Psyllid ID: psy8797

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120--
Protein Sequence
MKGTIRIRLKLKFHSNMVKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR
Secondary Structure (PSIPRED)
ccccHHHHccccccccccHHcccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHccccEEEHHHHHHHHccccEEEEEHHHHHcccccEEEcccccccccc
Secondary Structure Prediction (SSPRO)
cccEEEEEEEccccccHcEEEEccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccEcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccEEcc
Coil and Loop (DISEMBL)
MKGTIRIRLKLKFHSNMVKRRlnldqddeespfktpksvkkmrvnppttpakekgtrydtsLGLLTKKFVKLLqsspqgvvdlnvasesldvqkRRIYDITNVLEGIGILEkksknniqckr
Flexible Loop (DISEMBL)
mkgtirirlklkfhsnmvkrrlnldqddeespfktpksvkkmrvnppttpakekgtrydtSLGLLTKKFVKLLqsspqgvvdlnvasesldvqkrrIYDITNVlegigilekksknniqckr
Low Complexity Region (SEG)
MKGTIRIRLKLKFHSNMVKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR
Disordered region (IsUnstruct)
*******RLKLK***********************************************TSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE***********
Disordered Region (DISOPRED)
***************************************************************LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN*IQCK*
Disordered Region (DISEMBL)
MKGTIRIRLKLKFHSNMVKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR
Disordered Region (DISPRO)
*KGTIRIRLKLKFHSNMVKRRLNLD******************************TRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN***C**
Transmembrane Helix (TMHMM)
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Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
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Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MKGTIRIRLKLKFHSNMVKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR
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	122	2.2.26 [Sep-21-2011]
O00716	465	Transcription factor E2F3	yes	N/A	0.836	0.219	0.559	5e-24
O35261	457	Transcription factor E2F3	yes	N/A	0.827	0.221	0.564	6e-24
P56931	443	Transcription factor E2F2	no	N/A	0.696	0.191	0.673	5e-23
Q14209	437	Transcription factor E2F2	no	N/A	0.696	0.194	0.663	2e-22
Q90977	403	Transcription factor E2F1	no	N/A	0.819	0.248	0.567	4e-22
Q27368	805	Transcription factor E2f	yes	N/A	0.516	0.078	0.841	4e-21
Q9FV71	469	Transcription factor E2FB	yes	N/A	0.581	0.151	0.619	2e-19
Q9FV70	396	Transcription factor E2FC	no	N/A	0.532	0.164	0.676	3e-19
Q61501	430	Transcription factor E2F1	no	N/A	0.778	0.220	0.522	3e-19
Q01094	437	Transcription factor E2F1	no	N/A	0.819	0.228	0.528	1e-18

>sp|O00716|E2F3_HUMAN Transcription factor E2F3 OS=Homo sapiens GN=E2F3 PE=1 SV=1

 Score =  109 bits (273), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 61/109 (55%), Positives = 74/109 (67%), Gaps = 7/109 (6%)

Query: 18  VKRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFV 70
            KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF+
Sbjct: 132 AKRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFI 191

Query: 71  KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           +LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct: 192 QLLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 240

Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-3 binds specifically to RB1 protein, in a cell-cycle dependent manner.
Homo sapiens (taxid: 9606)

>sp|O35261|E2F3_MOUSE Transcription factor E2F3 OS=Mus musculus GN=E2f3 PE=1 SV=2

 Score =  109 bits (272), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 61/108 (56%), Positives = 74/108 (68%), Gaps = 7/108 (6%)

Query: 19  KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
           KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct: 125 KRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 184

Query: 72  LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct: 185 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 232

Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-3 binds specifically to RB1 protein, in a cell-cycle dependent manner.

Mus musculus (taxid: 10090)

>sp|P56931|E2F2_MOUSE Transcription factor E2F2 OS=Mus musculus GN=E2f2 PE=1 SV=2

 Score =  106 bits (264), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 62/92 (67%), Positives = 70/92 (76%), Gaps = 7/92 (7%)

Query: 33  FKTPKSVKKMRVN---PPTTPAKEKG--TRYDTSLGLLTKKFVKLLQSSPQGVVDLNVAS 87
           F+TPK  K +RV+    P TP K  G  TRYDTSLGLLTKKF+ LL  S  GV+DLN A+
Sbjct: 104 FRTPKG-KCIRVDGLPSPKTP-KSPGEKTRYDTSLGLLTKKFIYLLSESEDGVLDLNWAA 161

Query: 88  ESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           E LDVQKRRIYDITNVLEGI ++ KKSKNNIQ
Sbjct: 162 EVLDVQKRRIYDITNVLEGIQLIRKKSKNNIQ 193

Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F-2 binds specifically to RB1 protein, in a cell-cycle dependent manner.

Mus musculus (taxid: 10090)

>sp|Q14209|E2F2_HUMAN Transcription factor E2F2 OS=Homo sapiens GN=E2F2 PE=1 SV=1

 Score =  104 bits (259), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 61/92 (66%), Positives = 69/92 (75%), Gaps = 7/92 (7%)

Query: 33  FKTPKSVKKMRVN---PPTTPAKEKG--TRYDTSLGLLTKKFVKLLQSSPQGVVDLNVAS 87
           F TPK  K +RV+    P TP K  G  TRYDTSLGLLTKKF+ LL  S  GV+DLN A+
Sbjct: 102 FPTPKG-KCIRVDGLPSPKTP-KSPGEKTRYDTSLGLLTKKFIYLLSESEDGVLDLNWAA 159

Query: 88  ESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           E LDVQKRRIYDITNVLEGI ++ KK+KNNIQ
Sbjct: 160 EVLDVQKRRIYDITNVLEGIQLIRKKAKNNIQ 191

Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from g1 to s phase. E2F-2 binds specifically to RB1 protein, in a cell-cycle dependent manner.

Homo sapiens (taxid: 9606)

>sp|Q90977|E2F1_CHICK Transcription factor E2F1 OS=Gallus gallus GN=E2F1 PE=2 SV=1

 Score =  103 bits (256), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 59/104 (56%), Positives = 73/104 (70%), Gaps = 4/104 (3%)

Query: 18  VKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKG--TRYDTSLGLLTKKFVKLLQS 75
           VKR+LNL+ D +      P +  + R+  P   AK  G  +RY+TSL L TK+F++LL  
Sbjct: 65  VKRKLNLETDHQYIAESLPAARGRARI--PGRGAKSPGEKSRYETSLNLTTKRFLELLSQ 122

Query: 76  SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           SP GVVDLN A+E L VQKRRIYDITNVLEGI ++ KKSKNNIQ
Sbjct: 123 SPDGVVDLNWAAEVLKVQKRRIYDITNVLEGIQLITKKSKNNIQ 166

Transcription activator that binds DNA cooperatively with dp proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-1 binds preferentially RB1 protein, in a cell-cycle dependent manner. It can mediate both cell proliferation and p53-dependent apoptosis.

Gallus gallus (taxid: 9031)

>sp|Q27368|E2F_DROME Transcription factor E2f OS=Drosophila melanogaster GN=E2f PE=1 SV=2

 Score = 99.8 bits (247), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 53/63 (84%), Positives = 54/63 (85%)

Query: 57  RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116
           R DTSLG+LTKKFV LLQ SP GVVDLN AS  L VQKRRIYDITNVLEGI ILEKKSKN
Sbjct: 254 RADTSLGILTKKFVDLLQESPDGVVDLNEASNRLHVQKRRIYDITNVLEGINILEKKSKN 313

Query: 117 NIQ 119
           NIQ
Sbjct: 314 NIQ 316

Transcriptional activator that binds to E2f sites. Required for wild-type growth in mitotic and polytene tissues, Contributes to the expression of replication genes at the G1-S transition and Cyclin E. Activates cell proliferation in wing imaginal disk, which requires expression of vg.

Drosophila melanogaster (taxid: 7227)

>sp|Q9FV71|E2FB_ARATH Transcription factor E2FB OS=Arabidopsis thaliana GN=E2FB PE=1 SV=1

 Score = 94.4 bits (233), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/71 (61%), Positives = 58/71 (81%)

Query: 51  AKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL 110
           A+    RYD+SLGLLTKKF+ L++ +  G++DLN A+++L+VQKRRIYDITNVLEGIG++
Sbjct: 123 AQAGTCRYDSSLGLLTKKFINLIKQAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLI 182

Query: 111 EKKSKNNIQCK 121
           EK  KN IQ K
Sbjct: 183 EKTLKNRIQWK 193

Transcription activator that binds DNA cooperatively with DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The binding of retinoblastoma-related proteins represses transactivation. Involved in the control of cell-cycle progression from G1 to S phase and from G2 to M phase. Stimulates cell proliferation and delays differentiation. Represses cell enlargement and endoreduplication in auxin-free conditions.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FV70|E2FC_ARATH Transcription factor E2FC OS=Arabidopsis thaliana GN=E2FC PE=1 SV=1

 Score = 94.0 bits (232), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 44/65 (67%), Positives = 55/65 (84%)

Query: 57  RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN 116
           RYD+SLGLLTKKFVKL+Q +  G +DLN  +  L+VQKRRIYDITNVLEGIG++EK +KN
Sbjct: 155 RYDSSLGLLTKKFVKLIQEAEDGTLDLNYCAVVLEVQKRRIYDITNVLEGIGLIEKTTKN 214

Query: 117 NIQCK 121
           +I+ K
Sbjct: 215 HIRWK 219

Involved in transcriptional repression. May act by repressing E2F-regulated genes in mature differentiated cells, but is not an antagonist of E2FA. Restricts cell division and is involved in the coordination between cell proliferation and endoreduplication during development. May play a role during the transition from skotomorphogenesis to photomorphogenesis. Regulated by phosphorylation-dependent proteolysis via the protein-ubiquitin ligase SCF(SKP2A) complex.

Arabidopsis thaliana (taxid: 3702)

>sp|Q61501|E2F1_MOUSE Transcription factor E2F1 OS=Mus musculus GN=E2f1 PE=1 SV=1

 Score = 93.6 bits (231), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 57/109 (52%), Positives = 70/109 (64%), Gaps = 14/109 (12%)

Query: 18  VKRRLNLDQDDE-----ESPFKTPKSVKKMRVNPPTTPAKEKG--TRYDTSLGLLTKKFV 70
           VKRRL+L+ D +       PF+        R   P    K  G  +RY+TSL L TK+F+
Sbjct: 83  VKRRLDLETDHQYLAGSSGPFRG-------RGRHPGKGVKSPGEKSRYETSLNLTTKRFL 135

Query: 71  KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           +LL  S  GVVDLN A+E L VQKRRIYDITNVLEGI ++ KKSKN+IQ
Sbjct: 136 ELLSRSADGVVDLNWAAEVLKVQKRRIYDITNVLEGIQLIAKKSKNHIQ 184

Transcription activator that binds DNA cooperatively with dp proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-1 binds preferentially RB1 protein, in a cell-cycle dependent manner. It can mediate both cell proliferation and p53-dependent apoptosis.

Mus musculus (taxid: 10090)

>sp|Q01094|E2F1_HUMAN Transcription factor E2F1 OS=Homo sapiens GN=E2F1 PE=1 SV=1

 Score = 91.7 bits (226), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 55/104 (52%), Positives = 68/104 (65%), Gaps = 4/104 (3%)

Query: 18  VKRRLNLDQDDEESPFKTPKSVKKMRVNPPTTPAKEKG--TRYDTSLGLLTKKFVKLLQS 75
           VKRRL+L+ D +           + R   P    K  G  +RY+TSL L TK+F++LL  
Sbjct: 88  VKRRLDLETDHQY--LAESSGPARGRGRHPGKGVKSPGEKSRYETSLNLTTKRFLELLSH 145

Query: 76  SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
           S  GVVDLN A+E L VQKRRIYDITNVLEGI ++ KKSKN+IQ
Sbjct: 146 SADGVVDLNWAAEVLKVQKRRIYDITNVLEGIQLIAKKSKNHIQ 189

Transcription activator that binds DNA cooperatively with dp proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3' found in the promoter region of a number of genes whose products are involved in cell cycle regulation or in DNA replication. The DRTF1/E2F complex functions in the control of cell-cycle progression from G1 to S phase. E2F-1 binds preferentially RB1 protein, in a cell-cycle dependent manner. It can mediate both cell proliferation and p53-dependent apoptosis.

Homo sapiens (taxid: 9606)

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	122
156546407	447	PREDICTED: transcription factor E2F3-lik	0.844	0.230	0.657	1e-26
193673908	422	PREDICTED: transcription factor E2F2-lik	0.877	0.253	0.595	4e-26
328708308	394	PREDICTED: transcription factor E2F2-lik	0.877	0.271	0.603	4e-26
332016563	446	Transcription factor E2F3 [Acromyrmex ec	0.852	0.233	0.619	4e-26
357608368	381	E2F1 [Danaus plexippus]	0.877	0.280	0.578	5e-26
340719191	416	PREDICTED: transcription factor E2F3-lik	0.844	0.247	0.640	8e-26
350399050	416	PREDICTED: transcription factor E2F3-lik	0.844	0.247	0.640	9e-26
189242505	485	PREDICTED: similar to E2F transcription	0.811	0.204	0.623	9e-26
340719189	450	PREDICTED: transcription factor E2F3-lik	0.844	0.228	0.640	9e-26
350538465	456	E2F transcription factor 1 [Bombyx mori]	0.877	0.234	0.570	1e-25

>gi|156546407|ref|XP_001607080.1| PREDICTED: transcription factor E2F3-like isoform 1 [Nasonia vitripennis] gi|345498319|ref|XP_003428202.1| PREDICTED: transcription factor E2F3-like isoform 2 [Nasonia vitripennis]

 Score =  124 bits (310), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 73/111 (65%), Positives = 81/111 (72%), Gaps = 8/111 (7%)

Query: 18  VKRRLNLDQDDEESPFKTPKSVKKMRVNPPT----TPAKEKG---TRYDTSLGLLTKKFV 70
           VKRRLNL+    +S FK PK  K+ R    +    TP K K    TRYDTSL LLTKKF+
Sbjct: 87  VKRRLNLEVGPSQSTFKAPKG-KRRRSGSSSLTGHTPTKSKTVERTRYDTSLSLLTKKFI 145

Query: 71  KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
            L++ S  GVVDLNVASE L+VQKRRIYDITNVLEGIGILEKKSKNNIQ K
Sbjct: 146 NLVEDSNDGVVDLNVASEKLEVQKRRIYDITNVLEGIGILEKKSKNNIQWK 196

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193673908|ref|XP_001945228.1| PREDICTED: transcription factor E2F2-like isoform 1 [Acyrthosiphon pisum] gi|328708305|ref|XP_003243650.1| PREDICTED: transcription factor E2F2-like isoform 2 [Acyrthosiphon pisum]

 Score =  122 bits (305), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 72/121 (59%), Positives = 80/121 (66%), Gaps = 14/121 (11%)

Query: 15  SNMVKRRLNLDQDDEESPFKTPKSVKKMR--------------VNPPTTPAKEKGTRYDT 60
           S  VKRRLNL+  +      TP + K MR               N       E+ TRYDT
Sbjct: 65  SQGVKRRLNLESLNFGYDDVTPSTAKLMRKWSSSSAGSEPSPAQNVAAKKCSERPTRYDT 124

Query: 61  SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120
           SLGLLTKKF+ LL++S  GVVDLN+ASE LDVQKRRIYDITNVLEGIGILEKKSKNNIQ 
Sbjct: 125 SLGLLTKKFIGLLENSTDGVVDLNIASEKLDVQKRRIYDITNVLEGIGILEKKSKNNIQW 184

Query: 121 K 121
           K
Sbjct: 185 K 185

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328708308|ref|XP_003243651.1| PREDICTED: transcription factor E2F2-like isoform 3 [Acyrthosiphon pisum]

 Score =  122 bits (305), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 73/121 (60%), Positives = 83/121 (68%), Gaps = 14/121 (11%)

Query: 15  SNMVKRRLNLDQDDEESPFKTPKSVKKMR------VNPPTTPAK--------EKGTRYDT 60
           S  VKRRLNL+  +      TP + K MR           +PA+        E+ TRYDT
Sbjct: 37  SQGVKRRLNLESLNFGYDDVTPSTAKLMRKWSSSSAGSEPSPAQNVAAKKCSERPTRYDT 96

Query: 61  SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120
           SLGLLTKKF+ LL++S  GVVDLN+ASE LDVQKRRIYDITNVLEGIGILEKKSKNNIQ 
Sbjct: 97  SLGLLTKKFIGLLENSTDGVVDLNIASEKLDVQKRRIYDITNVLEGIGILEKKSKNNIQW 156

Query: 121 K 121
           K
Sbjct: 157 K 157

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332016563|gb|EGI57444.1| Transcription factor E2F3 [Acromyrmex echinatior]

 Score =  121 bits (304), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 70/113 (61%), Positives = 82/113 (72%), Gaps = 9/113 (7%)

Query: 18  VKRRLNLD---QDDEESPFKTPKSVKK------MRVNPPTTPAKEKGTRYDTSLGLLTKK 68
           VKRRLNL+       +S FKTP+  ++      +  + PT     + TRYDTSL LLTKK
Sbjct: 85  VKRRLNLEVGTTGPSQSAFKTPRGKRRRSGSNSLAGHTPTKSKTVERTRYDTSLSLLTKK 144

Query: 69  FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
           F+ L++SS  GVVDLNVASE L+VQKRRIYDITNVLEGIGILEKKSKNNIQ K
Sbjct: 145 FIHLVESSQDGVVDLNVASEKLEVQKRRIYDITNVLEGIGILEKKSKNNIQWK 197

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357608368|gb|EHJ65959.1| E2F1 [Danaus plexippus]

 Score =  121 bits (303), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 70/121 (57%), Positives = 83/121 (68%), Gaps = 14/121 (11%)

Query: 15  SNMVKRRLNLDQDDEESP---------FKTPKSVKKMRVNPPTTPAKE-----KGTRYDT 60
           S  VKRRLNL +    S          FKTPK  +   + P + P+       + +R+DT
Sbjct: 141 SEAVKRRLNLSESSSGSQGHVVPMKADFKTPKQKRVKVLTPYSRPSSSMKKYTERSRFDT 200

Query: 61  SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120
           SLGLLTKKFV LL+SSP GV+DLN+A+E L VQKRRIYDITNVLEGIGILEK+SKNNIQ 
Sbjct: 201 SLGLLTKKFVALLKSSPNGVLDLNIAAEHLSVQKRRIYDITNVLEGIGILEKRSKNNIQW 260

Query: 121 K 121
           K
Sbjct: 261 K 261

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719191|ref|XP_003398040.1| PREDICTED: transcription factor E2F3-like isoform 2 [Bombus terrestris]

 Score =  120 bits (302), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 82/114 (71%), Gaps = 11/114 (9%)

Query: 18  VKRRLNLDQDD---EESPFKTPKSVKKMRVNPPT----TPAKEKG---TRYDTSLGLLTK 67
           VKRRLNL+       +S FK P+  K+ R    +    TP K K    TRYDTSL LLTK
Sbjct: 86  VKRRLNLEMGTTGPSQSAFKAPRG-KRRRSGSSSLAGHTPTKSKTVERTRYDTSLSLLTK 144

Query: 68  KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
           KF+ L++SS  GVVDLNVASE L+VQKRRIYDITNVLEGIGILEKKSKNNIQ K
Sbjct: 145 KFIHLVESSQDGVVDLNVASEKLEVQKRRIYDITNVLEGIGILEKKSKNNIQWK 198

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350399050|ref|XP_003485399.1| PREDICTED: transcription factor E2F3-like isoform 2 [Bombus impatiens]

 Score =  120 bits (302), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 82/114 (71%), Gaps = 11/114 (9%)

Query: 18  VKRRLNLDQDD---EESPFKTPKSVKKMRVNPPT----TPAKEKG---TRYDTSLGLLTK 67
           VKRRLNL+       +S FK P+  K+ R    +    TP K K    TRYDTSL LLTK
Sbjct: 86  VKRRLNLEMGTTGPSQSAFKAPRG-KRRRSGSSSLAGHTPTKSKTVERTRYDTSLSLLTK 144

Query: 68  KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
           KF+ L++SS  GVVDLNVASE L+VQKRRIYDITNVLEGIGILEKKSKNNIQ K
Sbjct: 145 KFIHLVESSQDGVVDLNVASEKLEVQKRRIYDITNVLEGIGILEKKSKNNIQWK 198

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189242505|ref|XP_968025.2| PREDICTED: similar to E2F transcription factor 2 [Tribolium castaneum]

 Score =  120 bits (302), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 68/109 (62%), Positives = 80/109 (73%), Gaps = 10/109 (9%)

Query: 18  VKRRLNLDQDDE-----ESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKL 72
           VKRRLNL+ +       +  FK P+  K+ R+ P      +K TRYDTSLGLLT+KF  L
Sbjct: 46  VKRRLNLELERGRVVPLKQEFKPPQPRKQKRLTP-----TKKNTRYDTSLGLLTQKFSAL 100

Query: 73  LQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
           L+ SP GVVDLN AS+ L+VQKRRIYDITNVLEGIGI+EKKSKNNIQ K
Sbjct: 101 LEESPNGVVDLNKASQQLNVQKRRIYDITNVLEGIGIIEKKSKNNIQWK 149

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340719189|ref|XP_003398039.1| PREDICTED: transcription factor E2F3-like isoform 1 [Bombus terrestris] gi|350399047|ref|XP_003485398.1| PREDICTED: transcription factor E2F3-like isoform 1 [Bombus impatiens]

 Score =  120 bits (301), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 73/114 (64%), Positives = 82/114 (71%), Gaps = 11/114 (9%)

Query: 18  VKRRLNLDQDD---EESPFKTPKSVKKMRVNPPT----TPAKEKG---TRYDTSLGLLTK 67
           VKRRLNL+       +S FK P+  K+ R    +    TP K K    TRYDTSL LLTK
Sbjct: 86  VKRRLNLEMGTTGPSQSAFKAPRG-KRRRSGSSSLAGHTPTKSKTVERTRYDTSLSLLTK 144

Query: 68  KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK 121
           KF+ L++SS  GVVDLNVASE L+VQKRRIYDITNVLEGIGILEKKSKNNIQ K
Sbjct: 145 KFIHLVESSQDGVVDLNVASEKLEVQKRRIYDITNVLEGIGILEKKSKNNIQWK 198

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350538465|ref|NP_001233214.1| E2F transcription factor 1 [Bombyx mori] gi|341865523|dbj|BAG85354.2| E2F1 [Bombyx mori]

 Score =  120 bits (301), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 69/121 (57%), Positives = 82/121 (67%), Gaps = 14/121 (11%)

Query: 15  SNMVKRRLNLDQDDEESP---------FKTPKSVKKMRVNPPTTPAKE-----KGTRYDT 60
           S  VKRRLNL +    S          FKTPK  +   + P + P+       + +R+DT
Sbjct: 67  SEAVKRRLNLSESSSGSQGHVVPMKADFKTPKQKRVKVLTPYSRPSSSMKKYTERSRFDT 126

Query: 61  SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC 120
           SLGLLTKKFV LL+SS  GV+DLN+A+E L VQKRRIYDITNVLEGIGILEK+SKNNIQ 
Sbjct: 127 SLGLLTKKFVALLKSSQNGVLDLNIAAEHLSVQKRRIYDITNVLEGIGILEKRSKNNIQW 186

Query: 121 K 121
           K
Sbjct: 187 K 187

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	122
UNIPROTKB|J9P6U4	334	E2F3 "Uncharacterized protein"	0.827	0.302	0.564	1.6e-24
RGD|1561600	245	E2f3 "E2F transcription factor	0.827	0.412	0.564	1.6e-24
UNIPROTKB|F1NR90	342	E2F3 "Uncharacterized protein"	0.827	0.295	0.574	2e-24
UNIPROTKB|F1P324	348	E2F3 "Uncharacterized protein"	0.827	0.290	0.574	2e-24
UNIPROTKB|F1MYH2	463	E2F3 "Uncharacterized protein"	0.827	0.218	0.564	2.3e-24
UNIPROTKB|F1RUH1	358	E2F3 "Uncharacterized protein"	0.778	0.265	0.615	3.3e-24
MGI|MGI:1096340	457	E2f3 "E2F transcription factor	0.827	0.221	0.564	3.6e-24
UNIPROTKB|O00716	465	E2F3 "Transcription factor E2F	0.827	0.217	0.564	4e-24
UNIPROTKB|E1BD75	365	E2F2 "Uncharacterized protein"	0.852	0.284	0.601	6.8e-24
MGI|MGI:1096341	443	E2f2 "E2F transcription factor	0.811	0.223	0.629	8.5e-24

UNIPROTKB|J9P6U4 E2F3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 61/108 (56%), Positives = 74/108 (68%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct:     2 KRRLELGESGHQYLSDGLKTPKGKGRATLRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 61

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:    62 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 109

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

RGD|1561600 E2f3 "E2F transcription factor 3" [Rattus norvegicus (taxid:10116)]

 Score = 280 (103.6 bits), Expect = 1.6e-24, P = 1.6e-24
 Identities = 61/108 (56%), Positives = 74/108 (68%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct:   126 KRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 185

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:   186 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 233

GO:0001047 "core promoter binding" evidence=ISO

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

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

GO:0005667 "transcription factor complex" evidence=IEA

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

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

GO:0008284 "positive regulation of cell proliferation" evidence=ISO

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

UNIPROTKB|F1NR90 E2F3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 62/108 (57%), Positives = 73/108 (67%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +     P +P   K     TRYDTSLGLLTKKF++
Sbjct:     6 KRRLELGESGHQYLAEGLKTPKGKGRAATRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 65

