Citrus Sinensis ID: 045382

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-
Protein Sequence
FRMLYGDKDGMEMTGVARASDRYQPWPMELPETETKFGLGWRGDDRRRTIFRSVPTLAGGVEGNGNEIRVGSLYKVTYSSLKSFTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccHHHHHHHHcccEEEEEEHHHHHHccccEEEcccccEEEEccccHHHHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccEEEccccccEEEcHcHHHHcccccccccccEEEcccccccccccccEEEEEcccccHHccccccccccccccEcccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHcccccccEcHHHHHHHHcHHHHHHHHHHHHHHHHHHHHHHcccccEEccccccHHHHHHHHHHHcc
Coil and Loop (DISEMBL)
frmlygdkdgmemtgvarasdryqpwpmelpetetkfglgwrgddrrrtifrsvptlaggvegngneirVGSLYKVTYSSLKSftetmpqsssstkvqdpssrhyaysrKQKSLGLLCSNFLSlynrdgvesiglddaasklgverrRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Flexible Loop (DISEMBL)
frmlygdkdgmemtgvarasdryqpwpmelpetetkfglgwrgddRRRTIFRsvptlaggvegngneirvGSLYKVTYSSLKSftetmpqsssstkvqdpssRHYAYSRKQKSLGLLCSNFLSLYNrdgvesiglddaasklgverrriydivnvlesvgvltrraknkytwkgfkaiRGALQELKVLLRF
Low Complexity Region (SEG)
FRMLYGDKDGMEMTGVARASDRYQPWPMELPETETKFGLGWRGDDRRRTIFRSVPTLAGGVEGNGNEIRVGSLYKVTYSSLKSFTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Disordered region (IsUnstruct)
**********************************TKFGLGWRGDDRRRTIFRSVPTLAGGVEGNGNEIRVGSLYKVTYSS*******************************KSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLL**
Disordered Region (DISOPRED)
*RMLYG*KDGMEMTGVARASDRY**WP****************************************************************************************LLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Disordered Region (DISEMBL)
FRMLYGDKDGMEMTGVARASDRYQPWPMELPETETKFGLGWRGDDRRRTIFRSVPTLAGGVEGNGNEIRVGSLYKVTYSSLKSF**********************YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Disordered Region (DISPRO)
FRMLYGDKDGMEMTGVARASDRYQPWPMELPETETKFGLGWRGDDRRRTIFRSVPTLAG*V*********************************************YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
FRMLYGDKDGMEMTGVARASDRYQPWPMELPETETKFGLGWRGDDRRRTIFRSVPTLAGGVEGNGNEIRVGSLYKVTYSSLKSFTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVLLRF
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	191	2.2.26 [Sep-21-2011]
Q8LSZ4	403	E2F transcription factor-	yes	no	0.303	0.143	0.843	8e-37
Q8RWL0	354	E2F transcription factor-	no	no	0.340	0.183	0.7	4e-27
Q9LFQ9	359	E2F transcription factor-	no	no	0.345	0.183	0.675	5e-26
Q5RIX9	723	Transcription factor E2F7	yes	no	0.403	0.106	0.590	9e-18
F6YVB9	862	Transcription factor E2F7	yes	no	0.413	0.091	0.554	4e-17
Q6S7F2	904	Transcription factor E2F7	yes	no	0.424	0.089	0.529	1e-16
Q96AV8	911	Transcription factor E2F7	yes	no	0.424	0.088	0.529	1e-16
D4A4D7	902	Transcription factor E2F7	yes	no	0.424	0.089	0.529	1e-16
E1BE02	911	Transcription factor E2F7	yes	no	0.424	0.088	0.529	3e-16
E1BKK0	866	Transcription factor E2F8	no	no	0.413	0.091	0.542	1e-15

>sp|Q8LSZ4|E2FE_ARATH E2F transcription factor-like E2FE OS=Arabidopsis thaliana GN=E2FE PE=2 SV=1

 Score =  153 bits (386), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 80/83 (96%)

