.90  Aligned_cols=45  Identities=18%  Similarity=0.224  Sum_probs=38.4

Q ss_pred             CHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         49 PNSVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        49 S~dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      -.+++.+|+..+..|  ++..++|+.||||++||++-+++..+.|.+
T Consensus        11 ~d~l~~~Il~~l~~~~~ls~~eLa~~lgvSr~~vr~al~~L~~~Gli   57 (163)
T 2gqq_A           11 LDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI   57 (163)
T ss_dssp             CCSHHHHHHHHHHHCSSCCTTGGGTSSSCCTTTSSSTHHHHHHHTSE
T ss_pred             hhHHHHHHHHHHHhCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcE
Confidence            345677888876644  799999999999999999999999999965

>1p6r_A Penicillinase repressor; transcription regulation, DNA-binding, winged helix protein, bacterial resistance to antibiotics; NMR {Bacillus licheniformis} SCOP: a.4.5.39 PDB: 2p7c_B

Probab=89.76  E-value=0.54  Score=33.53  Aligned_cols=46  Identities=13%  Similarity=0.315  Sum_probs=36.4

Q ss_pred             CCHHHHHHHHHHHH--cCCCHHHHHHHhC----CCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQ--LGIRPCDISRQLR----VSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~--~G~S~~eIAr~LG----VSrsTVsRwikRyrEtGsl~   94 (258)
                      ++. .+..|+..+.  .+.+..+|++.|+    ++.+||++.+++..+.|-|.
T Consensus         7 lt~-~e~~vL~~L~~~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~   58 (82)
T 1p6r_A            7 ISD-AELEVMKVIWKHSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALN   58 (82)
T ss_dssp             CCH-HHHHHHHHHHTSSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCH-HHHHHHHHHHcCCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeE
Confidence            444 3445666553  3589999999997    79999999999999999874

>3cdl_A Transcriptional regulator AEFR; APC88582, TETR, pseudomonas syringae PV. tomato STR. DC3000, structural genomics, PSI-2; HET: MSE; 2.36A {Pseudomonas syringae PV}

Probab=89.75  E-value=0.36  Score=38.85  Aligned_cols=37  Identities=27%  Similarity=0.256  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.+.|.+|++..     +.|   .|..+||+..|||++|||+..
T Consensus         6 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvsk~tlY~~F   50 (203)
T 3cdl_A            6 LTDQKRESIVQAAIAEFGDRGFEITSMDRIAARAEVSKRTVYNHF   50 (203)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHTTS
T ss_pred             cchhHHHHHHHHHHHHHHHcCchhcCHHHHHHHhCCCHHHHHHHC
Confidence            4678888888864     234   699999999999999999853

>3trb_A Virulence-associated protein I; mobIle and extrachromosomal element functions, DNA binding P; 2.00A {Coxiella burnetii}

Probab=89.74  E-value=0.5  Score=36.06  Aligned_cols=26  Identities=15%  Similarity=0.226  Sum_probs=23.4

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -+.|++..++|+.+|||++||++|.+
T Consensus        24 ~~~gltq~eLA~~lGis~~~is~ie~   49 (104)
T 3trb_A           24 FLDKMSANQLAKHLAIPTNRVTAILN   49 (104)
T ss_dssp             HTTSCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            34799999999999999999999974

>3d0s_A Transcriptional regulatory protein; CAMP receptor protein (CRP), dimer, inactive(APO, unliganded allostery, DNA binding, cyclic AMP; 2.00A {Mycobacterium tuberculosis} PDB: 3i54_A* 3i59_A* 3mzh_A* 3h3u_A* 3r6s_A*

Probab=89.73  E-value=0.28  Score=40.26  Aligned_cols=32  Identities=25%  Similarity=0.310  Sum_probs=29.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.-
T Consensus       178 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~~  209 (227)
T 3d0s_A          178 LTQEEIAQLVGASRETVNKALADFAHRGWIRL  209 (227)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence            69999999999999999999999999998743

>2x48_A CAG38821; archeal virus, viral protein; 2.60A {Sulfolobus islandicus rod-shaped virusorganism_taxid}

Probab=89.72  E-value=0.32  Score=32.08  Aligned_cols=43  Identities=23%  Similarity=0.200  Sum_probs=32.3

Q ss_pred             CCCCCC--HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        102 KPRVTT--PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       102 RPrklT--~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      ++..++  ++..+.|..+..+  ..+..||++.|.          +|.+||++.|++
T Consensus        10 ~~~~l~~~~~~~~~i~~l~~~--g~s~~eIA~~lg----------is~~TV~~~l~~   54 (55)
T 2x48_A           10 VRYYVESEDDLVSVAHELAKM--GYTVQQIANALG----------VSERKVRRYLES   54 (55)
T ss_dssp             EEEEECSHHHHHHHHHHHHHT--TCCHHHHHHHHT----------SCHHHHHHHHTC
T ss_pred             HHHHHhcCHHHHHHHHHHHHc--CCCHHHHHHHHC----------cCHHHHHHHHHh
Confidence            555677  7777777777543  579999988883          499999999864

>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=89.70  E-value=0.31  Score=40.59  Aligned_cols=31  Identities=26%  Similarity=0.323  Sum_probs=29.4

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       187 ~t~~~lA~~lG~sr~tvsR~l~~l~~~glI~  217 (232)
T 1zyb_A          187 VKMDDLARCLDDTRLNISKTLNELQDNGLIE  217 (232)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             CCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999874

>3knw_A Putative transcriptional regulator (TETR/ACRR FAM; TETR-like protein, MCSG, PSI, structural genomics, protein S initiative; 2.45A {Acinetobacter SP}

Probab=89.69  E-value=0.52  Score=37.41  Aligned_cols=38  Identities=16%  Similarity=0.253  Sum_probs=30.2

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..+
T Consensus        11 ~~~~~r~~Il~aa~~l~~~~G~~~~ti~~IA~~agvs~~t~Y~~F~   56 (212)
T 3knw_A           11 KSEAKRQHILDSGFHLVLRKGFVGVGLQEILKTSGVPKGSFYHYFE   56 (212)
T ss_dssp             -CHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cchhhHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCChHHHHHHCC
Confidence            4568888888854     334   6999999999999999998644

>2fjr_A Repressor protein CI; genetic switch, regulation, cooperativity, transcription regulator; 1.95A {Enterobacteria phage 186} PDB: 2fkd_A

Probab=89.64  E-value=0.41  Score=39.07  Aligned_cols=34  Identities=15%  Similarity=0.240  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++-.|+.++...- +..++|+.+|||++||++|.+
T Consensus         9 ~~~~rl~~~r~~~-tq~elA~~~Gis~~~i~~~e~   42 (189)
T 2fjr_A            9 DVLDRICEAYGFS-QKIQLANHFDIASSSLSNRYT   42 (189)
T ss_dssp             HHHHHHHHHHTCS-SHHHHHHHTTCCHHHHHHHHH
T ss_pred             HHHHHHHHHHhhc-CHHHHHHHhCcCHHHHHHHHh
Confidence            4555666665444 999999999999999999987

>3anp_C Transcriptional repressor, TETR family; all alpha protein, DNA, acyl-COA; HET: DCC DAO; 1.95A {Thermus thermophilus} PDB: 3ang_C*

Probab=89.58  E-value=0.5  Score=37.77  Aligned_cols=36  Identities=25%  Similarity=0.330  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         8 ~~~r~~Il~aA~~lf~~~G~~~~t~~~Ia~~Agvs~gt~Y~yF~   51 (204)
T 3anp_C            8 KRRRERIFRAAMELFRNRGFQETTATEIAKAAHVSRGTFFNYYP   51 (204)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHcCcccccHHHHHHHcCCchHHHHHHcC
Confidence            35677787754     235   6999999999999999998643

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

Probab=89.56  E-value=0.21  Score=40.04  Aligned_cols=53  Identities=19%  Similarity=0.097  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598        105 VTTPKVVSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV  163 (258)
Q Consensus       105 klT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~  163 (258)
                      ++|+ ++..|.+++.+. ..+++.||.+.|++.+..+     |.+||+|.|..+....+-
T Consensus        11 r~T~-qR~~Il~~L~~~~~h~sa~eI~~~l~~~~~~i-----s~aTVYR~L~~L~e~Glv   64 (139)
T 3mwm_A           11 RATR-QRAAVSAALQEVEEFRSAQELHDMLKHKGDAV-----GLTTVYRTLQSLADAGEV   64 (139)
T ss_dssp             HHHH-HHHHHHHHHTTCSSCEEHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHHTTSS
T ss_pred             ccCH-HHHHHHHHHHhCCCCCCHHHHHHHHHHhCCCC-----CHHHHHHHHHHHHHCCCE
Confidence            3444 466677776654 3689999999999877664     999999999987666543

>3loc_A HTH-type transcriptional regulator RUTR; helix-turn-helix, putative transcriptional regulator, dimer, structural genomics, PSI; HET: MSE; 2.50A {Escherichia coli}

Probab=89.55  E-value=0.37  Score=38.21  Aligned_cols=36  Identities=22%  Similarity=0.218  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|++|++..     +.   +.|.++||+..|||++|||+...
T Consensus        17 ~~~R~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   60 (212)
T 3loc_A           17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFP   60 (212)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHhhhCC
Confidence            35788888754     23   57999999999999999998754

>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=89.53  E-value=0.66  Score=38.71  Aligned_cols=31  Identities=19%  Similarity=0.199  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|.++||+.||+|.+||++++++-.+.|.+.
T Consensus        25 ~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~   55 (196)
T 3k2z_A           25 PSVREIARRFRITPRGALLHLIALEKKGYIE   55 (196)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHcCCCcHHHHHHHHHHHHCCCEE
Confidence            7999999999999999999999999999874

>2bgc_A PRFA; bacterial infection, human pathogen, transcriptional regulat transcription; HET: PR3; 2.3A {Listeria monocytogenes} SCOP: a.4.5.4 b.82.3.3 PDB: 2beo_A* 1omi_A

Probab=89.50  E-value=0.51  Score=39.40  Aligned_cols=33  Identities=15%  Similarity=0.327  Sum_probs=29.7

Q ss_pred             CCCHHHHHHHhCCCHH-HHHHHHHHhhhhCCccc
Q psy15598         63 GIRPCDISRQLRVSHG-CVSKILARYHETGSILP   95 (258)
Q Consensus        63 G~S~~eIAr~LGVSrs-TVsRwikRyrEtGsl~p   95 (258)
                      .++..+||..+|+|++ ||+|.++++++.|.|.-
T Consensus       169 ~~t~~~lA~~lG~sr~etvsR~l~~l~~~glI~~  202 (238)
T 2bgc_A          169 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY  202 (238)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCCHHHHHHHhCCChHHHHHHHHHHHHHCCCEEe
Confidence            5788999999999995 99999999999998743

>3mlf_A Transcriptional regulator; structural genomics, helix-turn-helix XRE-family like protei transcription regulator, PSI-2; 2.60A {Staphylococcus aureus subsp}

Probab=89.50  E-value=0.38  Score=36.84  Aligned_cols=30  Identities=17%  Similarity=0.348  Sum_probs=25.2

Q ss_pred             HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         56 IVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |-.+. ..|++..++|+.+|||++||++|.+
T Consensus        28 Lk~~R~~~gltq~elA~~~gis~~~is~~E~   58 (111)
T 3mlf_A           28 LKELRTDYGLTQKELGDLFKVSSRTIQNMEK   58 (111)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHH
T ss_pred             HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            33443 4799999999999999999999975

>3lmm_A Uncharacterized protein; multi-domained alpha-beta protein, structural genomics, PSI- 2, protein structure initiative; 3.00A {Corynebacterium diphtheriae}

Probab=89.50  E-value=0.31  Score=48.18  Aligned_cols=97  Identities=9%  Similarity=-0.051  Sum_probs=32.5

Q ss_pred             HHHHHH-Hc-CCCHHHHHHHhCCCHHHHHHHHHHhhh-----hCCcccCCC-----------CCC---C------CCCCC
Q psy15598         55 RIVELA-QL-GIRPCDISRQLRVSHGCVSKILARYHE-----TGSILPGAI-----------GGS---K------PRVTT  107 (258)
Q Consensus        55 RIV~L~-~~-G~S~~eIAr~LGVSrsTVsRwikRyrE-----tGsl~pk~r-----------gG~---R------PrklT  107 (258)
                      .|+.++ ++ .++..++|+.|++|..+|.+.+++..+     .|.++....           -+.   +      -+.+.
T Consensus       434 ~iL~~l~~~~~it~~~la~~l~~s~~~~~~~L~~L~~~~~~~~glie~~g~~y~L~~~~~~~~~~~~~~~~~~~~~~~~~  513 (583)
T 3lmm_A          434 IVLYLLFQRPFITIDVVARGLQSGKEAARNALEAARQTTVAGAPLIIAHDGVWLLGNACREILRKVEPSPFSPVRYLSTD  513 (583)
T ss_dssp             HHHHHHHHSSSBCHHHHHHHHTSCHHHHHHHHHHHHTCEETTEESEEEETTEEEECHHHHHHHTSCC-------------
T ss_pred             HHHHHHHHCCCcCHHHHHHHhCcCHHHHHHHHHHHHhhhccccceEEEeCCEEEECHHHHHHhcccccccccccccccCC
Confidence            455544 44 489999999999999999999999998     444432100           000   0      00011


Q ss_pred             -HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        108 -PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       108 -~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                       ...++.|.++++++..++..+|++.+.          +|..+++|+|+++..+.
T Consensus       514 ~~~~~~~I~~~l~~~g~it~~di~~l~~----------ls~~qa~~~L~~Lv~~G  558 (583)
T 3lmm_A          514 QAELTNAAMLWLSEVGDLATSDLMAMCG----------VSRGTAKACVDGLVDEE  558 (583)
T ss_dssp             -------------------------------------------------------
T ss_pred             hhHHHHHHHHHHHHcCCcCHHHHHHHHC----------CCHHHHHHHHHHHHHCC
Confidence             123456888888888888888887663          38889999998877664

>1l9z_H Sigma factor SIGA; helix-turn-helix, coiled-coil, transcription/DNA complex; 6.50A {Thermus aquaticus} SCOP: i.8.1.1

Probab=89.47  E-value=0.5  Score=45.30  Aligned_cols=42  Identities=10%  Similarity=-0.001  Sum_probs=33.8

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+-    +|+|..+||+.||||+.+|+.++.|-.
T Consensus       375 ~L~ereR~VI~LRygL~~~e~~TleEIAe~LgIS~erVRqi~~RAl  420 (438)
T 1l9z_H          375 KLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL  420 (438)
T ss_pred             hCCHHHHHHHHHHHhccCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366666655555554    789999999999999999999998875

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

Probab=89.43  E-value=0.22  Score=39.75  Aligned_cols=57  Identities=16%  Similarity=0.264  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CC-CCCCCCCHHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GG-SKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG-~RPrklT~e~~~~I~~lv~  119 (258)
                      +++..+||+.++|+++||++.+++..+.|-|.-...  .+ ..--.+|++-.+.+.+...
T Consensus        62 ~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~~~~~DrR~~~l~LT~~G~~~~~~~~~  121 (168)
T 3u2r_A           62 GMATLQIADRLISRAPDITRLIDRLDDRGLVLRTRKPENRRVVEVALTDAGLKLLKDLEE  121 (168)
T ss_dssp             CEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeecCCCCCCCeeEeEECHHHHHHHHHHHH
Confidence            789999999999999999999999999998742221  11 0123477776666655543

>1r8e_A Multidrug-efflux transporter regulator; protein-DNA complex, MERR-family transcription activator, MU binding protein; HET: P4P; 2.40A {Bacillus subtilis} SCOP: a.6.1.3 d.60.1.1 PDB: 1exi_A* 1exj_A* 3iao_A 3q5p_A* 3d71_A* 3q3d_A* 3q1m_A* 3q2y_A* 3q5r_A* 3q5s_A* 3d70_A 3d6z_A* 3d6y_A* 1bow_A 2bow_A*

Probab=89.40  E-value=0.18  Score=43.77  Aligned_cols=65  Identities=18%  Similarity=0.121  Sum_probs=42.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC-CCCCCCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAI-GGSKPRVTTPKVV---SYIKELKQKDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r-gG~RPrklT~e~~---~~I~~lv~~nP~ita~EIr~~L~  134 (258)
                      ++..++|+.+|||.+|++.|    .+.|.+.|..+ ....-|..++++.   ..|..++..  .+++.+|++.|.
T Consensus         6 ~~i~e~a~~~gvs~~tlr~y----~~~gll~p~~~d~~~g~R~y~~~~~~~l~~i~~l~~~--g~~l~~i~~~~~   74 (278)
T 1r8e_A            6 YSIGEVSKLANVSIKALRYY----DKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYI--GTPLEEMKKAQD   74 (278)
T ss_dssp             EEHHHHHHHHTCCHHHHHHH----HHTTSSCCSEECTTTCCEEEETGGGGHHHHHHHHHHT--TCCHHHHHHHTT
T ss_pred             EeHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCccccCHHHHHHHHHHHHHHHC--CCCHHHHHHHHH
Confidence            68899999999999999866    44588876544 2112344554433   444444333  678888877663

>3bqz_B HTH-type transcriptional regulator QACR; multidrug resistance, TETR, malachite green, DNA- binding, plasmid, repressor; HET: MGR; 2.17A {Staphylococcus aureus} PDB: 3br1_B* 3br3_B* 3pm1_B* 1rkw_B* 1jt0_A* 1jty_B* 1jum_B* 1jup_B* 1jtx_B* 1jus_B* 2dtz_B 2gby_B* 2hq5_B 3br2_B* 3br5_B* 1qvt_B* 1qvu_B* 3br0_B* 3br6_B* 1jt6_B* ...

Probab=89.39  E-value=0.33  Score=38.04  Aligned_cols=23  Identities=13%  Similarity=0.099  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.++||+..|||++|+|+..+
T Consensus        22 ~~ti~~Ia~~agvs~~t~Y~~F~   44 (194)
T 3bqz_B           22 ATTTGEIVKLSESSKGNLYYHFK   44 (194)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHTS
T ss_pred             cCCHHHHHHHhCCCchhHHHhCC
Confidence            47999999999999999998643

>3q0w_A HTH-type transcriptional regulator EThr; TETR family, transcriptional repressor, transcription-transc inhibitor complex; HET: LL5; 1.60A {Mycobacterium tuberculosis} PDB: 3o8g_A* 3o8h_A* 3q0u_A* 3q0v_A* 3g1m_A* 3q3s_A* 3sdg_A* 3sfi_A* 1u9n_A* 1u9o_A* 3tp3_A 3qpl_A 3g1l_A* 1t56_A 3tp0_A*

Probab=89.38  E-value=0.48  Score=39.13  Aligned_cols=42  Identities=17%  Similarity=0.193  Sum_probs=30.9

Q ss_pred             CCCCCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..++-..+.|.+|++..     +.|   .|.++||+..|||++|||+..+
T Consensus        37 ~~~~~~~~~r~~Il~aA~~lf~e~G~~~~t~~~IA~~aGvs~~tlY~~F~   86 (236)
T 3q0w_A           37 TARPSGDDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFP   86 (236)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             CCCCChHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCcHHHHHHHCC
Confidence            45556778898988864     345   6999999999999999998644

>3ppb_A Putative TETR family transcription regulator; DNA-binding, helix-turn-helix motif, HTH motif, DNA/RNA-BIND helical bundle fold; HET: MSE PG4; 2.10A {Shewanella loihica}

Probab=89.37  E-value=0.3  Score=38.09  Aligned_cols=35  Identities=23%  Similarity=0.341  Sum_probs=26.9

Q ss_pred             HHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++..     +.|   .|.++||+..|||++|+|+..+
T Consensus         9 ~~r~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~   51 (195)
T 3ppb_A            9 TKKQAILETALQLFVSQGFHGTSTATIAREAGVATGTLFHHFP   51 (195)
T ss_dssp             CHHHHHHHHHHHHHHHTCSTTSCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCChhHHHHHcC
Confidence            4566666653     344   6999999999999999998643

>3dew_A Transcriptional regulator, TETR family; S genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 1.75A {Geobacter sulfurreducens}

Probab=89.33  E-value=0.35  Score=37.94  Aligned_cols=37  Identities=22%  Similarity=0.303  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|+|+..+.
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   51 (206)
T 3dew_A            7 ADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGG   51 (206)
T ss_dssp             -CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHSCH
T ss_pred             hHHHHHHHHHHHHHHhcCCcccCcHHHHHHHhCCCHHHHHHHcCC
Confidence            35677777753     234   79999999999999999987543

>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=89.33  E-value=0.23  Score=37.58  Aligned_cols=33  Identities=6%  Similarity=0.069  Sum_probs=25.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .+|+..+ .-++.+.||+.+||+.+||+||..-+
T Consensus        16 s~iL~~L-a~~gQ~~vAe~~GvdeStISR~k~~~   48 (83)
T 1zs4_A           16 SALLNKI-AMLGTEKTAEAVGVDKSQISRWKRDW   48 (83)
T ss_dssp             HHHHHHH-HHHCHHHHHHHHTSCHHHHHHHHHHT
T ss_pred             HHHHHHH-HHHhhHHHHHHhCCCHHHHhhhhhhH
Confidence            3343333 34788999999999999999998865

>3eyy_A Putative iron uptake regulatory protein; NUR, nickel-uptake regulator, D-domain, dimerization domain, DB-domain, DNA-binding domain; 2.40A {Streptomyces coelicolor}

Probab=89.32  E-value=0.58  Score=37.63  Aligned_cols=43  Identities=21%  Similarity=0.261  Sum_probs=36.1

Q ss_pred             HHHHHHHHHHH--cCCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         51 SVRMRIVELAQ--LGIRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        51 dlR~RIV~L~~--~G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      ..|..|++.+.  ...+..+|.+.|     +||.+||||-++.+.+.|.+
T Consensus        19 ~qR~~Il~~l~~~~h~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Glv   68 (145)
T 3eyy_A           19 PQRQLVLEAVDTLEHATPDDILGEVRKTASGINISTVYRTLELLEELGLV   68 (145)
T ss_dssp             HHHHHHHHHHHHHSSBCHHHHHHHHHTTCTTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHHhcCCCCHHHHHHHHHhhCCCCCHhHHHHHHHHHHHCCcE
Confidence            35777877764  357999999988     79999999999999999975

>4a0z_A Transcription factor FAPR; lipid homeostasis; HET: MLC; 1.90A {Staphylococcus aureus} PDB: 4a0y_A 4a0x_A* 4a12_A

Probab=89.29  E-value=0.28  Score=41.72  Aligned_cols=41  Identities=17%  Similarity=0.153  Sum_probs=0.0

Q ss_pred             CCcccCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHH
Q psy15598         39 GGVFVNGRPLPNSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSK   82 (258)
Q Consensus        39 ~~~~~~gR~~S~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsR   82 (258)
                      |.+|.|.+   .+-+++|+++++ +| ++..++|+.|+||..||+|
T Consensus         3 g~~~~m~k---~eR~~~i~~~l~~~~~~~~~~la~~~~vs~~TiRr   45 (190)
T 4a0z_A            3 GETLKLKK---DKRREAIRQQIDSNPFITDHELSDLFQVSIQTIRL   45 (190)
T ss_dssp             ----CHHH---HHHHHHHHHHHHHCTTCCHHHHHHHHTSCHHHHHH
T ss_pred             ccccccCH---HHHHHHHHHHHHHCCCEeHHHHHHHHCCCHHHHHH

>1a04_A Nitrate/nitrite response regulator protein NARL; signal transduction protein, response regulators, two- component systems; 2.20A {Escherichia coli} SCOP: a.4.6.2 c.23.1.1 PDB: 1rnl_A

Probab=89.21  E-value=0.57  Score=38.09  Aligned_cols=40  Identities=23%  Similarity=0.294  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...+ +|+.++.+|.+.++||+.+++|.+||...+++-+
T Consensus       155 Lt~rE~-~vl~~l~~g~s~~~Ia~~l~is~~TV~~hi~~i~  194 (215)
T 1a04_A          155 LTPRER-DILKLIAQGLPNKMIARRLDITESTVKVHVKHML  194 (215)
T ss_dssp             SCHHHH-HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            565544 5888888999999999999999999999988876

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

Probab=89.19  E-value=0.38  Score=37.37  Aligned_cols=33  Identities=9%  Similarity=0.131  Sum_probs=30.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      .+..+||+.++|++++|+++++..++.|-+...
T Consensus        27 ~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           27 TSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             BCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHHHHHHCCceEec
Confidence            799999999999999999999999999987543

>2gau_A Transcriptional regulator, CRP/FNR family; structural genomics, porphyromona gingivalis, PSI, protein structure initiative; 1.90A {Porphyromonas gingivalis} SCOP: a.4.5.4 b.82.3.2

Probab=89.17  E-value=0.33  Score=40.03  Aligned_cols=31  Identities=3%  Similarity=0.100  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus       181 ~t~~~lA~~lg~sr~tvsR~l~~l~~~g~I~  211 (232)
T 2gau_A          181 LSREELATLSNMTVSNAIRTLSTFVSERMLA  211 (232)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             cCHHHHHHHhCCCHHHHHHHHHHHHHCCCEe
Confidence            5899999999999999999999999999874

>1pb6_A Hypothetical transcriptional regulator YCDC; helix-loop-helix, dimer, structural genomics, PSI, protein structure initiative; 2.50A {Escherichia coli} PDB: 3loc_A*

Probab=89.11  E-value=0.57  Score=37.15  Aligned_cols=37  Identities=22%  Similarity=0.183  Sum_probs=29.8

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        15 ~~~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~t~Y~~F   59 (212)
T 1pb6_A           15 AVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYF   59 (212)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHS
T ss_pred             chHHHHHHHHHHHHHHHHHcCcchhhHHHHHHHHCCChhHHHHhC
Confidence            3457888888854     334   699999999999999999874

>3c3w_A Two component transcriptional regulatory protein; response regulator, two-component regulatory system, DNA-BIN protein; 2.20A {Mycobacterium tuberculosis}

Probab=89.06  E-value=0.57  Score=38.82  Aligned_cols=41  Identities=17%  Similarity=0.284  Sum_probs=35.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...+ +|+.++.+|++.++||+.|++|.+||...+++-+
T Consensus       149 ~LT~rE~-~vL~~l~~g~s~~eIa~~l~is~~TV~~hi~~l~  189 (225)
T 3c3w_A          149 GLTDQER-TLLGLLSEGLTNKQIADRMFLAEKTVKNYVSRLL  189 (225)
T ss_dssp             TSCHHHH-HHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            3666554 5888888999999999999999999999988876

>3mky_B Protein SOPB; partition, F plasmid, centromere, DNA binding protein- complex; HET: DNA; 2.86A {Escherichia coli} PDB: 3mkw_B* 3mkz_A*

Probab=89.05  E-value=0.82  Score=39.43  Aligned_cols=108  Identities=11%  Similarity=0.067  Sum_probs=64.9

Q ss_pred             CCCCCCHHHHHHHHHH-HHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         44 NGRPLPNSVRMRIVEL-AQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L-~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      ..|++|.-.|.+--.. .++|  .+.+++|+.+|||++.|+|.++-.+=.-.+...-   ..|.-++...-+.|......
T Consensus        20 ~~rplS~yErg~~y~r~L~~g~~~~Q~~lA~~~giS~a~VSR~L~~A~LP~~lv~~f---p~p~dLs~~~~~~L~k~~~~   96 (189)
T 3mky_B           20 HYRPTSAYERGQRYASRLQNEFAGNISALADAENISRKIITRCINTAKLPKSVVALF---SHPGELSARSGDALQKAFTD   96 (189)
T ss_dssp             ---CCCHHHHHHHHHHHHHTTTTTCHHHHHHHHTSCHHHHHHHHHHHHSCHHHHHTS---SSGGGSCHHHHHHHHHHTTT
T ss_pred             cCCCCCHHHHHHHHHHHHhcCcccCHHHHHHHHCCCHHHHHHHHHHhcCCHHHHHHc---CCHHhcCchhHHHHHHHHhc
Confidence            4588999888665555 4566  7999999999999999999999876222111110   13455666666666554433


Q ss_pred             CCCCCHHHHHHHHH---hcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598        121 DPGIFAWEIRDRLL---SDGVCDKFNVPSVSSISRILRNKIGS  160 (258)
Q Consensus       121 nP~ita~EIr~~L~---~~Gv~v~~~~pS~STI~RiLrr~~~~  160 (258)
                      ..+ .+.+...++.   +.|+..     +..-|-+.|......
T Consensus        97 ~~~-ll~~~a~~l~e~~~~G~~~-----~~~evi~~L~~~~~~  133 (189)
T 3mky_B           97 KEE-LLKQQASNLHEQKKAGVIF-----EADEVITLLTSVLKT  133 (189)
T ss_dssp             CHH-HHHHHHHHHHHHHHTTCCC-----CHHHHHHHHHHTTSG
T ss_pred             cHH-HHHHHHHHHHHHhccCCcC-----CHHHHHHHHHHHHhc
Confidence            332 2333334443   356654     666666666655433

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=89.00  E-value=4.4  Score=35.61  Aligned_cols=34  Identities=15%  Similarity=0.103  Sum_probs=27.6

Q ss_pred             HHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVEL-AQLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L-~~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +-.+|... .+.|++..+||+.+|||.++|++|++
T Consensus        32 ~~~~Ik~~r~~~gltQ~evA~~tGISqS~ISq~e~   66 (221)
T 2h8r_A           32 AAKMIKGYMQQHNIPQREVVDVTGLNQSHLSQHLN   66 (221)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence            33444443 45799999999999999999999986

>3la7_A Global nitrogen regulator; activator, DNA-binding, transcription, transcription regulation; HET: BOG; 1.90A {Anabaena} PDB: 3la2_A* 3la3_A* 2xko_A* 2xgx_A* 2xhk_A* 2xkp_A*

Probab=88.98  E-value=0.34  Score=40.74  Aligned_cols=31  Identities=16%  Similarity=0.233  Sum_probs=29.3

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.|.
T Consensus       194 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~  224 (243)
T 3la7_A          194 LSHQAIAEAIGSTRVTVTRLLGDLREKKMIS  224 (243)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCcHHHHHHHHHHHHHCCCEE
Confidence            5899999999999999999999999999875

>3vpr_A Transcriptional regulator, TETR family; all alpha, helix-turn-helix, transcriptional repressor, DNA protein; 2.27A {Thermus thermophilus}

Probab=88.93  E-value=0.46  Score=37.54  Aligned_cols=35  Identities=23%  Similarity=0.284  Sum_probs=26.6

Q ss_pred             HHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         52 VRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        52 lR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .|.+|++..     +.   +.|..+||+..|||++|+|+..+.
T Consensus         4 tr~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~t~Y~~F~s   46 (190)
T 3vpr_A            4 TRDRILEEAAKLFTEKGYEATSVQDLAQALGLSKAALYHHFGS   46 (190)
T ss_dssp             HHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             hHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcCC
Confidence            455666543     33   469999999999999999987654

>3crj_A Transcription regulator; APC88200, TETR, structura genomics, PSI-2, protein structure initiative; HET: MSE; 2.60A {Haloarcula marismortui atcc 43049}

Probab=88.88  E-value=0.42  Score=38.52  Aligned_cols=37  Identities=14%  Similarity=0.097  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.+.|.+|++..     +.|   .|.++||+..|||++|||+..
T Consensus        11 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~tlY~yF   55 (199)
T 3crj_A           11 TFSDQTEEIMQATYRALREHGYADLTIQRIADEYGKSTAAVHYYY   55 (199)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTTTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             cchhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCChhHHhhhc
Confidence            4567888898864     234   799999999999999999754

>3kxa_A NGO0477 protein, putative uncharacterized protein; NEW protein fold, OPPF, STRU genomics, oxford protein production facility; 2.80A {Neisseria gonorrhoeae}

Probab=88.87  E-value=0.37  Score=38.70  Aligned_cols=25  Identities=12%  Similarity=0.263  Sum_probs=23.3

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..|++..++|+.+|||+++|++|.+
T Consensus        79 ~~glTq~elA~~lGis~s~is~~E~  103 (141)
T 3kxa_A           79 KKGFTQSELATAAGLPQPYLSRIEN  103 (141)
T ss_dssp             HTTCCHHHHHHHTTCCHHHHHHHHH
T ss_pred             HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence            4799999999999999999999976

>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=88.86  E-value=0.39  Score=40.34  Aligned_cols=54  Identities=20%  Similarity=0.203  Sum_probs=39.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDP  122 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP  122 (258)
                      .++..+||..+|+|+.||+|.++++++.|-+.-..  + +-.++.   .+.+.++....+
T Consensus       177 ~~t~~~iA~~lG~sr~tvsR~l~~L~~~g~I~~~~--~-~i~i~d---~~~L~~~a~~~~  230 (250)
T 3e6c_C          177 PLSQKSIGEITGVHHVTVSRVLASLKRENILDKKK--N-KIIVYN---LGELKHLSEQTS  230 (250)
T ss_dssp             CCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECS--S-EEEESC---HHHHHHHHTSSC
T ss_pred             CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCeEeCC--C-EEEEec---HHHHHHHHccCc
Confidence            35999999999999999999999999999885331  1 223343   445556655544

>3f1b_A TETR-like transcriptional regulator; APC5888, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.40A {Rhodococcus}

Probab=88.83  E-value=0.63  Score=36.54  Aligned_cols=36  Identities=11%  Similarity=0.087  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        12 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   55 (203)
T 3f1b_A           12 RAVREQQMLDAAVDVFSDRGFHETSMDAIAAKAEISKPMLYLYY   55 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHHcCcccccHHHHHHHhCCchHHHHHHh
Confidence            345677787754     234   699999999999999999863