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNNIQ
Sbjct:    66 LLSQSPDGVLDLNRAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNIQ 113

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

UNIPROTKB|F1P324 E2F3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 62/108 (57%), Positives = 73/108 (67%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +     P +P   K     TRYDTSLGLLTKKF++
Sbjct:    13 KRRLELGESGHQYLAEGLKTPKGKGRAATRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 72

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNNIQ
Sbjct:    73 LLSQSPDGVLDLNRAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNIQ 120

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0001047 "core promoter binding" evidence=IEA

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

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

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

UNIPROTKB|F1MYH2 E2F3 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 282 (104.3 bits), Expect = 2.3e-24, P = 2.3e-24
 Identities = 61/108 (56%), Positives = 75/108 (69%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +  ++      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct:   131 KRRLELGESGQQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 190

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:   191 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 238

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

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

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

GO:0001047 "core promoter binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

UNIPROTKB|F1RUH1 E2F3 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 64/104 (61%), Positives = 77/104 (74%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLLTKKFVKLLQS 75
             KRRL L +  ++      KTPK   K R   P +P+ EK TRYDTSLGLLTKKF++LL  
Sbjct:    13 KRRLELGESGQQYLADGLKTPKG--KGRA--PKSPS-EK-TRYDTSLGLLTKKFIQLLSQ 66

Query:    76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:    67 SPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 110

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

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

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

GO:0001047 "core promoter binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

MGI|MGI:1096340 E2f3 "E2F transcription factor 3" [Mus musculus (taxid:10090)]

 Score = 280 (103.6 bits), Expect = 3.6e-24, P = 3.6e-24
 Identities = 61/108 (56%), Positives = 74/108 (68%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct:   125 KRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 184

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:   185 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 232

GO:0001047 "core promoter binding" evidence=ISO

GO:0003677 "DNA binding" evidence=IDA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

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

GO:0007049 "cell cycle" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IDA

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

UNIPROTKB|O00716 E2F3 "Transcription factor E2F3" [Homo sapiens (taxid:9606)]

 Score = 280 (103.6 bits), Expect = 4.0e-24, P = 4.0e-24
 Identities = 61/108 (56%), Positives = 74/108 (68%)

Query:    19 KRRLNLDQDDEE---SPFKTPKSVKKMRVNPPTTPAKEKG----TRYDTSLGLLTKKFVK 71
             KRRL L +   +      KTPK   +  +  P +P   K     TRYDTSLGLLTKKF++
Sbjct:   133 KRRLELGESGHQYLSDGLKTPKGKGRAALRSPDSPKTPKSPSEKTRYDTSLGLLTKKFIQ 192

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  SP GV+DLN A+E L VQKRRIYDITNVLEGI +++KKSKNN+Q
Sbjct:   193 LLSQSPDGVLDLNKAAEVLKVQKRRIYDITNVLEGIHLIKKKSKNNVQ 240

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0008284 "positive regulation of cell proliferation" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0001047 "core promoter binding" evidence=IDA

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0000080 "G1 phase of mitotic cell cycle" evidence=TAS

GO:0000085 "G2 phase of mitotic cell cycle" evidence=TAS

GO:0000278 "mitotic cell cycle" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

UNIPROTKB|E1BD75 E2F2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 274 (101.5 bits), Expect = 6.8e-24, P = 6.8e-24
 Identities = 68/113 (60%), Positives = 81/113 (71%)

Query:    14 HSNMVKRRLNLDQDDEES-P-FKTPKSVKKMRVN--P-PTTPAKEKG--TRYDTSLGLLT 66
             H    KR+L+L+     + P F+TPK  K +RV+  P P TP K  G  TRYDTSLGLLT
Sbjct:    11 HLPGAKRKLDLEGIGRPTVPEFRTPKG-KCIRVDGLPSPKTP-KSPGEKTRYDTSLGLLT 68

Query:    67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             KKF+ LL  S  GV+DLN A+E LDVQKRRIYDITNVLEGI ++ KK+KNNIQ
Sbjct:    69 KKFIYLLSESEDGVLDLNWAAEVLDVQKRRIYDITNVLEGIQLIRKKAKNNIQ 121

GO:0051726 "regulation of cell cycle" evidence=IEA

GO:0008134 "transcription factor binding" evidence=IEA

GO:0006915 "apoptotic process" evidence=IEA

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

GO:0001047 "core promoter binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

MGI|MGI:1096341 E2f2 "E2F transcription factor 2" [Mus musculus (taxid:10090)]

 Score = 276 (102.2 bits), Expect = 8.5e-24, P = 8.5e-24
 Identities = 68/108 (62%), Positives = 80/108 (74%)

Query:    19 KRRLNLDQDDEES-P-FKTPKSVKKMRVN--P-PTTPAKEKG--TRYDTSLGLLTKKFVK 71
             KR+L+L+     + P F+TPK  K +RV+  P P TP K  G  TRYDTSLGLLTKKF+ 
Sbjct:    88 KRKLDLEGIGRPTVPEFRTPKG-KCIRVDGLPSPKTP-KSPGEKTRYDTSLGLLTKKFIY 145

Query:    72 LLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ 119
             LL  S  GV+DLN A+E LDVQKRRIYDITNVLEGI ++ KKSKNNIQ
Sbjct:   146 LLSESEDGVLDLNWAAEVLDVQKRRIYDITNVLEGIQLIRKKSKNNIQ 193

GO:0001047 "core promoter binding" evidence=ISO

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IEA

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

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

GO:0006915 "apoptotic process" evidence=IDA

GO:0007049 "cell cycle" evidence=IEA

GO:0008134 "transcription factor binding" evidence=ISO

GO:0051726 "regulation of cell cycle" 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)
O35261	E2F3_MOUSE	No assigned EC number	0.5648	0.8278	0.2210	yes	N/A
Q27368	E2F_DROME	No assigned EC number	0.8412	0.5163	0.0782	yes	N/A
O00716	E2F3_HUMAN	No assigned EC number	0.5596	0.8360	0.2193	yes	N/A
Q9FV71	E2FB_ARATH	No assigned EC number	0.6197	0.5819	0.1513	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	122
pfam02319	67	pfam02319, E2F_TDP, E2F/DP family winged-helix DNA	3e-28

>gnl|CDD|202203 pfam02319, E2F_TDP, E2F/DP family winged-helix DNA-binding domain

 Score = 97.6 bits (244), Expect = 3e-28
 Identities = 44/66 (66%), Positives = 54/66 (81%), Gaps = 1/66 (1%)

Query: 57  RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSK 115
           R + SLGLLT+KF+KL + SP G+ DLN A++ LDV QKRRIYDITNVLEGIG++EKKSK
Sbjct: 1   RKEKSLGLLTQKFLKLCEKSPDGITDLNEAAKELDVKQKRRIYDITNVLEGIGLIEKKSK 60

Query: 116 NNIQCK 121
           N I+  
Sbjct: 61  NEIRWI 66

This family contains the transcription factor E2F and its dimerisation partners TDP1 and TDP2, which stimulate E2F-dependent transcription. E2F binds to DNA as a homodimer or as a heterodimer in association with TDP1/2, the heterodimer having increased binding efficiency. The crystal structure of an E2F4-DP2-DNA complex shows that the DNA-binding domains of the E2F and DP proteins both have a fold related to the winged-helix DNA-binding motif. Recognition of the central c/gGCGCg/c sequence of the consensus DNA-binding site is symmetric, and amino acids that contact these bases are conserved among all known E2F and DP proteins. Length = 67

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	122
KOG2577|consensus	354		99.97
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	99.94
KOG2578|consensus	388		99.86
KOG2578|consensus	388		99.63
KOG2829|consensus	326		98.24
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	96.83
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	96.14
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	95.94
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	95.77
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	95.66
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	95.24
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	95.21
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	94.77
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	94.67
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	94.29
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	94.22
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	94.01
PF13730	55	HTH_36: Helix-turn-helix domain	93.11
PF01047	59	MarR: MarR family; InterPro: IPR000835 The MarR-ty	92.69
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	92.52
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	92.3
PF09079	85	Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The	92.25
PF13463	68	HTH_27: Winged helix DNA-binding domain; PDB: 3GFL	92.04
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	91.92
cd08768	87	Cdc6_C Winged-helix domain of essential DNA replic	91.84
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	91.14
TIGR00738	132	rrf2_super rrf2 family protein (putative transcrip	90.34
PF01726	65	LexA_DNA_bind: LexA DNA binding domain; InterPro:	89.53
PF01022	47	HTH_5: Bacterial regulatory protein, arsR family;	88.97
COG3355	126	Predicted transcriptional regulator [Transcription	88.94
PF09012	69	FeoC: FeoC like transcriptional regulator; InterPr	88.68
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	88.45
PF04182	75	B-block_TFIIIC: B-block binding subunit of TFIIIC;	88.1
PRK09834	263	DNA-binding transcriptional activator MhpR; Provis	87.15
PF08220	57	HTH_DeoR: DeoR-like helix-turn-helix domain; Inter	86.95
TIGR00122	69	birA_repr_reg BirA biotin operon repressor domain.	86.94
cd07377	66	WHTH_GntR Winged helix-turn-helix (WHTH) DNA-bindi	86.77
smart00344	108	HTH_ASNC helix_turn_helix ASNC type. AsnC: an auto	86.33
smart00347	101	HTH_MARR helix_turn_helix multiple antibiotic resi	86.23
COG1378	247	Predicted transcriptional regulators [Transcriptio	86.18
PF12840	61	HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_	86.13
PF08784	102	RPA_C: Replication protein A C terminal; InterPro:	85.78
TIGR02716	306	C20_methyl_CrtF C-20 methyltransferase BchU. Membe	85.51
TIGR01610	95	phage_O_Nterm phage replication protein O, N-termi	84.69
TIGR02010	135	IscR iron-sulfur cluster assembly transcription fa	84.03
PF01325	60	Fe_dep_repress: Iron dependent repressor, N-termin	83.94
COG2739	105	Uncharacterized protein conserved in bacteria [Fun	83.89
TIGR01764	49	excise DNA binding domain, excisionase family. An	83.85
PF13518	52	HTH_28: Helix-turn-helix domain	83.73
PF08280	59	HTH_Mga: M protein trans-acting positive regulator	83.25
PRK11511	127	DNA-binding transcriptional activator MarA; Provis	82.95
TIGR01889	109	Staph_reg_Sar staphylococcal accessory regulator f	82.78
PRK09954	362	putative kinase; Provisional	82.49
PRK10857	164	DNA-binding transcriptional regulator IscR; Provis	82.26
TIGR02431	248	pcaR_pcaU beta-ketoadipate pathway transcriptional	82.11
PF13545	76	HTH_Crp_2: Crp-like helix-turn-helix domain; PDB:	82.01
PRK10219	107	DNA-binding transcriptional regulator SoxS; Provis	82.0
COG1414	246	IclR Transcriptional regulator [Transcription]	80.96
PRK00215	205	LexA repressor; Validated	80.87
PRK15090	257	DNA-binding transcriptional regulator KdgR; Provis	80.38

>KOG2577|consensus

Probab=99.97  E-value=3.9e-32  Score=228.26  Aligned_cols=107  Identities=55%  Similarity=0.723  Sum_probs=88.6

Q ss_pred             hhhhhhcCCCCCCC-CC--CccCCCccccc--cCC-CCCCCCC-CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHh
Q psy8797          16 NMVKRRLNLDQDDE-ES--PFKTPKSVKKM--RVN-PPTTPAK-EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASE   88 (122)
Q Consensus        16 ~~~~r~~~l~~~~~-~~--~~~tp~~~~~~--~~~-~~~~~k~-~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~   88 (122)
                      .++|++..+++... ..  .+.+|.+.++.  +.+ ++..+++ +.+.|+++|||+||+|||.|++++|+|++|||.||+
T Consensus        20 ~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~   99 (354)
T KOG2577|consen   20 LPAKEDSRLEEMDPQSVESGLPSPISPGSRMDRKPDSSKSSSSPSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAE   99 (354)
T ss_pred             cchhhhhhhhcccccccccCCCCCCCCCcccccCCCCcccccCCCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHH
Confidence            67888888877433 11  14444444433  333 4455555 788999999999999999999999999999999999


Q ss_pred             HhccchhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797          89 SLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR  122 (122)
Q Consensus        89 ~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G  122 (122)
                      .|+|+|||||||||||||||||+|++||+|+|+|
T Consensus       100 ~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G  133 (354)
T KOG2577|consen  100 VLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIG  133 (354)
T ss_pred             Hhccccceeeehhhhhhcccceeeccccceeeec
Confidence            9999999999999999999999999999999998

>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle

Probab=99.94  E-value=3.2e-27  Score=158.11  Aligned_cols=66  Identities=47%  Similarity=0.790  Sum_probs=62.9

Q ss_pred             CCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh---cc--chhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797          57 RYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESL---DV--QKRRIYDITNVLEGIGILEKKSKNNIQCKR  122 (122)
Q Consensus        57 R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L---~v--~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G  122 (122)
                      |+++||+.+|++|+++|...+++.++++++|+.|   ++  ++||||||+|||||+|+|+|.+++.|.|+|
T Consensus         1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G   71 (71)
T PF02319_consen    1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG   71 (71)
T ss_dssp             TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred             CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence            7899999999999999999999999999999999   99  999999999999999999999999999998

Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.

>KOG2578|consensus

Probab=99.86  E-value=1.4e-22  Score=169.60  Aligned_cols=70  Identities=40%  Similarity=0.622  Sum_probs=67.4

Q ss_pred             CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797          53 EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCKR  122 (122)
Q Consensus        53 ~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G  122 (122)
                      .-++|++||||+||++|+.++..+....+.|++||.+|||+|||||||+||||+||+++|.+||.|.|.|
T Consensus        17 qvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkG   86 (388)
T KOG2578|consen   17 QVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKG   86 (388)
T ss_pred             hhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccc
Confidence            4589999999999999999998888889999999999999999999999999999999999999999998

>KOG2578|consensus

Probab=99.63  E-value=3.3e-16  Score=131.43  Aligned_cols=121  Identities=28%  Similarity=0.335  Sum_probs=88.2

Q ss_pred             CchhhhHHHHhhcChhhhh-hcCCC-----C--------CCC--CCCccCCCccccccCCCCCCCCCCCCCCCcCcHHHH
Q psy8797           2 KGTIRIRLKLKFHSNMVKR-RLNLD-----Q--------DDE--ESPFKTPKSVKKMRVNPPTTPAKEKGTRYDTSLGLL   65 (122)
Q Consensus         2 ~~~~~~~~~~~~~~~~~~r-~~~l~-----~--------~~~--~~~~~tp~~~~~~~~~~~~~~k~~~~~R~~kSLg~L   65 (122)
                      +|---||.+|....+..-+ .|.--     .        +++  +|-..||+.+..+.+-+-.++.+....|+++||++|
T Consensus        85 kGf~aiPral~eLqeEgvke~l~~~~~~~~~~m~s~e~~~ee~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekSL~lL  164 (388)
T KOG2578|consen   85 KGFGAIPRALFELQEEGVKEGLPERVLRVNSAMVSFEEESEERGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKSLWLL  164 (388)
T ss_pred             cchhhhhHHHHHHHHHHHhhcccceeeecccccccccccccccCCccccCCCCCCCCCcchhcCCCCcccchhhhHHHHH
Confidence            5777899999988776533 22211     1        011  233455554422221112233345678899999999


Q ss_pred             HHHHHHHHhhCCCC-cccHHHHHhHh----------ccchhhhhhHHHhhhhccceeec-----cCCceeecC
Q psy8797          66 TKKFVKLLQSSPQG-VVDLNVASESL----------DVQKRRIYDITNVLEGIGILEKK-----SKNNIQCKR  122 (122)
Q Consensus        66 t~kFi~ll~~sp~~-~idL~~aa~~L----------~v~kRRiYDI~NVLE~igLI~K~-----~Kn~~~W~G  122 (122)
                      |++||.+|.++++. .|.|+.||..|          ..+-||||||.|||.+++||+|+     .|..|.|.|
T Consensus       165 ~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG  237 (388)
T KOG2578|consen  165 AQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLG  237 (388)
T ss_pred             HHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeC
Confidence            99999999999987 89999999988          35889999999999999999998     688999987

>KOG2829|consensus

Probab=98.24  E-value=2.5e-06  Score=71.67  Aligned_cols=61  Identities=26%  Similarity=0.427  Sum_probs=45.6

Q ss_pred             cCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh----------------------ccchhhhhhHHHhhhhccceeeccCC
Q psy8797          59 DTSLGLLTKKFVKLLQSSPQGVVDLNVASESL----------------------DVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        59 ~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L----------------------~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      ...|..++.+..+-++.  .+...-+++|..|                      .--|||+||..|||.++.+|.|. |.
T Consensus        43 g~gLRhfs~kVCeKve~--Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KK  119 (326)
T KOG2829|consen   43 GGGLRHFSMKVCEKVER--KGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KK  119 (326)
T ss_pred             CcchhhhhHHHHHHHHh--cCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cc
Confidence            44477777776666654  3445556666655                      23799999999999999999999 66


Q ss_pred             ceeecC
Q psy8797         117 NIQCKR  122 (122)
Q Consensus       117 ~~~W~G  122 (122)
                      .|+|+|
T Consensus       120 EIrW~G  125 (326)
T KOG2829|consen  120 EIRWIG  125 (326)
T ss_pred             eeeeec
Confidence            699998

>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=96.83  E-value=0.0027  Score=40.79  Aligned_cols=51  Identities=20%  Similarity=0.289  Sum_probs=41.9

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      +....+.  ..+..+..++|+.+++.+..+|+++|-|+..|+|++...+.+.|
T Consensus        12 ~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y   62 (68)
T PF01978_consen   12 KVYLALL--KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVY   62 (68)
T ss_dssp             HHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEE
T ss_pred             HHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEE
Confidence            3444443  35678999999999999999999999999999999987666554

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.

>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=96.14  E-value=0.022  Score=34.91  Aligned_cols=41  Identities=29%  Similarity=0.353  Sum_probs=34.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      .+.+.++..+.+. +...++|+.|+|++|-+|.-++.|+..|
T Consensus         3 ~~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~   43 (55)
T PF08279_consen    3 KQILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG   43 (55)
T ss_dssp             HHHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence            4567777666555 9999999999999999999999999998

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 ....

>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=95.94  E-value=0.036  Score=34.45  Aligned_cols=54  Identities=13%  Similarity=0.191  Sum_probs=42.6

Q ss_pred             HHHHHHHHHhhC-----CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          65 LTKKFVKLLQSS-----PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        65 Lt~kFi~ll~~s-----p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      ++.-|+++....     .+..+...++|+.+++.+.-++.+++.|+.-|+|.+.....|
T Consensus         5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~   63 (67)
T cd00092           5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKY   63 (67)
T ss_pred             HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence            444555555443     345789999999999999999999999999999998863444

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=95.77  E-value=0.034  Score=32.61  Aligned_cols=46  Identities=28%  Similarity=0.353  Sum_probs=39.0

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .++.++.+.  +.+++.++|+.+++.++-+|..++-|+..|+|.+...
T Consensus         4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            456666654  3489999999999999999999999999999998753

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=95.66  E-value=0.046  Score=36.02  Aligned_cols=48  Identities=23%  Similarity=0.377  Sum_probs=40.7

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +...++++.+.+ +.+.+.++|+.+++.+.-+|-+++.|+..|+|.+..
T Consensus         7 ~~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~   54 (91)
T smart00346        7 GLAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG   54 (91)
T ss_pred             HHHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence            345667776653 469999999999999999999999999999999874

>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=95.24  E-value=0.039  Score=33.94  Aligned_cols=46  Identities=17%  Similarity=0.265  Sum_probs=38.4

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      -..++++..++.+ +.+.++|+.+++.+=-+|-+++.|+..|++++.
T Consensus         6 l~iL~~l~~~~~~-~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    6 LRILEALAESGGP-LTLSEIARALGLPKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHHCHHCTBSC-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHcCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence            3456667766555 699999999999999999999999999999875

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.

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

Probab=95.21  E-value=0.07  Score=34.94  Aligned_cols=55  Identities=16%  Similarity=0.195  Sum_probs=46.2

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      -.+.+++|..+++..+.+.++|..||+.++-+.-++.-|+.-|+|.+.+-+-=.|
T Consensus         8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W   62 (68)
T smart00550        8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW   62 (68)
T ss_pred             HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence            3678888888765458999999999999999999999999999999976442355

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

>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=94.77  E-value=0.1  Score=31.28  Aligned_cols=43  Identities=21%  Similarity=0.450  Sum_probs=36.3

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE  111 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~  111 (122)
                      .+.+.++.+.|.  ++..++|+.+++.+..++.+++-|+.-|+|+
T Consensus         6 ~~Il~~l~~~~~--~t~~ela~~~~is~~tv~~~l~~L~~~g~I~   48 (48)
T PF13412_consen    6 RKILNYLRENPR--ITQKELAEKLGISRSTVNRYLKKLEEKGLIE   48 (48)
T ss_dssp             HHHHHHHHHCTT--S-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHcCC--CCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence            567788887555  9999999999999999999999999999985

...

>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=94.67  E-value=0.11  Score=32.04  Aligned_cols=46  Identities=22%  Similarity=0.355  Sum_probs=40.3

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+.++...++..+.+.++|+.+++.+=.+--+++-||.-|+|++.
T Consensus         9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~   54 (62)
T PF12802_consen    9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE   54 (62)
T ss_dssp             HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            4566677777777899999999999999999999999999999987

...

>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=94.29  E-value=0.24  Score=32.99  Aligned_cols=49  Identities=20%  Similarity=0.344  Sum_probs=40.0

Q ss_pred             HHHHHHHHHhhCCCC-cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          65 LTKKFVKLLQSSPQG-VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~-~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+-+++.++...+++ .+++.++|+.+++..+.+..|++-|+.-|+|+..
T Consensus         9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~   58 (83)
T PF02082_consen    9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS   58 (83)
T ss_dssp             HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence            455666777666654 4999999999999999999999999999999865

(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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=94.22  E-value=0.12  Score=30.74  Aligned_cols=37  Identities=16%  Similarity=0.267  Sum_probs=33.6

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+.++++++++.|++.+--++++++.|+.-|+|....
T Consensus         8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~   44 (66)
T smart00418        8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRR   44 (66)
T ss_pred             cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeee
Confidence            4557899999999999999999999999999998764

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=94.01  E-value=0.15  Score=36.43  Aligned_cols=48  Identities=15%  Similarity=0.135  Sum_probs=41.3

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-+.+.++...+++.+++.++|+.+++.+..++.+++.|+.-|+|+..
T Consensus        11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~   58 (130)
T TIGR02944        11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK   58 (130)
T ss_pred             HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            334566666666788999999999999999999999999999999864

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.

>PF13730 HTH_36: Helix-turn-helix domain

Probab=93.11  E-value=0.19  Score=30.63  Aligned_cols=29  Identities=21%  Similarity=0.367  Sum_probs=27.8

Q ss_pred             cHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797          82 DLNVASESLDVQKRRIYDITNVLEGIGIL  110 (122)
Q Consensus        82 dL~~aa~~L~v~kRRiYDI~NVLE~igLI  110 (122)
                      +...+|+.+|+.+|.++-.++.||..|+|
T Consensus        27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   27 SQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            79999999999999999999999999986

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

Probab=92.69  E-value=0.24  Score=30.36  Aligned_cols=44  Identities=18%  Similarity=0.379  Sum_probs=36.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++.++.+.++  +.+.++|+.+++.+--+-.+++-|+.-|+|+|..
T Consensus         8 iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~   51 (59)
T PF01047_consen    8 ILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER   51 (59)
T ss_dssp             HHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence            3444555444  8999999999999999999999999999999873

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 ....

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

Probab=92.52  E-value=0.45  Score=28.74  Aligned_cols=45  Identities=20%  Similarity=0.399  Sum_probs=37.8

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..++..+...+   +...++++.+++.+.-++-++|.|+.-|+|....
T Consensus        10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~   54 (78)
T cd00090          10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRR   54 (78)
T ss_pred             HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEE
Confidence            44555555544   8999999999999999999999999999998763

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.

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=92.30  E-value=0.28  Score=28.44  Aligned_cols=38  Identities=16%  Similarity=0.267  Sum_probs=33.7

Q ss_pred             cccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .+...++|+.+++.+--++.+++.|+.-|++++.. +.|
T Consensus         8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~   45 (48)
T smart00419        8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRI   45 (48)
T ss_pred             ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEE
Confidence            46789999999999999999999999999999874 444

>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8)

Probab=92.25  E-value=0.12  Score=34.57  Aligned_cols=30  Identities=37%  Similarity=0.472  Sum_probs=23.1

Q ss_pred             HHHhHhcc---chhhhhhHHHhhhhccceeecc
Q psy8797          85 VASESLDV---QKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        85 ~aa~~L~v---~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+|+.+++   ..||+||++|-|+.+|+|.-..
T Consensus        27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~   59 (85)
T PF09079_consen   27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESER   59 (85)
T ss_dssp             HHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence            34555554   7899999999999999997653

It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.