Query: 104 HYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           H++YSRKQKSLGLLC+NFL+LYNR+G+E +GLDDAASKLGVERRRIYDIVNVLESVGVLT
Sbjct: 29  HHSYSRKQKSLGLLCTNFLALYNREGIEMVGLDDAASKLGVERRRIYDIVNVLESVGVLT 88

Query: 164 RRAKNKYTWKGFKAIRGALQELK 186
           RRAKN+YTWKGF AI GAL+EL+
Sbjct: 89  RRAKNQYTWKGFSAIPGALKELQ 111

Inhibitor of E2F-dependent activation of gene expression. Binds specifically the E2 recognition site without interacting with DP proteins and prevents transcription activation by E2F/DP heterodimers. Controls the timing of endocycle onset and inhibits endoreduplication.
Arabidopsis thaliana (taxid: 3702)

>sp|Q8RWL0|E2FF_ARATH E2F transcription factor-like E2FF OS=Arabidopsis thaliana GN=E2FF PE=2 SV=1

 Score =  120 bits (302), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 56/80 (70%), Positives = 68/80 (85%)

Query: 107 YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166
           YSRK+KSLG+L SNFL LYNRD V+ IGLDDAA +LGVERRRIYD+VN+LES+G++ RR 
Sbjct: 19  YSRKEKSLGVLVSNFLRLYNRDDVDLIGLDDAAGQLGVERRRIYDVVNILESIGIVARRG 78

Query: 167 KNKYTWKGFKAIRGALQELK 186
           KN+Y+WKGF  I  +L ELK
Sbjct: 79  KNQYSWKGFGEIPRSLDELK 98

Inhibitor of E2F-dependent activation of gene expression. Binds specifically the E2 recognition site without interacting with DP proteins and prevents transcription activation by E2F/DP heterodimers. Does not bind retinoblastoma-related proteins. Acts as a growth regulator but is not associated with changes in the expression of cell cycle marker genes or in nuclear ploidy levels. Has no effect on cell proliferation, but may repress cell wall biosynthesis genes during cell elongation in differentiated cells.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LFQ9|E2FD_ARATH E2F transcription factor-like E2FD OS=Arabidopsis thaliana GN=E2FD PE=1 SV=1

 Score =  117 bits (293), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 54/80 (67%), Positives = 67/80 (83%)

Query: 107 YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166
           YSRK KSLG+L +NFL+LYNR  V+  GLDDAA+KLGVERRRIYD+VN+LES+G++ R  
Sbjct: 11  YSRKDKSLGVLVANFLTLYNRPDVDLFGLDDAAAKLGVERRRIYDVVNILESIGLVARSG 70

Query: 167 KNKYTWKGFKAIRGALQELK 186
           KN+Y+WKGF A+  AL ELK
Sbjct: 71  KNQYSWKGFGAVPRALSELK 90

Inhibitor of E2F-dependent regulation of gene expression. Binds specifically the E2 recognition site as a monomer without interacting with DP proteins. May be up-regulating E2FA and down-regulating repressors of cell cycle progression. Promotes cell proliferation and represses cell elongation. Regulated by proteolysis via an ubiquitin-proteasome pathway.

Arabidopsis thaliana (taxid: 3702)

>sp|Q5RIX9|E2F7_DANRE Transcription factor E2F7 OS=Danio rerio GN=e2f7 PE=3 SV=2

 Score = 89.7 bits (221), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 49/83 (59%), Positives = 58/83 (69%), Gaps = 6/83 (7%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES-----IGLDDAASKLGVERRRIYDIVNVLESVGVL 162
           SRKQKSLGLLC  FL+LY  D  ES     I LD+ A+ LGVERRRIYDIVNVLES+ ++
Sbjct: 146 SRKQKSLGLLCQKFLALYP-DYPESSESINISLDEVATCLGVERRRIYDIVNVLESLMLV 204

Query: 163 TRRAKNKYTWKGFKAIRGALQEL 185
           +R+AKN Y W G   +   LQ L
Sbjct: 205 SRKAKNMYVWHGRSRLPQTLQGL 227

Atypical E2F transcription factor that participates to various processes such as angiogenesis and polyploidization of specialized cells. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'-TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as e2f1. Acts as a regulator of S-phase by recognizing and binding the E2-related site 5'-TTCCCGCC-3' and mediating repression of G1/S-regulated genes (By similarity). Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator and promoting expression of vegfa.