>3pas_A TETR family transcription regulator; structural genomics, joint center for structural genomics, J protein structure initiative; HET: MSE; 1.90A {Marinobacter aquaeolei}

Probab=88.78  E-value=0.46  Score=36.98  Aligned_cols=36  Identities=14%  Similarity=0.149  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|+|+..+
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   50 (195)
T 3pas_A            7 DSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYE   50 (195)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHcChHhcCHHHHHHHhCCCchHHHHHcC
Confidence            46778887754     23   47999999999999999998643

>2g7s_A Transcriptional regulator, TETR family; APC5906, PSI, protein structure initiat midwest center for structural genomics, MCSG; HET: MSE; 1.40A {Agrobacterium tumefaciens str} SCOP: a.4.1.9 a.121.1.1

Probab=88.77  E-value=0.21  Score=38.97  Aligned_cols=36  Identities=17%  Similarity=0.200  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus         7 ~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   50 (194)
T 2g7s_A            7 QSKADDILQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHFP   50 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             hhhHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcC
Confidence            46778887753     23   47999999999999999998643

>2oer_A Probable transcriptional regulator; helix-turn-helix, alpha-beta, structural genomics, PSI-2, protein structure initiative; 2.00A {Pseudomonas aeruginosa}

Probab=88.74  E-value=0.46  Score=38.61  Aligned_cols=37  Identities=16%  Similarity=0.216  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHHH-----c---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELAQ-----L---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~~-----~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.+.|.+|++...     .   +.|..+||+..|||++|||+..+
T Consensus        22 ~~~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~aGvskgtlY~yF~   66 (214)
T 2oer_A           22 SSELVASILEAAVQVLASEGAQRFTTARVAERAGVSIGSLYQYFP   66 (214)
T ss_dssp             -CHHHHHHHHHHHHC------CCCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHhhCcccccHHHHHHHhCCCCchHHHhCC
Confidence            4567888998753     3   46999999999999999998743

>2np5_A Transcriptional regulator; TETR family, structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; HET: MSE LMT NDS; 1.80A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=88.72  E-value=0.39  Score=38.72  Aligned_cols=38  Identities=16%  Similarity=0.263  Sum_probs=28.3

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -+...|.+|++..     +.|   .|.++||+..|||++|||+..+
T Consensus         6 ~~~~tr~~Il~AA~~lf~~~G~~~~s~~~IA~~AGvs~gtlY~~F~   51 (203)
T 2np5_A            6 YSSTSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFS   51 (203)
T ss_dssp             ---CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccchhHHHHHHHHHHHHHHhChhhccHHHHHHHhCCCHHHHHHHcC
Confidence            3456678888754     344   7999999999999999998743

>1ixc_A CBNR, LYSR-type regulatory protein; long alpha helix connecting DNA binding and regulatory domai binding protein; 2.20A {Cupriavidus necator} SCOP: a.4.5.37 c.94.1.1 PDB: 1iz1_A

Probab=88.71  E-value=1.1  Score=37.51  Aligned_cols=57  Identities=11%  Similarity=0.111  Sum_probs=37.2

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      +++..+.+-.|.+++|+.|+||.++|++-+++.++ -|. +-.+  .+ |.-.+|++=+.++
T Consensus         7 ~~f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R--~~-~~~~lT~~G~~l~   65 (294)
T 1ixc_A            7 KYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLER--SH-RGIELTAAGHAFL   65 (294)
T ss_dssp             HHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC--------CCBCHHHHHHH
T ss_pred             HHHHHHHHcCCHHHHHHHhCCCcchHHHHHHHHHHHHCCEEEEe--CC-CCeeECHhHHHHH
Confidence            44555544459999999999999999999999986 443 2222  23 4566776644433

>3bru_A Regulatory protein, TETR family; structural genomics, APC88928, PSI-2, protein structur initiative; 2.30A {Rhodobacter sphaeroides 2}

Probab=88.68  E-value=0.46  Score=38.14  Aligned_cols=37  Identities=14%  Similarity=0.260  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+..+
T Consensus        28 ~~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~aGvs~~t~Y~~F~   72 (222)
T 3bru_A           28 ASLAHQSLIRAGLEHLTEKGYSSVGVDEILKAARVPKGSFYHYFR   72 (222)
T ss_dssp             GGGHHHHHHHHHHHHHHHSCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hhhHHHHHHHHHHHHHHHcCCCcCcHHHHHHHhCCCcchhhhhCC
Confidence            456788888764     244   6999999999999999998753

>2id3_A Putative transcriptional regulator; structural genomics, PSI-2, prote structure initiative; 1.70A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=88.65  E-value=0.47  Score=38.95  Aligned_cols=38  Identities=18%  Similarity=0.219  Sum_probs=30.2

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+....
T Consensus        38 ~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~s   83 (225)
T 2id3_A           38 TARIREAVLLAAGDALAADGFDALDLGEIARRAGVGKTTVYRRWGT   83 (225)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHCS
T ss_pred             chHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCHHHHHHHCCC
Confidence            346788888754     234   79999999999999999987654

>3lfp_A CSP231I C protein; transcriptional regulator, DNA binding protein, helix-turn-H restriction-modification, transcription; 2.00A {Citrobacter SP} PDB: 3lis_A

Probab=88.62  E-value=0.6  Score=34.30  Aligned_cols=30  Identities=10%  Similarity=0.193  Sum_probs=23.3

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHH----HHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGC----VSKIL   84 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsT----VsRwi   84 (258)
                      +|-.+. ..|++..++|+.+|||++|    |++|.
T Consensus         5 ~lk~~R~~~glsq~~lA~~~gis~~~~~~~is~~E   39 (98)
T 3lfp_A            5 RLKDARLRAGISQEKLGVLAGIDEASASARMNQYE   39 (98)
T ss_dssp             HHHHHHHHHTCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCcchhhhHHHHHH
Confidence            344443 4799999999999999999    55554

>2o7t_A Transcriptional regulator; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: UNL; 2.10A {Corynebacterium glutamicum} SCOP: a.4.1.9 a.121.1.1

Probab=88.60  E-value=0.59  Score=37.22  Aligned_cols=36  Identities=14%  Similarity=0.101  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+...
T Consensus         7 ~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F~   50 (199)
T 2o7t_A            7 LKRREHIITTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNFP   50 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHcC
Confidence            45677787754     344   6999999999999999998754

>3hhg_A Transcriptional regulator, LYSR family; transcription factor, structur genomics, oxford protein production facility, OPPF; 3.20A {Neisseria meningitidis serogroup B}

Probab=88.60  E-value=1.1  Score=37.56  Aligned_cols=58  Identities=19%  Similarity=0.219  Sum_probs=40.8

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .+++..+.+-.|.+++|+.|+||.++|++-+++.++ -|. +-.+  .+ +.-.+|++-+.++
T Consensus         8 l~~f~~v~~~gs~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R--~~-~~~~lT~~G~~l~   67 (306)
T 3hhg_A            8 LTVFVQVVESGSFSRAAEQLAMANSAVSRIVKRLEEKLGVNLLNR--TT-RQLSLTEEGAQYF   67 (306)
T ss_dssp             HHHHHHHHHSSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEET--TS-SSCEECHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEee--cC-CCeeECHhHHHHH
Confidence            345555556669999999999999999999999986 453 2222  23 5567777644433

>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=88.54  E-value=0.41  Score=40.80  Aligned_cols=32  Identities=22%  Similarity=0.267  Sum_probs=29.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||..+|+|+.||+|.++++++.|.|.-
T Consensus       218 lt~~~lA~~lG~sr~tvsR~l~~L~~~GlI~~  249 (260)
T 3kcc_A          218 ITRQEIGQIVGCSRETVGRILKMLEDQNLISA  249 (260)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence            57899999999999999999999999998753

>3gzi_A Transcriptional regulator, TETR family; TETR family transcriptional regulator, structural genomics, center for structural genomics, JCSG; 2.05A {Shewanella loihica pv-4}

Probab=88.54  E-value=0.66  Score=37.07  Aligned_cols=37  Identities=11%  Similarity=0.125  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHH-----cC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-----LG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        50 ~dlR~RIV~L~~-----~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|.+|++...     .|   .|.++||+..|||++|||+..+.
T Consensus        16 ~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   60 (218)
T 3gzi_A           16 TQNRDKLILAARNLFIERPYAQVSIREIASLAGTDPGLIRYYFGS   60 (218)
T ss_dssp             HHHHHHHHHHHHHHHHTSCCSCCCHHHHHHHHTSCTHHHHHHHSS
T ss_pred             hHHHHHHHHHHHHHHHHCCCCcCCHHHHHHHhCCCHHHHHHHcCC
Confidence            457888888643     34   69999999999999999987643

>3bdn_A Lambda repressor; repressor, allostery; HET: DNA; 3.91A {Enterobacteria phage lambda}

Probab=88.50  E-value=0.25  Score=41.71  Aligned_cols=35  Identities=9%  Similarity=0.234  Sum_probs=27.5

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +..+|-.+.+ .|++.+++|+.+|||++||++|.+.
T Consensus        18 ~~~~l~~~r~~~g~t~~~lA~~~gis~~~i~~~~~g   53 (236)
T 3bdn_A           18 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALFNG   53 (236)
T ss_dssp             HHHHHHHHTTTTTCCSHHHHHHHTSCHHHHHHHTTT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcC
Confidence            3444555543 5999999999999999999999753

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

Probab=88.49  E-value=0.21  Score=43.79  Aligned_cols=42  Identities=12%  Similarity=0.211  Sum_probs=35.7

Q ss_pred             HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      -.+|++++.   .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus        23 ~l~iL~~l~~~~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~   67 (265)
T 2ia2_A           23 GLAVIRCFDHRNQRRTLSDVARATDLTRATARRFLLTLVELGYVA   67 (265)
T ss_dssp             HHHHHHTCCSSCSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            346777653   368999999999999999999999999999774

>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=88.45  E-value=0.63  Score=36.96  Aligned_cols=37  Identities=19%  Similarity=0.295  Sum_probs=28.4

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        29 ~~~~r~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F~   73 (218)
T 3dcf_A           29 GNDRRTQIIKVATELFREKGYYATSLDDIADRIGFTKPAIYYYFK   73 (218)
T ss_dssp             -CHHHHHHHHHHHHHHHHTCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             ccchHHHHHHHHHHHHHHcCcccCcHHHHHHHhCCCHHHHHHHcC
Confidence            345677777754     245   6999999999999999998644

>2ibd_A Possible transcriptional regulator; probable transcriptional regulatory protein, rhodococcus SP. structural genomics, PSI-2; 1.50A {Rhodococcus SP}

Probab=88.40  E-value=0.67  Score=37.11  Aligned_cols=36  Identities=14%  Similarity=0.243  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|..+||+..|||++|+|+..+
T Consensus        13 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvs~~tlY~~F~   56 (204)
T 2ibd_A           13 SGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFD   56 (204)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHTTSCHHHHHHHCS
T ss_pred             chhHHHHHHHHHHHHHHcCchhcCHHHHHHHhCCCchhHHHhcC
Confidence            46788888754     23   46999999999999999998653

>3g1o_A Transcriptional regulatory repressor protein (TETR-family) EThr; TERT family, transcriptional repressor, DNA-binding; HET: RF1; 1.85A {Mycobacterium tuberculosis}

Probab=88.40  E-value=0.45  Score=39.75  Aligned_cols=42  Identities=17%  Similarity=0.199  Sum_probs=30.1

Q ss_pred             CCCCCCHHHHHHHHHHHH-----cC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         44 NGRPLPNSVRMRIVELAQ-----LG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~-----~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++++-..+.|.+|++...     .|   .+.++||+..|||++|+|+..+
T Consensus        36 ~~~~~~~~~r~~Il~AA~~lf~~~G~~~~t~~~IA~~aGvs~~tlY~~F~   85 (255)
T 3g1o_A           36 TARPSGDDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFP   85 (255)
T ss_dssp             -----CCHHHHHHHHHHHHHHTTSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             CCCcCHHHHHHHHHHHHHHHHHHcCCccCcHHHHHHHhCCCHHHHHHHcC
Confidence            344456678888888653     34   6999999999999999998643

>4fx0_A Probable transcriptional repressor protein; helix-turn-helix, DNA binding, transcription regulator; 2.70A {Mycobacterium tuberculosis} PDB: 4fx4_A*

Probab=88.39  E-value=1.8  Score=34.22  Aligned_cols=55  Identities=13%  Similarity=0.120  Sum_probs=37.6

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC-CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGA-IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~-rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ++.++||+.++|+++||++.+++..+.|-|+-.. ..+ .+--.+|++=.+.+.+..
T Consensus        53 ~t~~eLa~~l~~~~~tvsr~v~~Le~~glVr~~~~~DrR~~~v~LT~~G~~~~~~~~  109 (148)
T 4fx0_A           53 LTMSELAARIGVERTTLTRNLEVMRRDGLVRVMAGADARCKRIELTAKGRAALQKAV  109 (148)
T ss_dssp             -CHHHHHHHHTCCHHHHHHHHHHHHHTTSBC-----------CCBCHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeeCCCCCCeeEEEECHHHHHHHHHHH
Confidence            7999999999999999999999999999773211 111 123457777666655543

>3dpj_A Transcription regulator, TETR family; APC88616, silicibacter pomeroyi DSS, structural genomics, PSI-2, protein structure initiative; HET: MES; 1.90A {Silicibacter pomeroyi}

Probab=88.38  E-value=0.7  Score=36.29  Aligned_cols=37  Identities=27%  Similarity=0.276  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus         6 ~~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~Agvs~~tly~~F~   50 (194)
T 3dpj_A            6 QAQTRDQIVAAADELFYRQGFAQTSFVDISAAVGISRGNFYYHFK   50 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hhhHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCChHHHHHHcC
Confidence            456788888764     334   6999999999999999998643

>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=88.37  E-value=0.5  Score=39.98  Aligned_cols=31  Identities=13%  Similarity=0.053  Sum_probs=25.7

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +|.++. +.|+|..++|+.||||++|+++|-+
T Consensus        94 ~lk~lR~~~glTQ~elA~~LGvsr~tis~yE~  125 (170)
T 2auw_A           94 MFGDWMHRNNLSLTTAAEALGISRRMVSYYRT  125 (170)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence            455555 4699999999999999999988754

>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=88.32  E-value=0.6  Score=33.15  Aligned_cols=24  Identities=13%  Similarity=0.056  Sum_probs=20.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...+..++|+.+|||++||++|.+
T Consensus        26 ~~~sq~~lA~~~gis~~~is~~E~   49 (86)
T 2ofy_A           26 GDMSMVTVAFDAGISVETLRKIET   49 (86)
T ss_dssp             TTSCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHCCHHHHHHHhCCCHHHHHHHHc
Confidence            334999999999999999999864

>2jj7_A Hemolysin II regulatory protein; DNA-binding protein, transcription regulation, DNA-binding, family, transcription, transcriptional regulator; 2.10A {Bacillus cereus} PDB: 2wv1_A 2jk3_A 2fx0_A

Probab=88.32  E-value=0.54  Score=36.78  Aligned_cols=38  Identities=16%  Similarity=0.187  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+..+.
T Consensus         5 ~~~~r~~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~tlY~~F~s   50 (186)
T 2jj7_A            5 REQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNG   50 (186)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHHcCCccCCHHHHHHHhCCChhhhhhhcCC
Confidence            356777777753     23   489999999999999999997653

>2nx4_A Transcriptional regulator, TETR family protein; HTH DNA binding motif, structural genomics, PSI-2, Pro structure initiative; 1.70A {Rhodococcus SP}

Probab=88.31  E-value=0.69  Score=36.92  Aligned_cols=36  Identities=22%  Similarity=0.256  Sum_probs=28.9

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   |.|.++||+..|||++|+|+..+
T Consensus         9 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~gtlY~yF~   52 (194)
T 2nx4_A            9 DERRRSITAAAWRLIAARGIEAANMRDIATEAGYTNGALSHYFA   52 (194)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCcchHHHhCc
Confidence            45678888764     23   46999999999999999998753

>4aci_A HTH-type transcriptional repressor ACNR; aconitase, citrate, TETR superfamily; HET: CIT; 1.65A {Corynebacterium glutamicum} PDB: 4ac6_A*

Probab=88.26  E-value=0.38  Score=37.78  Aligned_cols=39  Identities=21%  Similarity=0.245  Sum_probs=28.9

Q ss_pred             CCHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      -..+.|.+|++..     +.   +.|..+||+..|||++|+|++...
T Consensus        11 ~~~~~r~~Il~aA~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~s   57 (191)
T 4aci_A           11 KPTNSRQEILEGARRCFAEHGYEGATVRRLEEATGKSRGAIFHHFGD   57 (191)
T ss_dssp             ---CHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             chHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCchHHHHHCCC
Confidence            3446777777753     23   479999999999999999987653

>2zcx_A SCO7815, TETR-family transcriptional regulator; helix-turn-helix, DNA-binding, transcription regulation; 2.22A {Streptomyces coelicolor}

Probab=88.22  E-value=0.77  Score=38.26  Aligned_cols=37  Identities=16%  Similarity=0.257  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|||+..
T Consensus        20 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvs~~tlY~~F   64 (231)
T 2zcx_A           20 AKQQREEAILDAARELGTERGIREITLTDIAATVGMHKSALLRYF   64 (231)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHhCCcccCCHHHHHHHhCCCHHHHHHhC
Confidence            4567788888764     234   799999999999999999864

>3jsj_A Putative TETR-family transcriptional regulator; DNA-binding, transcription regulation; 2.10A {Streptomyces avermitilis ma-4680}

Probab=88.15  E-value=0.41  Score=37.65  Aligned_cols=37  Identities=24%  Similarity=0.306  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHH-----HcC--CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG--IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G--~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|  .|.++||+..|||++|||+..+
T Consensus         7 ~~~~r~~Il~aA~~lf~~~G~~~t~~~IA~~aGvs~~tly~~F~   50 (190)
T 3jsj_A            7 KQSPRERLLEAAAALTYRDGVGIGVEALCKAAGVSKRSMYQLFE   50 (190)
T ss_dssp             CCCHHHHHHHHHHHHHHHHCTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cchHHHHHHHHHHHHHHHhCccccHHHHHHHhCCCHHHHHHHcC
Confidence            456777887754     235  6999999999999999998643

>3cta_A Riboflavin kinase; structural genomics, transferase, PSI-2, protein structure initiative; 2.20A {Thermoplasma acidophilum dsm 1728} SCOP: a.4.5.28 b.43.5.2

Probab=88.11  E-value=0.33  Score=41.43  Aligned_cols=55  Identities=15%  Similarity=0.133  Sum_probs=38.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l  117 (258)
                      |.+.+++|+.|++|++||++.+++..+.|-+.-.+.++.+.-.+|++=+.++...
T Consensus        27 ~~s~s~aA~~L~isq~avSr~I~~LE~~~L~~R~~~~R~~~v~LT~~G~~l~~~~   81 (230)
T 3cta_A           27 YLTSSKLADMLGISQQSASRIIIDLEKNGYITRTVTKRGQILNITEKGLDVLYTE   81 (230)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEEETTEEEEEECHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEcCCeEEEEECHHHHHHHHHH
Confidence            3679999999999999999999999998866322111113345777655555443

>3ljl_A Transcriptional regulator LUXT; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; HET: MES; 3.20A {Vibrio parahaemolyticus}

Probab=88.03  E-value=0.4  Score=37.35  Aligned_cols=38  Identities=18%  Similarity=0.243  Sum_probs=29.9

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.+.|.+|++..     +.   +.|.++||+..|||++|+|+....
T Consensus        12 ~~~~r~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~s   57 (156)
T 3ljl_A           12 TEITIQKIMDAVVDQLLRLGYDKMSYTTLSQQTGVSRTGISHHFPK   57 (156)
T ss_dssp             HHHHHHHHHHHHHHHHHHTHHHHCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             hHhHHHHHHHHHHHHHHHhChhhcCHHHHHHHHCCCHHHHHHHCCC
Confidence            456788888754     23   479999999999999999987543

>3bjb_A Probable transcriptional regulator, TETR family P; APC7331, rhodococcus SP. RHA1, structural genomics, PS protein structure initiative; 2.50A {Rhodococcus SP}

Probab=88.02  E-value=0.65  Score=37.68  Aligned_cols=37  Identities=14%  Similarity=0.329  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|..+||+..|||++|+|+...
T Consensus        20 ~~~~r~~Il~AA~~lf~e~G~~~~s~~~IA~~AGVsk~tlY~~F~   64 (207)
T 3bjb_A           20 QRARHVRMLEAAIELATEKELARVQMHEVAKRAGVAIGTLYRYFP   64 (207)
T ss_dssp             HHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            446788888764     345   6999999999999999998754

>1iuf_A Centromere ABP1 protein; riken structural genomics/proteomics initiative, RSGI, structural genomics, DNA binding protein; NMR {Schizosaccharomyces pombe} SCOP: a.4.1.7 a.4.1.7

Probab=87.99  E-value=0.25  Score=39.72  Aligned_cols=52  Identities=19%  Similarity=0.084  Sum_probs=42.4

Q ss_pred             CCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHh-cCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        103 PRVTTPKVVSYIKELK-QKDPGIFAWEIRDRLLS-DGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       103 PrklT~e~~~~I~~lv-~~nP~ita~EIr~~L~~-~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      ...+|.++...|.++. +++|.++..+|+.+..+ +|..     ||.+||+++|++...
T Consensus         9 R~~lT~~qK~~i~~~~~~~~~~~~q~~la~wa~~~f~~~-----is~stis~ilk~k~~   62 (144)
T 1iuf_A            9 RRAITEHEKRALRHYFFQLQNRSGQQDLIEWFREKFGKD-----ISQPSVSQILSSKYS   62 (144)
T ss_dssp             SSCCCSHHHHHHHHHHHSSSSCCCHHHHHHHHHHHHSSC-----CSSSSTTHHHHHHHH
T ss_pred             CccCCHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHCCC-----CcHHHHHHHHhhHHH
Confidence            3568888899999998 78999999999998874 6554     499999999998543

>2qtq_A Transcriptional regulator, TETR family; transcription regulator, DNA/RNA-binding 3-helical bundle FO turn helix motif, HTH motif; HET: MSE; 1.85A {Novosphingobium aromaticivorans} PDB: 2rha_A*

Probab=87.94  E-value=0.59  Score=36.98  Aligned_cols=38  Identities=13%  Similarity=0.129  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+..+.
T Consensus        14 ~~~~r~~Il~aa~~lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~s   59 (213)
T 2qtq_A           14 TPGARDLLLQTASNIMREGDVVDISLSELSLRSGLNSALVKYYFGN   59 (213)
T ss_dssp             CTTHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHCCCHHHHHHHHSS
T ss_pred             ChhHHHHHHHHHHHHHHHcCcccccHHHHHHHhCCChhhHhHhcCC
Confidence            446777777754     23   479999999999999999987643

>3mnl_A KSTR, transcriptional regulatory protein (probably TETR; TETR family of transcriptional regulator, all-helical; 1.80A {Mycobacterium tuberculosis}

Probab=87.88  E-value=0.55  Score=36.97  Aligned_cols=37  Identities=14%  Similarity=0.256  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus        18 ~~~~r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   62 (203)
T 3mnl_A           18 QRERRKRILDATMAIASKGGYEAVQMRAVADRADVAVGTLYRYFP   62 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             chHHHHHHHHHHHHHHHHcCCccCCHHHHHHHcCCChhHHHHHcC
Confidence            356788888754     23   47999999999999999998643

>2hyt_A TETR-family transcriptional regulator; structural genomics, center for structural genomics, JCSG, protein structure INI PSI-2; HET: MSE; 1.64A {Pectobacterium atrosepticum}

Probab=87.88  E-value=0.32  Score=38.96  Aligned_cols=37  Identities=16%  Similarity=0.266  Sum_probs=29.4

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus        10 ~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~~tlY~~F~   54 (197)
T 2hyt_A           10 MEETRATLLATARKVFSERGYADTSMDDLTAQASLTRGALYHHFG   54 (197)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCTTHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            346778888754     334   6999999999999999998754

>3on4_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics; HET: MSE; 1.85A {Legionella pneumophila subsp}

Probab=87.81  E-value=0.51  Score=36.71  Aligned_cols=35  Identities=14%  Similarity=0.244  Sum_probs=27.4

Q ss_pred             HHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++..     +.   +.|.++||+..|||++|+|+..+
T Consensus        10 ~~r~~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F~   52 (191)
T 3on4_A           10 NTKERILAVAEALIQKDGYNAFSFKDIATAINIKTASIHYHFP   52 (191)
T ss_dssp             CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCcchhhhcCC
Confidence            5677777653     33   47999999999999999998643

>2gfn_A HTH-type transcriptional regulator PKSA related P; transcriptional regulato PSI-2, regulatory protein, structural genomics, protein STR initiative; 1.90A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=87.78  E-value=0.61  Score=37.93  Aligned_cols=36  Identities=11%  Similarity=0.255  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|||+...
T Consensus         8 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvs~gtlY~yF~   51 (209)
T 2gfn_A            8 DERRRALADAVLALIAREGISAVTTRAVAEESGWSTGVLNHYFG   51 (209)
T ss_dssp             CHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCCCcchHHhcCC
Confidence            46788888764     334   7999999999999999998753

>3n0r_A Response regulator; sigma factor, receiver, two-component SI transduction, signaling protein; HET: MSE GOL; 1.25A {Caulobacter vibrioides} PDB: 3t0y_A

Probab=87.78  E-value=0.48  Score=41.81  Aligned_cols=43  Identities=16%  Similarity=0.285  Sum_probs=34.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      ++...|.-++..+.+|++..+||..+|++.+||..++.+-+..
T Consensus       112 Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tVks~l~rA~~~  154 (286)
T 3n0r_A          112 IAPRSRQAFLLTALEGFTPTEAAQILDCDFGEVERLIGDAQAE  154 (286)
T ss_dssp             HSCHHHHHHHHHHTTCCCHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             CCHHHeeEEEEEeeCCCCHHHHHHHhCcCHHHHHHHHHHHHhh
Confidence            4556666555556699999999999999999999999887643

>3qbm_A TETR transcriptional regulator; DNA/RNA-binding three-helical bundle, structural genomics, J center for structural genomics, JCSG; HET: MSE PGE; 1.80A {Chloroflexus aurantiacus}

Probab=87.75  E-value=0.62  Score=36.43  Aligned_cols=35  Identities=23%  Similarity=0.287  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|+|+..
T Consensus         6 ~~~r~~Il~aa~~l~~~~G~~~~t~~~IA~~agvs~~t~Y~~F   48 (199)
T 3qbm_A            6 QETRERVVAQAAALFNVSGYAGTAISDIMAATGLEKGGIYRHF   48 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHHTTC
T ss_pred             hhHHHHHHHHHHHHHHHhCcCcCCHHHHHHHhCCCccHHHHhC
Confidence            46777777754     23   4799999999999999999753

>2qlz_A Transcription factor PF0095; 2.50A {Pyrococcus furiosus} PDB: 2quf_A

Probab=87.73  E-value=0.11  Score=45.78  Aligned_cols=48  Identities=23%  Similarity=0.198  Sum_probs=41.6

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++...|.+|+.+... .++..+||+.+|+|++||++-++...+.|-|..
T Consensus         9 L~~~~R~~IL~~L~~g~~s~~ELa~~lglS~stVs~hL~~Le~aGLV~~   57 (232)
T 2qlz_A            9 LGNKVRRDLLSHLTCMECYFSLLSSKVSVSSTAVAKHLKIMEREGVLQS   57 (232)
T ss_dssp             HTSHHHHHHHHHHTTTTTCSSSSCTTCCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            456788999988765 489999999999999999999999999997743

>2esn_A Probable transcriptional regulator; PA0477, APC5828,transcription, PSI, protein struc initiative, MCSG; 2.10A {Pseudomonas aeruginosa} SCOP: a.4.5.37 c.94.1.1

Probab=87.72  E-value=0.88  Score=38.53  Aligned_cols=59  Identities=12%  Similarity=0.119  Sum_probs=40.3

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYIK  115 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I~  115 (258)
                      .+++..+.+-.|.+++|+.|+||.++|++-+++.++ -|. +-.  |.+ |.-.+|++=+.++.
T Consensus        15 L~~f~~v~~~gs~s~AA~~L~isq~avS~~I~~LE~~lg~~Lf~--R~~-~~~~lT~~G~~l~~   75 (310)
T 2esn_A           15 LLVFDALYRHRNVGTAASELAISASAFSHALGRLRQGLDDELFL--RQG-NRMQPTQRAEHLAA   75 (310)
T ss_dssp             HHHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEE--EET-TEEEECHHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHhhCCccee--ecC-CCccccHHHHHHHH
Confidence            345555545559999999999999999999999986 443 222  223 45667776544443

>3nnr_A Transcriptional regulator, TETR family; TETR-family transcriptional regulator, structural genomics, center for structural genomics, JCSG; HET: MSE; 2.49A {Marinobacter aquaeolei}

Probab=87.64  E-value=0.39  Score=39.12  Aligned_cols=36  Identities=22%  Similarity=0.254  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|+|+..+
T Consensus         4 ~~tr~~Il~aA~~lf~~~G~~~~t~~~IA~~Agvs~~t~Y~~F~   47 (228)
T 3nnr_A            4 MKTRDKILLSSLELFNDKGERNITTNHIAAHLAISPGNLYYHFR   47 (228)
T ss_dssp             CCHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             chHHHHHHHHHHHHHHHhChhhcCHHHHHHHhCCCCccchhcCC
Confidence            35677777653     234   7999999999999999998643

>1vi0_A Transcriptional regulator; structural genomics; HET: MSE DCC; 1.65A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=87.60  E-value=0.51  Score=38.21  Aligned_cols=36  Identities=22%  Similarity=0.345  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         7 ~~~r~~Il~aA~~lf~~~Gy~~~s~~~IA~~AGvs~gt~Y~yF~   50 (206)
T 1vi0_A            7 RPKYMQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFK   50 (206)
T ss_dssp             -CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCChhHHHHHcC
Confidence            35677777653     344   6999999999999999998743

>3bni_A Putative TETR-family transcriptional regulator; structural genomics, APC7281; HET: PG4; 2.30A {Streptomyces coelicolor A3}

Probab=87.59  E-value=0.78  Score=37.74  Aligned_cols=37  Identities=14%  Similarity=0.274  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+..+
T Consensus        41 ~~~~r~~Il~aA~~l~~~~G~~~~tv~~IA~~AGvs~~t~Y~~F~   85 (229)
T 3bni_A           41 SAERLTRILDACADLLDEVGYDALSTRAVALRADVPIGSVYRFFG   85 (229)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhcChhhccHHHHHHHHCCCchhHHHHcC
Confidence            457788888754     23   47999999999999999998654

>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP}

Probab=87.53  E-value=0.38  Score=38.83  Aligned_cols=38  Identities=18%  Similarity=0.239  Sum_probs=29.5

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+....
T Consensus        26 ~~~~r~~Il~aa~~lf~~~G~~~~tv~~IA~~agvs~~t~Y~~F~s   71 (215)
T 2qko_A           26 NPERRAALVNAAIEVLAREGARGLTFRAVDVEANVPKGTASNYFPS   71 (215)
T ss_dssp             -CHHHHHHHHHHHHHHHHTCTTTCCHHHHHHHSSSTTTCHHHHCSC
T ss_pred             cHHHHHHHHHHHHHHHHHhChhhccHHHHHHHcCCCcchHHHhCCC
Confidence            457788888754     334   79999999999999999987543

>1okr_A MECI, methicillin resistance regulatory protein MECI; bacterial antibiotic resistance, MECI protein, transcriptional regulatory element; 2.4A {Staphylococcus aureus} SCOP: a.4.5.39 PDB: 1sax_A 1sd7_A 2d45_A 1sd6_A

Probab=87.50  E-value=0.68  Score=34.95  Aligned_cols=47  Identities=11%  Similarity=0.192  Sum_probs=36.4

Q ss_pred             CCHHHHHHHHHHH--HcCCCHHHHHHHhC----CCHHHHHHHHHHhhhhCCccc
Q psy15598         48 LPNSVRMRIVELA--QLGIRPCDISRQLR----VSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        48 ~S~dlR~RIV~L~--~~G~S~~eIAr~LG----VSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++... ..|+..+  ..+.+..+||+.++    ++++||++.+++..+.|-|.-
T Consensus         8 lt~~~-~~vL~~l~~~~~~t~~ela~~l~~~~~~s~~tv~~~l~~L~~~Glv~r   60 (123)
T 1okr_A            8 ISSAE-WEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDR   60 (123)
T ss_dssp             CCHHH-HHHHHHHHHHSSEEHHHHHHHHHHHCCCCHHHHHHHHHHHHHHTSEEE
T ss_pred             CCHHH-HHHHHHHHhCCCcCHHHHHHHHhccCCCcHhhHHHHHHHHHHCCCeEE
Confidence            44432 3344443  35799999999999    899999999999999998743

>3c2b_A Transcriptional regulator, TETR family; structural genomics, APC5923, PSI-2, PR structure initiative; 2.10A {Agrobacterium tumefaciens str}

Probab=87.45  E-value=0.75  Score=36.92  Aligned_cols=37  Identities=14%  Similarity=0.239  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|+|+..+.
T Consensus        14 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvs~~t~Y~~F~s   58 (221)
T 3c2b_A           14 SPRQNAVLDQALRLLVEGGEKALTTSGLARAANCSKESLYKWFGD   58 (221)
T ss_dssp             CHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHhCCcccCCHHHHHHHhCCCHHHHHHhCCC
Confidence            35677887753     234   79999999999999999998654

>2gen_A Probable transcriptional regulator; APC6095, TETR family, structural genomics, PSI, protein structure initiative; 1.70A {Pseudomonas aeruginosa PAO1} SCOP: a.4.1.9 a.121.1.1