>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=92.04  E-value=0.52  Score=29.33  Aligned_cols=38  Identities=26%  Similarity=0.393  Sum_probs=31.7

Q ss_pred             CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..++.+.+.++|+.+++.+--+..+++-|+..|+|++.
T Consensus        14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~   51 (68)
T PF13463_consen   14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE   51 (68)
T ss_dssp             --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence            36788899999999999999999999999999999887

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=91.92  E-value=0.55  Score=27.98  Aligned_cols=40  Identities=15%  Similarity=0.316  Sum_probs=35.3

Q ss_pred             CCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          77 PQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        77 p~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      ++..+ +..++|+.+++++=-+...++.|+.-|+|.+....
T Consensus        16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~   56 (60)
T smart00345       16 PGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS   56 (60)
T ss_pred             CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence            45566 89999999999999999999999999999877544

>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding

Probab=91.84  E-value=0.18  Score=33.18  Aligned_cols=22  Identities=41%  Similarity=0.685  Sum_probs=19.7

Q ss_pred             cchhhhhhHHHhhhhccceeec
Q psy8797          92 VQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        92 v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ...||++|++|-||..|+|.-.
T Consensus        44 l~~~~~~~~l~~L~~~gli~~~   65 (87)
T cd08768          44 LTQRRISDLLSELEMLGLLETE   65 (87)
T ss_pred             CcHHHHHHHHHHHHHcCCeEEE
Confidence            4789999999999999999754

This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases

>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=91.14  E-value=0.51  Score=29.87  Aligned_cols=40  Identities=18%  Similarity=0.321  Sum_probs=34.1

Q ss_pred             CCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          77 PQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        77 p~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      ++..+ +..++|+.++|++.=+.+.++.|+.-|+|+.....
T Consensus        20 ~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~   60 (64)
T PF00392_consen   20 PGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGR   60 (64)
T ss_dssp             TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred             CCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence            56678 99999999999999999999999999999887543

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 ....

>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator)

Probab=90.34  E-value=1.1  Score=31.58  Aligned_cols=36  Identities=19%  Similarity=0.341  Sum_probs=33.4

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ...++..++|+.+++.+..+++|++.|+..|+|...
T Consensus        23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~   58 (132)
T TIGR00738        23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV   58 (132)
T ss_pred             CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence            348999999999999999999999999999999864

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.

>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=89.53  E-value=0.65  Score=30.51  Aligned_cols=47  Identities=13%  Similarity=0.186  Sum_probs=36.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccc-hhhhhhHHHhhhhccceeeccC
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQ-KRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~-kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      ||.-+....+..-.+.++|+.||+. ..-+++-+..||.-|+|++...
T Consensus        14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~   61 (65)
T PF01726_consen   14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG   61 (65)
T ss_dssp             HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred             HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence            4444444446677999999999996 9999999999999999998743

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.

>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=88.97  E-value=1.1  Score=26.88  Aligned_cols=41  Identities=24%  Similarity=0.413  Sum_probs=34.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK  112 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K  112 (122)
                      .+.++.+   +..++.++|+.+++.+=-++-=+++|+..|+|+|
T Consensus         7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~   47 (47)
T PF01022_consen    7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK   47 (47)
T ss_dssp             HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence            4444544   6689999999999999999999999999999986

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 ....

>COG3355 Predicted transcriptional regulator [Transcription]

Probab=88.94  E-value=0.74  Score=34.43  Aligned_cols=44  Identities=20%  Similarity=0.413  Sum_probs=38.7

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      |..+++  +++..+.+++|+.|+..|=.+|=.+|=|...|+|.|.-
T Consensus        33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek   76 (126)
T COG3355          33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREK   76 (126)
T ss_pred             HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeee
Confidence            445554  57889999999999999999999999999999999873

>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif

Probab=88.68  E-value=0.37  Score=31.24  Aligned_cols=45  Identities=16%  Similarity=0.228  Sum_probs=35.6

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      .+++.+  .+.+++.++|..|+++..-+=+.+.+|+.-|.|++...+
T Consensus         6 ~~~l~~--~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~   50 (69)
T PF09012_consen    6 RDYLRE--RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMS   50 (69)
T ss_dssp             HHHHHH--S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred             HHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence            344443  567999999999999999999999999999999987543

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

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=88.45  E-value=1.4  Score=35.35  Aligned_cols=48  Identities=19%  Similarity=0.272  Sum_probs=40.3

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +-..+++|..++ ..+.+.++|+.+++.|=.+|.+++-|+..|++.+..
T Consensus        27 ~l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~   74 (271)
T PRK10163         27 GIAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS   74 (271)
T ss_pred             HHHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence            345667776553 458999999999999999999999999999998864

>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks

Probab=88.10  E-value=1.2  Score=29.58  Aligned_cols=49  Identities=20%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      ..+++.+-.+...-+.-.+++..++...|-++=+++.|+..|||.|+.-
T Consensus         5 ~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~   53 (75)
T PF04182_consen    5 YCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV   53 (75)
T ss_pred             HHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence            3566777666655566678889999999999999999999999999865

This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.

>PRK09834 DNA-binding transcriptional activator MhpR; Provisional

Probab=87.15  E-value=1.7  Score=34.52  Aligned_cols=51  Identities=10%  Similarity=0.265  Sum_probs=40.9

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc-CCcee
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS-KNNIQ  119 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~-Kn~~~  119 (122)
                      ..+++|..++ ..+.+.++|+.+++.|=-+|-+++-|+..|++++.. .+.|.
T Consensus        15 ~iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~   66 (263)
T PRK09834         15 MVLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR   66 (263)
T ss_pred             HHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence            3556665543 348999999999999999999999999999999863 44454

>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=86.95  E-value=1.7  Score=27.40  Aligned_cols=45  Identities=24%  Similarity=0.404  Sum_probs=37.7

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.++++.+  .+.+.+.++|+.|+|+..=+.==+|.|+.-|+|.|..
T Consensus         4 ~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~   48 (57)
T PF08220_consen    4 QILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH   48 (57)
T ss_pred             HHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence            45677765  4679999999999998887777788999999999874

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

>TIGR00122 birA_repr_reg BirA biotin operon repressor domain

Probab=86.94  E-value=1.6  Score=27.89  Aligned_cols=40  Identities=15%  Similarity=0.237  Sum_probs=33.0

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL  110 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI  110 (122)
                      +.+.++.+.   .+...++|+.++|+++-++.-++.|++-|++
T Consensus         4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~   43 (69)
T TIGR00122         4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVD   43 (69)
T ss_pred             HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence            455665543   3569999999999999999999999998884

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.

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

Probab=86.77  E-value=2.9  Score=25.27  Aligned_cols=34  Identities=21%  Similarity=0.338  Sum_probs=31.3

Q ss_pred             ccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          81 VDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        81 idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ....++|+.+++.+=.+...++-|+.-|+|++..
T Consensus        26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~   59 (66)
T cd07377          26 PSERELAEELGVSRTTVREALRELEAEGLVERRP   59 (66)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            4599999999999999999999999999998774

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

>smart00344 HTH_ASNC helix_turn_helix ASNC type

Probab=86.33  E-value=1.6  Score=29.64  Aligned_cols=47  Identities=15%  Similarity=0.280  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +=.+++.++++.  +.+...++|+.+++...-++..++-|+.-|+|.+.
T Consensus         4 ~D~~il~~L~~~--~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~   50 (108)
T smart00344        4 IDRKILEELQKD--ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY   50 (108)
T ss_pred             HHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence            346788888875  45889999999999999999999999999999854

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

>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein

Probab=86.23  E-value=2.2  Score=27.57  Aligned_cols=44  Identities=14%  Similarity=0.273  Sum_probs=36.9

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+.++...+  .+...++|+.+++.+--++-+++-|+.-|+|++.
T Consensus        14 ~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~   57 (101)
T smart00347       14 LVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL   57 (101)
T ss_pred             HHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence            3445555443  5889999999999999999999999999999876

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=86.18  E-value=0.9  Score=36.79  Aligned_cols=36  Identities=28%  Similarity=0.433  Sum_probs=32.3

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +...-.++|+..||.+=|+|||++-||.=|+|+...
T Consensus        29 g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~   64 (247)
T COG1378          29 GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE   64 (247)
T ss_pred             CCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC
Confidence            345778999999999999999999999999999873

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

Probab=86.13  E-value=1.2  Score=27.87  Aligned_cols=46  Identities=20%  Similarity=0.360  Sum_probs=37.6

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+.+.++.  .++..++.++|+.|++..=-+|-=+++|+..|+|+...
T Consensus        13 ~~Il~~L~--~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~   58 (61)
T PF12840_consen   13 LRILRLLA--SNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER   58 (61)
T ss_dssp             HHHHHHHH--HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHh--cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence            34566662  35678999999999999999999999999999998763

...

>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A)

Probab=85.78  E-value=1.9  Score=29.59  Aligned_cols=50  Identities=16%  Similarity=0.347  Sum_probs=40.7

Q ss_pred             cHHHHHHHHHHHHhhCC--CCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797          61 SLGLLTKKFVKLLQSSP--QGVVDLNVASESLDVQKRRIYDITNVLEGIGIL  110 (122)
Q Consensus        61 SLg~Lt~kFi~ll~~sp--~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI  110 (122)
                      +|..+.++.++++++.+  +.-+.+++++++|++....+.+++.-|..-|+|
T Consensus        44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I   95 (102)
T PF08784_consen   44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI   95 (102)
T ss_dssp             -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred             CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence            78889999999998732  345899999999999999999999999999987

RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.

>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU

Probab=85.51  E-value=0.91  Score=36.52  Aligned_cols=40  Identities=13%  Similarity=0.196  Sum_probs=35.3

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      ++..++.++|+++++..|.++-+.+.|.++|++++.. +.|
T Consensus        21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~-~~y   60 (306)
T TIGR02716        21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED-GKW   60 (306)
T ss_pred             cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC-CcE
Confidence            3578999999999999999999999999999999864 444

Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.

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

Probab=84.69  E-value=3.7  Score=28.28  Aligned_cols=37  Identities=19%  Similarity=0.218  Sum_probs=33.7

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ...+.-.++|+.+++.|--+..+++.||.-|+|.+..
T Consensus        45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~   81 (95)
T TIGR01610        45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG   81 (95)
T ss_pred             CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence            4567889999999999999999999999999999764

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

>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR

Probab=84.03  E-value=3.1  Score=30.04  Aligned_cols=37  Identities=19%  Similarity=0.217  Sum_probs=33.5

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .++.+.+.++|+.+++..+-+..|+..|.-.|+|.-.
T Consensus        22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~   58 (135)
T TIGR02010        22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV   58 (135)
T ss_pred             CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence            3458999999999999999999999999999999743

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

>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=83.94  E-value=4.7  Score=25.83  Aligned_cols=41  Identities=22%  Similarity=0.297  Sum_probs=36.2

Q ss_pred             HhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          73 LQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        73 l~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+ .++.+...++|+.|+|.+=-..+.++-|+.-|+|....
T Consensus        16 l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~   56 (60)
T PF01325_consen   16 LSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP   56 (60)
T ss_dssp             HHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred             HHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence            344 78899999999999999999999999999999998874

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 ....

>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]

Probab=83.89  E-value=1.3  Score=32.42  Aligned_cols=41  Identities=29%  Similarity=0.332  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797          63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV  103 (122)
Q Consensus        63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV  103 (122)
                      ++||.+=..++.-.-..-++|.++|+.++|+|-.|||=|+-
T Consensus        16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr   56 (105)
T COG2739          16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKR   56 (105)
T ss_pred             HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHH
Confidence            35777766665555555689999999999999999997763

>TIGR01764 excise DNA binding domain, excisionase family

Probab=83.85  E-value=1.1  Score=25.71  Aligned_cols=23  Identities=26%  Similarity=0.440  Sum_probs=20.6

Q ss_pred             ccHHHHHhHhccchhhhhhHHHh
Q psy8797          81 VDLNVASESLDVQKRRIYDITNV  103 (122)
Q Consensus        81 idL~~aa~~L~v~kRRiYDI~NV  103 (122)
                      +++.++|+.|++.+..||..++-
T Consensus         2 lt~~e~a~~lgis~~ti~~~~~~   24 (49)
T TIGR01764         2 LTVEEAAEYLGVSKDTVYRLIHE   24 (49)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHc
Confidence            57899999999999999999863

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).

>PF13518 HTH_28: Helix-turn-helix domain

Probab=83.73  E-value=1.4  Score=26.02  Aligned_cols=37  Identities=16%  Similarity=0.316  Sum_probs=30.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI  109 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL  109 (122)
                      .|+++.+   +. ++.++|..++|.+..+|.+++-++.-|+
T Consensus         5 iv~~~~~---g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~   41 (52)
T PF13518_consen    5 IVELYLE---GE-SVREIAREFGISRSTVYRWIKRYREGGI   41 (52)
T ss_pred             HHHHHHc---CC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence            4555553   33 9999999999999999999999988664

>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []

Probab=83.25  E-value=2.7  Score=26.54  Aligned_cols=36  Identities=25%  Similarity=0.377  Sum_probs=28.0

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhh
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLE  105 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE  105 (122)
                      +.++++..  +..+.+.++|+.|+++.|-|..-+|-|.
T Consensus         9 ~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~   44 (59)
T PF08280_consen    9 KLLELLLK--NKWITLKELAKKLNISERTIKNDINELN   44 (59)
T ss_dssp             HHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred             HHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence            46677766  5668999999999999999877776665

; PDB: 2WTE_A 3SQN_A.

>PRK11511 DNA-binding transcriptional activator MarA; Provisional

Probab=82.95  E-value=3.2  Score=29.64  Aligned_cols=45  Identities=11%  Similarity=0.143  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhh
Q psy8797          62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEG  106 (122)
Q Consensus        62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~  106 (122)
                      -.....++++++.++....++++++|+.+++..|.|.-+..---|
T Consensus         7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G   51 (127)
T PRK11511          7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETG   51 (127)
T ss_pred             cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence            345668899999999999999999999999999888766654433

>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family

Probab=82.78  E-value=3.2  Score=28.81  Aligned_cols=45  Identities=18%  Similarity=0.276  Sum_probs=38.9

Q ss_pred             HHHHh--hCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          70 VKLLQ--SSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        70 i~ll~--~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.++.  .++++.+.+.++|+.+++.+=.+-=+++-||.-|+|.|..
T Consensus        31 L~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~   77 (109)
T TIGR01889        31 LYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER   77 (109)
T ss_pred             HHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence            44444  5567889999999999999999999999999999999873

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.

>PRK09954 putative kinase; Provisional

Probab=82.49  E-value=2.2  Score=34.98  Aligned_cols=46  Identities=20%  Similarity=0.349  Sum_probs=40.2

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      -++.++++++++  .++..++|+.|++.+..++..++-|+.-|+|+..
T Consensus         5 ~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~   50 (362)
T PRK09954          5 EKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK   50 (362)
T ss_pred             HHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence            456888888655  7999999999999999999999999999999654

>PRK10857 DNA-binding transcriptional regulator IscR; Provisional

Probab=82.26  E-value=2.6  Score=32.06  Aligned_cols=38  Identities=21%  Similarity=0.204  Sum_probs=34.4

Q ss_pred             CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+..+.+.++|+.+++..+-+..|++-|.--|||.-.
T Consensus        21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~   58 (164)
T PRK10857         21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV   58 (164)
T ss_pred             CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence            34568999999999999999999999999999999854

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

Probab=82.11  E-value=3.4  Score=32.31  Aligned_cols=50  Identities=8%  Similarity=0.116  Sum_probs=40.8

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      -..+++|..+ ...+.+.++|+.+++.|=.+|-+++-|+..|++++.. ..|
T Consensus        12 l~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~-~~Y   61 (248)
T TIGR02431        12 LAVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDG-RLF   61 (248)
T ss_pred             HHHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC-CEE
Confidence            3456666554 4568999999999999999999999999999999863 344

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.

>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=82.01  E-value=2.6  Score=26.77  Aligned_cols=36  Identities=22%  Similarity=0.296  Sum_probs=33.1

Q ss_pred             cccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .++..++|+.+|+.+..+--+++-|+.-|+|+...+
T Consensus        28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~   63 (76)
T PF13545_consen   28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG   63 (76)
T ss_dssp             ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence            578999999999999999999999999999997744

...

>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional

Probab=82.00  E-value=3.9  Score=27.85  Aligned_cols=43  Identities=5%  Similarity=0.145  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhh
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEG  106 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~  106 (122)
                      .+..+++.++.+.....+++.++|+.++++.|.|.-+++=.-|
T Consensus         5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g   47 (107)
T PRK10219          5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTH   47 (107)
T ss_pred             HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence            3567788899888888999999999999999888766654433

>COG1414 IclR Transcriptional regulator [Transcription]

Probab=80.96  E-value=4.5  Score=32.25  Aligned_cols=51  Identities=22%  Similarity=0.406  Sum_probs=43.4

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC-ce
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN-NI  118 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn-~~  118 (122)
                      -..+++|...|.+ +.+.++|+.+|..|=-.|=+.+.|+..|++++...+ .|
T Consensus         7 l~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y   58 (246)
T COG1414           7 LAILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRY   58 (246)
T ss_pred             HHHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcE
Confidence            3567777775544 889999999999999999999999999999999865 44

>PRK00215 LexA repressor; Validated

Probab=80.87  E-value=3.7  Score=31.24  Aligned_cols=42  Identities=10%  Similarity=0.133  Sum_probs=36.4

Q ss_pred             hCCCCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeeccCC
Q psy8797          75 SSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        75 ~sp~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      ...+....+.++|+.+++ .+=-++.+++-||.-|+|++....
T Consensus        18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~   60 (205)
T PRK00215         18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR   60 (205)
T ss_pred             HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence            334566899999999999 999999999999999999887543

>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional

Probab=80.38  E-value=4.7  Score=31.76  Aligned_cols=47  Identities=11%  Similarity=0.274  Sum_probs=39.5

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      -..+++|...  ..+.+.++|+.+++.|=-+|-+++.|+..|++++...
T Consensus        17 l~IL~~l~~~--~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~   63 (257)
T PRK15090         17 FGILQALGEE--REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE   63 (257)
T ss_pred             HHHHHHhhcC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence            4466666543  3589999999999999999999999999999998643

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	122
1cf7_A	76	Structural Basis Of Dna Recognition By The Heterodi		3e-20

>pdb|1CF7|A Chain A, Structural Basis Of Dna Recognition By The Heterodimeric Cell Cycle Transcription Factor E2f-Dp Length = 76

Iteration: 1
 Score = 93.6 bits (231), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 49/77 (63%), Positives = 61/77 (79%), Gaps = 6/77 (7%)
Query: 46  PPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVL 104
           PP TP     +R++ SLGLLT KFV LLQ +  GV+DL +A+++L V QKRRIYDITNVL
Sbjct: 1   PPGTP-----SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVL 55
Query: 105 EGIGILEKKSKNNIQCK 121
           EGIG++EKKSKN+IQ K
Sbjct: 56  EGIGLIEKKSKNSIQWK 72

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	122
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	2e-26

>1cf7_A Protein (transcription factor E2F-4); E2F, winged-helix, DNA-binding domain, cell cycle, transcription/DNA complex; HET: DNA; 2.60A {Homo sapiens} SCOP: a.4.5.17 Length = 76

 Score = 92.7 bits (230), Expect = 2e-26
 Identities = 49/77 (63%), Positives = 61/77 (79%), Gaps = 6/77 (7%)

Query: 46  PPTTPAKEKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVL 104
           PP TP     +R++ SLGLLT KFV LLQ +  GV+DL +A+++L V QKRRIYDITNVL
Sbjct: 1   PPGTP-----SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVL 55

Query: 105 EGIGILEKKSKNNIQCK 121
           EGIG++EKKSKN+IQ K
Sbjct: 56  EGIGLIEKKSKNSIQWK 72

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	122
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	99.97
1cf7_B	95	Protein (transcription factor DP-2); E2F, winged-h	99.51
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	96.08
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	95.94
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	95.7
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	95.58
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	95.52
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	94.48
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	94.11
3r0a_A	123	Putative transcriptional regulator; structural gen	93.53
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	93.4
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	93.32
1y0u_A	96	Arsenical resistance operon repressor, putative; s	92.97
1sfx_A	109	Conserved hypothetical protein AF2008; structural	92.97
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	92.9
2kko_A	108	Possible transcriptional regulatory protein (possi	92.83
2fu4_A	83	Ferric uptake regulation protein; DNA binding doma	92.62
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	92.13
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	91.33
1ku9_A	152	Hypothetical protein MJ223; putative transcription	90.94
3jth_A	98	Transcription activator HLYU; transcription factor	90.81
2frh_A	127	SARA, staphylococcal accessory regulator A; winged	90.81
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	90.62
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	90.47
3rkx_A	323	Biotin-[acetyl-COA-carboxylase] ligase; biotin pro	90.24
3jw4_A	148	Transcriptional regulator, MARR/EMRR family; DNA-b	90.23
1j5y_A	187	Transcriptional regulator, biotin repressor famil;	90.2
2jt1_A	77	PEFI protein; solution structure, winged helix-tur	90.02
3deu_A	166	Transcriptional regulator SLYA; MARR, WING-helix,	89.98
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	89.88
2hzt_A	107	Putative HTH-type transcriptional regulator YTCD;	89.71
4b8x_A	147	SCO5413, possible MARR-transcriptional regulator;	89.67
2pg4_A	95	Uncharacterized protein; structural genomics, join	89.57
1ylf_A	149	RRF2 family protein; structural genomics, transcri	89.56
1sfu_A	75	34L protein; protein/Z-DNA complex, DNA binding pr	89.41
3mkl_A	120	HTH-type transcriptional regulator GADX; PSI2, MCS	89.3
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	89.25
3nqo_A	189	MARR-family transcriptional regulator; structural	89.17
3oio_A	113	Transcriptional regulator (ARAC-type DNA-binding c	89.11
3oou_A	108	LIN2118 protein; protein structure initiative, PSI	89.05
2cfx_A	144	HTH-type transcriptional regulator LRPC; transcrip	89.02
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	88.98
3g3z_A	145	NMB1585, transcriptional regulator, MARR family; t	88.84
3u2r_A	168	Regulatory protein MARR; structural genomics, PSI-	88.8
2gxg_A	146	146AA long hypothetical transcriptional regulator;	88.76
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	88.72
3tgn_A	146	ADC operon repressor ADCR; helix-turn-helix, trans	88.59
1on2_A	142	Transcriptional regulator MNTR; helix-turn-helix,	88.56
2x4h_A	139	Hypothetical protein SSO2273; transcription; 2.30A	88.49
2dbb_A	151	Putative HTH-type transcriptional regulator PH006;	88.33
1p6r_A	82	Penicillinase repressor; transcription regulation,	88.29
2nnn_A	140	Probable transcriptional regulator; structural gen	88.28
3nrv_A	148	Putative transcriptional regulator (MARR/EMRR FAM;	88.16
2fbi_A	142	Probable transcriptional regulator; MARR, APC5816,	88.04
3mn2_A	108	Probable ARAC family transcriptional regulator; st	88.04
3k69_A	162	Putative transcription regulator; putative transcr	88.03
2ip2_A	334	Probable phenazine-specific methyltransferase; pyo	87.93
1xn7_A	78	Hypothetical protein YHGG; alpha+beta, GFT structu	87.91
3i53_A	332	O-methyltransferase; CO-complex, rossmann-like fol	87.88
2xrn_A	241	HTH-type transcriptional regulator TTGV; DNA-bindi	87.8
3bja_A	139	Transcriptional regulator, MARR family, putative;	87.75
2cg4_A	152	Regulatory protein ASNC; DNA binding, FFRP, LRP fa	87.74
3fm5_A	150	Transcriptional regulator; MCSG, PF04017, PSI, MAR	87.65
2p5v_A	162	Transcriptional regulator, LRP/ASNC family; NMB057	87.64
2hr3_A	147	Probable transcriptional regulator; MCSG, structur	87.59
1tbx_A	99	ORF F-93, hypothetical 11.0 kDa protein; sulfolobu	87.59
3f3x_A	144	Transcriptional regulator, MARR family, putative;	87.57
3bpv_A	138	Transcriptional regulator; MARR, DNA binding, tran	87.52
3oop_A	143	LIN2960 protein; protein structure initiative, PSI	87.45
2qww_A	154	Transcriptional regulator, MARR family; YP_013417.	87.42
2o0y_A	260	Transcriptional regulator; ICLR-family, structural	87.42
1mkm_A	249	ICLR transcriptional regulator; structural genomic	87.4
3pfi_A	338	Holliday junction ATP-dependent DNA helicase RUVB;	87.23
1i1g_A	141	Transcriptional regulator LRPA; helix-turn-helix,	87.22
2fsw_A	107	PG_0823 protein; alpha-beta structure, helix-turn-	87.13
2fa5_A	162	Transcriptional regulator MARR/EMRR family; multip	87.03
1z7u_A	112	Hypothetical protein EF0647; winged-helix-turn-hel	87.02
2a61_A	145	Transcriptional regulator TM0710; APC4350, MCSG, m	86.88
3f6o_A	118	Probable transcriptional regulator, ARSR family pr	86.8
2w25_A	150	Probable transcriptional regulatory protein; trans	86.7
2bv6_A	142	MGRA, HTH-type transcriptional regulator MGRA; mul	86.67
2eth_A	154	Transcriptional regulator, putative, MAR family; M	86.59
2k02_A	87	Ferrous iron transport protein C; FEOC, iron-sulfu	86.45
3ech_A	142	MEXR, multidrug resistance operon repressor; winge	86.45
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	86.43
3gwz_A	369	MMCR; methyltransferase, mitomycin, S-adenosyl met	86.32
2dk5_A	91	DNA-directed RNA polymerase III 39 kDa polypeptide	86.32
3bdd_A	142	Regulatory protein MARR; putative multiple antibio	86.25
2fbh_A	146	Transcriptional regulator PA3341; MARR, transcript	86.23
3cdh_A	155	Transcriptional regulator, MARR family; helix-turn	86.23
3lsg_A	103	Two-component response regulator YESN; structural	86.21
2wte_A	244	CSA3; antiviral protein, viral resistance, winged	86.19
1bl0_A	129	Protein (multiple antibiotic resistance protein),	86.18
2vn2_A	128	DNAD, chromosome replication initiation protein; D	86.16
1lj9_A	144	Transcriptional regulator SLYA; HTH DNA binding pr	86.13
2jsc_A	118	Transcriptional regulator RV1994C/MT2050; cadmium,	86.09
3bj6_A	152	Transcriptional regulator, MARR family; helix-turn	85.98
3lst_A	348	CALO1 methyltransferase; calicheamicin, enediyne,	85.72
2r3s_A	335	Uncharacterized protein; methyltransferase domain,	85.6
2cyy_A	151	Putative HTH-type transcriptional regulator PH151;	85.59
3cjn_A	162	Transcriptional regulator, MARR family; silicibact	85.19
2k9s_A	107	Arabinose operon regulatory protein; activator, ar	85.18
3r4k_A	260	Transcriptional regulator, ICLR family; DNA/RNA-bi	85.18
1qzz_A	374	RDMB, aclacinomycin-10-hydroxylase; anthracycline,	85.16
2g7u_A	257	Transcriptional regulator; ICLR family, structural	85.09
2qko_A	215	Possible transcriptional regulator, TETR family P;	85.07
2pn6_A	150	ST1022, 150AA long hypothetical transcriptional re	84.96
4hbl_A	149	Transcriptional regulator, MARR family; HTH, trans	84.82
3hsr_A	140	HTH-type transcriptional regulator SARZ; helix-tur	84.81
1yyv_A	131	Putative transcriptional regulator; reductive meth	84.6
1v4r_A	102	Transcriptional repressor; helix-turn-helix, winge	84.59
3boq_A	160	Transcriptional regulator, MARR family; MARR famil	84.33
3k0l_A	162	Repressor protein; helix-turn-helix, structural ge	84.3
3s2w_A	159	Transcriptional regulator, MARR family; structural	84.04
1r7j_A	95	Conserved hypothetical protein SSO10A; winged heli	84.01
3t8r_A	143	Staphylococcus aureus CYMR; transcriptional regula	84.0
1s3j_A	155	YUSO protein; structural genomics, MARR transcript	83.96
1q1h_A	110	TFE, transcription factor E, TFE; TFIIE, transcrip	83.76
3qph_A	342	TRMB, A global transcription regulator; transcript	83.61
2rdp_A	150	Putative transcriptional regulator MARR; PFAM PF01	83.57
1jgs_A	138	Multiple antibiotic resistance protein MARR; trans	83.57
2pex_A	153	Transcriptional regulator OHRR; transcription regu	83.43
3tqn_A	113	Transcriptional regulator, GNTR family; regulatory	83.42
1z91_A	147	Organic hydroperoxide resistance transcriptional;	82.88
2nyx_A	168	Probable transcriptional regulatory protein, RV14;	82.8
2f2e_A	146	PA1607; transcription factor, helix-TRUN-helix, AP	82.72
2v79_A	135	DNA replication protein DNAD; primosome, DNA-bindi	82.53
3e6m_A	161	MARR family transcriptional regulator; APC88769, s	82.47
2ia2_A	265	Putative transcriptional regulator; SAD, PSI-2, st	82.43
2ia0_A	171	Putative HTH-type transcriptional regulator PF086;	82.39
1tw3_A	360	COMT, carminomycin 4-O-methyltransferase; anthracy	82.34
2h09_A	155	Transcriptional regulator MNTR; transcription regu	82.05
1x19_A	359	CRTF-related protein; methyltransferase, bacterioc	81.68
2ek5_A	129	Predicted transcriptional regulators; helix-turn-h	81.61
4a5n_A	131	Uncharacterized HTH-type transcriptional regulato;	81.55
2fbk_A	181	Transcriptional regulator, MARR family; winged-hel	81.48
3f6v_A	151	Possible transcriptional regulator, ARSR family pr	81.36
3k2z_A	196	LEXA repressor; winged helix-turn-helix, SOS syste	81.13
1xmk_A	79	Double-stranded RNA-specific adenosine deaminase;	80.89
2e1c_A	171	Putative HTH-type transcriptional regulator PH151;	80.66