Danio rerio (taxid: 7955)

>sp|F6YVB9|E2F7_XENTR Transcription factor E2F7 OS=Xenopus tropicalis GN=e2f7 PE=3 SV=1

 Score = 87.8 bits (216), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 46/83 (55%), Positives = 58/83 (69%), Gaps = 4/83 (4%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRKQKSLGLLC  FL+ Y    + +    I LD+AAS LGVERRRIYDIVNVLES+ +++
Sbjct: 139 SRKQKSLGLLCQKFLARYPSYPISTEKMTISLDEAASSLGVERRRIYDIVNVLESLHLVS 198

Query: 164 RRAKNKYTWKGFKAIRGALQELK 186
           R AKN+Y W G   +   L+ L+
Sbjct: 199 RVAKNQYCWHGQHNLNETLRNLQ 221

Atypical E2F transcription factor that participates to various processes such as angiogenesis and polyploidization of specialized cells. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'-TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as e2f1. Acts as a regulator of S-phase by recognizing and binding the E2-related site 5'-TTCCCGCC-3' and mediating repression of G1/S-regulated genes. Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator.

Xenopus tropicalis (taxid: 8364)

>sp|Q6S7F2|E2F7_MOUSE Transcription factor E2F7 OS=Mus musculus GN=E2f7 PE=1 SV=1

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/85 (52%), Positives = 58/85 (68%), Gaps = 4/85 (4%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct: 142 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 201

Query: 164 RRAKNKYTWKGFKAIRGALQELKVL 188
           R AKN+Y W G  ++   L+ L+ L
Sbjct: 202 RVAKNQYGWHGRHSLPKTLRTLQRL 226

Along with E2F8, inhibitor of E2F-dependent transcription that is important for embryonic development and for the control of the E2f1-Tp53 apoptotic pathway. Directly represses E2F1 transcription. Binds DNA independently of DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3'. Appears to regulate a subset of E2F-dependent genes whose products are required for normal cell cycle progession.

Mus musculus (taxid: 10090)

>sp|Q96AV8|E2F7_HUMAN Transcription factor E2F7 OS=Homo sapiens GN=E2F7 PE=1 SV=3

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/85 (52%), Positives = 58/85 (68%), Gaps = 4/85 (4%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct: 141 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 200

Query: 164 RRAKNKYTWKGFKAIRGALQELKVL 188
           R AKN+Y W G  ++   L+ L+ L
Sbjct: 201 RVAKNQYGWHGRHSLPKTLRNLQRL 225

Along with E2F8, inhibitor of E2F-dependent transcription that is important for the control of the E2F1-TP53 apoptotic pathway. Directly represses E2F1 transcription (By similarity). Binds DNA independently of DP proteins through the E2 recognition site, 5'-TTTC[CG]CGC-3'. Appears to regulate a subset of E2F-dependent genes whose products are required for normal cell cycle progession.

Homo sapiens (taxid: 9606)

>sp|D4A4D7|E2F7_RAT Transcription factor E2F7 OS=Rattus norvegicus GN=E2f7 PE=3 SV=1

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/85 (52%), Positives = 58/85 (68%), Gaps = 4/85 (4%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct: 142 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 201