Probab=87.45  E-value=0.55  Score=37.61  Aligned_cols=36  Identities=19%  Similarity=0.154  Sum_probs=27.0

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         6 ~~~r~~Il~aA~~lf~~~G~~~ts~~~IA~~aGvs~gtlY~~F~   49 (197)
T 2gen_A            6 SSRKDEILQAALACFSEHGVDATTIEMIRDRSGASIGSLYHHFG   49 (197)
T ss_dssp             --CHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCChHHHHHHCC
Confidence            34577777653     345   6999999999999999998753

>3col_A Putative transcription regulator; structural genomics, PSI-2, protein structure initiative, midwest CENT structural genomics, MCSG; HET: MSE; 2.10A {Lactobacillus plantarum WCFS1}

Probab=87.40  E-value=0.43  Score=37.20  Aligned_cols=36  Identities=8%  Similarity=0.249  Sum_probs=27.1

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus         8 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   51 (196)
T 3col_A            8 DMNKQVKIQDAVAAIILAEGPAGVSTTKVAKRVGIAQSNVYLYF   51 (196)
T ss_dssp             --CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCcHHHHHHHh
Confidence            356677777754     234   799999999999999999753

>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=87.34  E-value=0.43  Score=39.44  Aligned_cols=29  Identities=17%  Similarity=0.307  Sum_probs=27.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      ++..+||..+|+|+.||+|.++++++.| +
T Consensus       179 ~t~~~iA~~lg~sr~tvsR~l~~L~~~g-i  207 (237)
T 3fx3_A          179 YDKMLIAGRLGMKPESLSRAFSRLKAAG-V  207 (237)
T ss_dssp             SCTHHHHHHTTCCHHHHHHHHHHHGGGT-E
T ss_pred             CCHHHHHHHhCCCHHHHHHHHHHHHHCC-e
Confidence            4689999999999999999999999999 5

>2ras_A Transcriptional regulator, TETR family; bacterial regulatory proteins, DNA-binding, DNA binding 3-helical bundle fold; 1.80A {Novosphingobium aromaticivorans}

Probab=87.34  E-value=0.26  Score=39.54  Aligned_cols=36  Identities=19%  Similarity=0.480  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~agvs~~t~Y~~F~   53 (212)
T 2ras_A           10 DAMRARLVDVAQAIVEERGGAGLTLSELAARAGISQANLSRYFE   53 (212)
T ss_dssp             HHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHTSCHHHHTTTCS
T ss_pred             hHHHHHHHHHHHHHHHHhCcccCcHHHHHHHhCCCHHHHHHHcC
Confidence            56788888754     23   47999999999999999998643

>3kkc_A TETR family transcriptional regulator; APC20805, structural genomics, PSI-2, protein structure initiative; 2.50A {Streptococcus agalactiae 2603V}

Probab=87.32  E-value=0.57  Score=36.24  Aligned_cols=35  Identities=11%  Similarity=0.026  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHH-----cC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELAQ-----LG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~~-----~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+|++...     .|   .|.++||+..|||++|+|+..
T Consensus        11 ~~tr~~Il~aa~~l~~~~G~~~~tv~~Ia~~agvs~~t~Y~~F   53 (177)
T 3kkc_A           11 QKTKVAIYNAFISLLQENDYSKITVQDVIGLANVGRSTFYSHY   53 (177)
T ss_dssp             HHHHHHHHHHHHHHTTTSCTTTCCHHHHHHHHCCCHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHhCChhHhhHHHHHHHhCCcHhhHHHHc
Confidence            467778887653     34   699999999999999998754

>3e7q_A Transcriptional regulator; structural genomics, PSI, MCSG, P structure initiative, midwest center for structural genomic binding; 2.20A {Pseudomonas aeruginosa}

Probab=87.25  E-value=0.58  Score=36.98  Aligned_cols=38  Identities=18%  Similarity=0.204  Sum_probs=30.2

Q ss_pred             CCCHHHHHHHHHHHH-----c---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQ-----L---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~-----~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .-..+.|.+|++...     .   +.|.++||+..|||++|+|+..
T Consensus        10 ~~~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   55 (215)
T 3e7q_A           10 LEPEQRKALLIEATLACLKRHGFQGASVRKICAEAGVSVGLINHHY   55 (215)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHHHHC
T ss_pred             CChHHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHc
Confidence            345677888888642     3   5799999999999999999874

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

Probab=87.23  E-value=0.33  Score=39.07  Aligned_cols=32  Identities=16%  Similarity=0.207  Sum_probs=29.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ++..+||+.++|++.+|.+++.+.++.|-|..
T Consensus        29 ~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s   60 (143)
T 3t8r_A           29 ISLKSIAEENNLSDLYLEQLVGPLRNAGLIRS   60 (143)
T ss_dssp             EEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEe
Confidence            68999999999999999999999999998753

>1ylf_A RRF2 family protein; structural genomics, transcription regulator, P protein structure initiative; 2.50A {Bacillus cereus atcc 14579} SCOP: a.4.5.55

Probab=87.17  E-value=0.47  Score=38.17  Aligned_cols=32  Identities=9%  Similarity=0.170  Sum_probs=29.9

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+.++||+.++||.++|.+++.+.++.|-|..
T Consensus        31 ~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s   62 (149)
T 1ylf_A           31 CTSDYMAESVNTNPVVIRKIMSYLKQAGFVYV   62 (149)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence            79999999999999999999999999998753

>2v57_A TETR family transcriptional repressor LFRR; DNA-binding, transcription regulation; HET: PRL; 1.90A {Mycobacterium smegmatis} PDB: 2wgb_A

Probab=87.17  E-value=0.86  Score=35.63  Aligned_cols=38  Identities=18%  Similarity=0.167  Sum_probs=29.8

Q ss_pred             CHHHHHHHHHHHH------cCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELAQ------LGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~~------~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++...      .+.|..+||+..|||++|+|+..+.
T Consensus        12 ~~~~r~~Il~aA~~lf~~~~~~t~~~Ia~~agvs~~t~Y~~F~s   55 (190)
T 2v57_A           12 RERTRRAILDAAMLVLADHPTAALGDIAAAAGVGRSTVHRYYPE   55 (190)
T ss_dssp             -CHHHHHHHHHHHHHHTTCTTCCHHHHHHHHTCCHHHHHHHCSS
T ss_pred             HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHcCC
Confidence            3467788887542      5789999999999999999987543

>3he0_A Transcriptional regulator, TETR family; ACRR, vibrio parahaemolytic structural genomics, PSI-2, protein structure initiative; HET: MSE; 2.20A {Vibrio parahaemolyticus}

Probab=87.16  E-value=0.37  Score=37.82  Aligned_cols=35  Identities=17%  Similarity=0.271  Sum_probs=25.7

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRw   83 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+.
T Consensus         9 ~~~~r~~il~aa~~lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~   51 (196)
T 3he0_A            9 AVDKRDQILAAAEQLIAESGFQGLSMQKLANEAGVAAGTIYRY   51 (196)
T ss_dssp             --CCHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHTT
T ss_pred             chHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCcchHHHh
Confidence            345566666643     234   79999999999999999864

>1rkt_A Protein YFIR; transcription regulator, structural genomics, PSI, protein S initiative, midwest center for structural genomics, MCSG; 1.95A {Bacillus subtilis} SCOP: a.4.1.9 a.121.1.1

Probab=87.16  E-value=0.6  Score=37.43  Aligned_cols=35  Identities=23%  Similarity=0.250  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..
T Consensus        11 ~~~r~~Il~aA~~lf~~~Gy~~ts~~~IA~~agvs~gtlY~yF   53 (205)
T 1rkt_A           11 DKRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYF   53 (205)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCCcchhhhhC
Confidence            46778888764     234   699999999999999999753

>3rh2_A Hypothetical TETR-like transcriptional regulator; DNA/RNA-binding 3-helical bundle, structural genomics, joint for structural genomics; 2.42A {Shewanella amazonensis}

Probab=87.14  E-value=0.56  Score=37.63  Aligned_cols=35  Identities=20%  Similarity=0.285  Sum_probs=26.5

Q ss_pred             HHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus         3 ~tr~~Il~aA~~lf~~~G~~~~s~~~IA~~Agvs~~t~Y~~F~   45 (212)
T 3rh2_A            3 KTRDKIIQASLELFNEHGERTITTNHIAAHLDISPGNLYYHFR   45 (212)
T ss_dssp             CHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            3466666643     33   47999999999999999998643

>1hqc_A RUVB; extended AAA-ATPase domain, complex with nucleotide, hydrolase; HET: ADE; 3.20A {Thermus thermophilus} SCOP: a.4.5.11 c.37.1.20 PDB: 1ixs_B* 1ixr_C*

Probab=87.10  E-value=0.89  Score=39.43  Aligned_cols=64  Identities=17%  Similarity=0.174  Sum_probs=43.3

Q ss_pred             CCCHHHHHHHHHHHHc--C--CCHHHHHHHhCCCHHHHHHHHHHhhh-hCCcccCCCCCCCCCCCCHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQL--G--IRPCDISRQLRVSHGCVSKILARYHE-TGSILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~--G--~S~~eIAr~LGVSrsTVsRwikRyrE-tGsl~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .++...|..|..+.+.  |  .+..++|+.||+|++|+++++++|.. .|-+...   + +.+++++....++
T Consensus       244 ~l~~~e~~~i~~~~~~~~g~~~~~~~~a~~lgi~~~tl~~~l~~~~i~~~li~~~---~-~g~~~~~~~~~~~  312 (324)
T 1hqc_A          244 GLEKRDREILEVLILRFGGGPVGLATLATALSEDPGTLEEVHEPYLIRQGLLKRT---P-RGRVPTELAYRHL  312 (324)
T ss_dssp             CCCHHHHHHHHHHHHHSCSSCCCHHHHHHHTTSCHHHHHHHTHHHHHHTTSEEEE---T-TEEEECHHHHHHT
T ss_pred             CCCHHHHHHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHHhHHHHHhcchhcC---C-ccceecHHHHHHH
Confidence            3555566666555542  2  46999999999999999999999764 4444322   1 3367777666654

>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=87.05  E-value=1.4  Score=33.82  Aligned_cols=47  Identities=30%  Similarity=0.288  Sum_probs=37.4

Q ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        103 PRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       103 PrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      .+.++.+.+..|++++.+++..+..+++..+   |       ||.+||+++|+....
T Consensus         5 r~~~t~e~K~~iv~~~~~~g~~~~~~~A~~~---g-------vs~stl~~~~~~~~~   51 (131)
T 1hlv_A            5 RRQLTFREKSRIIQEVEENPDLRKGEIARRF---N-------IPPSTLSTILKNKRA   51 (131)
T ss_dssp             SCCCCHHHHHHHHHHHHHCTTSCHHHHHHHH---T-------CCHHHHHHHHHTHHH
T ss_pred             ceeCCHHHHHHHHHHHHHCCCCcHHHHHHHh---C-------CCHHHHHHHHhchhh
Confidence            3568999999999988777777777888776   4       499999999987543

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=87.02  E-value=0.57  Score=37.60  Aligned_cols=42  Identities=10%  Similarity=0.021  Sum_probs=35.6

Q ss_pred             HHHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598         53 RMRIVELAQL-GIRPCDISRQL-RVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        53 R~RIV~L~~~-G~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~   94 (258)
                      +..|+..... .++..++++.+ |||.+++++-+++..+.|-|.
T Consensus        28 ~l~IL~~L~~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~   71 (131)
T 4a5n_A           28 KGILFYHMIDGKKRFNEFRRICPSITQRMLTLQLRELEADGIVH   71 (131)
T ss_dssp             HHHHHHHHTTSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHhcCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEE
Confidence            5556655544 58999999999 999999999999999999875

>2a6h_F RNA polymerase sigma factor RPOD; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: a.4.13.1 a.4.13.2 a.177.1.1 PDB: 1smy_F* 1zyr_F* 1iw7_F* 2a69_F* 2a6e_F 2a68_F* 2be5_F* 2cw0_F 3eql_F* 3dxj_F* 1l9u_H

Probab=86.96  E-value=0.54  Score=44.46  Aligned_cols=42  Identities=10%  Similarity=-0.008  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+-    +|+|..+||+.||||+.||+.+..+-.
T Consensus       360 ~L~~rer~Vl~lr~~L~~~e~~Tl~EIA~~lgiS~erVrqi~~rAl  405 (423)
T 2a6h_F          360 KLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKAL  405 (423)
T ss_dssp             SSCHHHHHHHHHHHHTTCC-----CHHHHSSSSCHHHHHHHHHHHH
T ss_pred             hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            366666655555555    789999999999999999999988764

>2g3b_A Putative TETR-family transcriptional regulator; transcription regulator, structural genomics, P protein structure initiative; HET: MSE; 2.00A {Rhodococcus SP} SCOP: a.4.1.9 a.121.1.1

Probab=86.95  E-value=0.74  Score=37.38  Aligned_cols=36  Identities=25%  Similarity=0.284  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|..+||+..|||++|+|+..+
T Consensus         2 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~AGvskgtlY~hF~   45 (208)
T 2g3b_A            2 SERRDAILKASATAIAQRGIRGLRVNDVAEVAGVSPGLLYYHFK   45 (208)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHHC
T ss_pred             chHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            35677777643     23   57999999999999999998754

>2w53_A Repressor, SMet; antibiotic resistance, multi-drug efflux pump, transcription regulation, transcriptional repressor, DNA binding; 2.00A {Stenotrophomonas maltophilia} PDB: 3p9t_A*

Probab=86.73  E-value=0.32  Score=39.38  Aligned_cols=35  Identities=20%  Similarity=0.188  Sum_probs=27.1

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+..
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvskgtlY~~F   52 (219)
T 2w53_A           10 QATREGILDAAEACFHEHGVARTTLEMIGARAGYTRGAVYWHF   52 (219)
T ss_dssp             GCCHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCchHHhhcC
Confidence            34577777653     334   699999999999999999754

>3npi_A TETR family regulatory protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI; 2.96A {Corynebacterium diphtheriae}

Probab=86.72  E-value=0.32  Score=40.63  Aligned_cols=36  Identities=11%  Similarity=0.189  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|||+...
T Consensus        17 ~~~r~~Il~AA~~lf~~~G~~~~t~~~IA~~aGvs~~tlY~~F~   60 (251)
T 3npi_A           17 EVSTDTVLDIALSLFSELGFSDAKLEAIAKKSGMSKRMIHYHFG   60 (251)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHCCCHHHHHHHHC
T ss_pred             hHHHHHHHHHHHHHHHHcCccccCHHHHHHHHCCCHHHHHHHcC
Confidence            34566666643     23   47999999999999999998764

>2o0m_A Transcriptional regulator, SORC family; structural genomics, protein structure initiative, midwest center for structural genomics, MCSG; 1.60A {Enterococcus faecalis} SCOP: c.124.1.8

Probab=86.63  E-value=0.13  Score=46.99  Aligned_cols=43  Identities=12%  Similarity=0.092  Sum_probs=0.0

Q ss_pred             HHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|..|+..+  .++++.++||+.|+||++||+|.+++.++.|.+.
T Consensus        21 r~~~iL~~l~~~~~~t~~eLa~~l~vs~~Tv~r~l~~Le~~Glv~   65 (345)
T 2o0m_A           21 ERFQILRNIYWMQPIGRRSLSETMGITERVLRTETDVLKQLNLIE   65 (345)
T ss_dssp             ---------------------------------------------
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            345566654  3679999999999999999999999999999874

>3r4k_A Transcriptional regulator, ICLR family; DNA/RNA-binding 3-helical bundle, profilin-like, structural joint center for structural genomics, JCSG; 2.46A {Ruegeria SP}

Probab=86.59  E-value=0.42  Score=41.83  Aligned_cols=41  Identities=17%  Similarity=0.346  Sum_probs=34.9

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .+|++++.   .+++.+|||+.+|++++||+|+++...+.|-+.
T Consensus         9 l~IL~~l~~~~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~   52 (260)
T 3r4k_A            9 LTLLTYFNHGRLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVE   52 (260)
T ss_dssp             HHHHTTCBTTBSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHhhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            45666653   358999999999999999999999999999875

>3eup_A Transcriptional regulator, TETR family; structural genomics, MCSG, protein structure initiative, midwest center for STRU genomics; 1.99A {Cytophaga hutchinsonii}

Probab=86.59  E-value=0.47  Score=37.30  Aligned_cols=35  Identities=17%  Similarity=0.264  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRw   83 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+.
T Consensus         9 ~~~~r~~Il~aA~~lf~~~G~~~~ti~~IA~~agvs~~t~Y~~   51 (204)
T 3eup_A            9 SDRTRQFIIESTAPVFNVKGLAGTSLTDLTEATNLTKGSIYGN   51 (204)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTCCHHHHTTT
T ss_pred             chHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCcHHHHHh
Confidence            567888888754     23   479999999999999999875

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

Probab=86.56  E-value=1.2  Score=33.51  Aligned_cols=44  Identities=11%  Similarity=0.319  Sum_probs=39.0

Q ss_pred             HHHHHHHHHHHH-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         50 NSVRMRIVELAQ-LG--IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        50 ~dlR~RIV~L~~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+..++|++.++ .|  ++..+||+.+||.+.-|.+.+++.+..|.|
T Consensus        18 ~d~eekVLe~LkeaG~PlkageIae~~GvdKKeVdKaik~LKkEgkI   64 (80)
T 2lnb_A           18 GHLEQRILQVLTEAGSPVKLAQLVKECQAPKRELNQVLYRMKKELKV   64 (80)
T ss_dssp             HHHHHHHHHHHHHHTSCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred             chHHHHHHHHHHHcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCc
Confidence            467899999886 45  688999999999999999999999999976

>3mvp_A TETR/ACRR transcriptional regulator; PSI, MCSG, structural genomics, midwest center for structura genomics, protein structure initiative; 1.85A {Streptococcus mutans}

Probab=86.54  E-value=0.93  Score=35.93  Aligned_cols=37  Identities=19%  Similarity=0.278  Sum_probs=29.6

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        23 ~~~~~r~~Il~aA~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   67 (217)
T 3mvp_A           23 RSIEKRNKILQVAKDLFSDKTYFNVTTNEIAKKADVSVGTLYAYF   67 (217)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTSCHHHHHHHC
T ss_pred             cchhHHHHHHHHHHHHHHHcCccccCHHHHHHHhCCChhHHHHHc
Confidence            3457788888764     234   799999999999999999854

>1ojl_A Transcriptional regulatory protein ZRAR; response regulator, two component system, AAA domain, NTRC family, DNA-binding; HET: ATP; 3.0A {Salmonella typhimurium}

Probab=86.51  E-value=0.5  Score=42.10  Aligned_cols=38  Identities=18%  Similarity=0.218  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +....|..|...++ .|...+++|+.||||++|+|+.++
T Consensus       265 ~~~~e~~~i~~~l~~~~gn~~~aA~~Lgi~r~tl~~kl~  303 (304)
T 1ojl_A          265 LVDVEKEVILAALEKTGGNKTEAARQLGITRKTLLAKLS  303 (304)
T ss_dssp             HHHHHHHHHHHHHHTTTTCHHHHHHHHTSCHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence            33456777777776 477999999999999999999875

>3ccy_A Putative TETR-family transcriptional regulator; APC88698, structural G PSI-2, protein structure initiative; HET: MSE; 2.01A {Bordetella parapertussis 12822}

Probab=86.47  E-value=0.33  Score=38.83  Aligned_cols=37  Identities=24%  Similarity=0.248  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        11 ~~~~~r~~Il~aA~~lf~~~G~~~~s~~~Ia~~agvs~~t~Y~yF   55 (203)
T 3ccy_A           11 DYENIRDTIIERAAAMFARQGYSETSIGDIARACECSKSRLYHYF   55 (203)
T ss_dssp             -CTTHHHHHHHHHHHHHHHTCTTTSCHHHHHHHTTCCGGGGTTTC
T ss_pred             hhhhHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCCcCeeeeee
Confidence            3456788888843     344   699999999999999998754

>1ui5_A A-factor receptor homolog; helix-turn-helix, alpha-helix-bundle, antibiotic; 2.40A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1 PDB: 1ui6_A

Probab=86.47  E-value=0.7  Score=37.71  Aligned_cols=37  Identities=22%  Similarity=0.282  Sum_probs=29.0

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.+.|.+|++..     +.|   .|..+||+..|||++|+|+..+
T Consensus         7 ~~~~r~~Il~aA~~lf~~~Gy~~ts~~~IA~~AGvskgtlY~~F~   51 (215)
T 1ui5_A            7 AEQTRATIIGAAADLFDRRGYESTTLSEIVAHAGVTKGALYFHFA   51 (215)
T ss_dssp             TTTHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCchhhHhhCC
Confidence            456778887754     234   6999999999999999998644

>3nrg_A TETR family transcriptional regulator; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2; 2.56A {Chloroflexus aurantiacus}

Probab=86.43  E-value=0.48  Score=37.75  Aligned_cols=37  Identities=19%  Similarity=0.397  Sum_probs=30.4

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        10 ~~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F   54 (217)
T 3nrg_A           10 LPEEKRSRLIDVLLDEFAQNDYDSVSINRITERAGIAKGSFYQYF   54 (217)
T ss_dssp             SCHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCTTGGGGTC
T ss_pred             ChHHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCcHHHHHHHc
Confidence            3678899998864     345   799999999999999998754

>2yve_A Transcriptional regulator; helix-turn-helix, TETR-family; HET: MBT; 1.40A {Corynebacterium glutamicum} PDB: 1v7b_A 2zoy_A 2yvh_A 2dh0_A* 2zoz_A*

Probab=86.38  E-value=0.87  Score=36.14  Aligned_cols=34  Identities=6%  Similarity=0.033  Sum_probs=26.0

Q ss_pred             HHHHHHHH----H-HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVEL----A-QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L----~-~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .|.+|++.    + +.|   .|.++||+..|||++|+|++..
T Consensus         5 ~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   46 (185)
T 2yve_A            5 KKEMILRTAIDYIGEYSLETLSYDSLAEATGLSKSGLIYHFP   46 (185)
T ss_dssp             HHHHHHHHHHHHHHHSCSTTCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHcChhhccHHHHHHHhCCChHHHHHhCc
Confidence            45556554    3 344   6999999999999999998754

>3f0c_A TETR-molecule A, transcriptional regulator; MCSG,PSI, SAD, structural genomics, protein structure initiative; 2.96A {Cytophaga hutchinsonii}

Probab=86.33  E-value=0.73  Score=36.74  Aligned_cols=36  Identities=11%  Similarity=0.172  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        10 ~~~r~~Il~aA~~lf~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   53 (216)
T 3f0c_A           10 DGKLELIINAAQKRFAHYGLCKTTMNEIASDVGMGKASLYYYFP   53 (216)
T ss_dssp             CCHHHHHHHHHHHHHHHHCSSSCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHhCCCHHHHHHHcC
Confidence            35677777753     344   6999999999999999998743

>2guh_A Putative TETR-family transcriptional regulator; helix-turn-helix, TETR fold, structural genomics, PSI, prote structure initiative; HET: MSE; 1.52A {Rhodococcus SP}

Probab=86.31  E-value=0.88  Score=37.34  Aligned_cols=39  Identities=26%  Similarity=0.199  Sum_probs=31.3

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|||+....
T Consensus        36 ~~~~~r~~Il~AA~~lf~e~G~~~~tv~~IA~~AGvs~~tlY~~F~s   82 (214)
T 2guh_A           36 TAEQSRSLIVDAAGRAFATRPYREITLKDIAEDAGVSAPLIIKYFGS   82 (214)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHSS
T ss_pred             chhhHHHHHHHHHHHHHHHcChhhcCHHHHHHHhCCCHHHHHHHcCC
Confidence            3457788888754     345   79999999999999999998654

>2qwt_A Transcriptional regulator, TETR family; structural genomics, PSI-2, protein structure initiative; 2.30A {Mycobacterium vanbaalenii pyr-1}

Probab=86.25  E-value=0.97  Score=36.11  Aligned_cols=35  Identities=29%  Similarity=0.424  Sum_probs=28.1

Q ss_pred             HHHHHHHHHH-----HcC--CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QLG--IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~-----~~G--~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++..     +.|  .|.++||+..|||++|+|+..+
T Consensus        13 ~~r~~Il~aA~~lf~~~G~~~t~~~IA~~agvs~~tlY~~F~   54 (196)
T 2qwt_A           13 RNRARVLEVAYDTFAAEGLGVPMDEIARRAGVGAGTVYRHFP   54 (196)
T ss_dssp             HHHHHHHHHHHHHHHHTCTTSCHHHHHHHTTSCHHHHHHHCS
T ss_pred             hHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHCC
Confidence            5677888754     345  7999999999999999998643

>1yio_A Response regulatory protein; transcription regulation, DNA binding protein; 2.20A {Pseudomonas fluorescens} SCOP: a.4.6.2 c.23.1.1 PDB: 1zn2_A

Probab=86.20  E-value=0.92  Score=36.50  Aligned_cols=40  Identities=15%  Similarity=0.164  Sum_probs=31.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++... .+|+.+..+|.+..+||+.|++|.+||...+++-+
T Consensus       143 Lt~rE-~~vl~~l~~g~s~~~Ia~~l~is~~TV~~~~~~i~  182 (208)
T 1yio_A          143 LTGRE-QQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIM  182 (208)
T ss_dssp             SCHHH-HHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCHHH-HHHHHHHHcCCcHHHHHHHcCCCHHHHHHHHHHHH
Confidence            44333 34677777899999999999999999988777765

>2zcm_A Biofilm operon icaabcd HTH-type negative transcri regulator ICAR; helix-turn-helix, TETR family, repressor; 1.33A {Staphylococcus epidermidis} PDB: 2zcn_A

Probab=86.14  E-value=0.72  Score=36.38  Aligned_cols=23  Identities=17%  Similarity=0.232  Sum_probs=20.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.++||++.|||++|+|+...
T Consensus        27 ~~t~~~IA~~agvs~~tlY~~F~   49 (192)
T 2zcm_A           27 GTTLDDISKSVNIKKASLYYHYD   49 (192)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHTC
T ss_pred             cCCHHHHHHHhCCChHHHHHHCC
Confidence            46999999999999999998643

>3klo_A Transcriptional regulator VPST; REC domain, HTH domain, DNA-binding, transcription regulation; HET: C2E TAR; 2.80A {Vibrio cholerae} PDB: 3kln_A*

Probab=86.07  E-value=0.85  Score=37.58  Aligned_cols=40  Identities=25%  Similarity=0.308  Sum_probs=33.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...+ +|+.++.+|.+..+||+.|++|.+||...+++-+
T Consensus       160 Lt~rE~-~vL~~l~~g~s~~~Ia~~l~~s~~Tv~~~i~~l~  199 (225)
T 3klo_A          160 LTKREQ-QIIKLLGSGASNIEIADKLFVSENTVKTHLHNVF  199 (225)
T ss_dssp             SCHHHH-HHHHHHTTTCCHHHHHHHTTCCHHHHHHHHHHHT
T ss_pred             CCHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            555443 5777777899999999999999999999999975

>1yg2_A Gene activator APHA; virulence factor, winged helix, transcripti factor, transcription; 2.20A {Vibrio cholerae} SCOP: a.4.5.61

Probab=86.05  E-value=2.5  Score=34.69  Aligned_cols=69  Identities=20%  Similarity=0.181  Sum_probs=49.7

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHh--------CCCHHHHHHHHHHhhhhCCcccCCC--CCCCCC---CCCHHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQL--------RVSHGCVSKILARYHETGSILPGAI--GGSKPR---VTTPKVVSYIKEL  117 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~L--------GVSrsTVsRwikRyrEtGsl~pk~r--gG~RPr---klT~e~~~~I~~l  117 (258)
                      ++..|+.+.. ..++..+|++.|        ++|.++||+.+++..+.|-|.....  +|++++   .+|+.=++.+.++
T Consensus         3 l~~~iL~lL~~~~~~gyel~~~l~~~~~~~~~~s~~~ly~~L~~Le~~GlI~~~~~~~~~~~~r~~Y~lT~~G~~~l~~~   82 (179)
T 1yg2_A            3 LPHVILTVLSTRDATGYDITKEFSASIGYFWKASHQQVYRELNKMGEQGLVTCVLEPQEGKPDRKVYSITQAGRSALGEW   82 (179)
T ss_dssp             HHHHHHHHHHHCCBCHHHHHHHHTTGGGGTCCCCHHHHHHHHHHHHHTTSEEECCC---------CEEECHHHHHHHHHH
T ss_pred             hHHHHHHHHhcCCCCHHHHHHHHHHHhCCccCCCcCcHHHHHHHHHHCCCeEEEeecCCCCCCceEEEeChHHHHHHHHH
Confidence            4666777765 458999999999        7999999999999999997743221  221223   3788878888887


Q ss_pred             HHh
Q psy15598        118 KQK  120 (258)
Q Consensus       118 v~~  120 (258)
                      +..
T Consensus        83 ~~~   85 (179)
T 1yg2_A           83 FDQ   85 (179)
T ss_dssp             HHS
T ss_pred             HhC
Confidence            764

>3g7r_A Putative transcriptional regulator; TETR, all-helical, structural genomics, PSI-2, protein structure initiative; 1.38A {Streptomyces coelicolor A3}

Probab=86.02  E-value=0.99  Score=36.78  Aligned_cols=38  Identities=18%  Similarity=0.323  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|||+...
T Consensus        32 ~~~~~r~~Il~aA~~lf~~~G~~~~t~~~IA~~AGvs~~tlY~~F~   77 (221)
T 3g7r_A           32 TPSEARARLLGTATRIFYAEGIHSVGIDRITAEAQVTRATLYRHFS   77 (221)
T ss_dssp             --CHHHHHHHHHHHHHHHHHCSTTSCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cchhHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHCC
Confidence            3457888888864     234   7999999999999999998654

>2iu5_A DHAS, YCEG, HTH-type dhaklm operon transcriptional activator; synthase, TETR family; 1.6A {Lactococcus lactis subsp} SCOP: a.4.1.9 a.121.1.1

Probab=85.99  E-value=0.42  Score=38.08  Aligned_cols=36  Identities=11%  Similarity=0.074  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        11 ~~~~r~~Il~aa~~lf~~~G~~~~tv~~Ia~~agvs~~t~Y~~F   54 (195)
T 2iu5_A           11 SIITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYF   54 (195)
T ss_dssp             TSHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             cHHHHHHHHHHHHHHHHhCCCCeeCHHHHHHHhCCCHHHHHHHc
Confidence            456788888754     345   799999999999999999753

>2wus_R RODZ, putative uncharacterized protein; structural protein, cell WALL morphogenesis, bacterial cytos bacterial actin; 2.90A {Thermotoga maritima}

Probab=85.86  E-value=1.3  Score=34.19  Aligned_cols=33  Identities=12%  Similarity=-0.003  Sum_probs=26.3

Q ss_pred             HHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         53 RMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        53 R~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -.+|-.+.+ .|+|..++|+.+|||+++|++|-+
T Consensus         9 G~~Lr~~R~~~glSq~eLA~~~gis~~~is~iE~   42 (112)
T 2wus_R            9 GETFRKKREERRITLLDASLFTNINPSKLKRIEE   42 (112)
T ss_dssp             HHHHHHHHHTTTCCHHHHHHHSSCCHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence            344555554 699999999999999999998754

>3rd3_A Probable transcriptional regulator; 2.40A {Pseudomonas aeruginosa}

Probab=85.77  E-value=0.53  Score=36.81  Aligned_cols=36  Identities=14%  Similarity=0.249  Sum_probs=27.3

Q ss_pred             CHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus         8 ~~~~r~~Il~aa~~lf~~~G~~~~t~~~IA~~agvs~~tlY~~F   51 (197)
T 3rd3_A            8 YDDTRQHLLDTGYRIMAVKGFSGVGLNEILQSAGVPKGSFYHYF   51 (197)
T ss_dssp             --CHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTCCHHHHTTTC
T ss_pred             hHhHHHHHHHHHHHHHHHCCcccCCHHHHHHHhCCChhhHHHHc
Confidence            456777777754     335   699999999999999998754

>2qib_A TETR-family transcriptional regulator; HTH DNA binding, STRU genomics, MCSG, PSI-2, protein structure initiative; HET: P6G; 1.70A {Streptomyces coelicolor A3}

Probab=85.74  E-value=1  Score=37.06  Aligned_cols=38  Identities=13%  Similarity=0.141  Sum_probs=29.5

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      -..+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        10 ~~~~~r~~Il~AA~~l~~~~G~~~~tv~~IA~~agvs~~t~Y~~F~   55 (231)
T 2qib_A           10 GVEERRQQLIGVALDLFSRRSPDEVSIDEIASAAGISRPLVYHYFP   55 (231)
T ss_dssp             CHHHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             CHHHHHHHHHHHHHHHHHHcCchhcCHHHHHHHhCCCHHHHHHHCC
Confidence            3456778888754     345   6999999999999999998643

>3fxq_A LYSR type regulator of TSAMBCD; transcriptional regulator, LTTR, TSAR, WHTH, DNA- transcription, transcription regulation; 1.85A {Comamonas testosteroni} PDB: 3fxr_A* 3fxu_A* 3fzj_A 3n6t_A 3n6u_A*

Probab=85.66  E-value=1.3  Score=37.61  Aligned_cols=58  Identities=9%  Similarity=0.036  Sum_probs=40.5

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .+++..+.+-.|.+.+|++|+||.++|++-+++.++. |. +-.  |.+ |.-.+|++=+.++
T Consensus         7 L~~f~~v~~~gs~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~--R~~-r~~~lT~~G~~l~   66 (305)
T 3fxq_A            7 LQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLV--RTK-RGVSLTSFGQAFM   66 (305)
T ss_dssp             HHHHHHHHHHSCHHHHHHHTTCCHHHHHHHHHHHHHHHTSCSEE--ECS-SSEEECHHHHHHH
T ss_pred             HHHHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEE--ecC-CCccCCHhHHHHH
Confidence            3455555555699999999999999999999999864 43 222  223 5566777644444