>1cf7_A Protein (transcription factor E2F-4); E2F, winged-helix, DNA-binding domain, cell cycle, transcription/DNA complex; HET: DNA; 2.60A {Homo sapiens} SCOP: a.4.5.17

Probab=99.97  E-value=7.3e-32  Score=183.09  Aligned_cols=69  Identities=65%  Similarity=0.949  Sum_probs=65.6

Q ss_pred             CCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797          54 KGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSKNNIQCKR  122 (122)
Q Consensus        54 ~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G  122 (122)
                      ..+|+++||++||++||++|.+++++.++|++||+.|+| +|||||||+|||||||||+|.+||.|+|+|
T Consensus         4 ~~~R~~~SL~~lt~kFi~l~~~~~~~~i~l~~aa~~L~v~~kRRiYDI~NVLe~igli~K~~k~~~~W~G   73 (76)
T 1cf7_A            4 TPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWKG   73 (76)
T ss_dssp             --CTTTTCHHHHHHHHHHHHHHSSTTEEEHHHHHHHTTTCCTHHHHHHHHHHHHHTSEEEEETTEEEEC-
T ss_pred             CCCCccCcHHHHHHHHHHHHHhCCCCcCcHHHHHHHhCCccceehhhHHHHHhHhcceeecCCCcEEEeC
Confidence            478999999999999999999999999999999999999 999999999999999999999999999998

>1cf7_B Protein (transcription factor DP-2); E2F, winged-helix, DNA-binding domain, cell cycle, transcription/DNA complex; HET: DNA; 2.60A {Homo sapiens} SCOP: a.4.5.17

Probab=99.51  E-value=7.3e-15  Score=103.65  Aligned_cols=65  Identities=28%  Similarity=0.447  Sum_probs=46.3

Q ss_pred             CCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHh-------------------ccchhhhhhHHHhhhhccceeeccC
Q psy8797          55 GTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESL-------------------DVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        55 ~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L-------------------~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      +.+..++|..++.+..+.+++.  +..+.+++|++|                   ...|||+||++|||+++|||+| .+
T Consensus         5 ~~k~~~GLr~fS~kVcekVk~k--~~Tty~eVAdeLV~e~~~~~~~~~~~~~~d~~~~rRRvYD~~NVl~a~gii~K-~k   81 (95)
T 1cf7_B            5 GDKNGKGLRHFSMKVCEKVQRK--GTTSYNEVADELVSEFTNSNNHLAADSAYDQKNIRRRVYDALNVLMAMNIISK-EK   81 (95)
T ss_dssp             ----CCHHHHHHHHHHHHHHHH--SEECHHHHHHHHHHHHHTCTTCCGGGSHHHHHHHHHHHHHHHHHHHHTTSBCC-CS
T ss_pred             ccccCccHHHHHHHHHHHHHhc--CCccHHHHHHHHHHHHhcccccCccchhcccccchhhHHHHHHHHHHhcceec-CC
Confidence            3455666777777666666542  333555555544                   3489999999999999999999 79


Q ss_pred             CceeecC
Q psy8797         116 NNIQCKR  122 (122)
Q Consensus       116 n~~~W~G  122 (122)
                      +.|+|+|
T Consensus        82 ~~i~W~g   88 (95)
T 1cf7_B           82 KEIKWIG   88 (95)
T ss_dssp             SCEEBCC
T ss_pred             CEEEEec
Confidence            9999998

>2xvc_A ESCRT-III, SSO0910; cell cycle, cell division, cytokinesis, winged-helix; 2.15A {Sulfolobus solfataricus}

Probab=96.08  E-value=0.01  Score=38.37  Aligned_cols=44  Identities=16%  Similarity=0.428  Sum_probs=39.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcccee
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILE  111 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~  111 (122)
                      ++.++++.++ +|.+|+...|.+++|.|--+||+.+=||.=|||.
T Consensus        13 ~~lL~yIr~s-GGildI~~~a~kygV~kdeV~~~LrrLe~KGLI~   56 (59)
T 2xvc_A           13 RELLDYIVNN-GGFLDIEHFSKVYGVEKQEVVKLLEALKNKGLIA   56 (59)
T ss_dssp             HHHHHHHHHT-TSEEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEE
T ss_pred             HHHHHHHHHc-CCEEeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence            4567788775 8999999999999999999999999999999986

>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=95.94  E-value=0.014  Score=38.15  Aligned_cols=54  Identities=19%  Similarity=0.196  Sum_probs=46.6

Q ss_pred             HHHHHHHhhCC-CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          67 KKFVKLLQSSP-QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        67 ~kFi~ll~~sp-~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      ++.+.++.+.+ +..+...++|+.|++.++-+.-.+.-||.-|+|.+.+.+.=.|
T Consensus        17 ~~IL~~L~~~~~~~~~t~~eLA~~Lgvs~~tV~~~L~~L~~~G~I~~~g~~~~~W   71 (77)
T 1qgp_A           17 QRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLW   71 (77)
T ss_dssp             HHHHHHHHHHCSSSCEEHHHHHHHHCCCHHHHHHHHHHHHHHTSEEEECSSSCEE
T ss_pred             HHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence            66778887765 5679999999999999999999999999999999987655666

>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=95.70  E-value=0.022  Score=37.91  Aligned_cols=55  Identities=18%  Similarity=0.192  Sum_probs=46.0

Q ss_pred             HHHHHHHHhhCC-CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          66 TKKFVKLLQSSP-QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        66 t~kFi~ll~~sp-~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      -++.++++.+.+ +..+...++|+.|++.++-+.-.+.-|+.-|+|.+.+.+.=.|
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~~~~~W   67 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLW   67 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESSSSCEE
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCCee
Confidence            356777776554 6679999999999999999999999999999999886655566

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

Probab=95.58  E-value=0.028  Score=38.02  Aligned_cols=59  Identities=12%  Similarity=0.102  Sum_probs=50.8

Q ss_pred             CcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceeec
Q psy8797          60 TSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQCK  121 (122)
Q Consensus        60 kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~  121 (122)
                      -.-..+.++.+++|..  ++ +...++|++|++.+.-++=.++-||.=|+|.+.+-+--.|.
T Consensus        13 ~~~~~~~~~IL~lL~~--~g-~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~~PP~W~   71 (82)
T 1oyi_A           13 RSNAEIVCEAIKTIGI--EG-ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDIPPRWF   71 (82)
T ss_dssp             CCSHHHHHHHHHHHSS--ST-EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSSSSCEEE
T ss_pred             cchHHHHHHHHHHHHH--cC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCcce
Confidence            3445677889999984  34 99999999999999999999999999999999998888883

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

Probab=95.52  E-value=0.027  Score=35.51  Aligned_cols=53  Identities=17%  Similarity=0.209  Sum_probs=43.3

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .-.+.+++|.++ +..+.+.++|+.|++.+--++-+++.|+.-|+|.......|
T Consensus        11 ~~~~IL~~L~~~-~~~~s~~eLA~~lglsr~tv~~~l~~L~~~G~I~~~~~G~y   63 (67)
T 2heo_A           11 LEQKILQVLSDD-GGPVAIFQLVKKCQVPKKTLNQVLYRLKKEDRVSSPSPKYW   63 (67)
T ss_dssp             HHHHHHHHHHHH-CSCEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEEEETTEE
T ss_pred             HHHHHHHHHHHc-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEecCCCceE
Confidence            345678888763 45699999999999999999999999999999987544433

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

Probab=94.48  E-value=0.092  Score=33.42  Aligned_cols=44  Identities=16%  Similarity=0.207  Sum_probs=37.4

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.++++...  +.+...++|+.+++.+.-++-.++.|+.-|+|++.
T Consensus         4 ~Il~~L~~~--~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~~   47 (81)
T 2htj_A            4 EILEFLNRH--NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQRS   47 (81)
T ss_dssp             HHHHHHHHS--CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            456666653  45899999999999999999999999999999853

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

Probab=94.11  E-value=0.13  Score=35.25  Aligned_cols=48  Identities=10%  Similarity=0.209  Sum_probs=39.8

Q ss_pred             HHHHHHHHhhC-CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSS-PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~s-p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-+.+.++... +++.+...++|+.+++.++-++.|++.|+..|+|+..
T Consensus        11 al~iL~~la~~~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           11 GLTIMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             HHHHHHHHHHTTTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEec
Confidence            33445555544 3678999999999999999999999999999999876

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

Probab=93.53  E-value=0.12  Score=35.51  Aligned_cols=47  Identities=19%  Similarity=0.270  Sum_probs=39.5

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..++..+..+++..+...++|+.+++.+-.+|-.++.|+..|+|.+.
T Consensus        29 ~~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           29 LNVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            34566666654433899999999999999999999999999999985

>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=93.40  E-value=0.13  Score=34.41  Aligned_cols=46  Identities=13%  Similarity=0.117  Sum_probs=40.4

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+.++...+++.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        35 ~vL~~l~~~~~~~~t~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   80 (139)
T 3eco_A           35 HTLGYLYAHQQDGLTQNDIAKALQRTGPTVSNLLRNLERKKLIYRY   80 (139)
T ss_dssp             HHHHHHHHSTTTCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHhcCCCCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeec
Confidence            3555566666678999999999999999999999999999999987

>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=93.32  E-value=0.15  Score=33.93  Aligned_cols=45  Identities=11%  Similarity=0.086  Sum_probs=39.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++...+++.+...++|+.+++.+--++.+++-||.-|+|++.
T Consensus        39 iL~~l~~~~~~~~~~~ela~~l~~~~~tvs~~l~~Le~~Gli~r~   83 (141)
T 3bro_A           39 IIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   83 (141)
T ss_dssp             HHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHCCCCCcCHHHHHHHHCCCcchHHHHHHHHHHCCCEEee
Confidence            455566666557899999999999999999999999999999986

>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=92.97  E-value=0.15  Score=33.09  Aligned_cols=45  Identities=16%  Similarity=0.156  Sum_probs=37.7

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .+.++    ++.+.+.++|+.|++.+--++-.++.|+..|+|.+.. +.|
T Consensus        36 Il~~L----~~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~-g~y   80 (96)
T 1y0u_A           36 ILRML----DKGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG-ERW   80 (96)
T ss_dssp             HHHHH----HTTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TEE
T ss_pred             HHHHH----cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC-CEE
Confidence            44555    2458999999999999999999999999999999875 444

>1sfx_A Conserved hypothetical protein AF2008; structural genomics, HTH MOT protein structure initiative, midwest center for structural genomics; 1.55A {Archaeoglobus fulgidus} SCOP: a.4.5.50

Probab=92.97  E-value=0.14  Score=32.59  Aligned_cols=45  Identities=22%  Similarity=0.322  Sum_probs=37.4

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..+.++...  +.+...++|+.+++.+--+|.+++.|+.-|+|++..
T Consensus        24 ~il~~l~~~--~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~~   68 (109)
T 1sfx_A           24 RIYSLLLER--GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRREI   68 (109)
T ss_dssp             HHHHHHHHH--CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHc--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            345555442  348999999999999999999999999999999863

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

Probab=92.90  E-value=0.21  Score=31.72  Aligned_cols=45  Identities=4%  Similarity=0.069  Sum_probs=37.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .+.++..  ++.+.+.++|+.|++.+--++-.++.|+..|+|.+...
T Consensus        29 il~~l~~--~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~   73 (99)
T 3cuo_A           29 ILCMLSG--SPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRD   73 (99)
T ss_dssp             HHHHHTT--CCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEEC
T ss_pred             HHHHHHh--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEec
Confidence            4444433  45689999999999999999999999999999987643

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

Probab=92.83  E-value=0.16  Score=34.08  Aligned_cols=38  Identities=11%  Similarity=0.163  Sum_probs=34.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      +.+.+.++|+.|++.+--++-.++.|+..|+|++...+
T Consensus        37 ~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~g   74 (108)
T 2kko_A           37 GERAVEAIATATGMNLTTASANLQALKSGGLVEARREG   74 (108)
T ss_dssp             CCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEET
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeC
Confidence            56799999999999999999999999999999866433

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

Probab=92.62  E-value=0.14  Score=32.30  Aligned_cols=47  Identities=19%  Similarity=0.374  Sum_probs=39.8

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHh-----ccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESL-----DVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L-----~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..++++.+++++.+++.++++.|     ++.+=-+|-.++.|+..|+|.+..
T Consensus        21 ~IL~~l~~~~~~~~s~~el~~~l~~~~~~is~~TVyR~L~~L~~~Glv~~~~   72 (83)
T 2fu4_A           21 KILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHN   72 (83)
T ss_dssp             HHHHHHTSGGGSSBCHHHHHHHHHHTTCCCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             HHHHHHHhCCCCCCCHHHHHHHHHHhCCCCCHhhHHHHHHHHHHCCCeEEEe
Confidence            35666665543679999999999     899999999999999999999874

>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=92.13  E-value=0.14  Score=32.63  Aligned_cols=37  Identities=8%  Similarity=0.191  Sum_probs=34.0

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++.+...++|+.+++.+--+|.+++.|+.-|+|++..
T Consensus        34 ~~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           34 EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            4558999999999999999999999999999999874

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

Probab=91.33  E-value=0.39  Score=31.39  Aligned_cols=44  Identities=18%  Similarity=0.234  Sum_probs=36.6

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+.++..   +.+.+.++|+.+++.+--++-.++.|+.-|+|++..
T Consensus        25 ~IL~~L~~---~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~   68 (114)
T 2oqg_A           25 EILTELGR---ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVK   68 (114)
T ss_dssp             HHHHHHHH---SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEe
Confidence            34555532   348999999999999999999999999999998753

>1ku9_A Hypothetical protein MJ223; putative transcription factor, homodimeric winged-helix fold, structural genomics, PSI; 2.80A {Methanocaldococcus jannaschii} SCOP: a.4.5.36

Probab=90.94  E-value=0.38  Score=31.95  Aligned_cols=45  Identities=20%  Similarity=0.231  Sum_probs=37.3

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.++..+ ++.+.+.++|+.+++.+=-++.+++.|+.-|+|++.
T Consensus        30 ~il~~L~~~-~~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           30 AVYAILYLS-DKPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             HHHHHHHHC-SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            344455323 256899999999999999999999999999999986

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

Probab=90.81  E-value=0.5  Score=30.45  Aligned_cols=37  Identities=8%  Similarity=0.151  Sum_probs=34.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      +.+.+.++|+.+++.+--++--++.|+..|+|++...
T Consensus        35 ~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~   71 (98)
T 3jth_A           35 QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKE   71 (98)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECC
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            6789999999999999999999999999999987643

>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=90.81  E-value=0.32  Score=32.92  Aligned_cols=45  Identities=11%  Similarity=0.191  Sum_probs=38.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++...+++.+...++|+.|++.+=-+.-+++-||.-|+|++.
T Consensus        42 vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   86 (127)
T 2frh_A           42 VLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKK   86 (127)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCB
T ss_pred             HHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            445555555577999999999999999999999999999999985

>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=90.62  E-value=0.35  Score=31.94  Aligned_cols=44  Identities=14%  Similarity=0.303  Sum_probs=36.5

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .+.++.   ++.+.+.++|+.+++.+--++-.++.|+..|+|.+...
T Consensus        31 IL~~L~---~~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~   74 (106)
T 1r1u_A           31 IMELLS---VSEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQ   74 (106)
T ss_dssp             HHHHHH---HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEE
T ss_pred             HHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            445554   24479999999999999999999999999999987543

>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=90.47  E-value=0.61  Score=30.30  Aligned_cols=44  Identities=18%  Similarity=0.301  Sum_probs=36.6

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .+.++.+   +...+.++|+.+++.+--++.-++.|+..|+|.+...
T Consensus        28 Il~~L~~---~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~   71 (102)
T 3pqk_A           28 LVCTLVE---GEFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRN   71 (102)
T ss_dssp             HHHHHHT---CCBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECS
T ss_pred             HHHHHHh---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEe
Confidence            4455543   4589999999999999999999999999999987543

>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=90.24  E-value=0.41  Score=38.52  Aligned_cols=54  Identities=13%  Similarity=0.250  Sum_probs=43.9

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc-eeeccCCcee
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI-LEKKSKNNIQ  119 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL-I~K~~Kn~~~  119 (122)
                      -++.++++.++++..++-.++|+.|+++|.-++.-++.|+..|+ |+.....-|.
T Consensus         5 ~~~iL~~L~~~~g~~~Sg~eLa~~lgvSr~aV~k~i~~L~~~G~~i~~~~~~GY~   59 (323)
T 3rkx_A            5 SQDVLQLLYKNKPNYISGQSIAESLNISRTAVKKVIDQLKLEGCKIDSVNHKGHL   59 (323)
T ss_dssp             HHHHHHHHHHHTTSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEEETTTEEE
T ss_pred             HHHHHHHHHhCCCCccCHHHHHHHHCCCHHHHHHHHHHHHhcCCeEEEeCCCeEE
Confidence            35678888776777899999999999999999999999999998 5543333444

>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=90.23  E-value=0.22  Score=33.81  Aligned_cols=45  Identities=11%  Similarity=0.164  Sum_probs=33.0

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++...+++.+...++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        46 vL~~l~~~~~~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   90 (148)
T 3jw4_A           46 MIGYIYENQESGIIQKDLAQFFGRRGASITSMLQGLEKKGYIERR   90 (148)
T ss_dssp             HHHHHHHHTTTCCCHHHHHHC------CHHHHHHHHHHTTSBCCC
T ss_pred             HHHHHHhCCCCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEee
Confidence            445555555577899999999999999999999999999999987

>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=90.20  E-value=0.56  Score=34.21  Aligned_cols=46  Identities=24%  Similarity=0.317  Sum_probs=38.2

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc-eeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI-LEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL-I~K~  113 (122)
                      .+.++++.+. +..+...++|+.|+|++|-+|.=++.|+..|+ |...
T Consensus        24 ~~Il~~L~~~-~~~~s~~eLa~~l~vS~~Ti~rdi~~L~~~G~~I~~~   70 (187)
T 1j5y_A           24 KSIVRILERS-KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVAT   70 (187)
T ss_dssp             HHHHHHHHHC-SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEE
T ss_pred             HHHHHHHHHc-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            3466667654 34589999999999999999999999999999 8764

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

Probab=90.02  E-value=0.45  Score=31.22  Aligned_cols=47  Identities=17%  Similarity=0.253  Sum_probs=38.2

Q ss_pred             HHHHHHHhhC----CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSS----PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~s----p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +..++++.+.    .++++++.++|+.|+|+.--+..=++.||.-|+|.+.
T Consensus         7 ~~IL~~I~~~i~~~~g~~psv~EIa~~lgvS~~TVrr~L~~Le~kG~I~R~   57 (77)
T 2jt1_A            7 TKIISIVQERQNMDDGAPVKTRDIADAAGLSIYQVRLYLEQLHDVGVLEKV   57 (77)
T ss_dssp             HHHHHHHHHHHHHHTTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHhhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence            3444555443    3577999999999999888888999999999999887

>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=89.98  E-value=0.71  Score=32.43  Aligned_cols=36  Identities=8%  Similarity=0.213  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+.+.++|+.+++.+=-+.-+++-||.-|+|++..
T Consensus        67 ~~~t~~eLa~~l~i~~~tvs~~l~~Le~~GlV~r~~  102 (166)
T 3deu_A           67 PDQSQIQLAKAIGIEQPSLVRTLDQLEDKGLISRQT  102 (166)
T ss_dssp             SSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC-
T ss_pred             CCCCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEeeC
Confidence            458999999999999999999999999999999873

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

Probab=89.88  E-value=0.49  Score=36.74  Aligned_cols=51  Identities=16%  Similarity=0.309  Sum_probs=40.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      -..+++|..++ ..+.+.++|+.+++.|=-+|-+++.|+..|++++.....|
T Consensus        33 l~IL~~l~~~~-~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~~~~Y   83 (275)
T 3mq0_A           33 VRILDLVAGSP-RDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSADGTL   83 (275)
T ss_dssp             HHHHHHHHHCS-SCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECTTSEE
T ss_pred             HHHHHHHhhCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCcE
Confidence            44667777664 5689999999999999999999999999999999764444

>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=89.71  E-value=0.58  Score=31.08  Aligned_cols=37  Identities=11%  Similarity=0.217  Sum_probs=34.3

Q ss_pred             CCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++...+.++|+.+ ++.+--++..++.||.-|+|++..
T Consensus        25 ~~~~~~~eLa~~l~~is~~tls~~L~~Le~~GlI~r~~   62 (107)
T 2hzt_A           25 HGKKRTSELKRLMPNITQKMLTQQLRELEADGVINRIV   62 (107)
T ss_dssp             TCCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             hCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence            4668999999999 999999999999999999999874

>4b8x_A SCO5413, possible MARR-transcriptional regulator; winged helix motif; HET: CME; 1.25A {Streptomyces coelicolor}

Probab=89.67  E-value=0.38  Score=33.36  Aligned_cols=44  Identities=23%  Similarity=0.319  Sum_probs=39.3

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.++..++++.+...++|+.+++.+=-+--+++-||.-|+|++.
T Consensus        41 L~~L~~~~~~~~t~~eLa~~l~~~~~tvs~~v~~Le~~Glv~r~   84 (147)
T 4b8x_A           41 LVLLTFSKSGELPMSKIGERLMVHPTSVTNTVDRLVRSGLVAKR   84 (147)
T ss_dssp             HHHHHTSGGGEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHhCCCEEEe
Confidence            44455667888999999999999999999999999999999987

>2pg4_A Uncharacterized protein; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, DNA binding protein; HET: MSE CIT; 2.21A {Aeropyrum pernix} SCOP: a.4.5.48