Query: 164 RRAKNKYTWKGFKAIRGALQELKVL 188
           R AKN+Y W G  ++   L+ L+ L
Sbjct: 202 RVAKNQYGWHGRHSLPKTLRTLQRL 226

Atypical E2F transcription factor that participates to various processes such as angiogenesis, polyploidization of specialized cells and DNA damage response. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'-TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as E2F1. Acts as a regulator of S-phase by recognizing and binding the E2-related site 5'-TTCCCGCC-3' and mediating repression of G1/S-regulated genes. Plays a key role in polyploidization of cells in placenta and liver by regulating the endocycle, probably by repressing genes promoting cytokinesis and antagonizing action of classical E2F proteins (E2F1, E2F2 and/or E2F3). Required for placental development by promoting polyploidization of trophoblast giant cells. Also involved in DNA damage response: up-regulated by p53/TP53 following genotoxic stress and acts as a downstream effector of p53/TP53-dependent repression by mediating repression of indirect p53/TP53 target genes involved in DNA replication. Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator: associates with HIF1A, recognizes and binds the VEGFA promoter, which is different from canonical E2 recognition site, and activates expression of the VEGFA gene. Acts as a negative regulator of keratinocyte differentiation.

Rattus norvegicus (taxid: 10116)

>sp|E1BE02|E2F7_BOVIN Transcription factor E2F7 OS=Bos taurus GN=E2F7 PE=3 SV=1

 Score = 85.1 bits (209), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 45/85 (52%), Positives = 59/85 (69%), Gaps = 4/85 (4%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct: 140 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 199

Query: 164 RRAKNKYTWKGFKAIRGALQELKVL 188
           R AKN+Y+W G  ++   L+ L+ L
Sbjct: 200 RVAKNQYSWHGRHSLPKTLRNLQRL 224

Atypical E2F transcription factor that participates to various processes such as angiogenesis, polyploidization of specialized cells and DNA damage response. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'-TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as E2F1. Acts as a regulator of S-phase by recognizing and binding the E2-related site 5'-TTCCCGCC-3' and mediating repression of G1/S-regulated genes. Plays a key role in polyploidization of cells in placenta and liver by regulating the endocycle, probably by repressing genes promoting cytokinesis and antagonizing action of classical E2F proteins (E2F1, E2F2 and/or E2F3). Required for placental development by promoting polyploidization of trophoblast giant cells. Also involved in DNA damage response: up-regulated by p53/TP53 following genotoxic stress and acts as a downstream effector of p53/TP53-dependent repression by mediating repression of indirect p53/TP53 target genes involved in DNA replication. Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator: associates with HIF1A, recognizes and binds the VEGFA promoter, which is different from canonical E2 recognition site, and activates expression of the VEGFA gene. Acts as a negative regulator of keratinocyte differentiation.

Bos taurus (taxid: 9913)

>sp|E1BKK0|E2F8_BOVIN Transcription factor E2F8 OS=Bos taurus GN=E2F8 PE=3 SV=2

 Score = 83.2 bits (204), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/83 (54%), Positives = 56/83 (67%), Gaps = 4/83 (4%)

Query: 108 SRKQKSLGLLCSNFLSLY----NRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           SRK+KSLGLLC  FL+ Y    N      I LD+ A +L VERRRIYDIVNVLES+ +++
Sbjct: 112 SRKEKSLGLLCHKFLARYPNYPNPAVNNDICLDEVAEELNVERRRIYDIVNVLESLHMVS 171

Query: 164 RRAKNKYTWKGFKAIRGALQELK 186
           R AKN+YTW G   +   L+ LK
Sbjct: 172 RLAKNRYTWHGRHNLNQILETLK 194

Atypical E2F transcription factor that participates to various processes such as angiogenesis and polyploidization of specialized cells. Mainly acts as a transcription repressor that binds DNA independently of DP proteins and specifically recognizes the E2 recognition site 5'-TTTC[CG]CGC-3'. Directly represses transcription of classical E2F transcription factors such as E2F1: component of a feedback loop in S phase by repressing the expression of E2F1, thereby preventing p53/TP53-dependent apoptosis. Plays a key role in polyploidization of cells in placenta and liver by regulating the endocycle, probably by repressing genes promoting cytokinesis and antagonizing action of classical E2F proteins (E2F1, E2F2 and/or E2F3). Required for placental development by promoting polyploidization of trophoblast giant cells. Acts as a promoter of sprouting angiogenesis, possibly by acting as a transcription activator: associates with HIF1A, recognizes and binds the VEGFA promoter, which is different from canonical E2 recognition site, and activates expression of the VEGFA gene.