>3v6g_A Probable transcriptional regulatory protein (PROB family); helix-turn-helix DNA binding domain; 1.82A {Mycobacterium tuberculosis}

Probab=85.66  E-value=0.82  Score=37.46  Aligned_cols=36  Identities=22%  Similarity=0.300  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|||+...
T Consensus        13 ~~~R~~Il~AA~~lf~~~G~~~~s~~~IA~~AGvs~~tlY~~F~   56 (208)
T 3v6g_A           13 AGRRQAIVEAAERVIARQGLGGLSHRRVAAEANVPVGSTTYYFN   56 (208)
T ss_dssp             -CHHHHHHHHHHHHHHHHCTTCCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCchhHHHHcC
Confidence            34678888753     344   6999999999999999998643

>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=85.63  E-value=0.41  Score=41.21  Aligned_cols=50  Identities=18%  Similarity=0.151  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC----CCCCCCHHHHHHHHHhc
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD----KFNVPSVSSISRILRNK  157 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v----~~~~pS~STI~RiLrr~  157 (258)
                      ++++..|.++.+++|...+++|++.+...|++-    +...+|.+||+++|+..
T Consensus        14 ~~~~~~ie~~~~e~p~~l~~~Ik~~l~~~gitQ~~lA~~~GiSqs~ISr~l~~~   67 (194)
T 1ic8_A           14 AHQKAVVETLLQEDPWRVAKMVKSYLQQHNIPQREVVDTTGLNQSHLSQHLNKG   67 (194)
T ss_dssp             HHHHHHHHHHTTSCHHHHHHHHHHHHHHTTCCHHHHHHHHCCCHHHHHHHHHSB
T ss_pred             HHHHHHHHHHHccCHHHHHHHHHHHHHHcCCCHHHHHHHhCCChHHHHHHHhcC
Confidence            457889999998999999999999998888741    12236999999998653

>2ijl_A AGR_C_4647P, molybdenum-binding transcriptional repressor; structural GE DNA-binding protein, PSI-2, PROT structure initiative; 2.30A {Agrobacterium tumefaciens str}

Probab=85.61  E-value=1.8  Score=34.93  Aligned_cols=65  Identities=9%  Similarity=0.077  Sum_probs=43.0

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCC--CCCCCCCHHHHHHHHHH
Q psy15598         53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGG--SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG--~RPrklT~e~~~~I~~l  117 (258)
                      ..+++..+.+--|.+.+|+.|+||.++|++.+++.++. |. +-.+..+|  ++.-.+|++=+.++...
T Consensus        28 ~L~~f~av~e~gS~s~AA~~L~iSqsavS~~I~~LE~~lG~~Lf~R~~~G~~grg~~LT~~G~~ll~~a   96 (135)
T 2ijl_A           28 KVELMQLIAETGSISAAGRAMDMSYRRAWLLVDALNHMFRQPVICSQRGGKQGGGAALTVFGAELLERY   96 (135)
T ss_dssp             HHHHHHHHHHHSCHHHHHHHTTCCHHHHHHHHHHHHHHBSSCSEEECCC------EEECHHHHHHHHHH
T ss_pred             HHHHHHHHHHhCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCeeEEecCCCCCCCceeECHHHHHHHHHH
Confidence            34566666555699999999999999999999999864 42 32332221  14567887766555444

>3s5r_A Transcriptional regulator TETR family; DNA/RNA-binding 3-helical bundle, tetracyclin repressor-like structural genomics; 2.60A {Syntrophus aciditrophicus}

Probab=85.45  E-value=0.76  Score=36.54  Aligned_cols=37  Identities=11%  Similarity=0.187  Sum_probs=28.0

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus         8 ~~~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F~   52 (216)
T 3s5r_A            8 DKNTRELLLDAATTLFAEQGIAATTMAEIAASVGVNPAMIHYYFK   52 (216)
T ss_dssp             -CCHHHHHHHHHHHHHHHHCTTTCCHHHHHHTTTCCHHHHHHHCS
T ss_pred             chHHHHHHHHHHHHHHHHcCcccCCHHHHHHHHCCCHHHHHHHcC
Confidence            345677777653     23   47999999999999999998743

>2of7_A Putative TETR-family transcriptional regulator; APC7240, streptomyces coelicolor A3, structural genomics, PSI-2; 2.30A {Streptomyces coelicolor}

Probab=85.44  E-value=1.1  Score=37.63  Aligned_cols=38  Identities=18%  Similarity=0.143  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ..+.|.+|++..     +.   +.|..+||+..|||++|||+....
T Consensus        46 ~~~tr~~Il~AA~~lf~e~G~~~~Ti~~IA~~AGvs~~t~Y~yF~s   91 (260)
T 2of7_A           46 KTRTREAIRAATYGLIRQQGYEATTVEQIAERAEVSPSTVLRYFPT   91 (260)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHCSS
T ss_pred             hHHHHHHHHHHHHHHHHHhCcccccHHHHHHHhCCChHHHHHHcCC
Confidence            346778888753     23   479999999999999999987543

>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=85.37  E-value=1.2  Score=34.52  Aligned_cols=43  Identities=12%  Similarity=-0.037  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHhCC----CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        109 KVVSYIKELKQKDP----GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       109 e~~~~I~~lv~~nP----~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      ..+..|.+++.+||    .++..||++.+.          +|.+||.|+.+..|...
T Consensus        21 ~~e~~ia~yil~~~~~~~~~si~elA~~~~----------vS~aTv~Rf~kklG~~g   67 (111)
T 2o3f_A           21 PSERKLADYILAHPHXAIESTVNEISALAN----------SSDAAVIRLCXSLGLKG   67 (111)
T ss_dssp             HHHHHHHHHHHHCHHHHHTCCHHHHHHHTT----------CCHHHHHHHHHHTTCSS
T ss_pred             HHHHHHHHHHHHChHHHHhcCHHHHHHHHC----------CCHHHHHHHHHHcCCCC

>1hsj_A Fusion protein consisting of staphylococcus accessary regulator protein R and maltose...; novel fold for DNA binding; HET: GLC; 2.30A {Escherichia coli} SCOP: a.4.5.28 c.94.1.1

Probab=85.24  E-value=0.78  Score=42.59  Aligned_cols=57  Identities=12%  Similarity=0.049  Sum_probs=40.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-CC--CCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-KP--RVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-RP--rklT~e~~~~I~~lv  118 (258)
                      .|++.++||+.++++++||.+.++|-.+.|-|.-.+.... |-  -.+|++-++.+.++.
T Consensus       419 ~~~~~~~l~~~~~~~~~~~t~~~~~le~~g~v~r~~~~~D~R~~~i~lT~~g~~~~~~~~  478 (487)
T 1hsj_A          419 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKLI  478 (487)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeecCCCCCCCeEEEEECHHHHHHHHHHH
Confidence            3589999999999999999999999999998743221111 21  236666555554443

>2of5_A Death domain-containing protein cradd; death domain complex, apoptosis; 3.20A {Homo sapiens}

Probab=85.22  E-value=4.3  Score=31.79  Aligned_cols=73  Identities=15%  Similarity=0.013  Sum_probs=56.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCC
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD-PGIFAWEIRDRLLSDGVCD  140 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v  140 (258)
                      -|...+.+|+.||++...|..+..++.               .-+.+.....+..+.+++ ...+...|...|.+.|+..
T Consensus        34 lG~~Wk~LAR~LGlse~dId~I~~~~p---------------~~l~eq~~qmL~~W~~r~G~~AT~~~L~~AL~~~~l~~   98 (114)
T 2of5_A           34 LGPEWEPMVLSLGLSQTDIYRCKANHP---------------HNVQSQVVEAFIRWRQRFGKQATFQSLHNGLRAVEVDP   98 (114)
T ss_dssp             CCSTHHHHHHTTTCCHHHHHHHHHHCS---------------SCHHHHHHHHHHHHHHHHGGGCCHHHHHHHHHHTTCCT
T ss_pred             HhhhHHHHHHHcCCCHHHHHHHHHHCC---------------CCHHHHHHHHHHHHHHHHCcCcHHHHHHHHHHHcCCCH
Confidence            589999999999999999999998873               123345566666666654 4678999999999888875


Q ss_pred             CCCCCCHHHHHHHHHhc
Q psy15598        141 KFNVPSVSSISRILRNK  157 (258)
Q Consensus       141 ~~~~pS~STI~RiLrr~  157 (258)
                              ||+++|...
T Consensus        99 --------~v~~~~~~~  107 (114)
T 2of5_A           99 --------SLLLHMLEL  107 (114)
T ss_dssp             --------HHHHHHCC-
T ss_pred             --------HHHHHHHHH
Confidence                    788877643

>3him_A Probable transcriptional regulator; TETR, bacterial, RHA1, PSI-2, MCSG, structural midwest center for structural genomics; 2.20A {Rhodococcus jostii}

Probab=85.22  E-value=0.33  Score=38.31  Aligned_cols=38  Identities=24%  Similarity=0.196  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        47 ~~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .-..+.|.+|++..     +.|   .|.++||+..|||++|+|+..
T Consensus        12 ~~~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   57 (211)
T 3him_A           12 LGTSKAAARIRAAAIEVFAAKGYGATTTREIAASLDMSPGAVYPHY   57 (211)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHTTCCTTSSTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHhCCCcChhhhcC
Confidence            34567888888864     234   799999999999999998753

>2oi8_A Putative regulatory protein SCO4313; TETR, structural genomics, PSI-2, P structure initiative; 2.50A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=85.20  E-value=0.99  Score=37.17  Aligned_cols=38  Identities=18%  Similarity=0.288  Sum_probs=30.1

Q ss_pred             CCHHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        48 ~S~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...+.|.+|++..     +.|   .|.++||+..|||++|+|+...
T Consensus        13 ~~~~~r~~il~aA~~l~~~~G~~~~s~~~IA~~agvs~~t~Y~~F~   58 (216)
T 2oi8_A           13 YRTQVRAEIKDHAWEQIATAGASALSLNAIAKRMGMSGPALYRYFD   58 (216)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHCTTSCCHHHHHHHTTCCHHHHHTTCS
T ss_pred             hHHHHHHHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence            4567888888754     234   7999999999999999987543

>2hyj_A Putative TETR-family transcriptional regulator; HTH DNA binding motif, structural genomics, PSI-2, Pro structure initiative; 2.19A {Streptomyces coelicolor} SCOP: a.4.1.9 a.121.1.1

Probab=85.18  E-value=0.89  Score=36.55  Aligned_cols=36  Identities=28%  Similarity=0.344  Sum_probs=29.1

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.|.+|++..     +.   +.|..+||+..|||++|||+..
T Consensus        10 ~~~~r~~Il~aA~~lf~~~G~~~~s~~~IA~~aGvsk~tlY~hF   53 (200)
T 2hyj_A           10 AQATRGRILGRAAEIASEEGLDGITIGRLAEELEMSKSGVHKHF   53 (200)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHTTC
T ss_pred             hhccHHHHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHHHHc
Confidence            457888888764     23   4799999999999999999753

>1xwr_A Regulatory protein CII; all-alpha fold, DNA binding protein; 2.56A {Bacteriophage lambda} SCOP: a.35.1.9 PDB: 1zpq_A

Probab=85.17  E-value=0.57  Score=36.21  Aligned_cols=27  Identities=7%  Similarity=0.049  Sum_probs=24.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+.+.+.+|+.+||+.+||+||...+.
T Consensus        22 a~~gq~~vA~~iGV~~StISR~k~~~~   48 (97)
T 1xwr_A           22 AMLGTEKTAEAVGVDKSQISRWKRDWI   48 (97)
T ss_dssp             HHHCHHHHHHHHTCCTTTHHHHHHHHH
T ss_pred             HHHhHHHHHHHhCCCHHHHHHHHhhhH
Confidence            578999999999999999999988663

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

Probab=85.10  E-value=1.5  Score=31.22  Aligned_cols=41  Identities=17%  Similarity=-0.010  Sum_probs=31.8

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +..|.+++.++..++..||++.+.          +|.+||++.|+.+..+.
T Consensus         2 r~~Il~~L~~~~~~s~~eLa~~lg----------vs~~tv~r~L~~L~~~G   42 (81)
T 2htj_A            2 KNEILEFLNRHNGGKTAEIAEALA----------VTDYQARYYLLLLEKAG   42 (81)
T ss_dssp             HHHHHHHHHHSCCCCHHHHHHHHT----------SCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            345777777777899999999883          49999999998865543

>2elh_A CG11849-PA, LD40883P; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Drosophila melanogaster}

Probab=85.06  E-value=2.5  Score=30.70  Aligned_cols=45  Identities=16%  Similarity=0.084  Sum_probs=34.2

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      .+++.+++....+++++..  ..+..+|+..+   |       ||.+||+|+++...
T Consensus        19 ~~~~ys~e~k~~~v~~~~~--g~s~~~iA~~~---g-------Is~sTl~rW~k~~~   63 (87)
T 2elh_A           19 PLRSLTPRDKIHAIQRIHD--GESKASVARDI---G-------VPESTLRGWCKNED   63 (87)
T ss_dssp             CCSSCCHHHHHHHHHHHHH--TCCHHHHHHHH---T-------CCHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHHHC--CCCHHHHHHHH---C-------cCHHHHHHHHHHHH
Confidence            4567888887777777754  47888887776   3       49999999997644

>3nxc_A HTH-type protein SLMA; nucleoid occlusion, cell division, TETR family member, DNA B protein; 2.50A {Escherichia coli}

Probab=85.03  E-value=0.42  Score=37.95  Aligned_cols=36  Identities=17%  Similarity=0.254  Sum_probs=25.8

Q ss_pred             CHHHHHHHHHH----H--HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         49 PNSVRMRIVEL----A--QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        49 S~dlR~RIV~L----~--~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..+.|.+|++.    +  +.|   .|.++||+..|||++|+|+..
T Consensus        22 ~~~~r~~Il~aA~~~lf~~~G~~~~t~~~Ia~~agvs~~t~Y~~F   66 (212)
T 3nxc_A           22 KRNRREEILQSLALMLESSDGSQRITTAKLAASVGVSEAALYRHF   66 (212)
T ss_dssp             -CTTHHHHHHHHHHHHHC------CCHHHHHHHTTSCHHHHHTTC
T ss_pred             chHHHHHHHHHHHHHHHhcCChhhcCHHHHHHHhCCChhHHHHHC
Confidence            44566777665    2  224   799999999999999999754

>1t33_A Putative transcriptional repressor (TETR/ACRR FAM; structural genomics, TETR/CCRR FA helix turn helix DNA binding domain, PSI; 2.20A {Salmonella typhimurium} SCOP: a.4.1.9 a.121.1.1

Probab=84.95  E-value=1.4  Score=35.43  Aligned_cols=37  Identities=11%  Similarity=0.218  Sum_probs=29.4

Q ss_pred             HHHHHHHHHHH-----HcC--CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG--IRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G--~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .+.|.+|++..     +.|  .|.++||+..|||++|||+....
T Consensus        11 ~~~r~~Il~aA~~lf~~~G~~~s~~~IA~~agvs~~tiY~~F~s   54 (224)
T 1t33_A           11 EQAKSQLIAAALAQFGEYGLHATTRDIAALAGQNIAAITYYFGS   54 (224)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGSCHHHHHHHHTSCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHHhCccccHHHHHHHhCCCHHHHHHhcCC
Confidence            45777787753     234  89999999999999999987653

>3fzv_A Probable transcriptional regulator; LYSR, structural genomics, PSI-2, structure initiative; 2.71A {Pseudomonas aeruginosa PA01}

Probab=84.92  E-value=2.4  Score=35.47  Aligned_cols=57  Identities=14%  Similarity=0.155  Sum_probs=34.1

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHHH
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVSY  113 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~~  113 (258)
                      +++..+.+-.|.+++|+.|+||.++|++-+++.++. |. +-.+. ++ |.-.+|++=+.+
T Consensus        10 ~~f~~v~~~~s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~-~~-~~~~lT~~G~~l   68 (306)
T 3fzv_A           10 KYFVTTVECGSVAEASRKLYIAQPSISTAVKGLEESFGVQLFIRH-HA-QGVSLTPAGARF   68 (306)
T ss_dssp             HHHHHHHHSSSHHHHHHHHTCCC-CHHHHHHHHHHHC-CCCC-----------CCHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHhCCCchHHHHHHHHHHHHhCCeeEeec-CC-CCceECHhHHHH
Confidence            444455555699999999999999999999999864 42 22221 12 456677654433

>2rek_A Putative TETR-family transcriptional regulator; sulfur, SAD, structural genomics, PSI-2, protein structure initiative; 1.86A {Streptomyces coelicolor A3}

Probab=84.78  E-value=1.2  Score=35.36  Aligned_cols=36  Identities=22%  Similarity=0.274  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHH-----HcC--CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG--IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G--~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|  .|.++||+..|||++|+|+..+
T Consensus        15 ~~~r~~Il~aA~~lf~~~G~~~s~~~Ia~~agvs~~t~Y~~F~   57 (199)
T 2rek_A           15 RRNYDRIIEAAAAEVARHGADASLEEIARRAGVGSATLHRHFP   57 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHhCCchHHHHHHCC
Confidence            35677888753     234  6999999999999999998654

>2fbq_A Probable transcriptional regulator; PA3006, APC5893, structural genom protein structure initiative; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.1.9 a.121.1.1

Probab=84.75  E-value=1.3  Score=36.54  Aligned_cols=36  Identities=19%  Similarity=0.177  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|.++||+..|||++|||+..+
T Consensus         6 ~~~r~~Il~AA~~lF~e~G~~~ts~~~IA~~AGvs~~tlY~hF~   49 (235)
T 2fbq_A            6 SETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFG   49 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHTC
T ss_pred             hhHHHHHHHHHHHHHHHcCccccCHHHHHHHhCCCHHHHHHHcC
Confidence            46788888754     234   6999999999999999998643

>3szp_A Transcriptional regulator, LYSR family; winged helix-turn helix, DNA-binding, transcription factor; 2.20A {Vibrio cholerae} PDB: 3t1b_B

Probab=84.73  E-value=1.2  Score=36.89  Aligned_cols=58  Identities=7%  Similarity=0.079  Sum_probs=40.9

Q ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      .+++..+.+-.|.+++|+.|+||.++|++-+++.++ -|. +-.+  .+ +.-.+|++-+.++
T Consensus         6 l~~f~~v~~~~s~t~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R--~~-~~~~lT~~G~~l~   65 (291)
T 3szp_A            6 LNLFRLVVENGSYTSTSKKTMIPVATITRRIQALEDSLNLRLLNR--HA-RKLTLTEAGERFY   65 (291)
T ss_dssp             HHHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCEEE--ET-TEEEECHHHHHHH
T ss_pred             HHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCceEee--cC-CCcccCHhHHHHH
Confidence            345555566779999999999999999999999985 443 2222  23 4566777644444

---

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	258
d1pdnc_	123	a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Dros	5e-54
d1k78a2	61	a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [Ta	2e-35
d6paxa2	65	a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [Ta	4e-35
d1k78a1	63	a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [Tax	1e-30

>d1pdnc_ a.4.1.5 (C:) Paired protein (prd) {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 123

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]

 Score =  168 bits (427), Expect = 5e-54
 Identities = 82/122 (67%), Positives = 104/122 (85%)

Query: 33  GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92
           G VNQLGGVF+NGRPLPN++R++IVE+A  GIRPC ISRQLRVSHGCVSKIL RY ETGS
Sbjct: 2   GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGS 61

Query: 93  ILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISR 152
           I PG IGGSKPR+ TP++ + I+E K+  PG+F+WEIR++L+ +GVCD+   PSVS+ISR
Sbjct: 62  IRPGVIGGSKPRIATPEIENRIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISR 121

Query: 153 IL 154
           ++
Sbjct: 122 LV 123

>d1k78a2 a.4.1.5 (A:82-142) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 61

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]

 Score =  118 bits (299), Expect = 2e-35
 Identities = 40/60 (66%), Positives = 49/60 (81%)

Query: 98  IGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK 157
           IGGSKP+V TPKVV  I E K+++P +FAWEIRDRLL++ VCD   VPSVSSI+RI+R K
Sbjct: 2   IGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK 61

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]} Length = 65

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  118 bits (297), Expect = 4e-35
 Identities = 42/61 (68%), Positives = 49/61 (80%)

Query: 99  GGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI 158
           GGSKPRV TP+VVS I + KQ+ P IFAWEIRDRLLS+GVC   N+PSVSSI+R+LRN  
Sbjct: 1   GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLA 60

Query: 159 G 159
            
Sbjct: 61  S 61

>d1k78a1 a.4.1.5 (A:19-81) Pax-5 {Human (Homo sapiens) [TaxId: 9606]} Length = 63

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]

 Score =  106 bits (267), Expect = 1e-30
 Identities = 53/62 (85%), Positives = 56/62 (90%)

Query: 35 VNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94
          VNQLGGVFVNGRPLP+ VR RIVELA  G+RPCDISRQLRVSHGCVSKIL RY+ETGSI 
Sbjct: 2  VNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIK 61

Query: 95 PG 96
          PG
Sbjct: 62 PG 63

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	258
d1pdnc_	123	Paired protein (prd) {Fruit fly (Drosophila melano	100.0
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.87
d6paxa2	65	Pax-6 {Human (Homo sapiens) [TaxId: 9606]}	99.51
d1k78a2	61	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	99.5
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	98.86
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	98.33
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	98.17
d1hlva1	66	DNA-binding domain of centromere binding protein B	97.99
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	97.11
d1rp3a2	71	Sigma factor sigma-28 (FliA) {Aquifex aeolicus [Ta	97.06
d1r1ua_	94	Metal-sensing transcriptional repressor CzrA {Stap	96.88
d1or7a1	68	SigmaE factor (RpoE) {Escherichia coli [TaxId: 562	96.78
d1ijwc_	47	HIN recombinase (DNA-binding domain) {Synthetic}	96.77
d1r1ta_	98	SmtB repressor {Cyanobacteria (Synechococcus), pcc	96.68
d2hoea1	62	N-acetylglucosamine kinase {Thermotoga maritima [T	96.65
d1umqa_	60	Photosynthetic apparatus regulatory protein PprA (	96.54
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	96.39
d1z6ra1	70	Mlc protein N-terminal domain {Escherichia coli [T	96.39
d1s7oa_	106	Hypothetical protein SPy1201 {Streptococcus pyogen	96.36
d1u2wa1	108	Cadmium efflux system accessory protein CadC {Stap	96.34
d1a04a1	67	Nitrate/nitrite response regulator (NarL) {Escheri	96.29
d1xsva_	106	Hypothetical protein SAV1236 {Staphylococcus aureu	96.23
d1fsea_	67	Germination protein GerE {Bacillus subtilis [TaxId	96.19
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	96.03
d2p4wa1	194	Transcriptional regulatory protein PF1790 {Pyrococ	95.96
d2p5ka1	63	Arginine repressor (ArgR), N-terminal DNA-binding	95.94
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	95.91
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	95.89
d1l3la1	65	Quorum-sensing transcription factor TraR, C-termin	95.84
d2ev0a1	61	Manganese transport regulator MntR {Bacillus subti	95.84
d1b4aa1	75	Arginine repressor (ArgR), N-terminal DNA-binding	95.78
d1g2ha_	61	Transcriptional regulator TyrR, C-terminal domain	95.73
d1yioa1	70	Response regulatory protein StyR, C-terminal domai	95.68
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	95.65
d1aoya_	78	Arginine repressor (ArgR), N-terminal DNA-binding	95.6
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	95.45
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	95.34
d2croa_	65	cro 434 {Bacteriophage 434 [TaxId: 10712]}	95.31
d2ppxa1	62	Uncharacterized protein Atu1735 {Agrobacterium tum	95.26
d2isya1	63	Iron-dependent regulator IdeR {Mycobacterium tuber	95.26
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	95.2
d1ulya_	190	Hypothetical protein PH1932 {Pyrococcus horikoshii	95.2
d1qpza1	57	Purine repressor (PurR), N-terminal domain {Escher	95.18
d2hsga1	57	Glucose-resistance amylase regulator CcpA, N-termi	95.05
d1q06a_	127	Transcriptional regulator CueR {Escherichia coli [	95.03
d1uxda_	59	Fructose repressor (FruR), N-terminal domain {Esch	95.01
d1i5za1	69	Catabolite gene activator protein (CAP), C-termina	95.01
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	94.91
d1etxa_	89	FIS protein {Escherichia coli [TaxId: 562]}	94.9
d1p4wa_	87	Transcriptional regulator RcsB {Erwinia amylovora	94.88
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	94.82
d1r8da_	109	Multidrug transporter activator MtaN {Bacillus sub	94.81
d1ft9a1	80	CO-sensing protein CooA, C-terminal domain {Rhodos	94.74
d1hw1a1	74	Fatty acid responsive transcription factor FadR, N	94.69
d2auwa1	67	Hypothetical protein NE0471 C-terminal domain {Nit	94.64
d2oa4a1	93	Uncharacterized protein SPO1678 {Silicibacter pome	94.63
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.6
d1jhga_	101	Trp repressor, TrpR {Escherichia coli [TaxId: 562]	94.57
d2gaua1	81	Transcriptional regulator PG0396, C-terminal domai	94.42
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	94.38
d1hlva1	66	DNA-binding domain of centromere binding protein B	94.38
d2r1jl1	66	P22 C2 repressor, DNA-binding domain {Salmonella b	94.37
d1zyba1	73	Probable transcription regulator BT4300, C-termina	94.36
d3e5ua1	80	Chlorophenol reduction protein CprK {Desulfitobact	94.32
d1rr7a_	94	Middle operon regulator, Mor {Bacteriophage Mu [Ta	94.29
d1jgsa_	138	Multiple antibiotic resistance repressor, MarR {Es	94.21
d2a6ca1	69	HTH-motif protein NE1354 {Nitrosomonas europaea [T	94.07
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	93.97
d2o38a1	89	Hypothetical protein RPA3824 {Rhodopseudomonas pal	93.89
d1lmb3_	87	lambda C1 repressor, DNA-binding domain {Bacteriop	93.86
d1y7ya1	69	Restriction-modification controller protein C.AhdI	93.85
d1utxa_	66	Putative transcription regulator CylR2 {Enterococc	93.76
d1r69a_	63	434 C1 repressor, DNA-binding domain {Bacteriophag	93.73
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.72
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	93.64
d2b5aa1	77	Regulatory protein C.BclI {Bacillus caldolyticus [	93.58
d1tc3c_	51	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	93.57
d1x57a1	78	Endothelial differentiation-related factor 1, EDF1	93.53
d1ku3a_	61	Sigma70 (SigA, RpoD) {Thermus aquaticus [TaxId: 27	93.5
d1b0na2	68	SinR repressor, DNA-binding domain {Bacillus subti	93.44
d1ntca_	91	DNA-binding domain of NTRC {Salmonella typhimurium	93.39
d2fbqa1	79	Transcriptional regulator PsrA {Pseudomonas aerugi	93.36
d1t56a1	73	Ethr repressor {Mycobacterium tuberculosis [TaxId:	93.33
d2zcwa1	82	Transcriptional regulator TTHA1359, C-terminal dom	93.27
d1efaa1	59	Lac repressor (LacR), N-terminal domain {Escherich	93.23
d1lnwa_	141	MexR repressor {Pseudomonas aeruginosa [TaxId: 287	93.16
d2etha1	140	Putative transcriptional regulator TM0816 {Thermot	93.15
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	93.04
d2icta1	87	Antitoxin HigA {Escherichia coli [TaxId: 562]}	92.97
d1jt6a1	71	Multidrug binding protein QacR {Staphylococcus aur	92.69
d2cg4a1	63	Regulatory protein AsnC {Escherichia coli [TaxId:	92.61
d2gfna1	77	Probable transcriptional regulator RHA1_ro04631 {R	92.4
d2fq4a1	69	Transcriptional regulator BC3163 {Bacillus cereus	92.35
d1y9qa1	79	Probable transcriptional regulator VC1968, N-termi	92.18
d2fxaa1	162	Protease production regulatory protein Hpr {Bacill	92.16
d1v4ra1	100	Transcriptional repressor TraR, N-terminal domain	92.04
d3c07a1	75	Putative transcriptional regulator SCO4850 {Strept	91.94
d2bgca1	100	Listeriolysin regulatory protein PrfA, C-terminal	91.84
d2cfxa1	63	Transcriptional regulator LrpC {Bacillus subtilis	91.83
d1s3ja_	143	Putative transcriptional regulator YusO {Bacillus	91.73
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	91.71
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	91.68
d1ui5a1	71	A-factor receptor homolog CprB {Streptomyces coeli	91.66
d1i1ga1	60	LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}	91.64
d2g7sa1	74	Putative transcriptional regulator Atu0279 {Agroba	91.62
d1z91a1	137	Organic hydroperoxide resistance transcriptional r	91.54
d2fx0a1	73	Hemolysin II regulatory protein, HlyIIR {Bacillus	91.48
d1gdta1	43	gamma,delta resolvase (C-terminal domain) {Escheri	91.47
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	91.38
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	91.34
d2esna1	89	Probable LysR-type transcriptional regulator PA047	91.23
d2o7ta1	78	Transcriptional regulator Cgl1640/Cg1846 {Coryneba	91.2
d1lj9a_	144	Transcriptional regulator SlyA {Enterococcus faeca	91.17
d2id3a1	68	Putative transcriptional regulator SCO5951 {Strept	91.15
d1pb6a1	72	Hypothetical transcriptional regulator YcdC {Esche	90.84
d2g3ba1	72	Putative transcriptional regulator {Rhodococcus sp	90.79
d2hkua1	70	Putative transcriptional regulator RHA1_ro03468 {R	90.7
d1sgma1	73	Putative transcriptional regulator YxaF {Bacillus	90.57
d2oi8a1	79	Putative regulatory protein Sco4313 {Streptomyces	90.5
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	90.48
d1r71a_	114	Transcriptional repressor protein KorB DNA-binding	90.45
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	90.24
d2vkva1	62	Tetracyclin repressor (Tet-repressor, TetR) {Esche	90.24
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	90.23
d1b9ma1	127	N-terminal domain of molybdate-dependent transcrip	90.02
d2gena1	70	Probable transcriptional regulator PA1836 {Pseudom	90.0
d2bv6a1	136	Transcriptional regulator MgrA {Staphylococcus aur	89.66
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	89.61
d2hyja1	75	Putative transcriptional regulator SCO4940 {Strept	89.48
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	89.48
d1v7ba1	74	Transcriptional regulator Cgl2612 {Corynebacterium	89.46
d2p7vb1	68	Sigma70 (SigA, RpoD) {Escherichia coli [TaxId: 562	89.43
d1r8ea1	118	Transcription activator BmrR {Bacillus subtilis [T	89.29
d1vz0a1	93	Putative partitioning protein ParB/Spo0J {Thermus	88.95
d2d6ya1	68	Putative regulator SCO4008 {Streptomyces coelicolo	88.94
d1j9ia_	68	Terminase gpNU1 subunit domain {Bacteriophage lamb	88.66
d2ao9a1	120	Phage protein BC1890 {Bacillus cereus [TaxId: 1396	88.59
d2id6a1	75	Transcriptional regulator TM1030 {Thermotoga marit	88.59
d2ofya1	82	Putative transcriptional regulator RHA1_ro04071 {R	88.53
d2g7ga1	65	Putative transcriptional regulator Rha04620 {Rhodo	88.53
d1ixca1	89	LysR-type regulatory protein CbnR {Ralstonia eutro	88.44
d2fbia1	136	Probable transcriptional regulator PA4135 {Pseudom	88.34
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	88.34
d2ezla_	99	Ibeta subdomain of the mu end DNA-binding domain o	88.28
d1xd7a_	127	Hypothetical protein ywnA {Bacillus subtilis [TaxI	87.97
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	87.91
d2iu5a1	71	Transcriptional activator DhaS {Lactococcus lactis	87.64
d3deua1	140	Transcriptional regulator SlyA {Salmonella typhimu	87.53
d1rkta1	81	Hypothetical transcriptional regulator YfiR {Bacil	87.47
d2fd5a1	76	Probable transcriptional regulator PA3133 {Pseudom	87.19
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	87.1
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	86.91
d1vi0a1	72	Hypothetical transcriptional regulator YsiA {Bacil	86.69
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	86.3
d1ttya_	87	Sigma70 (SigA, RpoD) {Thermotoga maritima [TaxId:	86.19
d2p8ta1	69	Hypothetical protein PH0730 {Pyrococcus horikoshii	85.77
d1t33a1	88	Putative transcriptional repressor YbiH {Salmonell	85.2
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	84.53
d1zk8a1	72	Transcriptional regulator BC5000 {Bacillus cereus	84.45
d2i10a1	69	Putative transcriptional regulator RHA1_ro09068 {R	84.11
d2np5a1	69	Transcriptional regulator RHA1_ro04179 {Rhodococcu	83.72
d1stza1	87	Heat-inducible transcription repressor HrcA, N-ter	83.67
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	83.44
d2o3fa1	83	Putative transcriptional regulator YbbH {Bacillus	83.43
d1sfua_	70	34L {Yaba-like disease virus, YLDV [TaxId: 132475]	83.1
d2ezia_	75	Transposase {Bacteriophage mu [TaxId: 10677]}	82.54
d2g7la1	68	Putative transcriptional regulator SCO7704 {Strept	82.54
d1k78a1	63	Pax-5 {Human (Homo sapiens) [TaxId: 9606]}	82.17
d1z0xa1	68	Transcriptional regulator EF0787 {Enterococcus fae	81.87
d1mzba_	134	Ferric uptake regulation protein, FUR {Pseudomonas	80.83
d1u78a2	50	Transposase tc3a1-65 {Caenorhabditis elegans [TaxI	80.76
d2jn6a1	89	Uncharacterized protein Cgl2762 {Corynebacterium g	80.13