Probab=89.57  E-value=0.48  Score=30.50  Aligned_cols=52  Identities=12%  Similarity=0.183  Sum_probs=39.8

Q ss_pred             CcHHHHHHHH--HHHHhhCCCCcccHHHHHhHhccchhh-hhhHHHhhhhccceee
Q psy8797          60 TSLGLLTKKF--VKLLQSSPQGVVDLNVASESLDVQKRR-IYDITNVLEGIGILEK  112 (122)
Q Consensus        60 kSLg~Lt~kF--i~ll~~sp~~~idL~~aa~~L~v~kRR-iYDI~NVLE~igLI~K  112 (122)
                      ..++.+.+-|  +.++...+ ..+.+.++|+.+++.+=- ++-+++-||.-|+|++
T Consensus         9 ~~~g~~~~~l~~L~~l~~~~-~~~t~~eLa~~l~is~~t~vs~~l~~Le~~Glv~~   63 (95)
T 2pg4_A            9 LQFGHLIRILPTLLEFEKKG-YEPSLAEIVKASGVSEKTFFMGLKDRLIRAGLVKE   63 (95)
T ss_dssp             SBHHHHHHHHHHHHHHHHTT-CCCCHHHHHHHHCCCHHHHHTTHHHHHHHTTSEEE
T ss_pred             HHhhhHHHHHHHHHHHHhcC-CCCCHHHHHHHHCCCchHHHHHHHHHHHHCCCeec
Confidence            3456555444  33344432 258999999999999999 9999999999999983

>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=89.56  E-value=0.66  Score=32.78  Aligned_cols=47  Identities=17%  Similarity=0.301  Sum_probs=39.2

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      -+.+.++...+++.+.+.++|+.+++..+-+..|+..|...|+|+-.
T Consensus        17 l~~L~~La~~~~~~~~~~~iA~~~~i~~~~l~kil~~L~~~Glv~s~   63 (149)
T 1ylf_A           17 VHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVN   63 (149)
T ss_dssp             HHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEc
Confidence            33444444456678999999999999999999999999999999865

>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=89.41  E-value=0.53  Score=31.42  Aligned_cols=58  Identities=19%  Similarity=0.113  Sum_probs=47.2

Q ss_pred             cHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          61 SLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        61 SLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      ....+..++|..|.  +++.....++|.+||++|+-+==++.-|+.-|.|.+...+--.|
T Consensus        12 ~~~~~v~~~i~~L~--~~~~~Ta~~IAkkLg~sK~~vNr~LY~L~kkG~V~~~~~~PP~W   69 (75)
T 1sfu_A           12 EIFSLVKKEVLSLN--TNDYTTAISLSNRLKINKKKINQQLYKLQKEDTVKMVPSNPPKW   69 (75)
T ss_dssp             HHHHHHHHHHHTSC--TTCEECHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEECCSSCEE
T ss_pred             HHHHHHHHHHHhCC--CCcchHHHHHHHHHCCCHHHHHHHHHHHHHCCCEecCCCCCCCc
Confidence            34445566666443  45559999999999999999999999999999999998888888

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

Probab=89.30  E-value=0.59  Score=31.35  Aligned_cols=43  Identities=5%  Similarity=-0.016  Sum_probs=36.8

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      +..++++++.++....++|+++|+.+++..|.|+-++.-. |+.
T Consensus         8 ~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~-G~s   50 (120)
T 3mkl_A            8 MRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE-ETS   50 (120)
T ss_dssp             HHHHHHHHHHTSTTSCCCHHHHHHHTTCCHHHHHHHHHHT-TCC
T ss_pred             HHHHHHHHHHHhccCCCCHHHHHHHHCcCHHHHHHHHHHc-CCC
Confidence            5678999999998889999999999999999998887653 443

>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=89.25  E-value=0.47  Score=29.98  Aligned_cols=43  Identities=16%  Similarity=0.229  Sum_probs=36.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++..  ++.+.+.++|+.+++.+--+|-.++.||.-|+|++.
T Consensus        21 iL~~L~~--~~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~   63 (100)
T 1ub9_A           21 IMIFLLP--RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             HHHHHHH--HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHh--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            4444443  346899999999999999999999999999999965

>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=89.17  E-value=0.52  Score=33.89  Aligned_cols=45  Identities=18%  Similarity=0.221  Sum_probs=39.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++...+++.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        46 vL~~L~~~~~~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   90 (189)
T 3nqo_A           46 TILSILHLPEEETTLNNIARKMGTSKQNINRLVANLEKNGYVDVI   90 (189)
T ss_dssp             HHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHhccCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            445566667788999999999999999999999999999999986

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

Probab=89.11  E-value=0.7  Score=30.58  Aligned_cols=44  Identities=11%  Similarity=0.124  Sum_probs=37.4

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      +..++++++.++....++++++|+.+++..|.|+-++.-.-|+.
T Consensus         8 ~i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s   51 (113)
T 3oio_A            8 KLTEAVSLMEANIEEPLSTDDIAYYVGVSRRQLERLFKQYLGTV   51 (113)
T ss_dssp             HHHHHHHHHHTCSSSCCCHHHHHHHHTSCHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHhhhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            56788999999988889999999999999999988877655543

>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=89.05  E-value=0.49  Score=31.08  Aligned_cols=44  Identities=5%  Similarity=0.064  Sum_probs=36.7

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      +..++++++.++....++++++|+.+++.+|.|+-++.-.-|+.
T Consensus         6 ~i~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~s   49 (108)
T 3oou_A            6 IIQNVLSYITEHFSEGMSLKTLGNDFHINAVYLGQLFQKEMGEH   49 (108)
T ss_dssp             HHHHHHHHHHHHTTSCCCHHHHHHHHTSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            45778888888888889999999999999999998877655543

>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=89.02  E-value=0.68  Score=32.08  Aligned_cols=47  Identities=11%  Similarity=0.275  Sum_probs=40.6

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-.+.+.+++..  +.+...++|+.+|+++.-+...++-|+.-|+|.+.
T Consensus         6 ~d~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   52 (144)
T 2cfx_A            6 IDLNIIEELKKD--SRLSMRELGRKIKLSPPSVTERVRQLESFGIIKQY   52 (144)
T ss_dssp             HHHHHHHHHHHC--SCCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            345678888764  56899999999999999999999999999999874

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

Probab=88.98  E-value=0.71  Score=30.66  Aligned_cols=36  Identities=14%  Similarity=0.326  Sum_probs=32.7

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +...+.++|+.|++.+--++-.++.||..|+|.+..
T Consensus        44 ~~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~   79 (119)
T 2lkp_A           44 GPLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDR   79 (119)
T ss_dssp             CCCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            357999999999999999999999999999997653

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

Probab=88.84  E-value=0.54  Score=31.60  Aligned_cols=33  Identities=18%  Similarity=0.321  Sum_probs=32.0

Q ss_pred             ccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          81 VDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        81 idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        46 ~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   78 (145)
T 3g3z_A           46 RTQKHIGEKWSLPKQTVSGVCKTLAGQGLIEWQ   78 (145)
T ss_dssp             BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            899999999999999999999999999999986

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

Probab=88.80  E-value=0.43  Score=33.19  Aligned_cols=45  Identities=16%  Similarity=0.186  Sum_probs=34.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++...+++.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        51 vL~~l~~~~~~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   95 (168)
T 3u2r_A           51 TLRLLRSVHPEGMATLQIADRLISRAPDITRLIDRLDDRGLVLRT   95 (168)
T ss_dssp             HHHHHHHHTTSCEEHHHHHHHC---CTHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHhcCCCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEeec
Confidence            334444444567899999999999999999999999999999986

>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=88.76  E-value=0.66  Score=30.91  Aligned_cols=36  Identities=17%  Similarity=0.240  Sum_probs=33.9

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        48 ~~~~~~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   83 (146)
T 2gxg_A           48 DGPKTMAYLANRYFVTQSAITASVDKLEEMGLVVRV   83 (146)
T ss_dssp             TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEee
Confidence            566899999999999999999999999999999986

>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=88.72  E-value=0.72  Score=31.38  Aligned_cols=46  Identities=13%  Similarity=0.053  Sum_probs=36.9

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      +.+.++..  ++.+.+.++|+.|++.+--++-.++.|+..|+|.+...
T Consensus        46 ~IL~~L~~--~~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~   91 (122)
T 1u2w_A           46 KITYALCQ--DEELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKE   91 (122)
T ss_dssp             HHHHHHHH--SSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC--
T ss_pred             HHHHHHHH--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEE
Confidence            34555553  34589999999999999999999999999999987533

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

Probab=88.59  E-value=0.65  Score=31.05  Aligned_cols=44  Identities=18%  Similarity=0.262  Sum_probs=36.2

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..+.++...  + +...++|+.+++.+=-+.-+++.||.-|+|++..
T Consensus        42 ~iL~~l~~~--~-~t~~eLa~~l~~s~~tvs~~l~~L~~~Glv~r~~   85 (146)
T 3tgn_A           42 HILMLLSEE--S-LTNSELARRLNVSQAAVTKAIKSLVKEGMLETSK   85 (146)
T ss_dssp             HHHHHHTTC--C-CCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             HHHHHHHhC--C-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEecc
Confidence            345555543  3 9999999999999999999999999999999863

>1on2_A Transcriptional regulator MNTR; helix-turn-helix, DNA-binding protein, metalloregulatory protein; 1.61A {Bacillus subtilis} SCOP: a.4.5.24 a.76.1.1 PDB: 2ev0_A 1on1_A 2ev5_A 2ev6_A* 2f5c_A 2f5d_A 2f5e_A 2f5f_A 2hyf_A* 2hyg_D 3r60_A* 3r61_A*

Probab=88.56  E-value=0.99  Score=30.59  Aligned_cols=36  Identities=17%  Similarity=0.200  Sum_probs=33.5

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+.+.++|+.|++.+=-+.-+++.||.-|+|.+..
T Consensus        21 ~~~~~~ela~~l~vs~~tvs~~l~~Le~~Glv~r~~   56 (142)
T 1on2_A           21 GYARVSDIAEALAVHPSSVTKMVQKLDKDEYLIYEK   56 (142)
T ss_dssp             SSCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEee
Confidence            458999999999999999999999999999999874

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

Probab=88.49  E-value=0.75  Score=31.01  Aligned_cols=38  Identities=18%  Similarity=0.350  Sum_probs=35.1

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .++.+.+.++|+.|++.+=-++-+++.||.-|+|++..
T Consensus        28 ~~~~~s~~ela~~l~is~~tv~~~l~~Le~~Gli~r~~   65 (139)
T 2x4h_A           28 SGEGAKINRIAKDLKIAPSSVFEEVSHLEEKGLVKKKE   65 (139)
T ss_dssp             TTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             cCCCcCHHHHHHHhCCChHHHHHHHHHHHHCCCEEecC
Confidence            45678999999999999999999999999999999875

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

Probab=88.33  E-value=0.77  Score=31.81  Aligned_cols=50  Identities=22%  Similarity=0.364  Sum_probs=42.3

Q ss_pred             HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      |..+-.+.+.+++.  ++.+...++|+.+|+++..+...++-|+.-|+|.+.
T Consensus         7 ld~~d~~il~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   56 (151)
T 2dbb_A            7 LDRVDMQLVKILSE--NSRLTYRELADILNTTRQRIARRIDKLKKLGIIRKF   56 (151)
T ss_dssp             CCHHHHHHHHHHHH--CTTCCHHHHHHHTTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             CCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            33445678888876  466899999999999999999999999999999864

>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=88.29  E-value=0.7  Score=28.99  Aligned_cols=46  Identities=15%  Similarity=0.182  Sum_probs=37.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhc----cchhhhhhHHHhhhhccceeecc
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLD----VQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~----v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..++.++..  ++.+...++++.|+    +.+=-+|-+++.|+.-|+|++..
T Consensus        12 ~~vL~~L~~--~~~~t~~ei~~~l~~~~~~s~~Tv~~~l~rL~~kGlv~r~~   61 (82)
T 1p6r_A           12 LEVMKVIWK--HSSINTNEVIKELSKTSTWSPKTIQTMLLRLIKKGALNHHK   61 (82)
T ss_dssp             HHHHHHHHT--SSSEEHHHHHHHHHHHSCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHHHc--CCCCCHHHHHHHHhhcCCccHHHHHHHHHHHHHCCCeEEEe
Confidence            445666665  45789999999997    56788999999999999999874

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

Probab=88.28  E-value=0.59  Score=30.84  Aligned_cols=34  Identities=12%  Similarity=0.191  Sum_probs=32.5

Q ss_pred             cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+...++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        52 ~~t~~ela~~l~~~~~tvs~~l~~L~~~glv~r~   85 (140)
T 2nnn_A           52 PCPQNQLGRLTAMDAATIKGVVERLDKRGLIQRS   85 (140)
T ss_dssp             SBCHHHHHHHTTCCHHHHHHHHHHHHHTTCEEEE
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            6899999999999999999999999999999986

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

Probab=88.16  E-value=0.75  Score=30.90  Aligned_cols=44  Identities=18%  Similarity=0.258  Sum_probs=36.6

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .++..+...+  .+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        44 ~iL~~l~~~~--~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   87 (148)
T 3nrv_A           44 RIISVLSSAS--DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN   87 (148)
T ss_dssp             HHHHHHHHSS--SBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHHcCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            3444455443  6899999999999999999999999999999987

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

Probab=88.04  E-value=0.62  Score=30.82  Aligned_cols=34  Identities=12%  Similarity=0.121  Sum_probs=32.5

Q ss_pred             cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+.++|+.+++.+--++-+++-||.-|+|++.
T Consensus        50 ~~t~~ela~~l~~s~~~vs~~l~~Le~~glv~r~   83 (142)
T 2fbi_A           50 EMESYQLANQACILRPSMTGVLARLERDGIVRRW   83 (142)
T ss_dssp             SEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            4899999999999999999999999999999986

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

Probab=88.04  E-value=0.68  Score=30.31  Aligned_cols=44  Identities=7%  Similarity=0.147  Sum_probs=36.6

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      +..+.++++.++....++++++|+.+++..|.|+-++.-.-|+.
T Consensus         3 ~i~~~~~~i~~~~~~~~~~~~lA~~~~~s~~~l~r~fk~~~G~s   46 (108)
T 3mn2_A            3 AVRQVEEYIEANWMRPITIEKLTALTGISSRGIFKAFQRSRGYS   46 (108)
T ss_dssp             HHHHHHHHHHHHTTSCCCHHHHHHHHTCCHHHHHHHHHHHTSSC
T ss_pred             HHHHHHHHHHHcccCCCCHHHHHHHHCCCHHHHHHHHHHHhCcC
Confidence            45678888888888889999999999999999988887655543

>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=88.03  E-value=1.1  Score=32.45  Aligned_cols=48  Identities=21%  Similarity=0.205  Sum_probs=40.8

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-+.+.++..+++..+...++|+.+++.+.-+.-|++.|..-|+|+-.
T Consensus        14 Alr~l~~La~~~~~~~s~~~IA~~~~is~~~l~kil~~L~~aGlv~s~   61 (162)
T 3k69_A           14 AVHSILYLDAHRDSKVASRELAQSLHLNPVMIRNILSVLHKHGYLTGT   61 (162)
T ss_dssp             HHHHHHHHHTTTTSCBCHHHHHHHHTSCGGGTHHHHHHHHHTTSSEEE
T ss_pred             HHHHHHHHHhCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            344555666667788999999999999999999999999999999765

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

Probab=87.93  E-value=0.54  Score=36.13  Aligned_cols=41  Identities=12%  Similarity=0.272  Sum_probs=36.6

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ  119 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~  119 (122)
                      +.+++.++|+.+++..+.++-+.++|.++|++++...+.|.
T Consensus        40 ~~~t~~ela~~~~~~~~~l~r~Lr~L~~~g~l~~~~~~~y~   80 (334)
T 2ip2_A           40 GIDSDETLAAAVGSDAERIHRLMRLLVAFEIFQGDTRDGYA   80 (334)
T ss_dssp             TCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETTTEEE
T ss_pred             CCCCHHHHHHHhCcCHHHHHHHHHHHHhCCceEecCCCeEe
Confidence            56899999999999999999999999999999987655553

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

Probab=87.91  E-value=0.96  Score=29.62  Aligned_cols=45  Identities=20%  Similarity=0.267  Sum_probs=37.4

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ...++++.+  .+.++++++|+.|+|+.=-|---+|.||.-|+|.|.
T Consensus         5 ~~Il~~L~~--~g~vsv~eLa~~l~VS~~TIRrdL~~Le~~G~l~R~   49 (78)
T 1xn7_A            5 IQVRDLLAL--RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI   49 (78)
T ss_dssp             HHHHHHHHH--SCSBCHHHHHHHTTCCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence            345667765  567999999999999777777778999999999998

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

Probab=87.88  E-value=0.43  Score=36.82  Aligned_cols=48  Identities=6%  Similarity=0.137  Sum_probs=40.8

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ  119 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~  119 (122)
                      +++.+.   ++.+++.++|+.+++..+.++-+.+.|.++|++++..++.|.
T Consensus        30 lf~~l~---~g~~t~~elA~~~~~~~~~l~rlLr~l~~~gl~~~~~~~~y~   77 (332)
T 3i53_A           30 VADHIA---AGHRTAAEIASAAGAHADSLDRLLRHLVAVGLFTRDGQGVYG   77 (332)
T ss_dssp             HHHHHH---TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEECTTSBEE
T ss_pred             hHHHHh---cCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEecCCCeEE
Confidence            445554   357999999999999999999999999999999998766654

>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=87.80  E-value=0.88  Score=34.38  Aligned_cols=50  Identities=16%  Similarity=0.207  Sum_probs=41.0

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC-Cce
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK-NNI  118 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K-n~~  118 (122)
                      ..++++... ++.+.+.++|+.+++.|=-+|-+++.|+..|+|++... ..|
T Consensus        10 ~iL~~l~~~-~~~~s~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~~~~~Y   60 (241)
T 2xrn_A           10 SIMRALGSH-PHGLSLAAIAQLVGLPRSTVQRIINALEEEFLVEALGPAGGF   60 (241)
T ss_dssp             HHHHHHHTC-TTCEEHHHHHHHTTSCHHHHHHHHHHHHTTTSEEECGGGCEE
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCeE
Confidence            456666654 34689999999999999999999999999999999753 344

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

Probab=87.75  E-value=0.83  Score=30.05  Aligned_cols=43  Identities=14%  Similarity=0.259  Sum_probs=36.5

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++...  +.+.+.++|+.+++.+--++-+++-||.-|+|++.
T Consensus        38 iL~~l~~~--~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~   80 (139)
T 3bja_A           38 VIQVLAKS--GKVSMSKLIENMGCVPSNMTTMIQRMKRDGYVMTE   80 (139)
T ss_dssp             HHHHHHHS--CSEEHHHHHHHCSSCCTTHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHc--CCcCHHHHHHHHCCChhHHHHHHHHHHHCCCeeec
Confidence            44445443  35899999999999999999999999999999986

>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=87.74  E-value=0.87  Score=31.64  Aligned_cols=48  Identities=13%  Similarity=0.155  Sum_probs=41.3

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+-.+.+.+++..  +.+...++|+.+|+++--++..++-|+.-|+|.+.
T Consensus         8 ~~d~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   55 (152)
T 2cg4_A            8 NLDRGILEALMGN--ARTAYAELAKQFGVSPETIHVRVEKMKQAGIITGA   55 (152)
T ss_dssp             HHHHHHHHHHHHC--TTSCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEEE
T ss_pred             HHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcceE
Confidence            3445778888764  56899999999999999999999999999999874

>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=87.65  E-value=0.67  Score=31.42  Aligned_cols=42  Identities=14%  Similarity=0.223  Sum_probs=34.7

Q ss_pred             HHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          71 KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        71 ~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .++...+ +.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        46 ~~l~~~~-~~~t~~eLa~~l~i~~~tvs~~l~~Le~~Glv~r~   87 (150)
T 3fm5_A           46 VLACEQA-EGVNQRGVAATMGLDPSQIVGLVDELEERGLVVRT   87 (150)
T ss_dssp             HHHHHST-TCCCSHHHHHHHTCCHHHHHHHHHHHHTTTSEEC-
T ss_pred             HHHHhCC-CCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            3343333 34899999999999999999999999999999986

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

Probab=87.64  E-value=0.95  Score=31.86  Aligned_cols=50  Identities=22%  Similarity=0.232  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      |...-.+.+.+++..  +.+...++|+.+|+++--++..++-|+.-|+|.+.
T Consensus         8 ld~~~~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   57 (162)
T 2p5v_A            8 LDKTDIKILQVLQEN--GRLTNVELSERVALSPSPCLRRLKQLEDAGIVRQY   57 (162)
T ss_dssp             CCHHHHHHHHHHHHC--TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEeee
Confidence            344556788888764  45899999999999999999999999999999874

>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=87.59  E-value=0.78  Score=30.69  Aligned_cols=45  Identities=11%  Similarity=0.144  Sum_probs=37.6

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+..+... ++.+...++|+.+++.+--++-+++-||.-|+|++.
T Consensus        39 ~iL~~l~~~-~~~~~~~~la~~l~i~~~~vs~~l~~Le~~glv~r~   83 (147)
T 2hr3_A           39 VVLGAIDRL-GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRH   83 (147)
T ss_dssp             HHHHHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeC
Confidence            344445442 456899999999999999999999999999999986

>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=87.59  E-value=1.1  Score=28.82  Aligned_cols=36  Identities=11%  Similarity=0.205  Sum_probs=32.6

Q ss_pred             CCcccHHHH----HhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVA----SESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~a----a~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+...++    |+.+++.+--++-+++-||.-|+|++.
T Consensus        20 ~~~~~~~el~~~la~~l~is~~tvs~~l~~Le~~gli~r~   59 (99)
T 1tbx_A           20 NEGIATYDLYKKVNAEFPMSTATFYDAKKFLIQEGFVKER   59 (99)
T ss_dssp             CTTCBHHHHHHHHHTTSCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCcCHHHHHHHHHHHcCCCHHHHHHHHHHHHHCCCEEEE
Confidence            355788888    999999999999999999999999985

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

Probab=87.57  E-value=0.75  Score=30.86  Aligned_cols=42  Identities=17%  Similarity=0.264  Sum_probs=36.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++..+...++   .+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        42 iL~~l~~~~~---~~~~la~~l~~~~~tvs~~l~~Le~~Glv~r~   83 (144)
T 3f3x_A           42 ILKATSEEPR---SMVYLANRYFVTQSAITAAVDKLEAKGLVRRI   83 (144)
T ss_dssp             HHHHHHHSCE---EHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHCCC---CHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            4455555544   99999999999999999999999999999987

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

Probab=87.52  E-value=0.99  Score=29.74  Aligned_cols=43  Identities=16%  Similarity=0.204  Sum_probs=36.4

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++..  ++.+...++|+.+++.+--++-+++-||.-|+|++.
T Consensus        34 iL~~l~~--~~~~~~~ela~~l~~s~~tvs~~l~~L~~~glv~~~   76 (138)
T 3bpv_A           34 CLLRIHR--EPGIKQDELATFFHVDKGTIARTLRRLEESGFIERE   76 (138)
T ss_dssp             HHHHHHH--STTCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHH--cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            3444444  356899999999999999999999999999999985

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

Probab=87.45  E-value=0.66  Score=31.10  Aligned_cols=35  Identities=9%  Similarity=0.058  Sum_probs=33.2

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+--+.-+++-||.-|+|++.
T Consensus        50 ~~~t~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   84 (143)
T 3oop_A           50 EPISQKEIALWTKKDTPTVNRIVDVLLRKELIVRE   84 (143)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCeecc
Confidence            56899999999999999999999999999999986

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

Probab=87.42  E-value=0.92  Score=30.64  Aligned_cols=42  Identities=12%  Similarity=0.179  Sum_probs=35.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceee
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEK  112 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K  112 (122)
                      ++..+...  +.+...++|+.+++.+--+.-+++-||.-|+|++
T Consensus        46 iL~~l~~~--~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r   87 (154)
T 2qww_A           46 MINVIYST--PGISVADLTKRLIITGSSAAANVDGLISLGLVVK   87 (154)
T ss_dssp             HHHHHHHS--TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE
T ss_pred             HHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence            34444444  3489999999999999999999999999999998

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

Probab=87.42  E-value=0.93  Score=34.63  Aligned_cols=49  Identities=10%  Similarity=0.240  Sum_probs=39.5

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .+++|... ++.+.+.++|+.+++.|=-+|-+++.|+..|+|++...+.|
T Consensus        28 iL~~l~~~-~~~~~~~eia~~~gl~kstv~r~l~tL~~~G~v~~~~~~~Y   76 (260)
T 2o0y_A           28 LLELFDAA-HPTRSLKELVEGTKLPKTTVVRLVATMCARSVLTSRADGSY   76 (260)
T ss_dssp             HHTTCBTT-BSSBCHHHHHHHHCCCHHHHHHHHHHHHHTTSEEECTTSCE
T ss_pred             HHHHHhhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCeE
Confidence            34444333 45689999999999999999999999999999999754444

>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=87.40  E-value=1.1  Score=33.75  Aligned_cols=50  Identities=18%  Similarity=0.341  Sum_probs=40.7

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      +.++++... +..+.+.++|+.+++.+=-+|-+++.|+..|+|++.....|
T Consensus        12 ~iL~~l~~~-~~~~~~~ela~~~gl~~stv~r~l~~L~~~G~v~~~~~~~Y   61 (249)
T 1mkm_A           12 EILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRY   61 (249)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCE
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEECCCCcE
Confidence            456666654 34689999999999999999999999999999999733334