Bos taurus (taxid: 9913)

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	191
255540801	389	E2F, putative [Ricinus communis] gi|2235	0.513	0.251	0.777	2e-36
224133412	384	repressor, antagonist of e2f-dp complex	0.413	0.205	0.776	3e-36
224119208	385	repressor, antagonist of e2f-dp complex	0.434	0.215	0.776	9e-36
30692988	379	protein DP-E2F-like 1 [Arabidopsis thali	0.303	0.153	0.843	3e-35
22331664	403	protein DP-E2F-like 1 [Arabidopsis thali	0.303	0.143	0.843	4e-35
357477293	385	E2F transcription factor-like protein [M	0.345	0.171	0.806	7e-35
357477291	391	E2F transcription factor-like protein [M	0.314	0.153	0.806	7e-35
449487782	381	PREDICTED: E2F transcription factor-like	0.303	0.152	0.833	4e-34
225457156	382	PREDICTED: E2F transcription factor-like	0.376	0.188	0.797	5e-34
356516714	374	PREDICTED: E2F transcription factor-like	0.413	0.211	0.823	6e-34

>gi|255540801|ref|XP_002511465.1| E2F, putative [Ricinus communis] gi|223550580|gb|EEF52067.1| E2F, putative [Ricinus communis]

 Score =  157 bits (398), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 77/99 (77%), Positives = 86/99 (86%), Gaps = 1/99 (1%)

Query: 88  MPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERR 147
           MP SS+    +  S RH+ YSRKQKSLGLLC+NFLSLY++DG+E IGLDDAASKLGVERR
Sbjct: 1   MPLSSNEAPTES-SCRHHTYSRKQKSLGLLCTNFLSLYDKDGIEVIGLDDAASKLGVERR 59

Query: 148 RIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELK 186
           RIYDIVNVLESVGVL+R+AKNKYTWKGF AI  ALQELK
Sbjct: 60  RIYDIVNVLESVGVLSRKAKNKYTWKGFGAIPKALQELK 98

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224133412|ref|XP_002321561.1| repressor, antagonist of e2f-dp complex [Populus trichocarpa] gi|222868557|gb|EEF05688.1| repressor, antagonist of e2f-dp complex [Populus trichocarpa]

 Score =  156 bits (395), Expect = 3e-36,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 84/94 (89%)

Query: 93  SSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDI 152
           S T + DP SRH+AYSRKQKSLGLLC+NFL+LYNRD ++ IGLDDAASKLGVERRRIYDI
Sbjct: 4   SYTDIIDPPSRHHAYSRKQKSLGLLCTNFLTLYNRDDIDVIGLDDAASKLGVERRRIYDI 63

Query: 153 VNVLESVGVLTRRAKNKYTWKGFKAIRGALQELK 186
           VNVLESVGVL R+AKNKY+WKGF ++  ALQ+LK
Sbjct: 64  VNVLESVGVLARKAKNKYSWKGFASVPKALQDLK 97

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224119208|ref|XP_002318015.1| repressor, antagonist of e2f-dp complex [Populus trichocarpa] gi|222858688|gb|EEE96235.1| repressor, antagonist of e2f-dp complex [Populus trichocarpa]

 Score =  155 bits (391), Expect = 9e-36,   Method: Compositional matrix adjust.
 Identities = 73/94 (77%), Positives = 83/94 (88%)

Query: 93  SSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDI 152
           S + + DPSSRH+ YSRKQKSLGLLC+NFL+LY+RD ++ IGLDDAASKLGVERRRIYDI
Sbjct: 4   SYSDIIDPSSRHHTYSRKQKSLGLLCTNFLTLYDRDDIDVIGLDDAASKLGVERRRIYDI 63

Query: 153 VNVLESVGVLTRRAKNKYTWKGFKAIRGALQELK 186
           VNVLESVGVL R+AKNKY WKGF A+  ALQELK
Sbjct: 64  VNVLESVGVLARKAKNKYLWKGFAAVPKALQELK 97