>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=100.00  E-value=1.4e-34  Score=233.51  Aligned_cols=122  Identities=67%  Similarity=1.216  Sum_probs=118.6

Q ss_pred             chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598         33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS  112 (258)
Q Consensus        33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~  112 (258)
                      +++|||||+|+|||+||.|+|.+||+++++|++.++||++|+||++||++|+++|+++|.+.+++++|++|++++++++.
T Consensus         2 ~~~n~~gg~~~~GrpLs~dlR~rIv~~~~~G~s~r~iA~~~~VS~~tV~k~l~r~~~~G~~~~~~~~~~rpr~~t~~~~~   81 (123)
T d1pdnc_           2 GRVNQLGGVFINGRPLPNNIRLKIVEMAADGIRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRIATPEIEN   81 (123)
T ss_dssp             EEECTTSCEEETTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHCCSSCCCCSCCCCCSSCSTHHH
T ss_pred             cCcccCCCcccCCcCCCHHHHHHHHHHHHhcCCHHHHHHHHCcCHHHHHHHHHHHHccCCcCcCCCCCCCCCCCCHHHHH
Confidence            68999999999999999999999999999999999999999999999999999999999999999887799999999999


Q ss_pred             HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHH
Q psy15598        113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL  154 (258)
Q Consensus       113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiL  154 (258)
                      +|.++++++|++++|||++.|.+.|++...++||+|||+|+|
T Consensus        82 ~I~~~~~~~P~~t~~El~~~L~~egv~~~~~~pSvStI~RiL  123 (123)
T d1pdnc_          82 RIEEYKRSSPGMFSWEIREKLIREGVCDRSTAPSVSAISRLV  123 (123)
T ss_dssp             HHHHTTTTCTTCCHHHHHHHHHHTSSSCSTTCCCHHHHHHHC
T ss_pred             HHHHHHHhCCCccHHHHHHHHHHcCCCCCCCCCChhhHhhcC
Confidence            999999999999999999999999999889999999999986

>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=99.87  E-value=9.5e-23  Score=147.13  Aligned_cols=63  Identities=84%  Similarity=1.338  Sum_probs=61.2

Q ss_pred             hhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         34 EVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        34 ~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      ++|||||.|+||||||.|+|+|||+++++|+|.++||++|+||++||.||+++|+|||+++|+
T Consensus         1 ~~n~~gg~~~~GrPls~DLR~Riv~~~~~G~s~r~aA~rf~VS~s~v~k~l~r~reTG~i~PG   63 (63)
T d1k78a1           1 GVNQLGGVFVNGRPLPDVVRQRIVELAHQGVRPCDISRQLRVSHGCVSKILGRYYETGSIKPG   63 (63)
T ss_dssp             CBCTTSCBCCTTSCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHHHSCCCCC
T ss_pred             CcCCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCC
Confidence            589999999999999999999999999999999999999999999999999999999999874

>d6paxa2 a.4.1.5 (A:69-133) Pax-6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Paired domain
domain: Pax-6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.51  E-value=1.6e-14  Score=103.52  Aligned_cols=63  Identities=67%  Similarity=1.046  Sum_probs=59.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598         99 GGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus        99 gG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      ||++|++.|++++..|.+++++||.+++|||++.|..+|+|..+++||+|+|+|+||++..++
T Consensus         1 GGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~egiC~~~~vPSvSsInRilR~~~~~~   63 (65)
T d6paxa2           1 GGSKPRVATPEVVSKIAQYKQECPSIFAWEIRDRLLSEGVCTNDNIPSVSSINRVLRNLASEK   63 (65)
T ss_dssp             SCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTCCCHHHHHHHHHHHHHHT
T ss_pred             CCCCcCcCCHHHHHHHHHHHHhCCccchHHHHHHHHHcCCCCCCCCCchHHHHHHHHHhhhhh
Confidence            578999999999999999999999999999999999999999999999999999999876654

>d1k78a2 a.4.1.5 (A:82-142) 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=99.50  E-value=3e-14  Score=100.91  Aligned_cols=60  Identities=67%  Similarity=1.099  Sum_probs=57.3

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598         98 IGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus        98 rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      .||++|++.|++++..|.+++++||.+++|||++.|.++|+|..+++||.|+|+|+||++
T Consensus         2 IGGSKPrvaTP~V~~kI~~yK~enP~iFaWEIRd~Li~egiC~~~nvPSvSsInRilR~k   61 (61)
T d1k78a2           2 IGGSKPKVATPKVVEKIAEYKRQNPTMFAWEIRDRLLAERVCDNDTVPSVSSINRIIRTK   61 (61)
T ss_dssp             CCCCCCSSSCHHHHHHHHHHHHHCTTCCHHHHHHHHHHTTSSCTTTSCCHHHHHHHHHCC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHhcCCcccHHHHHHHHHHcCCCCCCCCCchHHHHHHhhcC
Confidence            478899999999999999999999999999999999999999999999999999999963

>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=98.86  E-value=2e-09  Score=80.10  Aligned_cols=70  Identities=14%  Similarity=0.260  Sum_probs=53.1

Q ss_pred             CCCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy15598         46 RPLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD  121 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n  121 (258)
                      +.||.++|.++|.++.  +|.|.++||+.||||.+||++|+++|++.|.....     .+. ......+.|.++.++|
T Consensus         4 k~Ys~EfK~~aV~l~~~~~g~s~~~vA~~lGIs~~tl~~W~k~~~~~~~~~~~-----~~~-~~~~~~~ei~~L~~En   75 (89)
T d2jn6a1           4 KTYSEEFKRDAVALYENSDGASLQQIANDLGINRVTLKNWIIKYGSNHNVQGT-----TPS-AAVSEAEQIRQLKKEN   75 (89)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHHTSCHHHHHHHHHHHCCCSTTCSC-----CCC-HHHHTHHHHHHHHHCG
T ss_pred             CCCCHHHHHHHHHHHHHcCCCcHHHHHHHHCCCHHHHHHHHHHHhhcccccCC-----CCC-cchhHHHHHHHHHHHH
Confidence            3699999999999985  48999999999999999999999999876643211     222 2233455677776665

>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=98.33  E-value=3.5e-07  Score=61.14  Aligned_cols=40  Identities=10%  Similarity=0.150  Sum_probs=37.3

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.++.+..+.+..++.+|++.++||+.||||++|||||+
T Consensus         3 ~~~lt~~q~~~a~~l~~~G~s~~~iA~~~gVSr~TiYry~   42 (47)
T d1ijwc_           3 PRAINKHEQEQISRLLEKGHPRQQLAIIFGIGVSTLYRYF   42 (47)
T ss_dssp             CCSSCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHS
T ss_pred             CCcCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHhhC
Confidence            3568999999999999999999999999999999999996

>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=98.17  E-value=1.2e-06  Score=57.45  Aligned_cols=34  Identities=21%  Similarity=0.430  Sum_probs=31.7

Q ss_pred             HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      |.+|..|.++|++..+||++|||+|++|||+++.
T Consensus         8 ~~~V~~L~~~G~gat~IAk~lgI~R~SVYR~L~~   41 (43)
T d1gdta1           8 RDAVLNMWQQGLGASHISKTMNIARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHS
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhh
Confidence            5689999999999999999999999999999874

>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=97.99  E-value=5.9e-06  Score=58.76  Aligned_cols=44  Identities=23%  Similarity=0.365  Sum_probs=39.8

Q ss_pred             CCCCCCHHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         44 NGRPLPNSVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        44 ~gR~~S~dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .-+.|+.+.+.+||..++.|  ++..+||+.|||+++||+.|+++-
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~fGv~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLRKGEIARRFNIPPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcchHHHHHHHhCCChhHHHHHHHHH
Confidence            34579999999999999988  589999999999999999999874

>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=97.11  E-value=0.00036  Score=48.14  Aligned_cols=43  Identities=19%  Similarity=0.343  Sum_probs=37.9

Q ss_pred             HHHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         50 NSVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        50 ~dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      .+.+.+|+.+..++  +|..++|+.||||++||++-++..++.|.
T Consensus         4 ~~~~~~iL~~L~~~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~   48 (63)
T d1biaa1           4 NTVPLKLIALLANGEFHSGEQLGETLGMSRAAINKHIQTLRDWGV   48 (63)
T ss_dssp             CHHHHHHHHHHTTSSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTC
T ss_pred             cHHHHHHHHHHHHCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence            35677899988754  69999999999999999999999999995

>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=97.06  E-value=0.0006  Score=46.82  Aligned_cols=43  Identities=21%  Similarity=0.238  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-++..+-+|++..+||+.||||.+||++.+.|-+.
T Consensus        21 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~~~ra~~   63 (71)
T d1rp3a2          21 KLPEREKLVIQLIFYEELPAKEVAKILETSVSRVSQLKAKALE   63 (71)
T ss_dssp             TSCHHHHHHHHHHHTSCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHHHHhHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            4788888877777889999999999999999999999988753

>d1r1ua_ a.4.5.5 (A:) Metal-sensing transcriptional repressor CzrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Metal-sensing transcriptional repressor CzrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.88  E-value=0.00036  Score=51.73  Aligned_cols=54  Identities=28%  Similarity=0.312  Sum_probs=46.8

Q ss_pred             CCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598         46 RPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG   99 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg   99 (258)
                      +.+++..|.+|+.+..+| +++++||+.||+|++||++-++..++.|-|...+.|
T Consensus        13 kaL~d~~Rl~Il~~L~~~~~~v~el~~~l~~s~~~vS~HL~~L~~~glv~~~r~G   67 (94)
T d1r1ua_          13 KALGDYNRIRIMELLSVSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQG   67 (94)
T ss_dssp             HHTCSHHHHHHHHHHHHCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHhCCHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence            457889999999998654 899999999999999999999999999988655433

>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=96.78  E-value=0.0013  Score=45.23  Aligned_cols=42  Identities=26%  Similarity=0.320  Sum_probs=36.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...|.-++..+-+|++..+||+.+|||.+||...+.|-+.
T Consensus        19 Lp~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~   60 (68)
T d1or7a1          19 LPEDLRMAITLRELDGLSYEEIAAIMDCPVGTVRSRIFRARE   60 (68)
T ss_dssp             SCHHHHHHHHHHHTTCCCHHHHHHHTTSCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            677778777777779999999999999999999999998753

>d1ijwc_ a.4.1.2 (C:) HIN recombinase (DNA-binding domain) {Synthetic}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: HIN recombinase (DNA-binding domain)
species: Synthetic

Probab=96.77  E-value=0.0012  Score=43.37  Aligned_cols=41  Identities=24%  Similarity=0.301  Sum_probs=35.7

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHH
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL  154 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiL  154 (258)
                      ||+++|+++.+.+++++..  ..+..+|+..+   |       ||++||+|.|
T Consensus         2 R~~~lt~~q~~~a~~l~~~--G~s~~~iA~~~---g-------VSr~TiYry~   42 (47)
T d1ijwc_           2 RPRAINKHEQEQISRLLEK--GHPRQQLAIIF---G-------IGVSTLYRYF   42 (47)
T ss_dssp             CCCSSCHHHHHHHHHHHHT--TCCHHHHHHHH---T-------CCHHHHHHHS
T ss_pred             CCCcCCHHHHHHHHHHHHC--CCCHHHHHHHH---C-------cCHHHHHhhC
Confidence            8999999999999999976  46888888877   3       5999999987

>d1r1ta_ a.4.5.5 (A:) SmtB repressor {Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: SmtB repressor
species: Cyanobacteria (Synechococcus), pcc7942 [TaxId: 1129]

Probab=96.68  E-value=0.00051  Score=51.12  Aligned_cols=54  Identities=20%  Similarity=0.249  Sum_probs=46.5

Q ss_pred             CCCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598         46 RPLPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG   99 (258)
Q Consensus        46 R~~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg   99 (258)
                      +.+++..|.+|+.+..+ .+++++||+.||+|++||++-++.-++.|-|...+.|
T Consensus        18 kaL~~p~Rl~Il~~L~~~~~~v~ela~~l~is~stvS~HL~~L~~aglV~~~r~G   72 (98)
T d1r1ta_          18 AVLADPNRLRLLSLLARSELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQG   72 (98)
T ss_dssp             HHHCCHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHhCCHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEC
Confidence            45678899999999865 5899999999999999999999999999988655433

>d2hoea1 a.4.5.63 (A:10-71) N-acetylglucosamine kinase {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: N-acetylglucosamine kinase
species: Thermotoga maritima [TaxId: 2336]

Probab=96.65  E-value=0.00071  Score=46.49  Aligned_cols=38  Identities=16%  Similarity=0.309  Sum_probs=33.2

Q ss_pred             HHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         56 IVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        56 IV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      |+.+.. ..++..|||+.+|+|++||.+.++...+.|.+
T Consensus         4 Il~~i~~~pisr~eLa~~~gls~~TVs~~v~~L~~~GlV   42 (62)
T d2hoea1           4 ILKRIMKSPVSRVELAEELGLTKTTVGEIAKIFLEKGIV   42 (62)
T ss_dssp             SHHHHHHSCBCHHHHHHHHTCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence            455544 56999999999999999999999999999976

>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=96.54  E-value=0.0017  Score=44.31  Aligned_cols=41  Identities=15%  Similarity=0.184  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +....|..|+..++ .|...+++|+.||||++|+++.+++|.
T Consensus        17 l~~~Er~~I~~aL~~~~gn~~~aA~~LGIsR~TL~rkmkky~   58 (60)
T d1umqa_          17 ADRVRWEHIQRIYEMCDRNVSETARRLNMHRRTLQRILAKRS   58 (60)
T ss_dssp             HHHHHHHHHHHHHHHTTSCHHHHHHHHTSCHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHHHHHhcCcHHHHHHHHCCCHHHHHHHHHHcC
Confidence            34457888888876 588999999999999999999999984

>d1z05a1 a.4.5.63 (A:10-80) Transcriptional regulator VC2007 N-terminal domain {Vibrio cholerae [TaxId: 666]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Transcriptional regulator VC2007 N-terminal domain
species: Vibrio cholerae [TaxId: 666]

Probab=96.39  E-value=0.0026  Score=44.02  Aligned_cols=43  Identities=19%  Similarity=0.206  Sum_probs=37.2

Q ss_pred             HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      -+.+|+.++.  .++|..+||+.+|+|++||++.+++..+.|-+.
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~   51 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESELAPASITKITRELIDAHLIH   51 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            3567887764  468999999999999999999999999999763

>d1z6ra1 a.4.5.63 (A:12-81) Mlc protein N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ROK associated domain
domain: Mlc protein N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.39  E-value=0.0031  Score=43.84  Aligned_cols=43  Identities=16%  Similarity=0.204  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         52 VRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        52 lR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      -+.+|+.+...  .+|..+||+.+|+|++||.++++...+.|.+.
T Consensus         6 N~~~Il~~i~~~g~~sr~eLa~~~gLS~~Tvs~iv~~L~~~glv~   50 (70)
T d1z6ra1           6 NAGAVYRLIDQLGPVSRIDLSRLAQLAPASITKIVHEMLEAHLVQ   50 (70)
T ss_dssp             HHHHHHHHHHSSCSCCHHHHHHHTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence            35678888753  48999999999999999999999999999764

>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=96.36  E-value=0.0035  Score=47.50  Aligned_cols=42  Identities=17%  Similarity=0.093  Sum_probs=37.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++...|.-++..+-+|+|..+||..+|||++||+.-+.|-+.
T Consensus        17 Lp~~qR~v~~L~y~~~ls~~EIA~~lgiS~~aV~~~l~RA~~   58 (106)
T d1s7oa_          17 LTDKQMNYIELYYADDYSLAEIADEFGVSRQAVYDNIKRTEK   58 (106)
T ss_dssp             SCHHHHHHHHHHHHTCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence            788888888877889999999999999999999999988753

>d1u2wa1 a.4.5.5 (A:12-119) Cadmium efflux system accessory protein CadC {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: ArsR-like transcriptional regulators
domain: Cadmium efflux system accessory protein CadC
species: Staphylococcus aureus [TaxId: 1280]

Probab=96.34  E-value=0.0014  Score=49.44  Aligned_cols=55  Identities=22%  Similarity=0.238  Sum_probs=44.5

Q ss_pred             CCCCHHHHHHHHHHH-HcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         46 RPLPNSVRMRIVELA-QLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        46 R~~S~dlR~RIV~L~-~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +.+++..|.+|+... ..| +++++||+.||+|.+||++-++..++.|-|...+.|.
T Consensus        26 kaLadp~Rl~Il~~L~~~~~~~v~ela~~l~~s~s~vS~HL~~L~~aGlv~~~r~G~   82 (108)
T d1u2wa1          26 KAIADENRAKITYALCQDEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGK   82 (108)
T ss_dssp             HHHHSHHHHHHHHHHHHSSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----
T ss_pred             HHhCCHHHHHHHHHHHhCCCccHHHHHHHHccChhHHHHHHHHHHHCCeeEEEEECC
Confidence            447788999999765 554 7999999999999999999999999999887665443

>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=96.29  E-value=0.0033  Score=43.29  Aligned_cols=41  Identities=20%  Similarity=0.245  Sum_probs=34.4

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++... .+|+.++.+|++..+||+.|+||.+||...+++-.+
T Consensus         7 LT~rE-~~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   47 (67)
T d1a04a1           7 LTPRE-RDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK   47 (67)
T ss_dssp             SCHHH-HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            34433 468888899999999999999999999999888753

>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=96.23  E-value=0.0037  Score=47.41  Aligned_cols=41  Identities=20%  Similarity=0.132  Sum_probs=36.6

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-++..+-+|+|..+||..+|||++||+.-+.|-+
T Consensus        19 Lpe~QR~vl~L~~~e~ls~~EIA~~lgiS~~aV~~~l~Ra~   59 (106)
T d1xsva_          19 LTNKQRNYLELFYLEDYSLSEIADTFNVSRQAVYDNIRRTG   59 (106)
T ss_dssp             SCHHHHHHHHHHHTSCCCHHHHHHHTTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHHHhCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence            78888877777778999999999999999999999999875

>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=96.19  E-value=0.0043  Score=42.53  Aligned_cols=40  Identities=18%  Similarity=0.167  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +|... .+|+.++.+|++..+||+.|+||.+||...+++-.
T Consensus         5 LT~rE-~~vl~l~~~G~s~~eIA~~L~is~~TV~~~~~~i~   44 (67)
T d1fsea_           5 LTKRE-REVFELLVQDKTTKEIASELFISEKTVRNHISNAM   44 (67)
T ss_dssp             CCHHH-HHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44433 46888888999999999999999999999888865

>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=96.03  E-value=0.005  Score=42.11  Aligned_cols=42  Identities=17%  Similarity=0.222  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHH--cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         51 SVRMRIVELAQ--LG-IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        51 dlR~RIV~L~~--~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      +-+.+|+.+..  .+ ++..++|+.|+||+.||+|-++.-++.|.
T Consensus         7 eR~~~Il~~L~~~~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~   51 (65)
T d1j5ya1           7 ERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGY   51 (65)
T ss_dssp             HHHHHHHHHHHHCSSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence            44567888764  24 79999999999999999999999999885

>d2p4wa1 a.4.5.64 (A:1-194) Transcriptional regulatory protein PF1790 {Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PF1790-like
domain: Transcriptional regulatory protein PF1790
species: Pyrococcus furiosus [TaxId: 2261]

Probab=95.96  E-value=0.0023  Score=52.15  Aligned_cols=47  Identities=32%  Similarity=0.304  Sum_probs=42.1

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +++..|.+|+.+... .++..+||+.||||.+||++-++.-.+.|.|.
T Consensus        12 l~~~~R~~Il~~L~~~~~~~~ela~~l~~s~~~v~~HL~~L~~~Glv~   59 (194)
T d2p4wa1          12 LGNETRRRILFLLTKRPYFVSELSRELGVGQKAVLEHLRILEEAGLIE   59 (194)
T ss_dssp             HHSHHHHHHHHHHHHSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            566789999998865 48999999999999999999999999999764

>d2p5ka1 a.4.5.3 (A:2-64) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus subtilis [TaxId: 1423]

Probab=95.94  E-value=0.0089  Score=41.37  Aligned_cols=49  Identities=18%  Similarity=0.091  Sum_probs=44.1

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ  164 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~  164 (258)
                      ...|.+++.+++--+..||.+.|.+.|+.+     +.+||+|-|+..+..|...
T Consensus         6 q~~I~~li~~~~i~tQ~eL~~~L~~~G~~v-----TQaTlSRDL~eLg~vKv~~   54 (63)
T d2p5ka1           6 HIKIREIITSNEIETQDELVDMLKQDGYKV-----TQATVSRDIKELHLVKVPT   54 (63)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHHTTCCC-----CHHHHHHHHHHHTCEEEEE
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcCCCe-----eHHHHHHHHHHhCCEEeeC
Confidence            568899999999999999999999999986     9999999999999887543

>d1ub9a_ a.4.5.28 (A:) Hypothetical protein PH1061 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Hypothetical protein PH1061
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=95.91  E-value=0.0061  Score=44.17  Aligned_cols=69  Identities=16%  Similarity=0.153  Sum_probs=50.4

Q ss_pred             HHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCC---CCCCHHHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKP---RVTTPKVVSYIKELK  118 (258)
Q Consensus        50 ~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RP---rklT~e~~~~I~~lv  118 (258)
                      ...|.+|+... . ..++.++||+.|+++++||++.+++-.+.|-|.-....+.++   -.+|++-++.+.+++
T Consensus        15 ~p~r~~IL~~L~~~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~~~~~d~r~~~~~LT~~G~~~~~~~~   88 (100)
T d1ub9a_          15 NPVRLGIMIFLLPRRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTYKVIADRPRTVVEITDFGMEEAKRFL   88 (100)
T ss_dssp             SHHHHHHHHHHHHHSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEECSSSCEEEEEECHHHHHHHHHHH
T ss_pred             CHHHHHHHHHhccCCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEEEcCcCCccccccCCHHHHHHHHHHH
Confidence            35678888876 3 458999999999999999999999999999875332222233   237777666555543

>d2cfxa1 a.4.5.32 (A:1-63) Transcriptional regulator LrpC {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Transcriptional regulator LrpC
species: Bacillus subtilis [TaxId: 1423]

Probab=95.89  E-value=0.0083  Score=40.88  Aligned_cols=42  Identities=17%  Similarity=0.328  Sum_probs=36.0

Q ss_pred             HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +-.+|+...+ ++ .+.++||+.+|+|.+||++=+++.++.|.+
T Consensus         6 ~D~~IL~~L~~n~r~s~~~iA~~lgis~~tv~~Ri~~L~~~giI   49 (63)
T d2cfxa1           6 IDLNIIEELKKDSRLSMRELGRKIKLSPPSVTERVRQLESFGII   49 (63)
T ss_dssp             HHHHHHHHHHHCSCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSE
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            3456777765 44 899999999999999999999999999976

>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=95.84  E-value=0.0073  Score=41.19  Aligned_cols=40  Identities=15%  Similarity=0.035  Sum_probs=33.7

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      +|... .+|+.++.+|++.++||+.|+||.+||...+++-.
T Consensus         5 Lt~rE-~~vl~l~~~G~s~~eIA~~l~iS~~TV~~~~~~i~   44 (65)
T d1l3la1           5 LDPKE-ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM   44 (65)
T ss_dssp             CCHHH-HHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCHHH-HHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            44433 46888888999999999999999999999888865

>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=95.84  E-value=0.012  Score=40.19  Aligned_cols=47  Identities=21%  Similarity=0.251  Sum_probs=35.5

Q ss_pred             HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      ..|..+.+  ...+..+||+.||||++||..-++|..+.|-+.-.+.+|
T Consensus        10 k~I~~l~~~~~~v~~~~iA~~L~vs~~SVs~mikrL~~~GlV~~~~Y~~   58 (61)
T d2ev0a1          10 EQIYMLIEEKGYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEKYRG   58 (61)
T ss_dssp             HHHHHHHHHHSSCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC----C
T ss_pred             HHHHHHHhcCCCccHHHHHHHhCCCchhHHHHHHHHHHCCCEEEccCCC
Confidence            44555543  347999999999999999999999999999886555443

>d1b4aa1 a.4.5.3 (A:4-78) Arginine repressor (ArgR), N-terminal DNA-binding domain {Bacillus stearothermophilus [TaxId: 1422]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Bacillus stearothermophilus [TaxId: 1422]

Probab=95.78  E-value=0.0097  Score=42.53  Aligned_cols=49  Identities=18%  Similarity=0.106  Sum_probs=44.7

Q ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598        111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ  164 (258)
Q Consensus       111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~  164 (258)
                      ...|.+++.+++--+..||.+.|.+.|+.+     +.+||+|-|+..+..|...
T Consensus         4 ~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-----TQaTlSRDL~eLg~vKv~~   52 (75)
T d1b4aa1           4 HIKIREIIMSNDIETQDELVDRLREAGFNV-----TQATVSRDIKEMQLVKVPM   52 (75)
T ss_dssp             HHHHHHHHHHSCCCSHHHHHHHHHHTTCCC-----CHHHHHHHHHHTTCEEEEC
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHHHHcCCce-----eHHHHHHHHHHhCCEEeeC
Confidence            568999999999999999999999999986     9999999999999998653

>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=95.73  E-value=0.012  Score=40.10  Aligned_cols=42  Identities=14%  Similarity=0.082  Sum_probs=35.2

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ....-.|.-|..+++..-+.+++|+.||||++|+++-+++|.
T Consensus        17 ~~~~~Er~~I~~aL~~~gn~~~aA~~Lgisr~tL~rKlkk~g   58 (61)
T d1g2ha_          17 IIGFYEAQVLKLFYAEYPSTRKLAQRLGVSHTAIANKLKQYG   58 (61)
T ss_dssp             SCSHHHHHHHHHHHHHSCSHHHHHHHTTSCTHHHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence            466778888888876534788999999999999999999983

>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=95.68  E-value=0.0072  Score=41.94  Aligned_cols=41  Identities=15%  Similarity=0.174  Sum_probs=33.9

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ++.-. .+|+.++.+|++..+||..|+||.+||...+++-.+
T Consensus        13 LT~rE-~~vl~~l~~G~s~~eIA~~l~iS~~TV~~~~~~i~~   53 (70)
T d1yioa1          13 LTGRE-QQVLQLTIRGLMNKQIAGELGIAEVTVKVHRHNIMQ   53 (70)
T ss_dssp             SCHHH-HHHHHHHTTTCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             CCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence            44433 367778889999999999999999999999988763

>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=95.65  E-value=0.015  Score=39.02  Aligned_cols=42  Identities=19%  Similarity=0.363  Sum_probs=36.2

Q ss_pred             HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +-.+|+.+.+ ++ .+..+||+.+|+|.+||++=+++..+.|.+
T Consensus         4 ~D~~Il~~L~~n~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI   47 (60)
T d2cyya1           4 IDKKIIKILQNDGKAPLREISKITGLAESTIHERIRKLRESGVI   47 (60)
T ss_dssp             HHHHHHHHHHHCTTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            3457788776 33 799999999999999999999999999976

>d1aoya_ a.4.5.3 (A:) Arginine repressor (ArgR), 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: Arginine repressor (ArgR), N-terminal DNA-binding domain
domain: Arginine repressor (ArgR), N-terminal DNA-binding domain
species: Escherichia coli [TaxId: 562]

Probab=95.60  E-value=0.0093  Score=42.95  Aligned_cols=52  Identities=21%  Similarity=0.123  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH  165 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~  165 (258)
                      ..+.|.+++.+++--+..||.+.|.+.|+..    ++.+||+|-|+..+..|....
T Consensus        10 ~l~~I~~li~~~~i~tQ~eL~~~L~~~G~~~----vTQaTiSRDL~eLg~vKv~~~   61 (78)
T d1aoya_          10 LVKAFKALLKEEKFSSQGEIVAALQEQGFDN----INQSKVSRMLTKFGAVRTRNA   61 (78)
T ss_dssp             HHHHHHHHHHTCCCCSHHHHHHHHHHHTCSS----CCHHHHHHHHHHHTCEEEECT
T ss_pred             HHHHHHHHHHhCCcCCHHHHHHHHHHcCCcc----hhHHHHHHHHHHhCCEEeeCC
Confidence            4578899999999999999999999999952    399999999999999987654

>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=95.45  E-value=0.015  Score=39.16  Aligned_cols=40  Identities=25%  Similarity=0.313  Sum_probs=35.1

Q ss_pred             HHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         54 MRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        54 ~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      .+|+.+.+ ++ .+..+||+++|+|.+||++=+++..+.|.+
T Consensus         6 ~kIl~~L~~n~r~s~~~lA~~~gls~~~v~~Ri~~L~~~giI   47 (60)
T d1i1ga1           6 KIILEILEKDARTPFTEIAKKLGISETAVRKRVKALEEKGII   47 (60)
T ss_dssp             HHHHHHHHHCTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSS
T ss_pred             HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            46777765 44 799999999999999999999999999976

>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=95.34  E-value=0.018  Score=39.02  Aligned_cols=41  Identities=17%  Similarity=0.215  Sum_probs=35.4

Q ss_pred             HHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         53 RMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        53 R~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      =.+|+...+ + .++..+||+.+|+|.+||++=+++.++.|.+
T Consensus         7 D~~IL~~L~~~~r~s~~eiA~~l~ls~~~v~~Ri~rL~~~GiI   49 (63)
T d2cg4a1           7 DRGILEALMGNARTAYAELAKQFGVSPETIHVRVEKMKQAGII   49 (63)
T ss_dssp             HHHHHHHHHHCTTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence            346777765 4 4899999999999999999999999999975

>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=95.31  E-value=0.011  Score=39.78  Aligned_cols=34  Identities=15%  Similarity=0.205  Sum_probs=28.7

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +..+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         4 i~~rlr~~R~~~gltq~~lA~~~gvs~~ti~~~E~   38 (65)
T d2croa_           4 LSERLKKRRIALKMTQTELATKAGVKQQSIQLIEA   38 (65)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCcCHhHHHHHHC
Confidence            4566777764 699999999999999999999953

>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=95.26  E-value=0.01  Score=40.10  Aligned_cols=25  Identities=12%  Similarity=0.195  Sum_probs=22.8

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|+|..++|+.+|||++||++|-+
T Consensus        10 ~~gltQ~elA~~lGvs~~tvs~~E~   34 (62)
T d2ppxa1          10 ALKLTQEEFSARYHIPLGTLRDWEQ   34 (62)
T ss_dssp             HTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence            4799999999999999999999854

>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=95.26  E-value=0.028  Score=38.48  Aligned_cols=44  Identities=23%  Similarity=0.264  Sum_probs=36.0

Q ss_pred             HHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598         54 MRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGA   97 (258)
Q Consensus        54 ~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~   97 (258)
                      ..|..+.+++  .+..+||+.||||++||.+-++|..+.|-+.-.+
T Consensus        12 ~~I~~L~~~~~~v~~~~iA~~L~vs~~SVt~mvkrL~~~Glv~~~~   57 (63)
T d2isya1          12 RTIYDLEEEGVTPLRARIAERLDQSGPTVSQTVSRMERDGLLRVAG   57 (63)
T ss_dssp             HHHHHHHHTTCCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECT
T ss_pred             HHHHHHHhcCCCCcHHHHHHHhCCCchhHHHHHHHHHHCCCEEEcC
Confidence            4455555543  7999999999999999999999999999875443

>d3bwga1 a.4.5.6 (A:5-82) Transcriptional regulator YydK {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional regulator YydK
species: Bacillus subtilis [TaxId: 1423]

Probab=95.20  E-value=0.015  Score=40.83  Aligned_cols=51  Identities=24%  Similarity=0.281  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHH-HcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         50 NSVRMRIVELA-QLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        50 ~dlR~RIV~L~-~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .+++..|+.-. ..|  + +.+++|+.|+||+.||++-+++..+.|.+...++.|
T Consensus         5 ~~i~~~I~~g~l~~G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   59 (78)
T d3bwga1           5 TEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSG   59 (78)
T ss_dssp             HHHHHHHHHTTCCTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHHcCCCCCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCcE
Confidence            34555555542 334  4 889999999999999999999999999886655444

>d1ulya_ a.4.5.58 (A:) Hypothetical protein PH1932 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Hypothetical protein PH1932
domain: Hypothetical protein PH1932
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.20  E-value=0.0063  Score=48.82  Aligned_cols=47  Identities=15%  Similarity=0.244  Sum_probs=42.1

Q ss_pred             CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         48 LPNSVRMRIVELAQL-GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +++..|.+|+.+..+ .++..+||+.+|+|++||++-++.-.+.|-|.
T Consensus        16 l~~p~R~~Il~~L~~~~~s~~ela~~lg~s~~~v~~hl~~L~~~glv~   63 (190)
T d1ulya_          16 MLEDTRRKILKLLRNKEMTISQLSEILGKTPQTIYHHIEKLKEAGLVE   63 (190)
T ss_dssp             HHSHHHHHHHHHHTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             hCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence            556789999999865 48999999999999999999999999999763

>d1qpza1 a.35.1.5 (A:2-58) Purine repressor (PurR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Purine repressor (PurR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.18  E-value=0.018  Score=38.99  Aligned_cols=40  Identities=13%  Similarity=0.161  Sum_probs=32.2

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      +.++||+..|||.+||+|.++..               + ..+++.+++|.+..++
T Consensus         2 Ti~dvA~~agVS~sTVSr~ln~~---------------~-~vs~~tr~rV~~~a~~   41 (57)
T d1qpza1           2 TIKDVAKRANVSTTTVSHVINKT---------------R-FVAEETRNAVWAAIKE   41 (57)
T ss_dssp             CHHHHHHHHTSCHHHHHHHHHTC---------------S-CCCHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCcCHHHHHHHHCCC---------------C-ccCHHHHHHHHHHHHH
Confidence            67899999999999999999752               1 2567888888887765