>3pfi_A Holliday junction ATP-dependent DNA helicase RUVB; probable holliday junction DNA helicase; HET: ADP; 2.69A {Campylobacter jejuni subsp}

Probab=87.23  E-value=0.74  Score=35.21  Aligned_cols=55  Identities=20%  Similarity=0.370  Sum_probs=44.8

Q ss_pred             HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHH-hhhhccceeeccCC
Q psy8797          62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITN-VLEGIGILEKKSKN  116 (122)
Q Consensus        62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~N-VLE~igLI~K~~Kn  116 (122)
                      +..+-++++..+....+..+++.++|+.|++.+..+|+.+. .|...|+|......
T Consensus       261 l~~~e~~~l~~l~~~~~~~~~~~~~a~~lg~~~~tl~~~l~~~l~~~gli~~~~~g  316 (338)
T 3pfi_A          261 FDAMDLRYLELLTAAKQKPIGLASIAAALSEDENTIEDVIEPYLLANGYIERTAKG  316 (338)
T ss_dssp             CCHHHHHHHHHHHHSCSCCBCHHHHHHHTTCCHHHHHHTTHHHHHHTTSEEEETTE
T ss_pred             CCHHHHHHHHHHHHhcCCCchHHHHHHHhCCCHHHHHHHHhHHHHHcCceecCCCc
Confidence            33445677777666566788999999999999999999999 99999999887554

>1i1g_A Transcriptional regulator LRPA; helix-turn-helix, LRP/ASNC family; 2.90A {Pyrococcus furiosus} SCOP: a.4.5.32 d.58.4.2

Probab=87.22  E-value=0.66  Score=31.54  Aligned_cols=45  Identities=18%  Similarity=0.307  Sum_probs=38.5

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+.+++.  ++.+...++|+.+++++.-++..++-|+.-|+|.+.
T Consensus         7 ~~il~~L~~--~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   51 (141)
T 1i1g_A            7 KIILEILEK--DARTPFTEIAKKLGISETAVRKRVKALEEKGIIEGY   51 (141)
T ss_dssp             HHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEecc
Confidence            456677764  345799999999999999999999999999999865

>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=87.13  E-value=1  Score=29.75  Aligned_cols=37  Identities=16%  Similarity=0.381  Sum_probs=33.8

Q ss_pred             CCcccHHHHHhHhc-cchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLD-VQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~-v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++.....++++.++ +.+--++..++.||.-|+|++..
T Consensus        36 ~~~~~~~eL~~~l~gis~~~ls~~L~~Le~~GlV~r~~   73 (107)
T 2fsw_A           36 RRIIRYGELKRAIPGISEKMLIDELKFLCGKGLIKKKQ   73 (107)
T ss_dssp             TSCEEHHHHHHHSTTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             hCCcCHHHHHHHcccCCHHHHHHHHHHHHHCCCEEEee
Confidence            56789999999995 99999999999999999999874

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

Probab=87.03  E-value=0.93  Score=30.88  Aligned_cols=37  Identities=11%  Similarity=0.083  Sum_probs=32.8

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+.+...++|+.+++.+--++-+++-||.-|+|++..
T Consensus        61 ~~~~t~~ela~~l~is~~tvs~~l~~Le~~glv~r~~   97 (162)
T 2fa5_A           61 YPGSSASEVSDRTAMDKVAVSRAVARLLERGFIRRET   97 (162)
T ss_dssp             STTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEC--
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeec
Confidence            4568999999999999999999999999999999863

>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=87.02  E-value=0.94  Score=30.26  Aligned_cols=36  Identities=19%  Similarity=0.279  Sum_probs=33.4

Q ss_pred             CcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+...++|+.+ ++.+--++.+++.||.-|+|++..
T Consensus        34 ~~~~~~eLa~~l~~is~~tvs~~L~~Le~~GlI~r~~   70 (112)
T 1z7u_A           34 GTKRNGELMRALDGITQRVLTDRLREMEKDGLVHRES   70 (112)
T ss_dssp             SCBCHHHHHHHSTTCCHHHHHHHHHHHHHHTSEEEEE
T ss_pred             CCCCHHHHHHHhccCCHHHHHHHHHHHHHCCCEEEee
Confidence            457999999999 999999999999999999999874

>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=86.88  E-value=0.8  Score=30.47  Aligned_cols=35  Identities=26%  Similarity=0.248  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+--++-+++-||.-|+|++.
T Consensus        46 ~~~~~~~la~~l~~s~~tvs~~l~~L~~~glv~r~   80 (145)
T 2a61_A           46 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRT   80 (145)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            45899999999999999999999999999999986

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

Probab=86.80  E-value=1  Score=30.28  Aligned_cols=44  Identities=14%  Similarity=0.233  Sum_probs=37.0

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+.++.   ++.+.+.++|+.|++.+--++--+++|+..|+|.+..
T Consensus        22 ~Il~~L~---~~~~~~~eLa~~l~is~~tvs~hL~~L~~~GlV~~~~   65 (118)
T 3f6o_A           22 AVLGRLS---RGPATVSELAKPFDMALPSFMKHIHFLEDSGWIRTHK   65 (118)
T ss_dssp             HHHHHHH---TCCEEHHHHHTTCCSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             HHHHHHH---hCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEe
Confidence            3555555   3567999999999999999999999999999997653

>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=86.70  E-value=1.1  Score=30.97  Aligned_cols=48  Identities=15%  Similarity=0.207  Sum_probs=40.6

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..-.+.+.++..  ++.+...++|+.+++.+--++..++-|+.-|+|.+.
T Consensus         7 ~~~~~iL~~L~~--~~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (150)
T 2w25_A            7 DIDRILVRELAA--DGRATLSELATRAGLSVSAVQSRVRRLESRGVVQGY   54 (150)
T ss_dssp             HHHHHHHHHHHH--CTTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            344567777765  356899999999999999999999999999999764

>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=86.67  E-value=0.87  Score=30.34  Aligned_cols=36  Identities=8%  Similarity=0.275  Sum_probs=33.5

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+...++|+.+++.+--++-+++-||.-|+|++..
T Consensus        50 ~~~~~~ela~~l~~~~~tvs~~l~~L~~~gli~r~~   85 (142)
T 2bv6_A           50 SPVNVKKVVTELALDTGTVSPLLKRMEQVDLIKRER   85 (142)
T ss_dssp             SEEEHHHHHHHTTCCTTTHHHHHHHHHHTTSEEEEE
T ss_pred             CCcCHHHHHHHHCCChhhHHHHHHHHHHCCCEEeec
Confidence            458999999999999999999999999999999863

>2eth_A Transcriptional regulator, putative, MAR family; MARR family, structural genomics, joint center for structura genomics, JCSG; 2.30A {Thermotoga maritima} SCOP: a.4.5.28

Probab=86.59  E-value=0.83  Score=31.16  Aligned_cols=43  Identities=14%  Similarity=0.183  Sum_probs=36.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++...+  .+.+.++|+.+++.+--++-+++.||.-|+|++.
T Consensus        49 iL~~l~~~~--~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   91 (154)
T 2eth_A           49 AFLYVALFG--PKKMKEIAEFLSTTKSNVTNVVDSLEKRGLVVRE   91 (154)
T ss_dssp             HHHHHHHHC--CBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEee
Confidence            344444433  5899999999999999999999999999999986

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

Probab=86.45  E-value=1.1  Score=30.15  Aligned_cols=46  Identities=20%  Similarity=0.249  Sum_probs=37.8

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+.++++.+  .+.+++.++|+.|+|+.=-|--.++.||.-|+|.|..
T Consensus         5 ~~Il~~L~~--~g~vsv~eLA~~l~VS~~TIRrDL~~Le~~G~l~R~~   50 (87)
T 2k02_A            5 MEVRDMLAL--QGRMEAKQLSARLQTPQPLIDAMLERMEAMGKVVRIS   50 (87)
T ss_dssp             HHHHHHHHH--SCSEEHHHHHHHTTCCHHHHHHHHHHHHTTCCSEEEE
T ss_pred             HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEe
Confidence            345667765  5779999999999997777777789999999999983

>3ech_A MEXR, multidrug resistance operon repressor; winged helix, helix-turn-helix, protein-peptide complex; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.28 PDB: 1lnw_A 3mex_A

Probab=86.45  E-value=0.95  Score=30.33  Aligned_cols=43  Identities=19%  Similarity=0.250  Sum_probs=32.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++...  +.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        42 vL~~l~~~--~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   84 (142)
T 3ech_A           42 VLKLIDEQ--RGLNLQDLGRQMCRDKALITRKIRELEGRNLVRRE   84 (142)
T ss_dssp             HHHHHHHT--TTCCHHHHHHHHC---CHHHHHHHHHHHTTSEEC-
T ss_pred             HHHHHHhC--CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEeec
Confidence            44444443  35899999999999999999999999999999986

>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=86.43  E-value=1.2  Score=30.61  Aligned_cols=36  Identities=6%  Similarity=0.148  Sum_probs=32.9

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +...+.++|+.|++.+--++-.++.|+..|+|.+..
T Consensus        58 ~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~   93 (122)
T 1r1t_A           58 SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRK   93 (122)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEE
Confidence            558999999999999999999999999999998653

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

Probab=86.32  E-value=0.55  Score=37.18  Aligned_cols=41  Identities=10%  Similarity=0.322  Sum_probs=37.2

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCc
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNN  117 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~  117 (122)
                      +++.+++.++|+++++..+.++-+.++|.++|++++...+.
T Consensus        68 ~~g~~t~~eLA~~~g~~~~~l~rlLr~L~~~g~l~~~~~~~  108 (369)
T 3gwz_A           68 QEGPRTATALAEATGAHEQTLRRLLRLLATVGVFDDLGHDD  108 (369)
T ss_dssp             TTSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEECSSTT
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCCEEEeCCCc
Confidence            45789999999999999999999999999999999876655

>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=86.32  E-value=1.1  Score=29.88  Aligned_cols=47  Identities=11%  Similarity=0.069  Sum_probs=40.7

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..++.++.++.+.-++..++|+++++.+.-+-=|+.-||.-|+|.+.
T Consensus        23 ~~Vl~~I~~~g~~gi~qkeLa~~~~l~~~tvt~iLk~LE~kglIkr~   69 (91)
T 2dk5_A           23 KLVYQIIEDAGNKGIWSRDVRYKSNLPLTEINKILKNLESKKLIKAV   69 (91)
T ss_dssp             HHHHHHHHHHCTTCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45667777766667999999999999999999999999999999954

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

Probab=86.25  E-value=0.96  Score=29.87  Aligned_cols=36  Identities=17%  Similarity=0.242  Sum_probs=33.3

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+...++|+.+++.+--++.+++-||.-|+|++..
T Consensus        44 ~~~~~~ela~~l~is~~~vs~~l~~L~~~gli~~~~   79 (142)
T 3bdd_A           44 APLHQLALQERLQIDRAAVTRHLKLLEESGYIIRKR   79 (142)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence            358999999999999999999999999999999873

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

Probab=86.23  E-value=1  Score=29.81  Aligned_cols=37  Identities=14%  Similarity=0.201  Sum_probs=34.2

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .++.+...++|+.+++.+--++.+++-||.-|+|++.
T Consensus        49 ~~~~~t~~~la~~l~~s~~~vs~~l~~L~~~glv~r~   85 (146)
T 2fbh_A           49 HRDSPTQRELAQSVGVEGPTLARLLDGLESQGLVRRL   85 (146)
T ss_dssp             CSSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCeeec
Confidence            3556899999999999999999999999999999986

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

Probab=86.23  E-value=1.5  Score=29.70  Aligned_cols=36  Identities=8%  Similarity=0.221  Sum_probs=33.6

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+...++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        55 ~~~~t~~ela~~l~i~~~tvs~~l~~Le~~Glv~r~   90 (155)
T 3cdh_A           55 NDAMMITRLAKLSLMEQSRMTRIVDQMDARGLVTRV   90 (155)
T ss_dssp             CSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence            456899999999999999999999999999999986

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

Probab=86.21  E-value=1  Score=29.17  Aligned_cols=43  Identities=21%  Similarity=0.194  Sum_probs=34.4

Q ss_pred             HHHHHHHHHhhCCCC-cccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797          65 LTKKFVKLLQSSPQG-VVDLNVASESLDVQKRRIYDITNVLEGI  107 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~-~idL~~aa~~L~v~kRRiYDI~NVLE~i  107 (122)
                      +..++++++.++... .++++++|+.+++..|.|+-++.-.-|+
T Consensus         3 ~~~~i~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~g~   46 (103)
T 3lsg_A            3 AKELIQNIIEESYTDSQFTLSVLSEKLDLSSGYLSIMFKKNFGI   46 (103)
T ss_dssp             HHHHHHHHHHHHTTCTTCCHHHHHHHTTCCHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence            456777888777765 8999999999999999998877665444

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

Probab=86.19  E-value=1  Score=34.87  Aligned_cols=49  Identities=20%  Similarity=0.303  Sum_probs=40.5

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      ...+.+.++...  +.+.+.++|+.|++.+--++-+++.|+..|+|++...
T Consensus       153 ~~~~IL~~L~~~--~~~s~~eLA~~lglsksTv~r~L~~Le~~GlV~r~~r  201 (244)
T 2wte_A          153 EEMKLLNVLYET--KGTGITELAKMLDKSEKTLINKIAELKKFGILTQKGK  201 (244)
T ss_dssp             HHHHHHHHHHHH--TCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence            345566666543  3489999999999999999999999999999998743

>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=86.18  E-value=0.9  Score=30.86  Aligned_cols=44  Identities=11%  Similarity=0.156  Sum_probs=37.1

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGI  107 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~i  107 (122)
                      .+..++++++.++....++++++|+.+++..|.|+-++.-.-|+
T Consensus        11 ~~i~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~G~   54 (129)
T 1bl0_A           11 ITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGH   54 (129)
T ss_dssp             HHHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence            46788999999998888999999999999999998887655443

>2vn2_A DNAD, chromosome replication initiation protein; DNA replication, primosome; 2.3A {Geobacillus kaustophilus HTA426}

Probab=86.16  E-value=1  Score=31.19  Aligned_cols=36  Identities=11%  Similarity=0.079  Sum_probs=33.1

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..-++..++|+.+++...-+..+++-|+.-|+|++.
T Consensus        49 ~~~ps~~~LA~~l~~s~~~V~~~l~~Le~kGlI~~~   84 (128)
T 2vn2_A           49 VLFPTPAELAERMTVSAAECMEMVRRLLQKGMIAIE   84 (128)
T ss_dssp             CSSCCHHHHHHTSSSCHHHHHHHHHHHHHTTSSEEC
T ss_pred             CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            334799999999999999999999999999999986

>1lj9_A Transcriptional regulator SLYA; HTH DNA binding protein, structural genomics, PSI, protein structure initiative; 1.60A {Enterococcus faecalis} SCOP: a.4.5.28

Probab=86.13  E-value=1.2  Score=29.66  Aligned_cols=42  Identities=12%  Similarity=0.105  Sum_probs=35.8

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +..+...  +.+...++|+.+++.+--++-+++-||.-|+|++.
T Consensus        35 L~~l~~~--~~~t~~~la~~l~~s~~~vs~~l~~Le~~gli~r~   76 (144)
T 1lj9_A           35 LVRVCEN--PGIIQEKIAELIKVDRTTAARAIKRLEEQGFIYRQ   76 (144)
T ss_dssp             HHHHHHS--TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHC--cCcCHHHHHHHHCCCHhHHHHHHHHHHHCCCEEee
Confidence            3444443  35899999999999999999999999999999986

>3bj6_A Transcriptional regulator, MARR family; helix-turn-helix, trasnscription regulator, STR genomics, PSI-2, protein structure initiative; 2.01A {Silicibacter pomeroyi dss-3}

Probab=85.98  E-value=1.2  Score=29.92  Aligned_cols=35  Identities=14%  Similarity=0.273  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        53 ~~~t~~ela~~l~~~~~~vs~~l~~Le~~Glv~r~   87 (152)
T 3bj6_A           53 PGATAPQLGAALQMKRQYISRILQEVQRAGLIERR   87 (152)
T ss_dssp             TTEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence            35899999999999999999999999999999986

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

Probab=85.72  E-value=0.63  Score=36.36  Aligned_cols=41  Identities=7%  Similarity=0.089  Sum_probs=36.4

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .++.+++.++|+++++..+.++-+..+|.++|++++ ..+.|
T Consensus        52 ~~g~~t~~elA~~~g~~~~~l~rlLr~l~~~g~l~~-~~~~y   92 (348)
T 3lst_A           52 VDGPRTPAELAAATGTDADALRRVLRLLAVRDVVRE-SDGRF   92 (348)
T ss_dssp             TTSCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEE-ETTEE
T ss_pred             hCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEe-cCCEE
Confidence            356899999999999999999999999999999998 45544

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

Probab=85.60  E-value=0.59  Score=35.61  Aligned_cols=40  Identities=18%  Similarity=0.274  Sum_probs=35.3

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      ++.+++.++|+.+++..+.++-+.++|.+.|++++. .+.|
T Consensus        37 ~~~~t~~ela~~~~~~~~~l~r~L~~L~~~g~l~~~-~~~y   76 (335)
T 2r3s_A           37 QGIESSQSLAQKCQTSERGMRMLCDYLVIIGFMTKQ-AEGY   76 (335)
T ss_dssp             TSEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE-TTEE
T ss_pred             cCCCCHHHHHHHhCCCchHHHHHHHHHHhcCCeEec-CCEE
Confidence            378999999999999999999999999999999874 3444

>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=85.59  E-value=1.1  Score=31.19  Aligned_cols=48  Identities=25%  Similarity=0.340  Sum_probs=41.2

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+-.+.+.+++..  +.+...++|+.+|+++--+...++-|+.-|+|.+.
T Consensus         7 ~~~~~il~~L~~~--~~~s~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   54 (151)
T 2cyy_A            7 EIDKKIIKILQND--GKAPLREISKITGLAESTIHERIRKLRESGVIKKF   54 (151)
T ss_dssp             HHHHHHHHHHHHC--TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence            3445778888764  56899999999999999999999999999999874

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

Probab=85.19  E-value=1.4  Score=30.08  Aligned_cols=35  Identities=9%  Similarity=0.118  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        65 ~~~t~~ela~~l~is~~tvs~~l~~Le~~Gli~r~   99 (162)
T 3cjn_A           65 DGLPIGTLGIFAVVEQSTLSRALDGLQADGLVRRE   99 (162)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence            45899999999999999999999999999999986

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

Probab=85.18  E-value=1.5  Score=28.61  Aligned_cols=43  Identities=9%  Similarity=0.159  Sum_probs=35.2

Q ss_pred             HHHHHHHHHhhCCC-CcccHHHHHhHhccchhhhhhHHHhhhhc
Q psy8797          65 LTKKFVKLLQSSPQ-GVVDLNVASESLDVQKRRIYDITNVLEGI  107 (122)
Q Consensus        65 Lt~kFi~ll~~sp~-~~idL~~aa~~L~v~kRRiYDI~NVLE~i  107 (122)
                      ...+.++++.++.. ..++++++|+.++++.|.|.-++.-.-|+
T Consensus         4 ~i~~~~~~i~~~~~~~~~~~~~lA~~~~~S~~~l~r~fk~~~G~   47 (107)
T 2k9s_A            4 RVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGI   47 (107)
T ss_dssp             HHHHHHHHHHHTSSCSSCCHHHHHHHTTSCHHHHHHHHHHHHSS
T ss_pred             HHHHHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHCc
Confidence            35678888888887 89999999999999999988877654443

>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=85.18  E-value=0.61  Score=35.76  Aligned_cols=49  Identities=12%  Similarity=0.252  Sum_probs=40.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC-Cce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK-NNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K-n~~  118 (122)
                      .+++|..+ ++.+.+.++|+.+++.|=-+|-+++.|+..|++++... ..|
T Consensus        11 IL~~l~~~-~~~lsl~eia~~lgl~ksT~~RlL~tL~~~G~v~~~~~~~~Y   60 (260)
T 3r4k_A           11 LLTYFNHG-RLEIGLSDLTRLSGMNKATVYRLMSELQEAGFVEQVEGARSY   60 (260)
T ss_dssp             HHTTCBTT-BSEEEHHHHHHHHCSCHHHHHHHHHHHHHTTSEEECSSSSEE
T ss_pred             HHHHHhhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcE
Confidence            34444443 46789999999999999999999999999999999764 444

>1qzz_A RDMB, aclacinomycin-10-hydroxylase; anthracycline, methyltransferase, polyketide, tailoring enzymes, structural proteomics in E spine; HET: SAM; 2.10A {Streptomyces purpurascens} SCOP: a.4.5.29 c.66.1.12 PDB: 1r00_A* 1xds_A* 1xdu_A*

Probab=85.16  E-value=0.83  Score=35.51  Aligned_cols=45  Identities=22%  Similarity=0.315  Sum_probs=37.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      .++.+.   ++.+++.++|+.+++..+.++-+.++|.++|++++...+
T Consensus        41 i~~~l~---~~~~t~~eLA~~~g~~~~~l~r~Lr~L~~~Gll~~~~~~   85 (374)
T 1qzz_A           41 LVDHLL---AGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQ   85 (374)
T ss_dssp             HHHHHH---TTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECCCC-
T ss_pred             hHHHHh---CCCCCHHHHHHHhCcCHHHHHHHHHHHhhCCCEEEeCCC
Confidence            445553   356899999999999999999999999999999985444

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

Probab=85.09  E-value=0.81  Score=34.83  Aligned_cols=48  Identities=8%  Similarity=0.118  Sum_probs=38.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .++++... +..+.+.++|+.+++.|=-+|-+++.|+..|+|++.+ ..|
T Consensus        19 iL~~l~~~-~~~~~~~eia~~~gl~~stv~r~l~~L~~~G~v~~~~-~~Y   66 (257)
T 2g7u_A           19 VLLAFDAQ-RPNPTLAELATEAGLSRPAVRRILLTLQKLGYVAGSG-GRW   66 (257)
T ss_dssp             HHHTCSSS-CSSCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TEE
T ss_pred             HHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC-CEE
Confidence            34444433 4568999999999999999999999999999999874 444

>2qko_A Possible transcriptional regulator, TETR family P; TETR family protein, structural genomics, P protein structure initiative; 2.35A {Rhodococcus SP}

Probab=85.07  E-value=0.89  Score=31.80  Aligned_cols=47  Identities=9%  Similarity=0.058  Sum_probs=35.3

Q ss_pred             CCCCCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhh
Q psy8797          53 EKGTRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYD   99 (122)
Q Consensus        53 ~~~~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYD   99 (122)
                      +...|.+..=..|..-.+++|.+..-.-+.++++|+..||.+.-||-
T Consensus        21 ~R~~r~~~~r~~Il~aa~~lf~~~G~~~~tv~~IA~~agvs~~t~Y~   67 (215)
T 2qko_A           21 GHMAQNPERRAALVNAAIEVLAREGARGLTFRAVDVEANVPKGTASN   67 (215)
T ss_dssp             ------CHHHHHHHHHHHHHHHHTCTTTCCHHHHHHHSSSTTTCHHH
T ss_pred             ccccccHHHHHHHHHHHHHHHHHhChhhccHHHHHHHcCCCcchHHH
Confidence            33344555666788889999998877789999999999999998883

>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=84.96  E-value=1.2  Score=30.64  Aligned_cols=45  Identities=18%  Similarity=0.250  Sum_probs=38.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+.+++.  ++.+...++|+.+|+.+--+...++.|+.-|+|.+.
T Consensus         6 ~~il~~L~~--~~~~~~~ela~~lg~s~~tv~~~l~~L~~~G~i~~~   50 (150)
T 2pn6_A            6 LRILKILQY--NAKYSLDEIAREIRIPKATLSYRIKKLEKDGVIKGY   50 (150)
T ss_dssp             HHHHHHHTT--CTTSCHHHHHHHHTSCHHHHHHHHHHHHHTTSSCCC
T ss_pred             HHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEE
Confidence            456777764  456899999999999999999999999999999873

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

Probab=84.82  E-value=1.3  Score=30.09  Aligned_cols=35  Identities=20%  Similarity=0.300  Sum_probs=32.5

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        54 ~~~~~~eLa~~l~~~~~~vs~~l~~L~~~Glv~r~   88 (149)
T 4hbl_A           54 NPQTLNSIGRHLDLSSNTLTPMLKRLEQSGWVKRE   88 (149)
T ss_dssp             SSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEC-
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeeC
Confidence            56899999999999999999999999999999987

>3hsr_A HTH-type transcriptional regulator SARZ; helix-turn-helix, cysteine disulfide, MARR-family transcript regulator, DNA-binding; 1.90A {Staphylococcus aureus subsp} PDB: 3hse_A 3hrm_A 4gxo_A

Probab=84.81  E-value=1.6  Score=29.31  Aligned_cols=37  Identities=8%  Similarity=0.112  Sum_probs=34.5

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+.+...++|+.+++.+--+.-+++-||.-|+|++.
T Consensus        47 ~~~~~t~~eLa~~l~~~~~tvs~~l~~L~~~Glv~r~   83 (140)
T 3hsr_A           47 NDEKLNIKKLGERVFLDSGTLTPLLKKLEKKDYVVRT   83 (140)
T ss_dssp             TTCEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HcCCcCHHHHHHHHCCChhhHHHHHHHHHHCCCeEec
Confidence            3567899999999999999999999999999999987

>1yyv_A Putative transcriptional regulator; reductive methylation, D lysine, structural genomics, PSI; HET: MLY; 2.35A {Salmonella typhimurium} SCOP: a.4.5.69

Probab=84.60  E-value=1.1  Score=31.14  Aligned_cols=56  Identities=18%  Similarity=0.237  Sum_probs=42.9