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|30692988|ref|NP_851012.1| protein DP-E2F-like 1 [Arabidopsis thaliana] gi|19578315|emb|CAD10633.1| transcription factor E2Fe [Arabidopsis thaliana] gi|332644853|gb|AEE78374.1| protein DP-E2F-like 1 [Arabidopsis thaliana]

 Score =  153 bits (386), Expect = 3e-35,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 80/83 (96%)

Query: 104 HYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           H++YSRKQKSLGLLC+NFL+LYNR+G+E +GLDDAASKLGVERRRIYDIVNVLESVGVLT
Sbjct: 29  HHSYSRKQKSLGLLCTNFLALYNREGIEMVGLDDAASKLGVERRRIYDIVNVLESVGVLT 88

Query: 164 RRAKNKYTWKGFKAIRGALQELK 186
           RRAKN+YTWKGF AI GAL+EL+
Sbjct: 89  RRAKNQYTWKGFSAIPGALKELQ 111

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|22331664|ref|NP_190399.2| protein DP-E2F-like 1 [Arabidopsis thaliana] gi|75157824|sp|Q8LSZ4.1|E2FE_ARATH RecName: Full=E2F transcription factor-like E2FE; AltName: Full=DP-E2F-like protein 1; AltName: Full=E2F-like repressor E2L3 gi|20502508|dbj|BAB91414.1| E2F-like repressor E2L3 [Arabidopsis thaliana] gi|28393699|gb|AAO42262.1| putative DP-E2F protein 1 [Arabidopsis thaliana] gi|28973239|gb|AAO63944.1| putative DP-E2F protein 1 [Arabidopsis thaliana] gi|332644854|gb|AEE78375.1| protein DP-E2F-like 1 [Arabidopsis thaliana]

 Score =  153 bits (386), Expect = 4e-35,   Method: Compositional matrix adjust.
 Identities = 70/83 (84%), Positives = 80/83 (96%)

Query: 104 HYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
           H++YSRKQKSLGLLC+NFL+LYNR+G+E +GLDDAASKLGVERRRIYDIVNVLESVGVLT
Sbjct: 29  HHSYSRKQKSLGLLCTNFLALYNREGIEMVGLDDAASKLGVERRRIYDIVNVLESVGVLT 88

Query: 164 RRAKNKYTWKGFKAIRGALQELK 186
           RRAKN+YTWKGF AI GAL+EL+
Sbjct: 89  RRAKNQYTWKGFSAIPGALKELQ 111

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357477293|ref|XP_003608932.1| E2F transcription factor-like protein [Medicago truncatula] gi|355509987|gb|AES91129.1| E2F transcription factor-like protein [Medicago truncatula]

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 71/88 (80%), Positives = 78/88 (88%)

Query: 99  DPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLES 158
           DP SRH+ Y RKQKSLGLLC+NFLSLYN+D V  IGLDDAA+KLGVERRRIYDIVNVLES
Sbjct: 7   DPPSRHHTYDRKQKSLGLLCTNFLSLYNKDDVRLIGLDDAAAKLGVERRRIYDIVNVLES 66

Query: 159 VGVLTRRAKNKYTWKGFKAIRGALQELK 186
           +GVL R+AKN+YTWKGF AI  ALQELK
Sbjct: 67  IGVLARKAKNQYTWKGFAAIPVALQELK 94

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357477291|ref|XP_003608931.1| E2F transcription factor-like protein [Medicago truncatula] gi|355509986|gb|AES91128.1| E2F transcription factor-like protein [Medicago truncatula]

 Score =  152 bits (384), Expect = 7e-35,   Method: Compositional matrix adjust.
 Identities = 71/88 (80%), Positives = 78/88 (88%)

Query: 99  DPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLES 158
           DP SRH+ Y RKQKSLGLLC+NFLSLYN+D V  IGLDDAA+KLGVERRRIYDIVNVLES
Sbjct: 7   DPPSRHHTYDRKQKSLGLLCTNFLSLYNKDDVRLIGLDDAAAKLGVERRRIYDIVNVLES 66