>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=95.05  E-value=0.018  Score=38.88  Aligned_cols=41  Identities=22%  Similarity=0.353  Sum_probs=33.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+..+||+..|||.+||+|.++..               + ..+++.+++|.+..++
T Consensus         2 vTi~dvA~~agvS~~TVSr~Ln~~---------------~-~Vs~~tr~rV~~aa~~   42 (57)
T d2hsga1           2 VTIYDVAREASVSMATVSRVVNGN---------------P-NVKPSTRKKVLETIER   42 (57)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHTTC---------------T-TSCHHHHHHHHHHHHH
T ss_pred             cCHHHHHHHHCcCHHHHHHHhCCC---------------C-cCCHHHHHHHHHHHHH
Confidence            578999999999999999998641               1 2578888888887665

>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=95.03  E-value=0.033  Score=42.07  Aligned_cols=67  Identities=15%  Similarity=0.154  Sum_probs=47.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL  134 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~  134 (258)
                      |.+.++|+.+|||.+||+-|-    +.|.+.|..+..+.-|..++++...|..... ..-.+++.+|++.+.
T Consensus         1 m~Ige~A~~~gvs~~TlR~Ye----~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~   68 (127)
T d1q06a_           1 MNISDVAKITGLTSKAIRFYE----EKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN   68 (127)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHH----HTTCSCCCEECTTSCEECCHHHHHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred             CCHHHHHHHHCcCHHHHHHHH----HcCCCCCCccCCcCcccchHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence            578999999999999986654    4577776544322567888887766655433 233788999987765

>d1uxda_ a.35.1.5 (A:) Fructose repressor (FruR), N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: GalR/LacI-like bacterial regulator
domain: Fructose repressor (FruR), N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=95.01  E-value=0.0078  Score=41.01  Aligned_cols=24  Identities=21%  Similarity=0.220  Sum_probs=21.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      ++.++||+..|||.+||++.++..
T Consensus         1 vTl~diA~~agvS~sTVSrvLn~~   24 (59)
T d1uxda_           1 MKLDEIARLAGVSRTTASYVINGK   24 (59)
T ss_dssp             CCHHHHHHHHTSCTTHHHHHHHTC
T ss_pred             CCHHHHHHHHCcCHHHHHHHHcCC
Confidence            478999999999999999999864

>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=95.01  E-value=0.011  Score=40.47  Aligned_cols=31  Identities=23%  Similarity=0.273  Sum_probs=29.2

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.
T Consensus        30 lt~~~lA~~~G~sRetvsr~L~~l~~~glI~   60 (69)
T d1i5za1          30 ITRQEIGQIVGCSRETVGRILKMLEDQNLIS   60 (69)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            6899999999999999999999999999774

>d2d1ha1 a.4.5.50 (A:1-109) Hypothetical transcriptional regulator ST1889 {Sulfolobus tokodaii [TaxId: 111955]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical transcriptional regulator ST1889
species: Sulfolobus tokodaii [TaxId: 111955]

Probab=94.91  E-value=0.0083  Score=44.18  Aligned_cols=40  Identities=15%  Similarity=0.284  Sum_probs=33.4

Q ss_pred             HHHH-HHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         55 RIVE-LAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        55 RIV~-L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      .|+. +++ .| ++..+||+.++++++||++.+++..+.|-|.
T Consensus        25 ~iL~~L~~~~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~   67 (109)
T d2d1ha1          25 AVLLKMVEIEKPITSEELADIFKLSKTTVENSLKKLIELGLVV   67 (109)
T ss_dssp             HHHHHHHHHCSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHcCCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEE
Confidence            3443 444 45 8999999999999999999999999999763

>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=94.90  E-value=0.02  Score=41.63  Aligned_cols=40  Identities=13%  Similarity=0.126  Sum_probs=33.0

Q ss_pred             CHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         49 PNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        49 S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..-.|..|..+.+ .+-...++|+.|||||+|+++.+++|.
T Consensus        47 ~e~E~~~i~~aL~~~~gn~~~aA~~LGisR~tL~~klk~~g   87 (89)
T d1etxa_          47 AEVEQPLLDMVMQYTRGNATRAALMMGINRGTLRKKLKKYG   87 (89)
T ss_dssp             HHHHHHHHHHHHHHTTTCHHHHHHHHTSCHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHcCCcHHHHHHHHCCCHHHHHHHHHHhC
Confidence            3446666777665 578899999999999999999999984

>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=94.88  E-value=0.019  Score=41.25  Aligned_cols=41  Identities=17%  Similarity=0.149  Sum_probs=34.8

Q ss_pred             CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|...+ +|+.++.+|++..+||+.|+||.+||...+++-.
T Consensus        22 ~LT~rE~-~vl~ll~~G~s~~eIA~~l~iS~~TV~~~~~~i~   62 (87)
T d1p4wa_          22 RLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM   62 (87)
T ss_dssp             SCCHHHH-HHHHHHHHTCCHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred             CCCHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence            4666554 6888888999999999999999999998888765

>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=94.82  E-value=0.037  Score=38.51  Aligned_cols=42  Identities=17%  Similarity=0.281  Sum_probs=36.1

Q ss_pred             HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+|++.+.   .+++.++||+.+|++++||+|+++...+.|-+.-
T Consensus         8 l~IL~~~a~~~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~   52 (75)
T d1mkma1           8 FEILDFIVKNPGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLR   52 (75)
T ss_dssp             HHHHHHHHHCSSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHhCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            45777653   3689999999999999999999999999998753

>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=94.81  E-value=0.038  Score=40.60  Aligned_cols=68  Identities=15%  Similarity=0.106  Sum_probs=48.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS  135 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~  135 (258)
                      +++.++|+.+|||.+||+-|-    +.|.+.|..+..+.-|..++++...|..... .+-.+++.+|++.|..
T Consensus         3 ytI~e~A~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~   71 (109)
T d1r8da_           3 YQVKQVAEISGVSIRTLHHYD----NIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDH   71 (109)
T ss_dssp             BCHHHHHHHHSCCHHHHHHHH----HTTSSCCSEECTTCCEEBCHHHHHHHHHHHHHHHTTCCHHHHHHHHHC
T ss_pred             ccHHHHHHHHCcCHHHHHHHH----HcCCcCCcccCCcccccccHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence            578999999999999987665    4577776555322457888877665544433 2347899999888753

>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=94.74  E-value=0.018  Score=40.29  Aligned_cols=34  Identities=18%  Similarity=0.133  Sum_probs=30.6

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPG   96 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk   96 (258)
                      .++..+||..+|+|+.||+|.++++++.|-++-.
T Consensus        30 ~~t~~eiA~~lG~sretvsr~l~~l~~~g~I~~~   63 (80)
T d1ft9a1          30 DFTVEEIANLIGSSRQTTSTALNSLIKEGYISRQ   63 (80)
T ss_dssp             CCCHHHHHHHHCSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEC
Confidence            3689999999999999999999999999988543

>d1hw1a1 a.4.5.6 (A:5-78) Fatty acid responsive transcription factor FadR, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Fatty acid responsive transcription factor FadR, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.69  E-value=0.018  Score=40.38  Aligned_cols=36  Identities=14%  Similarity=0.151  Sum_probs=31.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      +.+++|+.|+||+.||.+-+++-.+.|-|.-.++.|
T Consensus        29 s~~eLa~~~~vSr~tvr~Al~~L~~~G~i~~~~g~G   64 (74)
T d1hw1a1          29 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP   64 (74)
T ss_dssp             CHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTEE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEeCce
Confidence            789999999999999999999999999886554433

>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=94.64  E-value=0.02  Score=39.85  Aligned_cols=29  Identities=14%  Similarity=0.075  Sum_probs=24.5

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRw   83 (258)
                      ++.++. +.|+|..++|+.||||+.||++|
T Consensus         5 ~~k~~R~~~gltQ~elA~~LGvs~~ti~~y   34 (67)
T d2auwa1           5 MFGDWMHRNNLSLTTAAEALGISRRMVSYY   34 (67)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTSCHHHHHHH
T ss_pred             HHHHHHHHcCCCHHHHHHHhCCCHHHHHHH
Confidence            444454 47999999999999999999998

>d2oa4a1 a.4.12.3 (A:1-93) Uncharacterized protein SPO1678 {Silicibacter pomeroyi [TaxId: 89184]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: SPO1678-like
domain: Uncharacterized protein SPO1678
species: Silicibacter pomeroyi [TaxId: 89184]

Probab=94.63  E-value=0.038  Score=40.96  Aligned_cols=50  Identities=18%  Similarity=0.214  Sum_probs=45.6

Q ss_pred             cCCCCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598         43 VNGRPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS   92 (258)
Q Consensus        43 ~~gR~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs   92 (258)
                      .+.+..+...+.+||.....| .|..|+++++++|..-+++|.+.+.+.|.
T Consensus        29 ~~trRWva~RKaaVV~av~~Gl~S~~EAcrrY~LS~eEf~~W~~a~~~hGe   79 (93)
T d2oa4a1          29 ANTRRWVASRKIAVVRGVIYGLITLAEAKQTYGLSDEEFNSWVSALAEHGK   79 (93)
T ss_dssp             SCCSCCCHHHHHHHHHHHHHTTCCHHHHHHTTCSSHHHHHHHHHHHHCCCS
T ss_pred             cccccccHHHHHHHHHHHHcCcCCHHHHHHHhCCCHHHHHHHHHHHHHHhH
Confidence            366789999999999999988 69999999999999999999999998775

>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=94.60  E-value=0.012  Score=43.57  Aligned_cols=34  Identities=26%  Similarity=0.346  Sum_probs=31.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ..+.+..+||+.+||+++||++.+++-.+.|-|.
T Consensus        32 ~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~   65 (109)
T d1sfxa_          32 RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVR   65 (109)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             cCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEE
Confidence            3569999999999999999999999999999874

>d1jhga_ a.4.12.1 (A:) Trp repressor, TrpR {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: TrpR-like
family: Trp repressor, TrpR
domain: Trp repressor, TrpR
species: Escherichia coli [TaxId: 562]

Probab=94.57  E-value=0.025  Score=42.58  Aligned_cols=38  Identities=16%  Similarity=0.269  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ..|.+|+.+...| ++.++|++.+|||..||.|.-+-.+
T Consensus        45 a~R~~ia~~L~~G~~s~reI~~~~gvs~aTItR~s~~Lk   83 (101)
T d1jhga_          45 GTRVRIIEELLRGEMSQRELKNELGAGIATITRGSNSLK   83 (101)
T ss_dssp             HHHHHHHHHHHHCCSCHHHHHHHHCCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHhCCChHHHHHHHHHHH
Confidence            5788999988888 8999999999999999998766554

>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=94.42  E-value=0.022  Score=39.59  Aligned_cols=31  Identities=3%  Similarity=0.100  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|.+.
T Consensus        30 lt~~eLA~~~G~sretvsr~L~~l~~~glI~   60 (81)
T d2gaua1          30 LSREELATLSNMTVSNAIRTLSTFVSERMLA   60 (81)
T ss_dssp             CCHHHHHHHTTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5889999999999999999999999999874

>d2hs5a1 a.4.5.6 (A:25-93) Putative transcriptional regulator RHA1_ro03477 {Rhodococcus sp. RHA1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Putative transcriptional regulator RHA1 ro03477
species: Rhodococcus sp. RHA1 [TaxId: 101510]

Probab=94.38  E-value=0.028  Score=38.58  Aligned_cols=50  Identities=22%  Similarity=0.219  Sum_probs=38.0

Q ss_pred             HHHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         51 SVRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        51 dlR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      .++.+|+.-. ..|  ++.+++|+.||||+.||.+-+++..+.|-+.-.++.|
T Consensus        10 ~l~~~I~~g~~~~G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~~G   62 (69)
T d2hs5a1          10 ILRDAIIDGTFRPGARLSEPDICAALDVSRNTVREAFQILIEDRLVAHELNRG   62 (69)
T ss_dssp             HHHHHHHHTSSCTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTE
T ss_pred             HHHHHHHcCCCCCcCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcCCE
Confidence            4555555542 234  4889999999999999999999999999886555444

>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=94.38  E-value=0.055  Score=37.57  Aligned_cols=46  Identities=33%  Similarity=0.331  Sum_probs=39.5

Q ss_pred             CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598        102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      +.+.+|-++...|.++++.+|.+...||+..+   |       ++.|||+.+|++.
T Consensus         4 kRk~LT~~eK~~ii~~~e~g~k~sq~eIA~~f---G-------v~~STvs~IlKnK   49 (66)
T d1hlva1           4 KRRQLTFREKSRIIQEVEENPDLRKGEIARRF---N-------IPPSTLSTILKNK   49 (66)
T ss_dssp             SSCCCCHHHHHHHHHHHHHCTTSCHHHHHHHH---T-------CCHHHHHHHHHTH
T ss_pred             ccccCCHHHHHHHHHHHHcCCcchHHHHHHHh---C-------CChhHHHHHHHHH
Confidence            45679999999999999999999988887766   4       4899999999974

>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=94.37  E-value=0.016  Score=38.91  Aligned_cols=34  Identities=24%  Similarity=0.265  Sum_probs=28.2

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +-.+|-.+.+ .|++..++|+.+|||++||++|.+
T Consensus         4 ig~rik~~R~~~g~tq~~lA~~~gvs~~~i~~~e~   38 (66)
T d2r1jl1           4 MGERIRARRKKLKIRQAALGKMVGVSNVAISQWER   38 (66)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            3456666654 799999999999999999999975

>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=94.36  E-value=0.021  Score=39.76  Aligned_cols=31  Identities=26%  Similarity=0.323  Sum_probs=29.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||+|.++++++.|-+.
T Consensus        28 lt~~elA~~lg~sr~tvsr~l~~l~~~g~I~   58 (73)
T d1zyba1          28 VKMDDLARCLDDTRLNISKTLNELQDNGLIE   58 (73)
T ss_dssp             CCHHHHHHHHTSCHHHHHHHHHHHHHTTSCE
T ss_pred             cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence            5889999999999999999999999999874

>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=94.32  E-value=0.02  Score=39.94  Aligned_cols=31  Identities=23%  Similarity=0.238  Sum_probs=29.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ++..+||..+|+|+.||.|.++++++.|-+.
T Consensus        31 lt~~elA~~~g~sretvsr~l~~l~~~glI~   61 (80)
T d3e5ua1          31 LSQKSIGEITGVHHVTVSRVLASLKRENILD   61 (80)
T ss_dssp             CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence            4889999999999999999999999999875

>d1rr7a_ a.4.1.14 (A:) Middle operon regulator, Mor {Bacteriophage Mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Middle operon regulator, Mor
domain: Middle operon regulator, Mor
species: Bacteriophage Mu [TaxId: 10677]

Probab=94.29  E-value=0.017  Score=42.57  Aligned_cols=53  Identities=21%  Similarity=0.277  Sum_probs=39.7

Q ss_pred             ccCC---cccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         37 QLGG---VFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        37 q~~~---~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      ..||   -++++..+....|.+-|..--+|.+..++|+.+++|..+|++++++-+.
T Consensus        37 ~~gG~~lYiP~~~~~~~~~Rn~~I~~ef~G~n~~eLA~kY~lS~~~I~~Ii~~~rk   92 (94)
T d1rr7a_          37 HLGGGQVYIPRGQALDSLIRDLRIWNDFNGRNVSELTTRYGVTFNTVYKAIRRMRR   92 (94)
T ss_dssp             HHCSSCCCCCCSHHHHHHHHHHHHHHHCCSSCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHCCeeEeeeccHHHHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHc
Confidence            3566   2335555556677555554448999999999999999999999998763

>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=94.21  E-value=0.31  Score=36.48  Aligned_cols=88  Identities=16%  Similarity=0.244  Sum_probs=54.8

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCCC-CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGGS-KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDG  137 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG~-RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~G  137 (258)
                      ..+.+.++||+.++++++||++.+++..+.|-|.  +.+..++ ..-.+|++-++.+.+....    ....+.+.+. .+
T Consensus        46 ~~~~t~~ela~~~~i~~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~----~~~~~~~~~~-~~  120 (138)
T d1jgsa_          46 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTGGAAICEQCHQL----VGQDLHQELT-KN  120 (138)
T ss_dssp             HSSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECTTCSSCEEEEECHHHHHHHHHHHHH----HHHHHHHHHH-TT
T ss_pred             CcCCCHHHHHHHHCCCHhHHHHHHHHHhhCCCEEEeeccCCCCeeEEEECHHHHHHHHHHHHH----HHHHHHHHHH-cC
Confidence            4689999999999999999999999999999874  3333331 2234777766655544321    0122333332 22


Q ss_pred             CCCCCCCCCHHHHHHHHHhc
Q psy15598        138 VCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       138 v~v~~~~pS~STI~RiLrr~  157 (258)
                      ++.    =-..++.++|++.
T Consensus       121 l~~----~e~~~l~~~L~kl  136 (138)
T d1jgsa_         121 LTA----DEVATLEYLLKKV  136 (138)
T ss_dssp             TTT----TCHHHHHHHHHTT
T ss_pred             CCH----HHHHHHHHHHHhh
Confidence            221    1456777777654

>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=94.07  E-value=0.04  Score=37.53  Aligned_cols=35  Identities=17%  Similarity=0.246  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++-.+|..+.+ .|++..++|+.+||++++|++|.+
T Consensus         6 ~l~~~i~~~r~~~gltq~elA~~~gv~~~~is~ie~   41 (69)
T d2a6ca1           6 QLLIVLQEHLRNSGLTQFKAAELLGVTQPRVSDLMR   41 (69)
T ss_dssp             HHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHcCHhHHHHHHc
Confidence            45566777765 699999999999999999999975

>d3ctaa1 a.4.5.28 (A:5-89) Ta1064 (RFK), N-terminal domain {Thermoplasma acidophilum [TaxId: 2303]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Ta1064 (RFK), N-terminal domain
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=93.97  E-value=0.02  Score=40.99  Aligned_cols=55  Identities=15%  Similarity=0.141  Sum_probs=41.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-CCCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      +++.++||+.+++++++|++.+++..+.|-|.- +..|+ .--.+|++=.+.+.+..
T Consensus        21 ~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r-~~D~R~~~i~LT~~G~~~l~~~~   76 (85)
T d3ctaa1          21 YLTSSKLADMLGISQQSASRIIIDLEKNGYITR-TVTKRGQILNITEKGLDVLYTEF   76 (85)
T ss_dssp             ECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE-EEETTEEEEEECHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee-ecccccccceECHHHHHHHHHHH
Confidence            589999999999999999999999999998753 22231 12336777666655544

>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=93.89  E-value=0.041  Score=39.44  Aligned_cols=34  Identities=9%  Similarity=0.137  Sum_probs=28.1

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +=.+|..+.+ .|+|..++|+.+|||++||++|.+
T Consensus        12 l~~~i~~~r~~~gltq~~lA~~~gis~~~is~ie~   46 (89)
T d2o38a1          12 LAYALNAVIDRARLSQAAAAARLGINQPKVSALRN   46 (89)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHHHhhHhHHHHHHc
Confidence            3445666654 699999999999999999999975

>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=93.86  E-value=0.14  Score=36.23  Aligned_cols=66  Identities=9%  Similarity=0.192  Sum_probs=42.8

Q ss_pred             HHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHH
Q psy15598         52 VRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIR  130 (258)
Q Consensus        52 lR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr  130 (258)
                      ++..|..+. +.|++..++|+.+|||+++|++|.     +|.           +..+-.....|.+.+.-++.....++.
T Consensus        13 l~~~i~~~R~~~gltq~~lA~~lgis~~~is~~E-----~g~-----------~~~s~~~l~~ia~~l~v~~~~~~~~~~   76 (87)
T d1lmb3_          13 LKAIYEKKKNELGLSQESVADKMGMGQSGVGALF-----NGI-----------NALNAYNAALLAKILKVSVEEFSPSIA   76 (87)
T ss_dssp             HHHHHHHHHHHHTCCHHHHHHHHTSCHHHHHHHH-----TTS-----------SCCCHHHHHHHHHHHTSCGGGTCHHHH
T ss_pred             HHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHH-----hcc-----------CCCcHHHHHHHHHHHCCCHHHHChhHH
Confidence            333344433 469999999999999999999984     322           223456677777777666654434444


Q ss_pred             HHH
Q psy15598        131 DRL  133 (258)
Q Consensus       131 ~~L  133 (258)
                      +.+
T Consensus        77 ~~~   79 (87)
T d1lmb3_          77 REI   79 (87)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            433

>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=93.85  E-value=0.047  Score=36.98  Aligned_cols=34  Identities=15%  Similarity=0.156  Sum_probs=27.6

Q ss_pred             HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +-.+|-.+.+ .|+|..++|+.+|||+++|++|.+
T Consensus        10 ~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~E~   44 (69)
T d1y7ya1          10 FGQRLRELRTAKGLSQETLAFLSGLDRSYVGGVER   44 (69)
T ss_dssp             HHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHcCCCHHHHHhHhCCCHHHHHHHHC
Confidence            3455666654 799999999999999999999853

>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=93.76  E-value=0.025  Score=38.16  Aligned_cols=30  Identities=17%  Similarity=0.221  Sum_probs=25.3

Q ss_pred             HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         56 IVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      |..+. +.|+|..++|+.+|||+++|++|.+
T Consensus         6 i~~lR~~~g~tq~elA~~~gis~~~is~~e~   36 (66)
T d1utxa_           6 LKLIREKKKISQSELAALLEVSRQTINGIEK   36 (66)
T ss_dssp             HHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHcCCCHHHHHHhcccCHHHHHHHHc
Confidence            44444 5799999999999999999999874

>d1r69a_ a.35.1.2 (A:) 434 C1 repressor, DNA-binding domain {Bacteriophage 434 [TaxId: 10712]}

class: All alpha proteins
fold: lambda repressor-like DNA-binding domains
superfamily: lambda repressor-like DNA-binding domains
family: Phage repressors
domain: 434 C1 repressor, DNA-binding domain
species: Bacteriophage 434 [TaxId: 10712]

Probab=93.73  E-value=0.039  Score=36.59  Aligned_cols=32  Identities=9%  Similarity=0.324  Sum_probs=26.5

Q ss_pred             HHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+.+ .|++..++|+.+|||+++|++|.+
T Consensus         4 ~rik~~R~~~g~sq~elA~~~gvs~~~is~~E~   36 (63)
T d1r69a_           4 SRVKSKRIQLGLNQAELAQKVGTTQQSIEQLEN   36 (63)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCcHHHHHHHhCcCHHHHHHHHC
Confidence            34555554 799999999999999999999864

>d1ku9a_ a.4.5.36 (A:) DNA-binding protein Mj223 {Archaeon Methanococcus jannaschii [TaxId: 2190]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: DNA-binding protein Mj223
domain: DNA-binding protein Mj223
species: Archaeon Methanococcus jannaschii [TaxId: 2190]

Probab=93.72  E-value=0.05  Score=41.18  Aligned_cols=32  Identities=31%  Similarity=0.432  Sum_probs=30.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      +++..+||+.+|||+++|++.+++..+.|.|.
T Consensus        41 plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~   72 (151)
T d1ku9a_          41 PLTISDIMEELKISKGNVSMSLKKLEELGFVR   72 (151)
T ss_dssp             CEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEE
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCEE
Confidence            48999999999999999999999999999875

>d2frha1 a.4.5.28 (A:102-216) Pleiotropic regulator of virulence genes, SarA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Pleiotropic regulator of virulence genes, SarA
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.64  E-value=0.096  Score=38.74  Aligned_cols=55  Identities=13%  Similarity=-0.023  Sum_probs=40.8

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCCC-CCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      ++..+||+.++++++||++.+++..+.|-+.-.+  ..++ .--.+|++-.+.+.++.
T Consensus        50 ~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~  107 (115)
T d2frha1          50 YYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKRNEHDERTVLILVNAQQRKKIESLL  107 (115)
T ss_dssp             EEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBCCSSSSCCCEEECCSHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeeecccCCceEEEEECHHHHHHHHHHH
Confidence            7999999999999999999999999999774322  2221 11237777777666654

>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=93.58  E-value=0.019  Score=39.70  Aligned_cols=35  Identities=6%  Similarity=0.148  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+-.+|-.+.+ .|+|..++|+.+|||+++|++|.+
T Consensus        10 ~~g~~ik~~R~~~gltq~~lA~~~gis~~~i~~~e~   45 (77)
T d2b5aa1          10 KFGRTLKKIRTQKGVSQEELADLAGLHRTYISEVER   45 (77)
T ss_dssp             HHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            34455555554 699999999999999999999864

>d1tc3c_ a.4.1.2 (C:) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase tc3a1-65
species: Caenorhabditis elegans [TaxId: 6239]

Probab=93.57  E-value=0.1  Score=34.22  Aligned_cols=46  Identities=20%  Similarity=0.327  Sum_probs=40.5

Q ss_pred             CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598         45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET   90 (258)
Q Consensus        45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt   90 (258)
                      +.-++.+.|.++-.+..-|.|..++||++.-|+.+|+++++.=.+-
T Consensus         3 ~~~L~~~e~aqlDVm~~L~~slhemaR~i~rSR~~ir~Yl~~Pl~Y   48 (51)
T d1tc3c_           3 GSALSDTERAQLDVMKLLNVSLHEMSRKISRSRHCIRVYLKDPVSY   48 (51)
T ss_dssp             SCCCCHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHHCSTTT
T ss_pred             chhhhHHHHHHHHHHHHhCCcHHHHHHHHHHhHHHHHHHhcChhhc
Confidence            4568999999999999999999999999999999999999864443

>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=93.53  E-value=0.059  Score=37.60  Aligned_cols=39  Identities=13%  Similarity=0.126  Sum_probs=31.8

Q ss_pred             CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ++.++=.+|..+.+ .|+|..++|+.+|||+++|++|-+-
T Consensus         3 ~~~~iG~~I~~~R~~~gltq~~lA~~~gis~~~is~~E~G   42 (78)
T d1x57a1           3 VTLEVGKVIQQGRQSKGLTQKDLATKINEKPQVIADYESG   42 (78)
T ss_dssp             CCCHHHHHHHHHHHTTTCCHHHHHHHHTSCHHHHHHHHHT
T ss_pred             ccHHHHHHHHHHHHHcCCChhHHHHcCCCCHHHHHHHHcc
Confidence            34556667777765 6999999999999999999999653

>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=93.50  E-value=0.075  Score=36.02  Aligned_cols=42  Identities=10%  Similarity=0.006  Sum_probs=33.1

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .++...|.-|...+    .+.++..+||+.||||+..|+.+.++..
T Consensus         8 ~L~~rer~Ii~~ryGl~~~~~~tl~eIa~~lgiS~erVrqi~~~al   53 (61)
T d1ku3a_           8 KLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKAL   53 (61)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHhCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            36666665555555    3568999999999999999999988764

>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=93.44  E-value=0.045  Score=36.88  Aligned_cols=31  Identities=19%  Similarity=0.294  Sum_probs=25.8

Q ss_pred             HHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         55 RIVELA-QLGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        55 RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +|-.+. +.|++..++|+.+|||++||++|.+
T Consensus         5 ~ik~~R~~~gltq~~la~~~gis~~~i~~~E~   36 (68)
T d1b0na2           5 RIKQYRKEKGYSLSELAEKAGVAKSYLSSIER   36 (68)
T ss_dssp             HHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHT
T ss_pred             HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence            344444 4799999999999999999999975

>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=93.39  E-value=0.043  Score=39.34  Aligned_cols=38  Identities=11%  Similarity=0.003  Sum_probs=30.4

Q ss_pred             HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      -.|..|....+ .+-...++|+.|||+|+|+++-+++|.
T Consensus        51 ~E~~lI~~aL~~~~Gn~~~AA~~LGI~R~TL~~Klk~~g   89 (91)
T d1ntca_          51 LERTLLTTALRHTQGHKQEAARLLGWGAATLTAKLKELG   89 (91)
T ss_dssp             HHHHHHHHHHHHTTTCTTHHHHHTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCcHHHHHHHHCCCHHHHHHHHHHHC
Confidence            35555666655 466778999999999999999999984

>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=93.36  E-value=0.066  Score=36.85  Aligned_cols=36  Identities=17%  Similarity=0.117  Sum_probs=28.6

Q ss_pred             HHHHHHHHHHH-----H---cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----Q---LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~---~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|++|++..     .   ++.+.++||+..|||++++|+...
T Consensus         3 ~~tre~Il~aa~~~~~~~G~~~~ti~~Ia~~agvs~~s~y~~F~   46 (79)
T d2fbqa1           3 SETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFG   46 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHHHTC
T ss_pred             hHHHHHHHHHHHHHHHHhCcccccHHHHHHHHCcChhHHHHHCc
Confidence            36778888753     2   357999999999999999988654

>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=93.33  E-value=0.061  Score=36.40  Aligned_cols=36  Identities=14%  Similarity=0.152  Sum_probs=27.9

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++.|.+|++..     +.   +.|.++||+..|||++|+|+...
T Consensus         2 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~Y~~F~   45 (73)
T d1t56a1           2 DDRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFP   45 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHCc
Confidence            35667777754     23   47999999999999999998654

>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=93.23  E-value=0.047  Score=37.05  Aligned_cols=41  Identities=15%  Similarity=0.174  Sum_probs=32.1

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK  120 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~  120 (258)
                      .+..|||+..|||.+||++.++..                ...+++..+.|.+..++
T Consensus         3 ~Ti~diA~~agvS~sTVSr~l~~~----------------~~vs~~tr~rI~~~a~~   43 (59)
T d1efaa1           3 VTLYDVAEYAGVSYQTVSRVVNQA----------------SHVSAKTREKVEAAMAE   43 (59)
T ss_dssp             CCHHHHHHTTTSCHHHHHHHHTTC----------------SSCCTHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHCCC----------------CcCCHHHHHHHHHHHHH
Confidence            578999999999999999988541                12467778888777665

>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=93.16  E-value=0.092  Score=39.71  Aligned_cols=63  Identities=11%  Similarity=0.144  Sum_probs=43.7

Q ss_pred             HHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCC-CCCCCCCHHHHHHHHHH
Q psy15598         55 RIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        55 RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG-~RPrklT~e~~~~I~~l  117 (258)
                      .|+....  .|++.++||+.+++++++|++.+++-.+.|-|.  +.+..+ ...-.+|+.-...+...
T Consensus        40 ~vL~~l~~~~~~t~~~la~~l~~~~~~vsr~l~~L~~~G~v~r~~~~~D~R~~~l~lT~~G~~~~~~~  107 (141)
T d1lnwa_          40 HVLKLIDEQRGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRERNPSDQRSFQLFLTDEGLAIHQHA  107 (141)
T ss_dssp             HHHHHHHSSTTCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEECSSSSSSEEEEECHHHHHHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHHHHHCccHhHHHHHHHHHHHhhceeeeccCCCCcchhhccCHHHHHHHHHH
Confidence            3444443  579999999999999999999999999999774  222222 12235777655555444

>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=93.15  E-value=0.17  Score=37.91  Aligned_cols=57  Identities=14%  Similarity=0.141  Sum_probs=41.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      .+++..+||+.++++++||++.+++..+.|-|.-.  +..+ .+--.+|+.-.+.+.+..
T Consensus        45 ~~~t~~~La~~l~i~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~  104 (140)
T d2etha1          45 GPKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVREMDPVDRRTYRVVLTEKGKEIFGEIL  104 (140)
T ss_dssp             CCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEEECTTTSSCEEEEECHHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeeecccccchhhhhcCHHHHHHHHHHH
Confidence            56999999999999999999999999999987422  2222 122346776665555543

>d1p4xa2 a.4.5.28 (A:126-250) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=93.04  E-value=0.072  Score=40.27  Aligned_cols=58  Identities=7%  Similarity=-0.017  Sum_probs=42.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-CC--CCCCHHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-KP--RVTTPKVVSYIKELKQ  119 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-RP--rklT~e~~~~I~~lv~  119 (258)
                      .|++..+||+.++++++||++.+++..+.|-+.-...... |-  -.+|++-.+.+.++..
T Consensus        48 ~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~~~~~D~R~v~i~LT~~G~~~~~~l~~  108 (125)
T d1p4xa2          48 NIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKERSTEDERKILIHMDDAQQDHAEQLLA  108 (125)
T ss_dssp             CCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEEECSSSTTCEEEECCHHHHHHHHHHHH
T ss_pred             CCccHHHHHHHHCCCcchHHHHHHHHHhccCEeeeecCCCCCeEEEEECHHHHHHHHHHHH
Confidence            3679999999999999999999999999998742221111 22  2477887777766653

>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=92.97  E-value=0.061  Score=38.35  Aligned_cols=26  Identities=15%  Similarity=0.404  Sum_probs=23.7

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.|+|..++|+.+|||++||++|.+-
T Consensus        12 ~~glsq~~LA~~lGvs~~~is~ie~g   37 (87)
T d2icta1          12 ELNVSLREFARAMEIAPSTASRLLTG   37 (87)
T ss_dssp             HHTCCHHHHHHHHTCCHHHHHHHHHT
T ss_pred             HcCCCHHHHHHHHhhcHHHHHHHHHh
Confidence            36999999999999999999999864

>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=92.69  E-value=0.069  Score=36.15  Aligned_cols=35  Identities=14%  Similarity=0.177  Sum_probs=27.0

Q ss_pred             HHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         52 VRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        52 lR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      .|.+|++..     +.   +.|.++||+..|||++|+|+....
T Consensus         2 ~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~~y~~F~~   44 (71)
T d1jt6a1           2 LKDKILGVAKELFIKNGYNATTTGEIVKLSESSKGNLYYHFKT   44 (71)
T ss_dssp             HHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTCCHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHCcC
Confidence            567777643     23   579999999999999999976543