Q ss_pred             CCCcCcHHHHHHHH----HHHHhhCCCCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797          56 TRYDTSLGLLTKKF----VKLLQSSPQGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        56 ~R~~kSLg~Lt~kF----i~ll~~sp~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.....|..+..++    +..+.   ++.....++++.+ ++.+.-+...++.||.-|+|++..
T Consensus        23 c~~~~~l~~l~~~w~l~IL~~L~---~g~~~~~eLa~~l~gis~~tls~~L~~Le~~GlV~r~~   83 (131)
T 1yyv_A           23 CPSREVLKHVTSRWGVLILVALR---DGTHRFSDLRRXMGGVSEXMLAQSLQALEQDGFLNRVS   83 (131)
T ss_dssp             CTHHHHHHHHHSHHHHHHHHHGG---GCCEEHHHHHHHSTTCCHHHHHHHHHHHHHHTCEEEEE
T ss_pred             CCHHHHHHHHcCCcHHHHHHHHH---cCCCCHHHHHHHhccCCHHHHHHHHHHHHHCCcEEEEe
Confidence            33445566666443    22232   4678999999999 799999999999999999999873

>1v4r_A Transcriptional repressor; helix-turn-helix, winged-helix, gene regulation; NMR {Streptomyces} SCOP: a.4.5.6

Probab=84.59  E-value=2.7  Score=27.42  Aligned_cols=52  Identities=15%  Similarity=0.321  Sum_probs=40.9

Q ss_pred             HHHHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          63 GLLTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        63 g~Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..+...+...+..   .++..+ ...++|+.|+|++=-+...++.|+.-|+|++..
T Consensus        14 ~~l~~~i~~~I~~~~l~~g~~lps~~eLa~~~~vSr~tvr~al~~L~~~Gli~~~~   69 (102)
T 1v4r_A           14 ADVATHFRTLIKSGELAPGDTLPSVADIRAQFGVAAKTVSRALAVLKSEGLVSSRG   69 (102)
T ss_dssp             HHHHHHHHHHTTTTSCCTTSBCCCHHHHHHHSSSCTTHHHHHTTTTTTSSCCEEET
T ss_pred             HHHHHHHHHHHHhCCCCCcCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence            3444555444443   356667 999999999999999999999999999998774

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

Probab=84.33  E-value=1.4  Score=29.86  Aligned_cols=36  Identities=19%  Similarity=0.222  Sum_probs=33.5

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.+.+.++|+.+++.+--+.-+++-||.-|+|++.
T Consensus        60 ~~~~~~~ela~~l~i~~~tvs~~l~~Le~~Gli~r~   95 (160)
T 3boq_A           60 PDGLSMGKLSGALKVTNGNVSGLVNRLIKDGMVVKA   95 (160)
T ss_dssp             TTCEEHHHHHHHCSSCCSCHHHHHHHHHHHTSEEEC
T ss_pred             CCCCCHHHHHHHHCCChhhHHHHHHHHHHCCCEEee
Confidence            345899999999999999999999999999999986

>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=84.30  E-value=1.8  Score=29.71  Aligned_cols=35  Identities=17%  Similarity=0.071  Sum_probs=33.1

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        59 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   93 (162)
T 3k0l_A           59 PNLSNAKLAERSFIKPQSANKILQDLLANGWIEKA   93 (162)
T ss_dssp             TTCCHHHHHHHHTSCGGGHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCcCeEec
Confidence            46899999999999999999999999999999987

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

Probab=84.04  E-value=1.6  Score=29.87  Aligned_cols=35  Identities=14%  Similarity=0.142  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+=-+.-+++-||.-|+|++.
T Consensus        63 ~~~t~~eLa~~l~~~~~tvs~~l~~Le~~Glv~r~   97 (159)
T 3s2w_A           63 DGINQESLSDYLKIDKGTTARAIQKLVDEGYVFRQ   97 (159)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            45799999999999999999999999999999987

>1r7j_A Conserved hypothetical protein SSO10A; winged helix-turn-helix, two-stranded antiparallel coiled CO structural genomics, PSI; 1.47A {Sulfolobus solfataricus} SCOP: a.4.5.49 PDB: 1xsx_A

Probab=84.01  E-value=3  Score=27.66  Aligned_cols=48  Identities=6%  Similarity=0.034  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          63 GLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        63 g~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..+.-..+..+.   .+ +...++|..+++.-|.+-.+++.|+.-|+|++..
T Consensus         7 ~eIi~~IL~~i~---~~-~~~t~La~~~~ls~~~~~~~l~~L~~~GLI~~~~   54 (95)
T 1r7j_A            7 LEIIQAILEACK---SG-SPKTRIMYGANLSYALTGRYIKMLMDLEIIRQEG   54 (95)
T ss_dssp             HHHHHHHHHHHT---TC-BCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHHH---cC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEC
Confidence            345555566555   33 8899999999999999999999999999999973

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

Probab=84.00  E-value=2.4  Score=29.92  Aligned_cols=48  Identities=15%  Similarity=0.250  Sum_probs=39.1

Q ss_pred             HHHHHHHHhhCC-CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSSP-QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~sp-~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-+.+.++...+ +..+.+.++|+.+++.+.-+..|+..|..-|+|+-.
T Consensus        13 Al~~L~~La~~~~~~~~s~~~IA~~~~i~~~~l~kil~~L~~aGlv~s~   61 (143)
T 3t8r_A           13 GLTLMISLAKKEGQGCISLKSIAEENNLSDLYLEQLVGPLRNAGLIRSV   61 (143)
T ss_dssp             HHHHHHHHHTTTTSCCEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCEEEec
Confidence            344455555444 458999999999999999999999999999999754

>1s3j_A YUSO protein; structural genomics, MARR transcriptional regulator family, PSI, protein structure initiative; HET: MSE; 2.25A {Bacillus subtilis} SCOP: a.4.5.28

Probab=83.96  E-value=1.2  Score=30.01  Aligned_cols=35  Identities=14%  Similarity=0.337  Sum_probs=33.1

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        50 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~   84 (155)
T 1s3j_A           50 GSLKVSEIAERMEVKPSAVTLMADRLEQKNLIART   84 (155)
T ss_dssp             SEEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEeec
Confidence            46899999999999999999999999999999986

>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=83.76  E-value=1  Score=29.55  Aligned_cols=37  Identities=14%  Similarity=0.196  Sum_probs=33.5

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++..++..++|+.|++.+=-+...++.|+.-|+|+..
T Consensus        30 ~g~~~s~~eLa~~lgvs~~tV~~~L~~L~~~GlV~~~   66 (110)
T 1q1h_A           30 KGTEMTDEEIANQLNIKVNDVRKKLNLLEEQGFVSYR   66 (110)
T ss_dssp             HCSCBCHHHHHHTTTSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3445899999999999999999999999999999876

>3qph_A TRMB, A global transcription regulator; transcriptional regulator; HET: SUC; 2.99A {Pyrococcus furiosus}

Probab=83.61  E-value=0.13  Score=41.63  Aligned_cols=49  Identities=18%  Similarity=0.205  Sum_probs=38.7

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      ++.++.   .+.....++|+.+++.+-++||+++.|+..|+|.....+...|
T Consensus        24 Y~~Ll~---~g~~t~~eia~~~gv~~~~Vy~~L~~L~~~GlV~~~~g~p~~y   72 (342)
T 3qph_A           24 YWTLLV---YGPSTAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEGTPKVY   72 (342)
T ss_dssp             SHHHHH---HHHHHHSCCSSSTTSSSCSCCHHHHHHHHHTSEEEECCTTCEE
T ss_pred             HHHHHH---cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceeEE
Confidence            445554   2356788899999999999999999999999999875544444

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

Probab=83.57  E-value=1.4  Score=29.48  Aligned_cols=35  Identities=14%  Similarity=0.251  Sum_probs=32.8

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+--++-+++.||.-|+|++.
T Consensus        55 ~~~t~~ela~~l~~~~~tvs~~l~~Le~~Glv~r~   89 (150)
T 2rdp_A           55 GDLTVGELSNKMYLACSTTTDLVDRMERNGLVARV   89 (150)
T ss_dssp             CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCCchhHHHHHHHHHHCCCeeec
Confidence            35899999999999999999999999999999986

>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=83.57  E-value=1.5  Score=28.97  Aligned_cols=35  Identities=14%  Similarity=0.118  Sum_probs=32.6

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+--++-+++-||.-|+|++.
T Consensus        47 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~gli~r~   81 (138)
T 1jgs_A           47 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL   81 (138)
T ss_dssp             SSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence            34789999999999999999999999999999986

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

Probab=83.43  E-value=1.9  Score=29.12  Aligned_cols=36  Identities=11%  Similarity=0.218  Sum_probs=33.3

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+...++|+.+++.+--+.-+++-||.-|+|++..
T Consensus        60 ~~~t~~ela~~l~~s~~tvs~~l~~Le~~glv~r~~   95 (153)
T 2pex_A           60 DERSVSEIGERLYLDSATLTPLLKRLQAAGLVTRTR   95 (153)
T ss_dssp             CSEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             CCcCHHHHHHHhCCCcccHHHHHHHHHHCCCEeecC
Confidence            458999999999999999999999999999999863

>3tqn_A Transcriptional regulator, GNTR family; regulatory functions; 2.80A {Coxiella burnetii}

Probab=83.42  E-value=1.6  Score=29.42  Aligned_cols=50  Identities=14%  Similarity=0.213  Sum_probs=39.8

Q ss_pred             HHHHHHHHHhh---CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          65 LTKKFVKLLQS---SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        65 Lt~kFi~ll~~---sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +...+.+.+..   .|+..+ +..++|+.|+|++=-+-..++.|+.-|+|+...
T Consensus        14 i~~~i~~~I~~g~~~~G~~lPs~~~La~~~~vSr~tvr~al~~L~~~Gli~~~~   67 (113)
T 3tqn_A           14 LRDKIVEAIIDGSYVEGEMIPSIRKISTEYQINPLTVSKAYQSLLDDNVIEKRR   67 (113)
T ss_dssp             HHHHHHHHHHHTSSCTTCEECCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             HHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence            33444444443   456667 899999999999999999999999999998764

>1z91_A Organic hydroperoxide resistance transcriptional; OHRR, MARR family, bacterial transcription factor, DNA bindi protein; 2.50A {Bacillus subtilis} SCOP: a.4.5.28 PDB: 1z9c_A*

Probab=82.88  E-value=1.2  Score=29.74  Aligned_cols=35  Identities=14%  Similarity=0.286  Sum_probs=33.0

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+...++|+.+++.+--++-+++-||.-|+|++.
T Consensus        53 ~~~~~~~la~~l~~~~~tvs~~l~~L~~~glv~r~   87 (147)
T 1z91_A           53 ETLTVKKMGEQLYLDSGTLTPMLKRMEQQGLITRK   87 (147)
T ss_dssp             SEEEHHHHHHTTTCCHHHHHHHHHHHHHHTSEECC
T ss_pred             CCCCHHHHHHHHCCCcCcHHHHHHHHHHCCCEEec
Confidence            36899999999999999999999999999999986

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

Probab=82.80  E-value=1.4  Score=30.68  Aligned_cols=35  Identities=20%  Similarity=0.326  Sum_probs=32.8

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        58 ~~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~   92 (168)
T 2nyx_A           58 GPINLATLATLLGVQPSATGRMVDRLVGAELIDRL   92 (168)
T ss_dssp             CSEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec
Confidence            35899999999999999999999999999999985

>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=82.72  E-value=1  Score=31.74  Aligned_cols=56  Identities=14%  Similarity=0.150  Sum_probs=43.4

Q ss_pred             CCCcCcHHHHHHH----HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          56 TRYDTSLGLLTKK----FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        56 ~R~~kSLg~Lt~k----Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +-....|..+..+    .+..+.   ++.....++++.+++.+--+...++.||.-|+|++..
T Consensus        12 c~~~~~l~~l~~~w~l~IL~~L~---~g~~~~~eLa~~lgis~~tls~~L~~Le~~GlI~r~~   71 (146)
T 2f2e_A           12 CPVARPLDVIGDGWSMLIVRDAF---EGLTRFGEFQKSLGLAKNILAARLRNLVEHGVMVAVP   71 (146)
T ss_dssp             CTTTTTHHHHCSSSHHHHHHHHH---TTCCSHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CcHHHHHHHhCCchHHHHHHHHH---hCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEEe
Confidence            3445567776533    233333   4568999999999999999999999999999999874

>2v79_A DNA replication protein DNAD; primosome, DNA-binding protein; HET: DNA; 2.00A {Bacillus subtilis}

Probab=82.53  E-value=1.6  Score=31.06  Aligned_cols=43  Identities=12%  Similarity=0.040  Sum_probs=36.2

Q ss_pred             HHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          71 KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        71 ~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+.+....-.+.+++|+.+++..+-++.+++-|+.=|+|++.
T Consensus        42 ~~~~~~g~~~ps~~~LA~~~~~s~~~v~~~L~~L~~KGlI~i~   84 (135)
T 2v79_A           42 KMHLEKGSYFPTPNQLQEGMSISVEECTNRLRMFIQKGFLFIE   84 (135)
T ss_dssp             HHHHTTTCCSCCHHHHHTTSSSCHHHHHHHHHHHHHHTSCEEE
T ss_pred             HHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            3334444456799999999999999999999999999999884

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

Probab=82.47  E-value=1.5  Score=30.14  Aligned_cols=36  Identities=8%  Similarity=0.076  Sum_probs=33.5

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+.+.++|+.+++.+=-+.-+++-||.-|+|++..
T Consensus        66 ~~~t~~eLa~~l~~~~~~vs~~l~~Le~~Glv~r~~  101 (161)
T 3e6m_A           66 GELTVGQLATLGVMEQSTTSRTVDQLVDEGLAARSI  101 (161)
T ss_dssp             SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECC
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeeC
Confidence            468999999999999999999999999999999873

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

Probab=82.43  E-value=1.2  Score=34.02  Aligned_cols=48  Identities=8%  Similarity=0.159  Sum_probs=39.2

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .+++|... +..+.+.++|+.+++.|=-+|-+++.|+..|++++.+ ..|
T Consensus        26 iL~~l~~~-~~~~~~~eia~~~gl~~stv~r~l~tL~~~G~v~~~~-~~Y   73 (265)
T 2ia2_A           26 VIRCFDHR-NQRRTLSDVARATDLTRATARRFLLTLVELGYVATDG-SAF   73 (265)
T ss_dssp             HHHTCCSS-CSSEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEESS-SEE
T ss_pred             HHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC-CEE
Confidence            44444433 4568999999999999999999999999999999974 444

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

Probab=82.39  E-value=1.9  Score=31.06  Aligned_cols=50  Identities=22%  Similarity=0.309  Sum_probs=42.5

Q ss_pred             HHHHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          62 LGLLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        62 Lg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      |..+-.+.+.+++..  +.+...++|+.+++++--+...++-|+.-|+|.+.
T Consensus        15 ld~~d~~IL~~L~~~--~~~s~~eLA~~lglS~~tv~~~l~~L~~~G~I~~~   64 (171)
T 2ia0_A           15 LDDLDRNILRLLKKD--ARLTISELSEQLKKPESTIHFRIKKLQERGVIERY   64 (171)
T ss_dssp             CCHHHHHHHHHHHHC--TTCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            344556788888764  46899999999999999999999999999999864

>1tw3_A COMT, carminomycin 4-O-methyltransferase; anthracycline, methylate, tailoring enzyme, polyketide, S-adenosyl-L-homocystein; HET: SAH ERT; 2.35A {Streptomyces peucetius} SCOP: a.4.5.29 c.66.1.12 PDB: 1tw2_A*

Probab=82.34  E-value=1.3  Score=34.23  Aligned_cols=47  Identities=17%  Similarity=0.337  Sum_probs=38.5

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .++.+.   ++..++.++|+.+++..+.++-+.++|.+.|++++...+.|
T Consensus        44 i~~~l~---~~~~t~~ela~~~~~~~~~l~r~L~~L~~~g~~~~~~~g~y   90 (360)
T 1tw3_A           44 LVDHIL---AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEF   90 (360)
T ss_dssp             HHHHHH---TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEETTEE
T ss_pred             HHHHHh---CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence            444453   35689999999999999999999999999999988544444

>2h09_A Transcriptional regulator MNTR; transcription regulator, diphtheria toxin, manganese transport, structural genomics, NPPSFA; 2.10A {Escherichia coli}

Probab=82.05  E-value=3.4  Score=28.32  Aligned_cols=36  Identities=17%  Similarity=0.239  Sum_probs=32.8

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+...++|+.|++.+=-+..+++.||.-|+|++..
T Consensus        53 ~~~~~~~la~~l~vs~~tvs~~l~~Le~~Glv~r~~   88 (155)
T 2h09_A           53 GEARQVDMAARLGVSQPTVAKMLKRLATMGLIEMIP   88 (155)
T ss_dssp             SCCCHHHHHHHHTSCHHHHHHHHHHHHHTTCEEEET
T ss_pred             CCcCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEec
Confidence            447889999999999999999999999999999874

>1x19_A CRTF-related protein; methyltransferase, bacteriochllochlorophyll, BCHU, SAM, SAH, adenosylmethyonine, S-adenosylhomocysteine, ADO-Met; 2.27A {Chlorobium tepidum} PDB: 1x1a_A* 1x1b_A* 1x1c_A* 1x1d_A*

Probab=81.68  E-value=1.4  Score=34.35  Aligned_cols=37  Identities=14%  Similarity=0.217  Sum_probs=34.3

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++.+++.++|+.+++..+.++-+..+|.++|++++..
T Consensus        62 ~~~~t~~eLA~~~g~~~~~l~rlLr~L~~~gll~~~~   98 (359)
T 1x19_A           62 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED   98 (359)
T ss_dssp             TCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCCCCHHHHHHHhCcChHHHHHHHHHHHhCCCeEeeC
Confidence            4679999999999999999999999999999999864

>2ek5_A Predicted transcriptional regulators; helix-turn-helix, interwined alpha helices; 2.20A {Corynebacterium glutamicum atcc 13032} PDB: 2du9_A

Probab=81.61  E-value=2.1  Score=29.78  Aligned_cols=40  Identities=23%  Similarity=0.110  Sum_probs=35.4

Q ss_pred             CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .|+..+ +..++|+.|+|++=-+-..++.|+.-|+|+....
T Consensus        23 ~~G~~LPse~~La~~~gvSr~tVr~Al~~L~~~Gli~~~~g   63 (129)
T 2ek5_A           23 SIDQRVPSTNELAAFHRINPATARNGLTLLVEAGILYKKRG   63 (129)
T ss_dssp             CTTSCBCCHHHHHHHTTCCHHHHHHHHHHHHTTTSEEEETT
T ss_pred             CCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence            366677 8999999999999999999999999999987643

>4a5n_A Uncharacterized HTH-type transcriptional regulato; activator, DNA binding, MARR-like; 1.81A {Bacillus subtilis} PDB: 4a5m_A

Probab=81.55  E-value=2.4  Score=29.96  Aligned_cols=37  Identities=19%  Similarity=0.205  Sum_probs=34.8

Q ss_pred             CCcccHHHHHhHh-ccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESL-DVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L-~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .+.....++++.+ ++...-|...+..||.-|||+|..
T Consensus        37 ~g~~rf~eL~~~l~gIs~~~Ls~~L~~Le~~GLV~R~~   74 (131)
T 4a5n_A           37 DGKKRFNEFRRICPSITQRMLTLQLRELEADGIVHREV   74 (131)
T ss_dssp             TSCBCHHHHHHHCTTSCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             cCCcCHHHHHHHhcccCHHHHHHHHHHHHHCCCEEEEe
Confidence            5678999999999 999999999999999999999874

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

Probab=81.48  E-value=1.9  Score=30.29  Aligned_cols=34  Identities=12%  Similarity=0.051  Sum_probs=32.5

Q ss_pred             cccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          80 VVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        80 ~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.+.++|+.+++.+=-++-+++-||.-|+|++.
T Consensus        86 ~~t~~eLa~~l~is~~tvs~~l~~Le~~GlV~r~  119 (181)
T 2fbk_A           86 GLRPTELSALAAISGPSTSNRIVRLLEKGLIERR  119 (181)
T ss_dssp             CBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECC
T ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCcCEEec
Confidence            4899999999999999999999999999999986

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

Probab=81.36  E-value=1.5  Score=31.38  Aligned_cols=46  Identities=20%  Similarity=0.344  Sum_probs=37.9

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCC
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKN  116 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn  116 (122)
                      +.+.++.   .+.+.+.++|+.|++.+=-++--+++|+..|+|++....
T Consensus        62 ~IL~~L~---~~~~t~~eLa~~lgls~stvs~hL~~L~~aGlV~~~~~G  107 (151)
T 3f6v_A           62 RLVQLLT---SGEQTVNNLAAHFPASRSAISQHLRVLTEAGLVTPRKDG  107 (151)
T ss_dssp             HHHHHGG---GCCEEHHHHHTTSSSCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHH---hCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecC
Confidence            3455554   355899999999999999999999999999999876433

>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=81.13  E-value=1.4  Score=32.18  Aligned_cols=39  Identities=15%  Similarity=0.096  Sum_probs=33.7

Q ss_pred             CCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          77 PQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        77 p~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .+....+.++|+.|++.+--++..++.||.-|+|.+...
T Consensus        21 ~g~~~s~~eia~~lgl~~~tv~~~l~~Le~~G~i~~~~~   59 (196)
T 3k2z_A           21 NGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKNG   59 (196)
T ss_dssp             HSSCCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEECC--
T ss_pred             hCCCCCHHHHHHHcCCCcHHHHHHHHHHHHCCCEEecCC
Confidence            355689999999999998899999999999999998643

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

Probab=80.89  E-value=6.1  Score=25.93  Aligned_cols=55  Identities=11%  Similarity=0.060  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchh-hhhhHHHhhhhccceeeccCCceee
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKR-RIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kR-RiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      ..-.+.+.++....  .....++|+.|++.+= -+=-..+.||.=|+|++.+.+.-.|
T Consensus        11 ~~~~~IL~~Lk~~g--~~ta~eiA~~Lgit~~~aVr~hL~~Le~eGlV~~~~~gRP~w   66 (79)
T 1xmk_A           11 EIKEKICDYLFNVS--DSSALNLAKNIGLTKARDINAVLIDMERQGDVYRQGTTPPIW   66 (79)
T ss_dssp             HHHHHHHHHHHHTC--CEEHHHHHHHHCGGGHHHHHHHHHHHHHTTSEEEECSSSCEE
T ss_pred             hHHHHHHHHHHHcC--CcCHHHHHHHcCCCcHHHHHHHHHHHHHCCCEEecCCCCCCe
Confidence            45678889988754  5789999999999764 6666777899999999887666677

---

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	122
d1cf7a_	67	a.4.5.17 (A:) Cell cycle transcription factor E2F-	6e-27

>d1cf7a_ a.4.5.17 (A:) Cell cycle transcription factor E2F-4 {Human (Homo sapiens) [TaxId: 9606]} Length = 67

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Cell cycle transcription factor e2f-dp
domain: Cell cycle transcription factor E2F-4
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.9 bits (231), Expect = 6e-27
 Identities = 45/67 (67%), Positives = 57/67 (85%), Gaps = 1/67 (1%)

Query: 56  TRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKS 114
           +R++ SLGLLT KFV LLQ +  GV+DL +A+++L V QKRRIYDITNVLEGIG++EKKS
Sbjct: 1   SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKS 60

Query: 115 KNNIQCK 121
           KN+IQ K
Sbjct: 61  KNSIQWK 67

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	122
d1cf7a_	67	Cell cycle transcription factor E2F-4 {Human (Homo	99.98
d1cf7b_	82	Cell cycle transcription factor DP-2 {Human (Homo	99.12
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	95.92
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	95.21
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.76
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	94.48
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	93.51
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	93.51
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	93.37
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	93.29
d3broa1	135	Transcriptional regulator OEOE1854 {Oenococcus oen	93.11
d1p4xa1	125	Staphylococcal accessory regulator A homolog, SarS	92.82
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	92.54
d1bl0a1	54	MarA {Escherichia coli [TaxId: 562]}	92.36
d1fnna1	112	CDC6, C-terminal domain {Archaeon Pyrobaculum aero	92.32
d1d5ya1	54	Rob transcription factor, N-terminal domain {Esche	91.11
d2frha1	115	Pleiotropic regulator of virulence genes, SarA {St	90.31
d1p4xa2	125	Staphylococcal accessory regulator A homolog, SarS	90.12
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	89.41
d1hsja1	115	Staphylococcal accessory regulator A homolog, SarR	88.58
d2a61a1	139	Transcriptional regulator TM0710 {Thermotoga marit	86.85
d2hs5a1	69	Putative transcriptional regulator RHA1_ro03477 {R	86.19
d1ub9a_	100	Hypothetical protein PH1061 {Archaeon Pyrococcus h	85.95
d1ylfa1	138	Hypothetical protein BC1842 {Bacillus cereus [TaxI	85.9
d3ctaa1	85	Ta1064 (RFK), N-terminal domain {Thermoplasma acid	85.84
d3bwga1	78	Transcriptional regulator YydK {Bacillus subtilis	85.32
d2fbha1	137	Transcriptional regulator PA3341 {Pseudomonas aeru	84.71
d2hr3a1	145	Probable transcriptional regulator PA3067 {Pseudom	84.65
d2cyya1	60	Putative transcriptional regulator PH1519 {Archaeo	84.14
d1z05a1	71	Transcriptional regulator VC2007 N-terminal domain	82.18
d2gxba1	59	Z-alpha domain of dsRNA-specific adenosine deamina	81.81
d2fbka1	172	Transcriptional regulator DR1159 {Deinococcus radi	81.13
d1w5sa1	110	CDC6-like protein APE0152, C-terminal domain {Aero	81.02

>d1cf7a_ a.4.5.17 (A:) Cell cycle transcription factor E2F-4 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Cell cycle transcription factor e2f-dp
domain: Cell cycle transcription factor E2F-4
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.98  E-value=2.5e-33  Score=185.68  Aligned_cols=66  Identities=68%  Similarity=1.004  Sum_probs=64.7

Q ss_pred             CCCcCcHHHHHHHHHHHHhhCCCCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeeccCCceeec
Q psy8797          56 TRYDTSLGLLTKKFVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKSKNNIQCK  121 (122)
Q Consensus        56 ~R~~kSLg~Lt~kFi~ll~~sp~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~Kn~~~W~  121 (122)
                      +|+|+||++||++|+++|.++|++.+||++||+.|+| +|||||||+|||||||||+|.+||+|+|.
T Consensus         1 sR~ekSLglLt~kFl~l~~~~~~~~~~L~~aa~~L~v~~kRRiYDI~NVLe~igli~K~~Kn~~~W~   67 (67)
T d1cf7a_           1 SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWK   67 (67)
T ss_dssp             CTTTTCHHHHHHHHHHHHHHSSTTEEEHHHHHHHTTTCCTHHHHHHHHHHHHHTSEEEEETTEEEEC
T ss_pred             ChhhhhHHHHHHHHHHHHhhCCCCeeeHHHHHHHhcCcchhhHHHHHHHHhhhhhhhcccCCccccC
Confidence            6999999999999999999999999999999999999 89999999999999999999999999995

>d1cf7b_ a.4.5.17 (B:) Cell cycle transcription factor DP-2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Cell cycle transcription factor e2f-dp
domain: Cell cycle transcription factor DP-2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=2.7e-11  Score=81.84  Aligned_cols=31  Identities=35%  Similarity=0.563  Sum_probs=27.8

Q ss_pred             ccchhhhhhHHHhhhhccceeeccCCceeecC
Q psy8797          91 DVQKRRIYDITNVLEGIGILEKKSKNNIQCKR  122 (122)
Q Consensus        91 ~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W~G  122 (122)
                      .-.|||+||.+|||.++|+|+|. |..+.|.|
T Consensus        50 KNIRRRVYDALNVLmA~~II~K~-kK~I~W~G   80 (82)
T d1cf7b_          50 KNIRRRVYDALNVLMAMNIISKE-KKEIKWIG   80 (82)
T ss_dssp             HHHHHHHHHHHHHHHHTTSBCCC-SSCEEBCC
T ss_pred             hhhhHHHHHHHHHHHHHhhhhhc-CceeEeec
Confidence            44799999999999999999999 55599998

>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=95.92  E-value=0.0089  Score=36.27  Aligned_cols=52  Identities=19%  Similarity=0.257  Sum_probs=41.7

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccc-eeeccCCceeec
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGI-LEKKSKNNIQCK  121 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igL-I~K~~Kn~~~W~  121 (122)
                      +.++++.++ +..++.+++|+.|+|++|-||-=++-|+..|+ |..... -|.+.
T Consensus        11 ~Il~~L~~~-~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~~~~g-GY~L~   63 (65)
T d1j5ya1          11 SIVRILERS-KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPR-GYVLA   63 (65)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEETT-EEECC
T ss_pred             HHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEEeCC-CEEeC
Confidence            356666664 57789999999999999999999999999997 766544 56654

>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=95.21  E-value=0.023  Score=35.14  Aligned_cols=50  Identities=18%  Similarity=0.341  Sum_probs=42.1

Q ss_pred             HHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          68 KFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        68 kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      +.++++..+ +..+.+.++|+.+++.+=.+|-+++.|+..|++++...+.|
T Consensus         9 ~IL~~~a~~-~~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~g~y   58 (75)
T d1mkma1           9 EILDFIVKN-PGDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKRY   58 (75)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSCE
T ss_pred             HHHHHHHhC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCCE
Confidence            456666665 45689999999999999999999999999999999754444

>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=94.76  E-value=0.012  Score=38.49  Aligned_cols=36  Identities=22%  Similarity=0.349  Sum_probs=33.2

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.....++|+.+++.+..+|++++-||.-|+|++.
T Consensus        32 ~g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          32 RGGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             HCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             cCCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEE
Confidence            356789999999999999999999999999999875

>d1biaa1 a.4.5.1 (A:1-63) Biotin repressor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Biotin repressor-like
domain: Biotin repressor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=94.48  E-value=0.038  Score=33.35  Aligned_cols=42  Identities=19%  Similarity=0.219  Sum_probs=36.4

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccce
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGIL  110 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI  110 (122)
                      .+.++++++  +..++..++|+.|+|+++-||-=++.|+..|++
T Consensus         8 ~~iL~~L~~--~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           8 LKLIALLAN--GEFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             HHHHHHHTT--SSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHH--CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            456777753  667999999999999999999999999999983

>d1qzza1 a.4.5.29 (A:10-101) Aclacinomycin-10-hydroxylase RdmB {Streptomyces purpurascens [TaxId: 1924]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Plant O-methyltransferase, N-terminal domain
domain: Aclacinomycin-10-hydroxylase RdmB
species: Streptomyces purpurascens [TaxId: 1924]

Probab=93.51  E-value=0.034  Score=36.01  Aligned_cols=47  Identities=21%  Similarity=0.287  Sum_probs=39.5

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCce
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNI  118 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~  118 (122)
                      .++.+.   +++.++.++|+++++..++++-+...|.++|++++...+.+
T Consensus        32 ifd~L~---~gp~t~~eLA~~~g~~~~~l~rLlr~L~a~gll~~~~d~~~   78 (92)
T d1qzza1          32 LVDHLL---AGADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQGR   78 (92)
T ss_dssp             HHHHHH---TTCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECCCC-CC
T ss_pred             chHHHh---CCCCCHHHHHHHHCcCchHHHHHHHHHHHCCCeeeecCCCc
Confidence            445554   46789999999999999999999999999999999866654

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

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

Probab=93.51  E-value=0.022  Score=36.10  Aligned_cols=42  Identities=17%  Similarity=0.324  Sum_probs=37.8

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ  119 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~  119 (122)
                      ++++++.++|+++++...+++-+..+|.++|++++.+.+.|.
T Consensus        32 ~gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~~~~y~   73 (85)
T d1tw3a1          32 AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFV   73 (85)
T ss_dssp             TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEETTEEE
T ss_pred             cCCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecCCCeEe
Confidence            567899999999999999999999999999999987766653

>d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: C-terminal fragment of elongation factor SelB
domain: C-terminal fragment of elongation factor SelB
species: Moorella thermoacetica [TaxId: 1525]

Probab=93.37  E-value=0.1  Score=31.59  Aligned_cols=56  Identities=14%  Similarity=0.117  Sum_probs=51.2

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCcee
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQ  119 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~  119 (122)
                      .|.++....+.++.-.+-.+.++|+.+++.-..+=++.+.|-..|.+-|...|.|.
T Consensus         7 ~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~~d~yf   62 (64)
T d1lvaa3           7 KLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYW   62 (64)
T ss_dssp             HHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBEE
T ss_pred             HHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecccccc
Confidence            46678888999988889999999999999999999999999999999999988774

>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=93.29  E-value=0.067  Score=35.37  Aligned_cols=48  Identities=19%  Similarity=0.184  Sum_probs=40.1

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..-+.+.++..++ +++++.++|+.+++.+=.+|=+++.|+..|+|.+.
T Consensus        27 ~~~~i~~~L~~~~-~plt~~ela~~l~vsk~~vs~~l~~L~~~GlV~r~   74 (151)
T d1ku9a_          27 SVGAVYAILYLSD-KPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (151)
T ss_dssp             HHHHHHHHHHHCS-SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHHhCC-CCcCHHHHHHHhCCCcchHHHHHHHHHHCCCEEEE
Confidence            3445566665554 45999999999999999999999999999999877

>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=93.11  E-value=0.078  Score=34.66  Aligned_cols=45  Identities=11%  Similarity=0.086  Sum_probs=40.3

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++...|++.+.+.++|+.+++.+-.+.-+++-|+.-|+|.+.
T Consensus        34 vL~~l~~~~~~~it~~ela~~~~~~~~~vs~~l~~L~~~g~v~r~   78 (135)
T d3broa1          34 IIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRK   78 (135)
T ss_dssp             HHHHHHHTTTSCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHcCCCCCCHHHHHHHHCcCHhHHHHHHHHHHHHHHHHHH
Confidence            445566678889999999999999999999999999999999887

>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=92.82  E-value=0.079  Score=35.09  Aligned_cols=44  Identities=11%  Similarity=0.120  Sum_probs=39.8

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.++...+++.+.+.++|+.+++.+=.+--+++.||.-|+|+|.
T Consensus        40 L~~l~~~~~~~~t~~eia~~~~~~~~~vs~~l~~L~~~g~v~r~   83 (125)
T d1p4xa1          40 LTYLFHQQENTLPFKKIVSDLCYKQSDLVQHIKVLVKHSYISKV   83 (125)
T ss_dssp             HHHHHSCSCSEEEHHHHHHHSSSCGGGTHHHHHHHHHTTSCEEE
T ss_pred             HHHHHHhccCCcCHHHHHHHhCCCcchHHHHHHHHHHCCCceee
Confidence            44456678889999999999999999999999999999999987

>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=92.54  E-value=0.073  Score=32.77  Aligned_cols=46  Identities=13%  Similarity=0.055  Sum_probs=38.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhcc-chhhhhhHHHhhhhccceeecc
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDV-QKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v-~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ||.-+....+....+.++|+.+|+ +.--+++.++.||.-|+|++..
T Consensus        13 ~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          13 LIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             HHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCC
Confidence            444444445677899999999999 6888999999999999999973

>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=92.36  E-value=0.072  Score=30.44  Aligned_cols=44  Identities=11%  Similarity=0.138  Sum_probs=37.9

Q ss_pred             HHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhcc
Q psy8797          65 LTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIG  108 (122)
Q Consensus        65 Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~ig  108 (122)
                      ...+.++++.++..+.++|+++|+.+++.+|.++-++.-.-|+.
T Consensus         4 ~i~~v~~yI~~~~~~~~tl~~lA~~~~~s~~~l~r~Fk~~~g~t   47 (54)
T d1bl0a1           4 TIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKETGHS   47 (54)
T ss_dssp             HHHHHHHHHHTTTTSCCCCHHHHHHSSSCHHHHHHHHHHHHSSC
T ss_pred             HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence            35788999999999999999999999999999998877655543

>d1fnna1 a.4.5.11 (A:277-388) CDC6, C-terminal domain {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6, C-terminal domain
species: Archaeon Pyrobaculum aerophilum [TaxId: 13773]

Probab=92.32  E-value=0.039  Score=36.85  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=24.0

Q ss_pred             HHHHhHhcc---chhhhhhHHHhhhhccceee
Q psy8797          84 NVASESLDV---QKRRIYDITNVLEGIGILEK  112 (122)
Q Consensus        84 ~~aa~~L~v---~kRRiYDI~NVLE~igLI~K  112 (122)
                      ..+|+..++   ..|||||++|-||.+|+|+-
T Consensus        42 ~~lc~~~~~~pls~rr~~~~l~~Le~lGiI~~   73 (112)
T d1fnna1          42 KIVCEEYGERPRVHSQLWSYLNDLREKGIVET   73 (112)
T ss_dssp             HHHHHHTTCCCCCHHHHHHHHHHHHHTTSSEE
T ss_pred             HHHHHHcCcchhhHHHHHHHHHHHHhCCCeee
Confidence            445666665   78999999999999999973

>d1d5ya1 a.4.1.8 (A:3-56) Rob transcription factor, N-terminal domain {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: AraC type transcriptional activator
domain: Rob transcription factor, N-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=91.11  E-value=0.12  Score=29.54  Aligned_cols=40  Identities=8%  Similarity=0.090  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHh
Q psy8797          64 LLTKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNV  103 (122)
Q Consensus        64 ~Lt~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NV  103 (122)
                      .+.++.++++.++..+.++|+++|+.++++++-|.-+.--
T Consensus         3 ~ii~~i~~yi~~~~~~~itl~~lA~~~~~S~~~l~r~Fk~   42 (54)
T d1d5ya1           3 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKD   42 (54)
T ss_dssp             HHHHHHHHHHHTTSSSSCCCHHHHTTTSSCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHccCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence            3678899999999999999999999999999988766543

>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=90.31  E-value=0.17  Score=32.86  Aligned_cols=46  Identities=11%  Similarity=0.186  Sum_probs=40.9

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++..+..++++.+.+.++|+.+++.+=-+-=+++.||.-|+|.|..
T Consensus        38 vL~~l~~~~~~~~t~~~la~~l~~~~~tvs~~i~~Le~~gli~r~~   83 (115)
T d2frha1          38 VLTYISENKEKEYYLKDIINHLNYKQPQVVKAVKILSQEDYFDKKR   83 (115)
T ss_dssp             HHHHHHHTCCSEEEHHHHHHHSSSHHHHHHHHHHHHHHTTSSCCBC
T ss_pred             HHHHHHcCCCCCCCHHHHHHHHCCCHhHHHHHHHHHHhhhhheeee
Confidence            3445677788889999999999999999999999999999999883

>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=90.12  E-value=0.2  Score=33.30  Aligned_cols=44  Identities=20%  Similarity=0.224  Sum_probs=38.8

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +.++...+++.+.+.++|+.+++.+-.+-=+++-||.-|+|+|.
T Consensus        39 L~~l~~~~~~~~~~~~ia~~l~~~~~~vs~~v~~L~~~glV~r~   82 (125)
T d1p4xa2          39 LAIITSQNKNIVLLKDLIETIHHKYPQTVRALNNLKKQGYLIKE   82 (125)
T ss_dssp             HHHHHTTTTCCEEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEEE
T ss_pred             HHHHHHccCCCccHHHHHHHHCCCcchHHHHHHHHHhccCEeee
Confidence            44455567777999999999999999999999999999999987

>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=89.41  E-value=0.25  Score=31.42  Aligned_cols=37  Identities=8%  Similarity=0.191  Sum_probs=33.9

Q ss_pred             CCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          78 QGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        78 ~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ++.+.+.++|+.+++.+--+.=+++-|+.-|+|.+..
T Consensus        34 ~~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~~   70 (109)
T d2d1ha1          34 EKPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             CSCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEee
Confidence            4468999999999999999999999999999998763

>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=88.58  E-value=0.24  Score=32.18  Aligned_cols=45  Identities=11%  Similarity=0.163  Sum_probs=40.1

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++.++..++++.+.+.++|+.+++.+=.+--+++-||.-|+|+|.
T Consensus        37 vL~~l~~~~~~~~t~~ela~~l~~~~~~vs~~i~~Le~~gli~r~   81 (115)
T d1hsja1          37 ILNHILRSESNEISSKEIAKCSEFKPYYLTKALQKLKDLKLLSKK   81 (115)
T ss_dssp             HHHHHHTCSCSEEEHHHHHHSSCCCHHHHHHHHHHHHTTTTSCCE
T ss_pred             HHHHHHccCCCCcCHHHHHHHHCCChhhHHHHHHHHHHcCCeEEE
Confidence            455566667888999999999999999999999999999999987

>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=86.85  E-value=0.14  Score=33.76  Aligned_cols=36  Identities=25%  Similarity=0.245  Sum_probs=33.3

Q ss_pred             CcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          79 GVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        79 ~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +.+++.++|+.+++.+--+.-++|-|+..|+|++..
T Consensus        43 ~~~t~~~la~~l~i~~~tvs~~l~~L~~~gli~r~~   78 (139)
T d2a61a1          43 GPKRPGELSVLLGVAKSTVTGLVKRLEADGYLTRTP   78 (139)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHhCCCcccchHHHHHHHhcCeeeeee
Confidence            357999999999999999999999999999999873

>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=86.19  E-value=0.54  Score=28.14  Aligned_cols=40  Identities=13%  Similarity=0.183  Sum_probs=36.1

Q ss_pred             CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccC
Q psy8797          76 SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSK  115 (122)
Q Consensus        76 sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~K  115 (122)
                      .|+..+...++|+.++|.+--+-+.++.|+.-|+|+....
T Consensus        21 ~~G~~l~~~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~~   60 (69)
T d2hs5a1          21 RPGARLSEPDICAALDVSRNTVREAFQILIEDRLVAHELN   60 (69)
T ss_dssp             CTTCEECHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEETT
T ss_pred             CCcCccCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEcC
Confidence            3677788999999999999999999999999999997744

>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=85.95  E-value=0.32  Score=30.33  Aligned_cols=43  Identities=16%  Similarity=0.229  Sum_probs=36.6

Q ss_pred             HHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          69 FVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        69 Fi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++..  .+.+++.++|+.+++.+--++-+++.||..|+|++.
T Consensus        21 IL~~L~~--~~~~~~~eLa~~l~is~~~vs~~l~~L~~~glV~~~   63 (100)
T d1ub9a_          21 IMIFLLP--RRKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             HHHHHHH--HSEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHhcc--CCCeeHHHHHHHHhhccccccHHHHHHhhhceeEEE
Confidence            4455543  345899999999999999999999999999999876

>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=85.90  E-value=0.67  Score=30.62  Aligned_cols=48  Identities=17%  Similarity=0.299  Sum_probs=40.9

Q ss_pred             HHHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          66 TKKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        66 t~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      +-+-+.++..+++..++..++|+.+++...-++-|++-|..-|+|+-.
T Consensus         9 Av~~L~~la~~~~~~vss~~IA~~~~i~~~~l~kil~~L~~aGlv~S~   56 (138)
T d1ylfa1           9 AVHILSILKNNPSSLCTSDYMAESVNTNPVVIRKIMSYLKQAGFVYVN   56 (138)
T ss_dssp             HHHHHHHHHHSCGGGCCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence            334455666678889999999999999999999999999999999654

>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=85.84  E-value=0.51  Score=29.42  Aligned_cols=40  Identities=15%  Similarity=0.211  Sum_probs=35.8

Q ss_pred             hhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          74 QSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        74 ~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ..+..+.+...++|+.+++.+=.+-.+++-||.-|+|++.
T Consensus        15 ~~~~~~~lt~~eLa~~l~i~~~~vs~~l~~Le~~GlV~r~   54 (85)
T d3ctaa1          15 EASNRAYLTSSKLADMLGISQQSASRIIIDLEKNGYITRT   54 (85)
T ss_dssp             TTSSEEECCHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             hccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence            3344568999999999999999999999999999999985

>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=85.32  E-value=0.55  Score=28.56  Aligned_cols=39  Identities=18%  Similarity=0.181  Sum_probs=35.1

Q ss_pred             CCCCcc-cHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          76 SPQGVV-DLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        76 sp~~~i-dL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      .|+..+ +..++|+.++|++--+-..++.|+.-|+|.+..
T Consensus        17 ~~G~~LPse~~La~~~~vSr~tvr~Al~~L~~~Gli~~~~   56 (78)
T d3bwga1          17 QQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVR   56 (78)
T ss_dssp             CTTCBCCCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEET
T ss_pred             CCcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEEEc
Confidence            366677 899999999999999999999999999998873

>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=84.71  E-value=0.78  Score=29.56  Aligned_cols=44  Identities=14%  Similarity=0.183  Sum_probs=37.0

Q ss_pred             HHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          70 VKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        70 i~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      +..+..+++ .+...++|+.+++.+=.+--+++-|+.-|+|++..
T Consensus        34 L~~l~~~~~-~~t~~~la~~~~~~~~~vs~~v~~L~~~gli~r~~   77 (137)
T d2fbha1          34 LLHLARHRD-SPTQRELAQSVGVEGPTLARLLDGLESQGLVRRLA   77 (137)
T ss_dssp             HHHHHHCSS-CCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHHcCC-CCcHHHHHHHHCCCHHHHHHHHHHHHHcCCccccC
Confidence            334445555 46999999999999999999999999999999873

>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=84.65  E-value=0.81  Score=29.92  Aligned_cols=43  Identities=12%  Similarity=0.158  Sum_probs=36.7

Q ss_pred             HHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          71 KLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        71 ~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ..+... ++.+.+.++|+.+++.+=.+.-+++.|+.-|+|++..
T Consensus        41 ~~L~~~-~g~~t~~~La~~~~~~~~~vs~~i~~L~~~glv~r~~   83 (145)
T d2hr3a1          41 GAIDRL-GGDVTPSELAAAERMRSSNLAALLRELERGGLIVRHA   83 (145)
T ss_dssp             HHHHHT-TSCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEEC
T ss_pred             HHHHHc-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeee
Confidence            334444 4569999999999999999999999999999999873

>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=84.14  E-value=0.82  Score=26.53  Aligned_cols=45  Identities=27%  Similarity=0.363  Sum_probs=39.9

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++.++..  ..++..++|+++++..--++.=++=|+.-|+|.+.
T Consensus         6 ~~Il~~L~~n--~r~s~~eiA~~l~ls~~~v~~Ri~~L~~~giI~~~   50 (60)
T d2cyya1           6 KKIIKILQND--GKAPLREISKITGLAESTIHERIRKLRESGVIKKF   50 (60)
T ss_dssp             HHHHHHHHHC--TTCCHHHHHHHHCSCHHHHHHHHHHHHHHTSSCCC
T ss_pred             HHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeE
Confidence            5678888874  66799999999999999999999999999999876

>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=82.18  E-value=1.1  Score=26.51  Aligned_cols=45  Identities=18%  Similarity=0.220  Sum_probs=38.4

Q ss_pred             HHHHHHHhhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeec
Q psy8797          67 KKFVKLLQSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        67 ~kFi~ll~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~  113 (122)
                      .+.++++...  +.+.-.++|+.+++.+--+..+++-|+.-|+|...
T Consensus         9 ~~Il~~l~~~--g~~sr~eLa~~~glS~~Tv~~~l~~L~~~Glv~e~   53 (71)
T d1z05a1           9 GRVYKLIDQK--GPISRIDLSKESELAPASITKITRELIDAHLIHET   53 (71)
T ss_dssp             HHHHHHHHHH--CSBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence            3566777654  46899999999999999999999999999999764

>d2gxba1 a.4.5.19 (A:140-198) Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Z-DNA binding domain
domain: Z-alpha domain of dsRNA-specific adenosine deaminase, ADAR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.81  E-value=2.6  Score=25.53  Aligned_cols=53  Identities=19%  Similarity=0.213  Sum_probs=42.2

Q ss_pred             HHHHHHhh-CCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeeccCCceee
Q psy8797          68 KFVKLLQS-SPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKSKNNIQC  120 (122)
Q Consensus        68 kFi~ll~~-sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~Kn~~~W  120 (122)
                      +.+.++.+ .|...+.-.++|.+|+|.|+.|--+.=-|+.-|.+.|.+..-=.|
T Consensus         3 ~vl~~l~~lg~~~~~tA~~LA~kl~vpKk~iNr~LYsL~~kgkl~k~~gtPPlW   56 (59)
T d2gxba1           3 RILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLW   56 (59)
T ss_dssp             HHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECSSSCEE
T ss_pred             HHHHHHHhcCCccchhHHHHHHHhCCcHHHHHHHHHHHHHccchhhcCCCCCCc
Confidence            34555554 577889999999999999998887777888889988887665555

>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=81.13  E-value=0.93  Score=30.91  Aligned_cols=41  Identities=15%  Similarity=0.137  Sum_probs=36.6

Q ss_pred             hhCCCCcccHHHHHhHhccchhhhhhHHHhhhhccceeecc
Q psy8797          74 QSSPQGVVDLNVASESLDVQKRRIYDITNVLEGIGILEKKS  114 (122)
Q Consensus        74 ~~sp~~~idL~~aa~~L~v~kRRiYDI~NVLE~igLI~K~~  114 (122)
                      ...++..+...++|+.+++.+=-+--+++-||.-|+|++..
T Consensus        73 ~~~~~~~lt~~eLa~~l~i~~~tvsr~l~~Le~~GlV~r~~  113 (172)
T d2fbka1          73 RSAPPEGLRPTELSALAAISGPSTSNRIVRLLEKGLIERRE  113 (172)
T ss_dssp             HHCCSSCBCHHHHHHHCSCCSGGGSSHHHHHHHHTSEECCC
T ss_pred             hhCCCCCcCHHHHHHHHCcCHhHHHHHHHHHHhCCCeeeec
Confidence            34566678999999999999999999999999999999884

>d1w5sa1 a.4.5.11 (A:300-409) CDC6-like protein APE0152, C-terminal domain {Aeropyrum pernix [TaxId: 56636]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: Helicase DNA-binding domain
domain: CDC6-like protein APE0152, C-terminal domain
species: Aeropyrum pernix [TaxId: 56636]

Probab=81.02  E-value=0.52  Score=31.49  Aligned_cols=27  Identities=15%  Similarity=0.176  Sum_probs=22.6

Q ss_pred             HhHhcc---chhhhhhHHHhhhhccceeec
Q psy8797          87 SESLDV---QKRRIYDITNVLEGIGILEKK  113 (122)
Q Consensus        87 a~~L~v---~kRRiYDI~NVLE~igLI~K~  113 (122)
                      ++..++   .-+||||++|-||.+|+|+..
T Consensus        43 c~~~~~~P~~~t~~~~~l~~Le~lGiI~~r   72 (110)
T d1w5sa1          43 LTMYNVKPRGYTQYHIYLKHLTSLGLVDAK   72 (110)
T ss_dssp             HHHSCCCCCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHhCCCCccHHHHHHHHHHHHHcCCeEEE
Confidence            455665   789999999999999999754