>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=92.61  E-value=0.086  Score=35.42  Aligned_cols=44  Identities=11%  Similarity=-0.052  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      ++.+..|++.+++|++++..||++.+.          +|.+||++.+++...++
T Consensus         4 D~~D~~IL~~L~~~~r~s~~eiA~~l~----------ls~~~v~~Ri~rL~~~G   47 (63)
T d2cg4a1           4 DNLDRGILEALMGNARTAYAELAKQFG----------VSPETIHVRVEKMKQAG   47 (63)
T ss_dssp             CHHHHHHHHHHHHCTTSCHHHHHHHHT----------SCHHHHHHHHHHHHHHT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            456788999999999999999999883          49999999999865543

>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=92.40  E-value=0.074  Score=36.48  Aligned_cols=35  Identities=9%  Similarity=0.199  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+|++..     +.   +.|.++||+..|||++|+|+..
T Consensus         5 ~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~lY~~F   47 (77)
T d2gfna1           5 DERRRALADAVLALIAREGISAVTTRAVAEESGWSTGVLNHYF   47 (77)
T ss_dssp             CHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHSSCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHHCCCHHHHHHHC
Confidence            35677777753     33   4699999999999999999764

>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=92.35  E-value=0.12  Score=34.88  Aligned_cols=37  Identities=14%  Similarity=0.158  Sum_probs=28.6

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.+.|.+|++..     +.   +.+..+||++.|||+++||+...
T Consensus         2 ~~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~   46 (69)
T d2fq4a1           2 NIETQKAILSASYELLLESGFKAVTVDKIAERAKVSKATIYKWWP   46 (69)
T ss_dssp             CHHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             cHHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCC
Confidence            456677777653     23   46999999999999999998654

>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=92.18  E-value=0.082  Score=36.41  Aligned_cols=32  Identities=16%  Similarity=0.164  Sum_probs=26.3

Q ss_pred             HHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         54 MRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        54 ~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+|-.+.+ .|+|..++|+.+|||+++|++|.+
T Consensus        11 ~~lr~~R~~~g~sq~~lA~~~gis~~~i~~~E~   43 (79)
T d1y9qa1          11 NQLKNLRKSRGLSLDATAQLTGVSKAMLGQIER   43 (79)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHSSCHHHHHHHHT
T ss_pred             HHHHHHHHHcCCCHHHHHHHHCcchhHHHHHHc
Confidence            44555543 699999999999999999999864

>d2fxaa1 a.4.5.28 (A:6-167) Protease production regulatory protein Hpr {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Protease production regulatory protein Hpr
species: Bacillus subtilis [TaxId: 1423]

Probab=92.16  E-value=0.18  Score=39.64  Aligned_cols=61  Identities=10%  Similarity=-0.051  Sum_probs=45.4

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHHHhC
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELKQKD  121 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv~~n  121 (258)
                      ..|++..+||+.++++++||++.+++-.+.|-+.-..  ..+ ..--.+|++-.+.+.+.....
T Consensus        53 ~~~~t~~~la~~~~l~~~tvs~~i~rL~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~~~~  116 (162)
T d2fxaa1          53 LNGASISEIAKFGVMHVSTAFNFSKKLEERGYLRFSKRLNDKRNTYVQLTEEGTEVFWSLLEEF  116 (162)
T ss_dssp             HTSEEHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEECC------CEEEECHHHHHHHHHHHHHC
T ss_pred             CCCcCHHHHHHHHcCCchhhHHHHHHHHHCCCceeecccccCeeeeeccCHhHHHHHHHHHHHH
Confidence            4689999999999999999999999999999774222  122 122347888888887776643

>d1v4ra1 a.4.5.6 (A:1-100) Transcriptional repressor TraR, N-terminal domain {Streptomyces sp. [TaxId: 1931]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: GntR-like transcriptional regulators
domain: Transcriptional repressor TraR, N-terminal domain
species: Streptomyces sp. [TaxId: 1931]

Probab=92.04  E-value=0.033  Score=40.93  Aligned_cols=36  Identities=28%  Similarity=0.294  Sum_probs=32.0

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598         65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG  100 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG  100 (258)
                      |.+++|++|+||+.||.+-+++-.+.|-|....+.|
T Consensus        35 s~r~La~~~~vSr~tvr~Al~~L~~~Gli~~~~g~G   70 (100)
T d1v4ra1          35 SVADIRAQFGVAAKTVSRALAVLKSEGLVSSRGALG   70 (100)
T ss_dssp             CHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEETTTE
T ss_pred             cHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEecCCE
Confidence            899999999999999999999999999886555444

>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=91.94  E-value=0.11  Score=35.22  Aligned_cols=36  Identities=28%  Similarity=0.262  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.|   .|..+||+..|||++|+|+...
T Consensus         4 e~tr~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~y~~F~   47 (75)
T d3c07a1           4 EQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFA   47 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSTTCCHHHHHHHHTSCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCc
Confidence            46777887753     234   7999999999999999988643

>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=91.84  E-value=0.072  Score=39.34  Aligned_cols=33  Identities=12%  Similarity=0.264  Sum_probs=29.8

Q ss_pred             CCCHHHHHHHhCCC-HHHHHHHHHHhhhhCCccc
Q psy15598         63 GIRPCDISRQLRVS-HGCVSKILARYHETGSILP   95 (258)
Q Consensus        63 G~S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~p   95 (258)
                      .+|..+||..+|+| |.||+|.++++++.|.|..
T Consensus        31 ~lTqeeLA~~lG~s~ReTVsR~L~~L~~~GlI~~   64 (100)
T d2bgca1          31 NLTMQELGYSSGIAHSSAVSRIISKLKQEKVIVY   64 (100)
T ss_dssp             CCCHHHHHHHTTCCCHHHHHHHHHHHHHTTSEEE
T ss_pred             ccCHHHHHHHhCCchHHHHHHHHHHHHHCCCEEE
Confidence            36899999999997 8999999999999998853

>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=91.83  E-value=0.12  Score=34.71  Aligned_cols=44  Identities=18%  Similarity=0.129  Sum_probs=36.8

Q ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      ++.+..|...+++|+.++..+|++.|.          +|.+||++.+++...++
T Consensus         4 D~~D~~IL~~L~~n~r~s~~~iA~~lg----------is~~tv~~Ri~~L~~~g   47 (63)
T d2cfxa1           4 DQIDLNIIEELKKDSRLSMRELGRKIK----------LSPPSVTERVRQLESFG   47 (63)
T ss_dssp             CHHHHHHHHHHHHCSCCCHHHHHHHHT----------CCHHHHHHHHHHHHHTT
T ss_pred             CHHHHHHHHHHHHcCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            345778888889999999999999883          49999999999876554

>d1s3ja_ a.4.5.28 (A:) Putative transcriptional regulator YusO {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Putative transcriptional regulator YusO
species: Bacillus subtilis [TaxId: 1423]

Probab=91.73  E-value=0.21  Score=37.43  Aligned_cols=57  Identities=12%  Similarity=0.113  Sum_probs=41.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCCC-CCCCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG~-RPrklT~e~~~~I~~l  117 (258)
                      ..|.+..+||+.++++++||.+.+++..+.|-+.  +.+..++ .--.+|++-++.+...
T Consensus        47 ~~~~t~~~la~~~~i~~~~vs~~l~~L~~~glv~r~~~~~D~R~~~v~lT~~G~~~~~~~  106 (143)
T d1s3ja_          47 HGSLKVSEIAERMEVKPSAVTLMADRLEQKNLIARTHNTKDRRVIDLSLTDEGDIKFEEV  106 (143)
T ss_dssp             HSEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHhhhheeeeecCCCCceEEEECHHHHHHHHHH
Confidence            3579999999999999999999999999999874  2222221 1134677656555544

>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=91.71  E-value=0.17  Score=37.96  Aligned_cols=57  Identities=21%  Similarity=0.204  Sum_probs=41.6

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ..|.+.++||+.++++++||++.+++..+.|-+.-..  ..+ ..--.+|+.-.+.+.++
T Consensus        42 ~~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~  101 (139)
T d2a61a1          42 EGPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTPDPADRRAYFLVITRKGEEVIEKV  101 (139)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeeeccCCCCeEEEEECHHHHHHHHHH
Confidence            3579999999999999999999999999999763221  111 12234777666665555

>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=91.68  E-value=0.11  Score=34.91  Aligned_cols=42  Identities=12%  Similarity=-0.039  Sum_probs=34.5

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      .+..|.+++.++..++..||++.|.          +|.+||+|.++.+....
T Consensus         6 ~~~~iL~~L~~~~~~s~~eLa~~l~----------vS~~ti~r~i~~L~~~G   47 (63)
T d1biaa1           6 VPLKLIALLANGEFHSGEQLGETLG----------MSRAAINKHIQTLRDWG   47 (63)
T ss_dssp             HHHHHHHHHTTSSCBCHHHHHHHHT----------SCHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHCCcCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            4567888888888999999999994          59999999998876543

>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=91.66  E-value=0.1  Score=35.34  Aligned_cols=36  Identities=19%  Similarity=0.230  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.+..+||+..|||++|+|++..
T Consensus         4 ~~~r~~il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~y~~F~   47 (71)
T d1ui5a1           4 EQTRATIIGAAADLFDRRGYESTTLSEIVAHAGVTKGALYFHFA   47 (71)
T ss_dssp             TTHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCHhHHHHHCc
Confidence            35677777653     23   57999999999999999988753

>d1i1ga1 a.4.5.32 (A:2-61) LprA {Archaeon Pyrococcus furiosus [TaxId: 2261]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: LprA
species: Archaeon Pyrococcus furiosus [TaxId: 2261]

Probab=91.64  E-value=0.1  Score=34.83  Aligned_cols=43  Identities=19%  Similarity=0.103  Sum_probs=36.3

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +.+..|...+++|+.++..+|++.+.          +|.+||++.+++...+.
T Consensus         3 ~~D~kIl~~L~~n~r~s~~~lA~~~g----------ls~~~v~~Ri~~L~~~g   45 (60)
T d1i1ga1           3 ERDKIILEILEKDARTPFTEIAKKLG----------ISETAVRKRVKALEEKG   45 (60)
T ss_dssp             SHHHHHHHHHHHCTTCCHHHHHHHHT----------SCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            35778899999999999999999884          49999999999876554

>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=91.62  E-value=0.11  Score=35.40  Aligned_cols=36  Identities=17%  Similarity=0.213  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHH-----H---cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----Q---LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~---~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +   ++.|.++||+..|||++|+|+...
T Consensus         3 ~~~r~~Il~aa~~l~~~~G~~~~s~~~Ia~~agvs~~~iY~~F~   46 (74)
T d2g7sa1           3 QSKADDILQCARTLIIRGGYNSFSYADISQVVGIRNASIHHHFP   46 (74)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHCCCHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHHCcCcchHHHHCc
Confidence            35667777653     2   357999999999999999987643

>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=91.54  E-value=0.14  Score=38.28  Aligned_cols=35  Identities=20%  Similarity=0.333  Sum_probs=32.3

Q ss_pred             HHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         60 AQLGIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        60 ~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      ...|++.++||+.++++++||.+.+++..+.|-|.
T Consensus        44 ~~~~~t~~~La~~~~i~~~~vsr~i~~L~~~glv~   78 (137)
T d1z91a1          44 EHETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLIT   78 (137)
T ss_dssp             HHSEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEE
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHhhccceE
Confidence            35789999999999999999999999999999874

>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=91.48  E-value=0.15  Score=34.83  Aligned_cols=36  Identities=17%  Similarity=0.209  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHH-----H---cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----Q---LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~---~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ...|.+|++..     +   ++.|..+||+..|||++|+|+..+
T Consensus         3 e~tr~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~~Y~~F~   46 (73)
T d2fx0a1           3 EQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFN   46 (73)
T ss_dssp             HHHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHTSCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCcHHHHHHHHCcChhHHHHHCc
Confidence            35677888754     2   357999999999999999998764

>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=91.47  E-value=0.22  Score=31.77  Aligned_cols=33  Identities=15%  Similarity=0.229  Sum_probs=26.5

Q ss_pred             HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598        112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN  156 (258)
Q Consensus       112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr  156 (258)
                      +.|.++..+  .+.+.+|+.+|.          ++++||+|+|+.
T Consensus         9 ~~V~~L~~~--G~gat~IAk~lg----------I~R~SVYR~L~~   41 (43)
T d1gdta1           9 DAVLNMWQQ--GLGASHISKTMN----------IARSTVYKVINE   41 (43)
T ss_dssp             HHHHHHHHT--TCCHHHHHHHHT----------CCHHHHHHHHHS
T ss_pred             HHHHHHHHc--CCCHHHHHHHHC----------CCHHHHHHHHhh
Confidence            456677655  789999999884          499999999985

>d2cyya1 a.4.5.32 (A:5-64) Putative transcriptional regulator PH1519 {Archaeon Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Lrp/AsnC-like transcriptional regulator N-terminal domain
domain: Putative transcriptional regulator PH1519
species: Archaeon Pyrococcus horikoshii [TaxId: 53953]

Probab=91.38  E-value=0.13  Score=33.99  Aligned_cols=43  Identities=21%  Similarity=0.073  Sum_probs=36.4

Q ss_pred             HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +.+..|+..+++|+.++..||++.|.          +|.+||++.+++...++
T Consensus         3 ~~D~~Il~~L~~n~r~s~~eiA~~l~----------ls~~~v~~Ri~~L~~~g   45 (60)
T d2cyya1           3 EIDKKIIKILQNDGKAPLREISKITG----------LAESTIHERIRKLRESG   45 (60)
T ss_dssp             HHHHHHHHHHHHCTTCCHHHHHHHHC----------SCHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHcCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCC
Confidence            45778899999999999999999883          49999999999876554

>d2hr3a1 a.4.5.28 (A:2-146) Probable transcriptional regulator PA3067 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA3067
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.34  E-value=0.19  Score=37.84  Aligned_cols=55  Identities=13%  Similarity=0.199  Sum_probs=39.7

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC--CCC-CCCCCCCHHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGA--IGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~--rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ++..+||+.++++++||.+.+++..+.|-|.-.+  ..+ ..--.+|++=.+.+.+..
T Consensus        50 ~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~~~~DrR~~~i~LT~~G~~~~~~~~  107 (145)
T d2hr3a1          50 VTPSELAAAERMRSSNLAALLRELERGGLIVRHADPQDGRRTRVSLSSEGRRNLYGNR  107 (145)
T ss_dssp             BCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC------CCEEEECHHHHHHHHHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeeeCccchhHHHhccCHHHHHHHHHHH
Confidence            8999999999999999999999999999874222  222 122347777666555543

>d2esna1 a.4.5.37 (A:3-91) Probable LysR-type transcriptional regulator PA0477 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: Probable LysR-type transcriptional regulator PA0477
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=91.23  E-value=0.21  Score=35.46  Aligned_cols=57  Identities=12%  Similarity=0.117  Sum_probs=38.3

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      +++..+.+-.+.+.+|+.|+||.++|++.+++.++ -|. +-.+  .+ +.-.+|+.-+..+
T Consensus        12 ~~f~~v~~~gs~t~AA~~l~isq~avs~~l~~lE~~~g~~Lf~R--~~-~~~~lT~~g~~l~   70 (89)
T d2esna1          12 LVFDALYRHRNVGTAASELAISASAFSHALGRLRQGLDDELFLR--QG-NRMQPTQRAEHLA   70 (89)
T ss_dssp             HHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCEEE--ET-TEEEECHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHHCCCCcHhhHHHHHHHhcCCceeEEE--CC-CceeECHHHHHHH
Confidence            34444433349999999999999999999999986 443 2222  23 4456776654443

>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=91.20  E-value=0.16  Score=35.01  Aligned_cols=35  Identities=14%  Similarity=0.118  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+||+..     +.   +.+..+||++.|||++|+|+..
T Consensus         6 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~t~y~~F   48 (78)
T d2o7ta1           6 LKRREHIITTTCNLYRTHHHDSLTMENIAEQAGVGVATLYRNF   48 (78)
T ss_dssp             HHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTCCHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCCHHHHHHHC
Confidence            35677888753     23   4799999999999999999764

>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=91.17  E-value=0.22  Score=37.70  Aligned_cols=57  Identities=21%  Similarity=0.185  Sum_probs=41.0

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc--CCCCC-CCCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILP--GAIGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p--k~rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      .|++..+||+.++|+++||.+.+++..+.|-|.-  .+..+ ..--.+|++-...+.++.
T Consensus        42 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~glI~r~~~~~D~R~~~l~LT~~G~~~~~~~~  101 (144)
T d1lj9a_          42 PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQEDASNKKIKRIYATEKGKNVYPIIV  101 (144)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTCEEEEECHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCccHhhHHHHHHHHHhhhcccccCCCCCCCccccccCHHHHHHHHHHH
Confidence            5799999999999999999999999999997742  22222 112346676555554443

>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=91.15  E-value=0.14  Score=34.34  Aligned_cols=36  Identities=17%  Similarity=0.175  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.+|++..     +.   +.+..+||+..|||++|+|+...
T Consensus         5 ~~~r~~Il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~iY~~F~   48 (68)
T d2id3a1           5 ARIREAVLLAAGDALAADGFDALDLGEIARRAGVGKTTVYRRWG   48 (68)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHHCcCHHHHHHHCc
Confidence            35677777643     23   47999999999999999998654

>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=90.84  E-value=0.2  Score=33.84  Aligned_cols=35  Identities=20%  Similarity=0.134  Sum_probs=26.7

Q ss_pred             HHHHHHHHH----H-H---cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         51 SVRMRIVEL----A-Q---LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        51 dlR~RIV~L----~-~---~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.+|++.    + +   ++.|.++||+..|||++|+|+...
T Consensus         4 ~rr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~y~~F~   46 (72)
T d1pb6a1           4 AKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFP   46 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHCTTTCCHHHHHHHTTSCHHHHHHHSS
T ss_pred             HHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCChHHHHHHCc
Confidence            346677654    2 2   357999999999999999998753

>d2g3ba1 a.4.1.9 (A:2-73) Putative transcriptional regulator {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
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=90.79  E-value=0.14  Score=34.60  Aligned_cols=36  Identities=25%  Similarity=0.273  Sum_probs=27.5

Q ss_pred             HHHHHHHHHH-----H---cCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598         51 SVRMRIVELA-----Q---LGIRPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        51 dlR~RIV~L~-----~---~G~S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      +.|.+|++..     +   .+.+..+||+..|||++|+|++...
T Consensus         2 err~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~ly~~F~~   45 (72)
T d2g3ba1           2 ERRDAILKASATAIAQRGIRGLRVNDVAEVAGVSPGLLYYHFKD   45 (72)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHTSCHHHHHHHHCS
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCcC
Confidence            4566666643     2   3589999999999999999987643

>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=90.70  E-value=0.14  Score=34.73  Aligned_cols=34  Identities=15%  Similarity=0.120  Sum_probs=26.0

Q ss_pred             HHHHHHHHH-----Hc--CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELA-----QL--GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~-----~~--G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .|++|++..     +.  +.|..+||+..|||++|+|++..
T Consensus         2 tr~~Il~aA~~l~~~~G~~~t~~~Ia~~agvs~~~~Y~~F~   42 (70)
T d2hkua1           2 TRDALFTAATELFLEHGEGVPITQICAAAGAHPNQVTYYYG   42 (70)
T ss_dssp             HHHHHHHHHHHHHHHHCTTSCHHHHHHHHTCCHHHHHHHHS
T ss_pred             hHHHHHHHHHHHHHhcccCchHHHHHHHHCCChhhHHhcCC
Confidence            355565543     22  57999999999999999998763

>d1sgma1 a.4.1.9 (A:5-77) Putative transcriptional regulator YxaF {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: Putative transcriptional regulator YxaF
species: Bacillus subtilis [TaxId: 1423]

Probab=90.57  E-value=0.095  Score=35.51  Aligned_cols=34  Identities=15%  Similarity=0.198  Sum_probs=26.3

Q ss_pred             HHHHHHHHHH-----H---cCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         51 SVRMRIVELA-----Q---LGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        51 dlR~RIV~L~-----~---~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      |.|++||+..     +   ++.|.++||+..|||++++|+..
T Consensus         2 etr~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~~iy~~F   43 (73)
T d1sgma1           2 DSREKILHTASRLSQLQGYHATGLNQIVKESGAPKGSLYHFF   43 (73)
T ss_dssp             CHHHHHHHHHHHHHHHHCTTTCCHHHHHHHHCCCSCHHHHST
T ss_pred             hHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHc
Confidence            3567777653     2   35799999999999999998754

>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=90.50  E-value=0.15  Score=34.99  Aligned_cols=35  Identities=17%  Similarity=0.239  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRw   83 (258)
                      ..+.|.+|++..     +.   +.+.++||++.|||++++|+.
T Consensus         7 ~~~~r~~il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~   49 (79)
T d2oi8a1           7 RTQVRAEIKDHAWEQIATAGASALSLNAIAKRMGMSGPALYRY   49 (79)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCTTSCCHHHHHHHTTCCHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHhCccccCHHHHHHHhCCCCCchhhh
Confidence            356777887653     23   579999999999999999864

>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=90.48  E-value=0.3  Score=36.10  Aligned_cols=54  Identities=11%  Similarity=0.085  Sum_probs=38.5

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYIKEL  117 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I~~l  117 (258)
                      ++..+||+.++++++||++.+++..+.|-+.-.  +..+ ..--.+|++-...+.+.
T Consensus        46 it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~  102 (135)
T d3broa1          46 VLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETII  102 (135)
T ss_dssp             CBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEECSSCTTSEEEEECHHHHTTHHHH
T ss_pred             CCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHHhhhhhhhhhhhcccHHHHHHHHHH
Confidence            899999999999999999999999999976321  1111 12234666655554444

>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=90.45  E-value=0.15  Score=37.66  Aligned_cols=41  Identities=12%  Similarity=0.161  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVEL-AQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L-~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++.-.+...+.. .+.|.+..+||+.+|+|+++|++.++-..
T Consensus        14 L~p~e~A~a~~~l~~~g~s~~eiA~~~G~s~~~V~~~l~L~~   55 (114)
T d1r71a_          14 LTPREIADFIGRELAKGKKKGDIAKEIGKSPAFITQHVTLLD   55 (114)
T ss_dssp             CCHHHHHHHHHHHHHTTCCHHHHHHHHTCCHHHHHHHHGGGS
T ss_pred             CCHHHHHHHHHHHHHhCCCHHHHHHHHCCcHHHHHHHHHHhC
Confidence            555555555554 46799999999999999999999988654

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=90.24  E-value=0.25  Score=37.21  Aligned_cols=52  Identities=13%  Similarity=0.128  Sum_probs=39.8

Q ss_pred             CCCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        105 VTTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       105 klT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      +.|+. +..|.+.+.+.  ...++.||.+.|.+.+..+     +.+||+|.|........
T Consensus        13 R~T~q-R~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i-----~~aTVYR~L~~l~e~gl   66 (134)
T d1mzba_          13 KVTLP-RVKILQMLDSAEQRHMSAEDVYKALMEAGEDV-----GLATVYRVLTQFEAAGL   66 (134)
T ss_dssp             CCCHH-HHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCC-----CHHHHHHHHHHHHHHTS
T ss_pred             CCCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCc-----cHHHHHHHHHHHHhccE
Confidence            35564 66676777643  3589999999999888775     99999999998766544

>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=90.24  E-value=0.1  Score=34.57  Aligned_cols=24  Identities=13%  Similarity=0.183  Sum_probs=21.2

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++.|.++||+..|||++|||++..
T Consensus        18 ~~~s~~~Ia~~agvs~~tiy~~F~   41 (62)
T d2vkva1          18 EGLTTRKLAQKLGVEQPTLYWHVK   41 (62)
T ss_dssp             HHCCHHHHHHHHTSCHHHHHHHSC
T ss_pred             ccCCHHHHHHHhCCCHHHHHHHCC
Confidence            468999999999999999998754

>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=90.23  E-value=0.17  Score=34.87  Aligned_cols=34  Identities=21%  Similarity=0.239  Sum_probs=30.5

Q ss_pred             cC--CCHHHHHHHhCC-CHHHHHHHHHHhhhhCCccc
Q psy15598         62 LG--IRPCDISRQLRV-SHGCVSKILARYHETGSILP   95 (258)
Q Consensus        62 ~G--~S~~eIAr~LGV-SrsTVsRwikRyrEtGsl~p   95 (258)
                      .|  -|.++||+.||+ |.+||++.+++..+.|-|.-
T Consensus        21 ~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r   57 (71)
T d1jhfa1          21 TGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEI   57 (71)
T ss_dssp             HSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEE
T ss_pred             hCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeec
Confidence            47  588999999999 89999999999999998753

>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=90.00  E-value=0.22  Score=33.21  Aligned_cols=24  Identities=13%  Similarity=-0.045  Sum_probs=20.9

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++.|.++||+..|||++|+|+...
T Consensus        19 ~~~si~~Ia~~agvs~~t~Y~~F~   42 (70)
T d2gena1          19 DATTIEMIRDRSGASIGSLYHHFG   42 (70)
T ss_dssp             TTCCHHHHHHHHCCCHHHHHHHTC
T ss_pred             ccCCHHHHHHHHCcCHHHHHHHCC
Confidence            357999999999999999988753

>d2bv6a1 a.4.5.28 (A:5-140) Transcriptional regulator MgrA {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator MgrA
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.66  E-value=0.19  Score=37.57  Aligned_cols=55  Identities=18%  Similarity=0.191  Sum_probs=40.6

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCCCCC--CCCHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGSKPR--VTTPKVVSYIKE  116 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~RPr--klT~e~~~~I~~  116 (258)
                      ..|.+.++||+.++++++||++.+++..+.|-+.-.  +..+ |-.  .+|++=.+.+.+
T Consensus        46 ~~~~t~~~la~~l~~~~~~~s~~l~~L~~~Gli~r~~~~~D~-R~~~l~lT~~G~~~~~~  104 (136)
T d2bv6a1          46 ESPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRERSEVDQ-REVFIHLTDKSETIRPE  104 (136)
T ss_dssp             SSEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEECSSST-TCEEEEECHHHHHHHHH
T ss_pred             CCCCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEEeecCCcc-cchhhccCHHHHHHHHH
Confidence            367999999999999999999999999999987422  2222 222  467765554443

>d2fbha1 a.4.5.28 (A:8-144) Transcriptional regulator PA3341 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator PA3341
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=89.61  E-value=0.24  Score=36.80  Aligned_cols=56  Identities=18%  Similarity=0.201  Sum_probs=39.3

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCCC-CCCCCCHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGGS-KPRVTTPKVVSYIKEL  117 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG~-RPrklT~e~~~~I~~l  117 (258)
                      +|.+.++||+.++++++||++.+++..+.|-|.  +.+..++ .--.+|++-.+.+.++
T Consensus        42 ~~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~~~~D~R~~~i~lT~~G~~~~~~~  100 (137)
T d2fbha1          42 DSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLAVAEDRRAKHIVLTPKADVLIADI  100 (137)
T ss_dssp             SCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCBTTBCSCEEEECTTHHHHHHHH
T ss_pred             CCCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccCCCCCCCchhhhcCHHHHHHHHHH
Confidence            468999999999999999999999999999764  2222221 1223565545544443

>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=89.48  E-value=0.2  Score=34.06  Aligned_cols=35  Identities=29%  Similarity=0.351  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      .+.|.+||+..     +.   +.|..+||+..|||++++|+..
T Consensus         4 ~~tr~~il~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~F   46 (75)
T d2hyja1           4 QATRGRILGRAAEIASEEGLDGITIGRLAEELEMSKSGVHKHF   46 (75)
T ss_dssp             HHHHHHHHHHHHHHHHHHCGGGCCHHHHHHHHTCCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccCcHHHHHHHHCcCHHHHHHHC
Confidence            45677777753     23   5799999999999999998653

>d1hsja1 a.4.5.28 (A:373-487) Staphylococcal accessory regulator A homolog, SarR {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarR
species: Staphylococcus aureus [TaxId: 1280]

Probab=89.48  E-value=0.14  Score=37.83  Aligned_cols=57  Identities=12%  Similarity=0.027  Sum_probs=39.8

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCCC-CCCCCCHHHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG~-RPrklT~e~~~~I~~lv  118 (258)
                      .|++..+||+.++++++||.+.+++..+.|-|.-.  +..++ .--.+|++-.+.+.+++
T Consensus        47 ~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~~~~~D~R~~~i~LT~~G~~~~~~~~  106 (115)
T d1hsja1          47 NEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKKRSLQDERTVIVYVTDTQKANIQKLI  106 (115)
T ss_dssp             SEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCEECCSSSSCCEEECCSSHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEEeecCCCceEEEEECHHHHHHHHHHH
Confidence            36899999999999999999999999999977422  22221 11236665555554443

>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=89.46  E-value=0.21  Score=33.74  Aligned_cols=23  Identities=4%  Similarity=-0.019  Sum_probs=20.3

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.|.++||+..|||++|+|+...
T Consensus        24 ~~s~~~Ia~~agvs~~t~Y~~F~   46 (74)
T d1v7ba1          24 TLSYDSLAEATGLSKSGLIYHFP   46 (74)
T ss_dssp             TCCHHHHHHHHCSCHHHHHHHCS
T ss_pred             ccCHHHHHHHhCcCcchHhhhCC
Confidence            57999999999999999987643

>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=89.43  E-value=0.3  Score=33.60  Aligned_cols=41  Identities=12%  Similarity=0.051  Sum_probs=30.8

Q ss_pred             CCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         48 LPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        48 ~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      ++...|.-|...+-    ..++..+||+.||||+..|+.+.++..
T Consensus         6 L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrerVrqie~~al   50 (68)
T d2p7vb1           6 LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKAL   50 (68)
T ss_dssp             CCHHHHHHHHHHTTTTSSSCCCHHHHHHHHTCCHHHHHHHHHHHH
T ss_pred             CCHHHHHHHHHHcCCCCCCcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence            55555544444431    347999999999999999999998875

>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=89.29  E-value=0.13  Score=38.09  Aligned_cols=64  Identities=19%  Similarity=0.110  Sum_probs=41.0

Q ss_pred             CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC-CCCCCCCCCHHHH---HHHHHHHHhCCCCCHHHHHHHH
Q psy15598         64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAI-GGSKPRVTTPKVV---SYIKELKQKDPGIFAWEIRDRL  133 (258)
Q Consensus        64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r-gG~RPrklT~e~~---~~I~~lv~~nP~ita~EIr~~L  133 (258)
                      .++.++|+.+|||..|++-|-+    .|.+.|... ..+.-|..++.+.   ..|..+..  -++++.+|++.+
T Consensus         4 ytI~evA~~~gvs~~tlR~Ye~----~GLl~P~~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~g~sl~eIk~~l   71 (118)
T d1r8ea1           4 YSIGEVSKLANVSIKALRYYDK----IDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKY--IGTPLEEMKKAQ   71 (118)
T ss_dssp             EEHHHHHHHHTCCHHHHHHHHH----TTSSCCSEECTTTCCEEEETGGGGHHHHHHHHHH--TTCCHHHHHHHT
T ss_pred             ccHHHHHHHHCcCHHHHHHHHH----cCCcccccccCCCCcccccHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence            3678999999999999976653    588876432 1112345555444   44444433  378888887654

>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=88.95  E-value=0.29  Score=35.51  Aligned_cols=32  Identities=16%  Similarity=0.340  Sum_probs=27.2

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         57 VELAQLGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        57 V~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      -.+.+.|++..+||+.||.|+++|++.++--.
T Consensus        13 ~~L~e~g~t~~~iA~~~Gks~~~V~~~LrLl~   44 (93)
T d1vz0a1          13 QALLEMGLTQEEVARRVGKARSTVANALRLLQ   44 (93)
T ss_dssp             HHHHHTTCCHHHHHHHHTCCHHHHHHHHHGGG
T ss_pred             HHHHHcCCCHHHHHHHHccchHHHHHHHHHHH
Confidence            33456799999999999999999999988754

>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=88.94  E-value=0.33  Score=32.45  Aligned_cols=34  Identities=24%  Similarity=0.286  Sum_probs=26.2

Q ss_pred             HHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         52 VRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        52 lR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .|.+|++..     +.   +.+.++||+..|||++|+|+...
T Consensus         3 tr~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~~~Y~~F~   44 (68)
T d2d6ya1           3 TKARIFEAAVAEFARHGIAGARIDRIAAEARANKQLIYAYYG   44 (68)
T ss_dssp             HHHHHHHHHHHHHHHHTTTSCCHHHHHHHHTCCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHhCccccCHHHHHHHHCcchhHHHHHCc
Confidence            466666643     23   57999999999999999997654

>d1j9ia_ a.6.1.5 (A:) Terminase gpNU1 subunit domain {Bacteriophage lambda [TaxId: 10710]}

class: All alpha proteins
fold: Putative DNA-binding domain
superfamily: Putative DNA-binding domain
family: Terminase gpNU1 subunit domain
domain: Terminase gpNU1 subunit domain
species: Bacteriophage lambda [TaxId: 10710]

Probab=88.66  E-value=0.06  Score=37.70  Aligned_cols=22  Identities=5%  Similarity=0.022  Sum_probs=19.5

Q ss_pred             CHHHHHHHhCCCHHHHHHHHHH
Q psy15598         65 RPCDISRQLRVSHGCVSKILAR   86 (258)
Q Consensus        65 S~~eIAr~LGVSrsTVsRwikR   86 (258)
                      ...++|+.||||.+||..|+++
T Consensus         4 nk~~lA~iFGVS~~TI~~W~~~   25 (68)
T d1j9ia_           4 NKKQLADIFGASIRTIQNWQEQ   25 (68)
T ss_dssp             EHHHHHHHTTCCHHHHHHHTTT
T ss_pred             CHHHHHHHhCCCHHHHHHHHHC
Confidence            4578999999999999999864

>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=88.59  E-value=0.45  Score=36.04  Aligned_cols=39  Identities=8%  Similarity=-0.001  Sum_probs=29.3

Q ss_pred             CCCHHHHHHHHHHHH---------cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         47 PLPNSVRMRIVELAQ---------LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        47 ~~S~dlR~RIV~L~~---------~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .++.+.|.....++.         +-.+..+||..+|||+.|+|||..
T Consensus        11 ~L~~~q~~AA~~l~~Ne~~~~~~~ekktqeqiAeelGisr~tLyrWrt   58 (120)
T d2ao9a1          11 KLTAKQIQAAYLLVENELMESNNEEKRTQDEMANELGINRTTLWEWRT   58 (120)
T ss_dssp             TSCHHHHHHHHHHHHHHHCC---CCCCCHHHHHHHHTCCHHHHHHHHH
T ss_pred             HhhHHHHHHHHHHhhchhccccchhhhhHHHHHHHhChhHHHHHHHhh
Confidence            366666666665553         124778999999999999999983

>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=88.59  E-value=0.17  Score=34.37  Aligned_cols=23  Identities=13%  Similarity=0.210  Sum_probs=20.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      +.+.++||+..|||++|||+...
T Consensus        23 ~~ti~~Ia~~agvs~~~iY~~F~   45 (75)
T d2id6a1          23 RATTDEIAEKAGVAKGLIFHYFK   45 (75)
T ss_dssp             HCCHHHHHHHHTCCTHHHHHHHS
T ss_pred             ccCHHHHHHHhCCCHHHHHHHCC
Confidence            58999999999999999998754

>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=88.53  E-value=0.25  Score=34.85  Aligned_cols=28  Identities=14%  Similarity=0.089  Sum_probs=23.8

Q ss_pred             HHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598         57 VELAQLGIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        57 V~L~~~G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      |..+..|++..++|+..|||+++|++|-
T Consensus        19 ir~~R~~~t~~eLA~~~Gvs~~~ls~iE   46 (82)
T d2ofya1          19 LRSARGDMSMVTVAFDAGISVETLRKIE   46 (82)
T ss_dssp             HHHHHTTSCHHHHHHHHTCCHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHcCCHHHHHHHH
Confidence            3344578999999999999999999885

>d2g7ga1 a.4.1.9 (A:9-73) Putative transcriptional regulator Rha04620 {Rhodococcus sp. rha1 [TaxId: 101510]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator Rha04620
species: Rhodococcus sp. rha1 [TaxId: 101510]

Probab=88.53  E-value=0.22  Score=33.36  Aligned_cols=24  Identities=21%  Similarity=0.207  Sum_probs=20.6

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      .+.|.++||+..|||++++|+..+
T Consensus        18 G~~ti~~Ia~~agvs~~~iY~~F~   41 (65)
T d2g7ga1          18 GDFRMPDLARHLNVQVSSIYHHAK   41 (65)
T ss_dssp             SSCCHHHHHHHTTSCHHHHHTTSC
T ss_pred             CCCCHHHHHHHhCccccchhhcCC
Confidence            368999999999999999987543

>d1ixca1 a.4.5.37 (A:1-89) LysR-type regulatory protein CbnR {Ralstonia eutropha [TaxId: 106590]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: LysR-like transcriptional regulators
domain: LysR-type regulatory protein CbnR
species: Ralstonia eutropha [TaxId: 106590]

Probab=88.44  E-value=0.77  Score=32.30  Aligned_cols=57  Identities=11%  Similarity=0.111  Sum_probs=36.8

Q ss_pred             HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598         55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI  114 (258)
Q Consensus        55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I  114 (258)
                      +++..+.+--+.+.+|+.|+||.++|++-+++..+ -|. +-.+  .+ +.-.+|+.-+..+
T Consensus         7 ~~f~~v~e~gs~~~AA~~L~isq~avs~~i~~LE~~lg~~Lf~R--~~-~~~~lT~~G~~l~   65 (89)
T d1ixca1           7 KYFIAVAEAGNMAAAAKRLHVSQPPITRQMQALEADLGVVLLER--SH-RGIELTAAGHAFL   65 (89)
T ss_dssp             HHHHHHHHHSSHHHHHHHHTCCHHHHHHHHHHHHHHHTSCCBC--------CCBCHHHHHHH
T ss_pred             HHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHhcCCceeeEe--cC-CccCccHhHHHHH
Confidence            44444444459999999999999999999999986 442 3222  22 4455676644433

>d2fbia1 a.4.5.28 (A:5-140) Probable transcriptional regulator PA4135 {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Probable transcriptional regulator PA4135
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=88.34  E-value=0.32  Score=36.11  Aligned_cols=58  Identities=14%  Similarity=0.071  Sum_probs=42.2

Q ss_pred             HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC--CCCC-CCCCCCCHHHHHHHHHHH
Q psy15598         61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPG--AIGG-SKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk--~rgG-~RPrklT~e~~~~I~~lv  118 (258)
                      ..+++..+||+.++|++++|++.+++..+.|-|.-.  +..+ ..--.+|++-.+.+.+..
T Consensus        42 ~~~~t~~~la~~~~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~lT~~G~~~~~~~~  102 (136)
T d2fbia1          42 QGEMESYQLANQACILRPSMTGVLARLERDGIVRRWKAPKDQRRVYVNLTEKGQQCFVSMS  102 (136)
T ss_dssp             HCSEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEEEEECHHHHHHHHHHH
T ss_pred             cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeecCccCchhhhccCHHHHHHHHHHH
Confidence            357999999999999999999999999999987322  2222 122347777666665554

>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=88.34  E-value=0.3  Score=34.52  Aligned_cols=46  Identities=13%  Similarity=0.078  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHhCC----CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        106 TTPKVVSYIKELKQKDP----GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       106 lT~e~~~~I~~lv~~nP----~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      +++. ++.|.+++.+||    ..+..+|++.+   |       ||.+||.|+.+..+....
T Consensus        16 Ls~~-e~~ia~yil~~~~~~~~~si~~lA~~~---~-------vS~sTi~Rf~kklG~~gf   65 (83)
T d2o3fa1          16 LPPS-ERKLADYILAHPHKAIESTVNEISALA---N-------SSDAAVIRLCKSLGLKGF   65 (83)
T ss_dssp             SCHH-HHHHHHHHHHCHHHHHTCCHHHHHHHT---T-------CCHHHHHHHHHHTTCSSH
T ss_pred             CCHH-HHHHHHHHHcCHHHHHHccHHHHHHHH---C-------CCHHHHHHHHHHhCCCCH
Confidence            4544 567888888887    46788887765   3       599999999999998754

>d2ezla_ a.4.1.2 (A:) Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Ibeta subdomain of the mu end DNA-binding domain of phage mu transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=88.28  E-value=0.35  Score=35.83  Aligned_cols=32  Identities=16%  Similarity=0.235  Sum_probs=26.0

Q ss_pred             HHHHHcCCCH----HHHHHHhCCCHHHHHHHHHHhh
Q psy15598         57 VELAQLGIRP----CDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        57 V~L~~~G~S~----~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      -.|.+.|.+.    .+||.++|||.+|+++|..+-+
T Consensus        43 ~~L~~~G~~~~~A~~~VA~~~~vs~~TL~nW~~~V~   78 (99)
T d2ezla_          43 DEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQ   78 (99)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHcCCcHHHHHHHHHHHhCCCHHHHHHHHHHHC
Confidence            3345678865    5699999999999999999875

>d1xd7a_ a.4.5.55 (A:) Hypothetical protein ywnA {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein ywnA
species: Bacillus subtilis [TaxId: 1423]

Probab=87.97  E-value=0.29  Score=36.47  Aligned_cols=46  Identities=4%  Similarity=0.028  Sum_probs=36.2

Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      ..++..+....++.++.++||+.++++...|.|++++-+..|-+..
T Consensus         5 ~Av~~L~~la~~~~~ss~~IA~~~~~~~~~v~kIl~~L~~aglV~s   50 (127)
T d1xd7a_           5 VAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTS   50 (127)
T ss_dssp             HHHHHHHHHHTCSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEC
T ss_pred             HHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHhCcccc
Confidence            3444433333445689999999999999999999999999997753

>d1p4xa1 a.4.5.28 (A:1-125) Staphylococcal accessory regulator A homolog, SarS {Staphylococcus aureus [TaxId: 1280]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Staphylococcal accessory regulator A homolog, SarS
species: Staphylococcus aureus [TaxId: 1280]

Probab=87.91  E-value=0.25  Score=36.88  Aligned_cols=57  Identities=11%  Similarity=-0.032  Sum_probs=42.2

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc--CCCCC-CCCCCCCHHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILP--GAIGG-SKPRVTTPKVVSYIKELKQ  119 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p--k~rgG-~RPrklT~e~~~~I~~lv~  119 (258)
                      +++..+||+.+++++++|.+.+++..+.|-|.-  .+..+ ..--.+|++-.+.+.+++.
T Consensus        50 ~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~~~~~D~R~~~i~lT~~G~~~~~~~~~  109 (125)
T d1p4xa1          50 TLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKVRSKIDERNTYISISEEQREKIAERVT  109 (125)
T ss_dssp             EEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEEECSSSTTSEEEECCHHHHHHHHHHHH
T ss_pred             CcCHHHHHHHhCCCcchHHHHHHHHHHCCCceeecccCCCCeEEEEECHHHHHHHHHHHH
Confidence            479999999999999999999999999997732  12222 1123478887777766643

>d2iu5a1 a.4.1.9 (A:1-71) Transcriptional activator DhaS {Lactococcus lactis [TaxId: 1358]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Transcriptional activator DhaS
species: Lactococcus lactis [TaxId: 1358]

Probab=87.64  E-value=0.16  Score=34.32  Aligned_cols=35  Identities=11%  Similarity=0.072  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHH-----HcC---CCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QLG---IRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~G---~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ...|++|++..     +.|   .+..+||+..|||++|+|+..
T Consensus         5 ~~t~~~I~~aa~~l~~~~G~~~~sv~~Ia~~agvs~~t~Y~~F   47 (71)
T d2iu5a1           5 IITQKIIAKAFKDLMQSNAYHQISVSDIMQTAKIRRQTFYNYF   47 (71)
T ss_dssp             SHHHHHHHHHHHHHHHHSCGGGCCHHHHHHHHTSCGGGGGGTC
T ss_pred             HHHHHHHHHHHHHHHHHcCcccCCHHHHHHHhCccccHHHHHc
Confidence            34566666653     234   699999999999999998653

>d3deua1 a.4.5.28 (A:2-141) Transcriptional regulator SlyA {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator SlyA
species: Salmonella typhimurium [TaxId: 90371]

Probab=87.53  E-value=0.24  Score=36.85  Aligned_cols=32  Identities=9%  Similarity=0.278  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL   94 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~   94 (258)
                      |++..+||+.++|++++|++.+++..+.|-|.
T Consensus        46 ~~t~~~la~~l~i~~~~vs~~l~~L~~~glI~   77 (140)
T d3deua1          46 DQSQIQLAKAIGIEQPSLVRTLDQLEDKGLIS   77 (140)
T ss_dssp             SEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred             CccHHHHHHHHCCCHhHHHHHHHHHHhCCCEE
Confidence            58999999999999999999999999999774

>d1rkta1 a.4.1.9 (A:2-82) Hypothetical transcriptional regulator YfiR {Bacillus subtilis [TaxId: 1423]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Hypothetical transcriptional regulator YfiR
species: Bacillus subtilis [TaxId: 1423]

Probab=87.47  E-value=0.32  Score=33.38  Aligned_cols=34  Identities=21%  Similarity=0.129  Sum_probs=26.5

Q ss_pred             HHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         51 SVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        51 dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ..|.+|++..     +.   +.+..+||+..|||++|+|+..
T Consensus        11 ~~r~~Il~aa~~l~~~~G~~~~ti~~Ia~~agvs~~t~Y~~F   52 (81)
T d1rkta1          11 KRQAEILEAAKTVFKRKGFELTTMKDVVEESGFSRGGVYLYF   52 (81)
T ss_dssp             HHHHHHHHHHHHHHHHHCSTTCCHHHHHHHHTSCHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHC
Confidence            4577777743     23   5799999999999999998653

>d2fd5a1 a.4.1.9 (A:1-76) Probable transcriptional regulator PA3133 {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 PA3133
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=87.19  E-value=0.21  Score=33.88  Aligned_cols=35  Identities=14%  Similarity=0.118  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         50 NSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        50 ~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      ...|.+|++..     +.   +.|..+||+..|||++|+|+..
T Consensus         6 ~~~r~~Il~aa~~l~~~~G~~~~si~~Ia~~agvs~~t~Y~~F   48 (76)
T d2fd5a1           6 TQTRARILGAATQALLERGAVEPSVGEVMGAAGLTVGGFYAHF   48 (76)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTTSCCHHHHHHHTTCCGGGGGGTC
T ss_pred             HHHHHHHHHHHHHHHHHhCcccccHHHHHHHhCCCccchhhcC
Confidence            35667777653     23   4699999999999999998654

>d1ylfa1 a.4.5.55 (A:5-142) Hypothetical protein BC1842 {Bacillus cereus [TaxId: 1396]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Transcriptional regulator Rrf2
domain: Hypothetical protein BC1842
species: Bacillus cereus [TaxId: 1396]

Probab=87.10  E-value=0.24  Score=37.45  Aligned_cols=45  Identities=9%  Similarity=0.124  Sum_probs=35.1

Q ss_pred             HHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598         51 SVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILP   95 (258)
Q Consensus        51 dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p   95 (258)
                      .+|..+....+.|  ++..+||+.+++++..+.|++++.++.|-|..
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S   55 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYV   55 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEe
Confidence            3444333333333  79999999999999999999999999998753

>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=86.91  E-value=0.42  Score=30.39  Aligned_cols=35  Identities=9%  Similarity=0.100  Sum_probs=29.0

Q ss_pred             HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598         54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH   88 (258)
Q Consensus        54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr   88 (258)
                      .+|++.++    +..+..++|+.+|+|++++.|+.++.-
T Consensus         6 ~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk~~~   44 (54)
T d1bl0a1           6 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKET   44 (54)
T ss_dssp             HHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHH
T ss_pred             HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence            45666654    467999999999999999999999873

>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=86.69  E-value=0.43  Score=31.84  Aligned_cols=22  Identities=18%  Similarity=0.262  Sum_probs=19.8

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.|..+||+..|||++++|+..
T Consensus        21 ~~ti~~Ia~~agvs~~~~y~~F   42 (72)
T d1vi0a1          21 QSQVSKIAKQAGVADGTIYLYF   42 (72)
T ss_dssp             GCCHHHHHHHHTSCHHHHHHHC
T ss_pred             cccHHHHHHHHCcCHHHHHHHC
Confidence            4799999999999999998754

>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=86.30  E-value=0.67  Score=30.83  Aligned_cols=37  Identities=11%  Similarity=0.085  Sum_probs=28.7

Q ss_pred             HHHHHHHHHhCC-CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598        111 VSYIKELKQKDP-GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK  157 (258)
Q Consensus       111 ~~~I~~lv~~nP-~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~  157 (258)
                      ...|..++.++. .+++.+|++.|.          ||.+||+|-|..+
T Consensus         9 ~~~Il~~L~~~~~~vs~~~La~~l~----------VS~~TI~rdi~~L   46 (65)
T d1j5ya1           9 LKSIVRILERSKEPVSGAQLAEELS----------VSRQVIVQDIAYL   46 (65)
T ss_dssp             HHHHHHHHHHCSSCBCHHHHHHHHT----------SCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHcCCCCcHHHHHHHHC----------CCHHHHHHHHHHH
Confidence            446677776655 489999999994          5999999988764

>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=86.19  E-value=0.78  Score=32.85  Aligned_cols=43  Identities=9%  Similarity=0.009  Sum_probs=32.5

Q ss_pred             CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598         47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHE   89 (258)
Q Consensus        47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrE   89 (258)
                      .++...|.-|...+    ...++..+||+.||||+..|+.+.++..+
T Consensus        18 ~L~~rE~~Ii~~rfGl~~~~~~tl~eI~~~lgiSrERVRQie~~al~   64 (87)
T d1ttya_          18 TLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALR   64 (87)
T ss_dssp             TSCHHHHHHHHHHHTTTTSSCCCHHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             cCCHHHHHHHHHHcCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence            36666664444444    14589999999999999999999998763

>d2p8ta1 a.4.5.72 (A:14-82) Hypothetical protein PH0730 {Pyrococcus horikoshii [TaxId: 53953]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: PH0730 N-terminal domain-like
domain: Hypothetical protein PH0730
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=85.77  E-value=1.4  Score=30.38  Aligned_cols=67  Identities=18%  Similarity=0.165  Sum_probs=51.5

Q ss_pred             CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHH
Q psy15598         48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELK  118 (258)
Q Consensus        48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv  118 (258)
                      |+.+-=.+++.+..+-++.+.+|+.++++.++|+.-+...++.|-+...+ .|   -.+|++=++.+.++.
T Consensus         2 ~~~~~vl~~l~ll~qPiGRr~La~~L~l~Er~vRte~~~Lk~~gLI~~~~-~G---m~lTe~G~~~l~~L~   68 (69)
T d2p8ta1           2 YTVEDVLAVIFLLKEPLGRKQISERLELGEGSVRTLLRKLSHLDIIRSKQ-RG---HFLTLKGKEIRDKLL   68 (69)
T ss_dssp             CCHHHHHHHHHHTTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC---C---EEECHHHHHHHHHHH
T ss_pred             CcHHHHHHHHHHHcCCccHHHHHHHcCCcHHHHHHHHHHHHHCCCeeeeC-CC---CEECHhHHHHHHHHh
Confidence            34444445666667889999999999999999999999999999886664 33   668888777776653

>d1t33a1 a.4.1.9 (A:1-88) Putative transcriptional repressor YbiH {Salmonella typhimurium [TaxId: 90371]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional repressor YbiH
species: Salmonella typhimurium [TaxId: 90371]

Probab=85.20  E-value=0.74  Score=31.92  Aligned_cols=37  Identities=11%  Similarity=0.205  Sum_probs=28.9

Q ss_pred             CHHHHHHHHHHH-----HcC--CCHHHHHHHhCCCHHHHHHHHH
Q psy15598         49 PNSVRMRIVELA-----QLG--IRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        49 S~dlR~RIV~L~-----~~G--~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ..+.|.+|++..     +.|  .+..+||+..|||++++|+...
T Consensus        10 ~~~tr~~Il~aa~~l~~~~G~~~t~~~Ia~~agvs~~~~Y~~F~   53 (88)
T d1t33a1          10 GEQAKSQLIAAALAQFGEYGLHATTRDIAALAGQNIAAITYYFG   53 (88)
T ss_dssp             HHHHHHHHHHHHHHHHHHHGGGSCHHHHHHHHTSCHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHHHHHHhccccCHHHHHHHhCCChhhhhccCC
Confidence            456788888863     234  3889999999999999998764

>d2fbka1 a.4.5.28 (A:8-179) Transcriptional regulator DR1159 {Deinococcus radiodurans [TaxId: 1299]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: MarR-like transcriptional regulators
domain: Transcriptional regulator DR1159
species: Deinococcus radiodurans [TaxId: 1299]

Probab=84.53  E-value=0.37  Score=37.65  Aligned_cols=56  Identities=23%  Similarity=0.260  Sum_probs=40.7

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKELK  118 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~lv  118 (258)
                      |++.++||+.++|+++||.+.+++..+.|-|.-...  .++ .--.+|++=.+.+.+..
T Consensus        79 ~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~~~~DrR~~~i~LT~~G~~l~~~~~  137 (172)
T d2fbka1          79 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERREDERDRRSASIRLTPQGRALVTHLL  137 (172)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC-------CCBEECHHHHHHHHHHH
T ss_pred             CcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeeccccchhhHHhhcCHHHHHHHHHHH
Confidence            589999999999999999999999999998743322  221 22347777666665554

>d1zk8a1 a.4.1.9 (A:6-77) Transcriptional regulator BC5000 {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 BC5000
species: Bacillus cereus [TaxId: 1396]

Probab=84.45  E-value=0.38  Score=32.26  Aligned_cols=21  Identities=10%  Similarity=0.148  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRw   83 (258)
                      +.+.++||+..|||++++|+.
T Consensus        23 ~~t~~~Ia~~agvs~~slY~y   43 (72)
T d1zk8a1          23 EVTLASLAQTLGVRSPSLYNH   43 (72)
T ss_dssp             GCCHHHHHHHHTSCHHHHTTT
T ss_pred             cccHHHHHHHhCCCHHHHHHH
Confidence            579999999999999999764

>d2i10a1 a.4.1.9 (A:10-78) Putative transcriptional regulator RHA1_ro09068 {Rhodococcus sp. [TaxId: 1831]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Tetracyclin repressor-like, N-terminal domain
domain: Putative transcriptional regulator RHA1 ro09068
species: Rhodococcus sp. [TaxId: 1831]

Probab=84.11  E-value=0.42  Score=31.90  Aligned_cols=24  Identities=13%  Similarity=0.238  Sum_probs=21.1

Q ss_pred             cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598         62 LGIRPCDISRQLRVSHGCVSKILA   85 (258)
Q Consensus        62 ~G~S~~eIAr~LGVSrsTVsRwik   85 (258)
                      ++.|..+||+..|||++|+|+..+
T Consensus        19 ~~~ti~~Ia~~agvs~~~~Y~~F~   42 (69)
T d2i10a1          19 EGTSITDLTKALGINPPSLYAAFG   42 (69)
T ss_dssp             TTCCHHHHHHHHTCCHHHHHHHHC
T ss_pred             ccCCHHHHHHHhCCChhHHHHHCc
Confidence            357999999999999999998764

>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=83.72  E-value=0.9  Score=29.86  Aligned_cols=22  Identities=23%  Similarity=0.380  Sum_probs=20.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.+.++||+..|||+++||+..
T Consensus        21 ~~ti~~Ia~~agvs~~~iy~~F   42 (69)
T d2np5a1          21 GASVREVAKRAGVSIGAVQHHF   42 (69)
T ss_dssp             GCCHHHHHHHHTCCHHHHHHHC
T ss_pred             ccCHHHHHHHhCCCHHHHHHHC
Confidence            5799999999999999998764

>d1stza1 a.4.5.51 (A:14-100) Heat-inducible transcription repressor HrcA, N-terminal domain {Thermotoga maritima [TaxId: 2336]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Heat-inducible transcription repressor HrcA, N-terminal domain
domain: Heat-inducible transcription repressor HrcA, N-terminal domain
species: Thermotoga maritima [TaxId: 2336]

Probab=83.67  E-value=3.3  Score=29.30  Aligned_cols=65  Identities=18%  Similarity=0.198  Sum_probs=43.7

Q ss_pred             HHHHHHH-HcC--CCHHHHHHHhC--CCHHHHHHHHHHhhhhCCcc-cCCCCCCCCCCCCHHH-HHHHHHHHHhC
Q psy15598         54 MRIVELA-QLG--IRPCDISRQLR--VSHGCVSKILARYHETGSIL-PGAIGGSKPRVTTPKV-VSYIKELKQKD  121 (258)
Q Consensus        54 ~RIV~L~-~~G--~S~~eIAr~LG--VSrsTVsRwikRyrEtGsl~-pk~rgG~RPrklT~e~-~~~I~~lv~~n  121 (258)
                      ..||+.+ +.|  .+.++||+.++  +|.+||+..++...+.|-|. +..-+|   ++-|+.- +-++..+++.+
T Consensus        11 ~~Ive~y~~~g~Pv~s~~i~~~~~l~~S~aTIRn~m~~LE~~G~l~~~h~s~G---riPT~~g~r~yv~~ll~~~   82 (87)
T d1stza1          11 YCIVREYIENKKPVSSQRVLEVSNIEFSSATIRNDMKKLEYLGYIYQPHTSAG---RIPTDKGLRFYYEEMLKIS   82 (87)
T ss_dssp             HHHHHHHHHHCSCBCHHHHHHHSCCCSCHHHHHHHHHHHHHTTSEECCSSCSC---BEECHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHcCCccCHHHHHHHhCCCCCHHHHHHHHHHHHHCCcccCCCCCCC---CcccHHHHHHHHHHHcccC
Confidence            3455555 356  58899999955  58999999999999999874 332233   5555543 44555555543

>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=83.44  E-value=0.52  Score=31.68  Aligned_cols=43  Identities=16%  Similarity=0.179  Sum_probs=35.4

Q ss_pred             HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598        110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI  162 (258)
Q Consensus       110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~  162 (258)
                      ....|.+++..++.++..||++.+.          +|.+||.++|+++..+.+
T Consensus         7 N~~~Il~~l~~~g~~sr~eLa~~~g----------lS~~Tv~~~l~~L~~~Gl   49 (71)
T d1z05a1           7 NAGRVYKLIDQKGPISRIDLSKESE----------LAPASITKITRELIDAHL   49 (71)
T ss_dssp             HHHHHHHHHHHHCSBCHHHHHHHHT----------CCHHHHHHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHcCCcCHHHHHHHHC----------CCHHHHHHHHHHHHHCCC
Confidence            3567888888888999999988883          499999999998876654

>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=83.43  E-value=0.46  Score=33.55  Aligned_cols=25  Identities=16%  Similarity=0.096  Sum_probs=23.9

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARY   87 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRy   87 (258)
                      .++.++||+..+||.+||.|..++.
T Consensus        36 ~~si~~lA~~~~vS~sTi~Rf~kkl   60 (83)
T d2o3fa1          36 ESTVNEISALANSSDAAVIRLCKSL   60 (83)
T ss_dssp             TCCHHHHHHHTTCCHHHHHHHHHHT
T ss_pred             HccHHHHHHHHCCCHHHHHHHHHHh
Confidence            6899999999999999999999996

>d1sfua_ a.4.5.19 (A:) 34L {Yaba-like disease virus, YLDV [TaxId: 132475]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: 34L
species: Yaba-like disease virus, YLDV [TaxId: 132475]

Probab=83.10  E-value=0.37  Score=33.65  Aligned_cols=31  Identities=10%  Similarity=0.262  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598         63 GIRPCDISRQLRVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl   93 (258)
                      +.+..+||+.||++++.|.|.+-+..+.|.+
T Consensus        24 ~~tA~~LAk~Lg~~Kk~VNr~LY~L~~~G~v   54 (70)
T d1sfua_          24 YTTAISLSNRLKINKKKINQQLYKLQKEDTV   54 (70)
T ss_dssp             EECHHHHHHHTTCCHHHHHHHHHHHHHTTSE
T ss_pred             CchHHHHHHHhCCCHHHHHHHHHHHHHCCCe
Confidence            4689999999999999999999999999987

>d2ezia_ a.4.1.2 (A:) Transposase {Bacteriophage mu [TaxId: 10677]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase
species: Bacteriophage mu [TaxId: 10677]

Probab=82.54  E-value=1.9  Score=29.55  Aligned_cols=51  Identities=8%  Similarity=-0.094  Sum_probs=36.1

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCC----HHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIF----AWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~it----a~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      ..++++.-++|...-.....-+    ..++...+.+.|+.+    ||.+||+|.++...
T Consensus         6 ~~~~~~~we~i~~~YL~~~~ps~~~~y~~i~~~c~~~gl~~----PS~~T~~rri~~l~   60 (75)
T d2ezia_           6 SEFDEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSI----PSRATAFRRIQQLD   60 (75)
T ss_dssp             CCSCHHHHHHHHHHHTSTTCCCHHHHHHHHHHHHHHHTCCC----CCHHHHHHHHHHHC
T ss_pred             ccCCHHHHHHHHHHHhCccCCCHHHHHHHHHHHHHHcCCCC----CCHHHHHHHHHhCC
Confidence            4578888888888644444444    345555556679876    99999999998643

>d2g7la1 a.4.1.9 (A:16-83) Putative transcriptional regulator SCO7704 {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 SCO7704
species: Streptomyces coelicolor [TaxId: 1902]

Probab=82.54  E-value=0.7  Score=30.73  Aligned_cols=21  Identities=5%  Similarity=0.083  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHhCCCHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKI   83 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRw   83 (258)
                      +.|.++||+.+|||++++|+.
T Consensus        24 ~~si~~ia~~~gvs~~~~y~h   44 (68)
T d2g7la1          24 KVTMRRLAQELDTGPASLYVY   44 (68)
T ss_dssp             SCCHHHHHHHTTSCHHHHTTT
T ss_pred             cCCHHHHHHHHCcCHhHhhHH
Confidence            579999999999999999764

>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=82.17  E-value=1.7  Score=29.37  Aligned_cols=44  Identities=27%  Similarity=0.283  Sum_probs=36.0

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIG  159 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~  159 (258)
                      +.++-+.+++|++++++  ..+..+++..+.          ||.+||.++|++...
T Consensus        13 rPls~DLR~Riv~~~~~--G~s~r~aA~rf~----------VS~s~v~k~l~r~re   56 (63)
T d1k78a1          13 RPLPDVVRQRIVELAHQ--GVRPCDISRQLR----------VSHGCVSKILGRYYE   56 (63)
T ss_dssp             SCCCHHHHHHHHHHHHT--TCCHHHHHHHHT----------CCHHHHHHHHHHHHH
T ss_pred             CcCCHHHHHHHHHHHHc--CCCHHHHHHHhC----------CCHHHHHHHHHHHHH
Confidence            45677889999999875  589999988884          599999999987643

>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=81.87  E-value=0.36  Score=32.29  Aligned_cols=22  Identities=14%  Similarity=0.166  Sum_probs=19.4

Q ss_pred             CCCHHHHHHHhCCCHHHHHHHH
Q psy15598         63 GIRPCDISRQLRVSHGCVSKIL   84 (258)
Q Consensus        63 G~S~~eIAr~LGVSrsTVsRwi   84 (258)
                      +.|.++||+..|||++++|+..
T Consensus        23 ~~t~~~Ia~~agvs~~~iy~hF   44 (68)
T d1z0xa1          23 QLSMRKVAKQLGVQAPAIYWYF   44 (68)
T ss_dssp             GCCHHHHHHHHTSCHHHHHTTC
T ss_pred             ccCHHHHHHHHCcchhHHHHhc
Confidence            3699999999999999998653

>d1mzba_ a.4.5.42 (A:) Ferric uptake regulation protein, FUR {Pseudomonas aeruginosa [TaxId: 287]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: FUR-like
domain: Ferric uptake regulation protein, FUR
species: Pseudomonas aeruginosa [TaxId: 287]

Probab=80.83  E-value=1.5  Score=32.54  Aligned_cols=42  Identities=19%  Similarity=0.436  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHc--C--CCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCc
Q psy15598         52 VRMRIVELAQL--G--IRPCDISRQL-----RVSHGCVSKILARYHETGSI   93 (258)
Q Consensus        52 lR~RIV~L~~~--G--~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl   93 (258)
                      .|..|++.+.+  +  .|..+|-+.+     .|+.+||||-+..+.+.|-+
T Consensus        17 qR~~Il~~L~~~~~~h~sa~ei~~~l~~~~~~i~~aTVYR~L~~l~e~gli   67 (134)
T d1mzba_          17 PRVKILQMLDSAEQRHMSAEDVYKALMEAGEDVGLATVYRVLTQFEAAGLV   67 (134)
T ss_dssp             HHHHHHHHHHCC-CCSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSE
T ss_pred             HHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCCccHHHHHHHHHHHHhccEE
Confidence            67888888752  3  6889998877     49999999999999999976

>d1u78a2 a.4.1.2 (A:55-104) Transposase tc3a1-65 {Caenorhabditis elegans [TaxId: 6239]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Recombinase DNA-binding domain
domain: Transposase tc3a1-65
species: Caenorhabditis elegans [TaxId: 6239]

Probab=80.76  E-value=4.1  Score=25.91  Aligned_cols=46  Identities=13%  Similarity=0.149  Sum_probs=34.7

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI  158 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~  158 (258)
                      +.++..+++-|++...+ -..++.+|+.+|+   +.     +|.+||-+.|++.+
T Consensus         5 k~ls~rdernviraasn-s~kta~dir~el~---l~-----~sk~tiln~i~~~g   50 (50)
T d1u78a2           5 KALSVRDERNVIRAASN-SCKTARDIRNELQ---LS-----ASKRTILNVIKRSG   50 (50)
T ss_dssp             CSSCHHHHHHHHHHHHH-CCCCHHHHHHHTT---CC-----SCHHHHHHHHHHTC
T ss_pred             cccchHHHHHHHHHHhc-chhhHHHHHHHHh---hh-----hHHHHHHHHHhhcC
Confidence            46777777766666544 5789999999884   55     49999999998753

>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=80.13  E-value=1.9  Score=30.04  Aligned_cols=48  Identities=10%  Similarity=0.077  Sum_probs=38.7

Q ss_pred             CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598        104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS  161 (258)
Q Consensus       104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~  161 (258)
                      +..+++....+++++......+..+|+..|   |       ||.+||++.++......
T Consensus         4 k~Ys~EfK~~aV~l~~~~~g~s~~~vA~~l---G-------Is~~tl~~W~k~~~~~~   51 (89)
T d2jn6a1           4 KTYSEEFKRDAVALYENSDGASLQQIANDL---G-------INRVTLKNWIIKYGSNH   51 (89)
T ss_dssp             CCCCHHHHHHHHHHHTTGGGSCHHHHHHHH---T-------SCHHHHHHHHHHHCCCS
T ss_pred             CCCCHHHHHHHHHHHHHcCCCcHHHHHHHH---C-------CCHHHHHHHHHHHhhcc
Confidence            358899999999888766678999998888   4       48999999999875543