Query: 159 VGVLTRRAKNKYTWKGFKAIRGALQELK 186
           +GVL R+AKN+YTWKGF AI  ALQELK
Sbjct: 67  IGVLARKAKNQYTWKGFAAIPVALQELK 94

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|449487782|ref|XP_004157798.1| PREDICTED: E2F transcription factor-like E2FE-like [Cucumis sativus]

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 70/84 (83%), Positives = 77/84 (91%)

Query: 103 RHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVL 162
           RH+ YSRKQKSLGLLCSNFLSLYN DGV SIGLDDAAS+LGVERRRIYDIVNVLESVGVL
Sbjct: 17  RHHTYSRKQKSLGLLCSNFLSLYNHDGVHSIGLDDAASRLGVERRRIYDIVNVLESVGVL 76

Query: 163 TRRAKNKYTWKGFKAIRGALQELK 186
           +R+AKN+Y+W GF AI  ALQ+LK
Sbjct: 77  SRKAKNQYSWNGFGAIPKALQDLK 100

Source: Cucumis sativus

Species: Cucumis sativus

Genus: Cucumis

Family: Cucurbitaceae

Order: Cucurbitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225457156|ref|XP_002280411.1| PREDICTED: E2F transcription factor-like E2FE-like [Vitis vinifera]

 Score =  149 bits (377), Expect = 5e-34,   Method: Compositional matrix adjust.
 Identities = 71/89 (79%), Positives = 79/89 (88%)

Query: 93  SSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDI 152
           SS+ +Q+ +S H  YSRKQKSLGLLCSNFLSLYNRDGVE IGLDDAAS+LGVERRRIYDI
Sbjct: 4   SSSTIQESASHHRTYSRKQKSLGLLCSNFLSLYNRDGVEPIGLDDAASRLGVERRRIYDI 63

Query: 153 VNVLESVGVLTRRAKNKYTWKGFKAIRGA 181
           VNVLESVGVL R+AKN+Y+WKGF AI  A
Sbjct: 64  VNVLESVGVLARKAKNQYSWKGFGAIPKA 92

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356516714|ref|XP_003527038.1| PREDICTED: E2F transcription factor-like E2FE-like [Glycine max]

 Score =  149 bits (376), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 70/85 (82%), Positives = 78/85 (91%)

Query: 102 SRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGV 161
           S H+ YSRKQKSLGLLC+NFLSLYN++GV  +GLDDAAS+LGVERRRIYDIVNVLESVGV
Sbjct: 5   STHHTYSRKQKSLGLLCTNFLSLYNKEGVRLVGLDDAASRLGVERRRIYDIVNVLESVGV 64

Query: 162 LTRRAKNKYTWKGFKAIRGALQELK 186
           LTR+AKN+YTWKGF AI  ALQELK
Sbjct: 65  LTRKAKNQYTWKGFCAIPAALQELK 89

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	191
TAIR|locus:2100444	403	DEL1 "DP-E2F-like 1" [Arabidop	0.492	0.233	0.74	6.5e-35
TAIR|locus:2100272	354	DEL3 "DP-E2F-like protein 3" [	0.502	0.271	0.628	1.2e-26
TAIR|locus:2147865	359	DEL2 "DP-E2F-like 2" [Arabidop	0.418	0.222	0.675	2.2e-25
ZFIN|ZDB-GENE-030131-3527	723	e2f7 "E2F transcription factor	0.408	0.107	0.585	5.4e-16
UNIPROTKB|H0YHW2	208	E2F7 "Transcription factor E2F	0.424	0.389	0.529	9.8e-16
UNIPROTKB|H0YIF4	219	E2F7 "Transcription factor E2F	0.424	0.369	0.529	9.8e-16
UNIPROTKB|F6YVB9	862	e2f7 "Transcription factor E2F	0.413	0.091	0.554	1.2e-15
UNIPROTKB|E9PP48	355	E2F8 "Transcription factor E2F	0.413	0.222	0.554	3.3e-15
UNIPROTKB|F1P135	829	F1P135 "Uncharacterized protei	0.413	0.095	0.566	4.8e-15
UNIPROTKB|E1BE02	911	E2F7 "Transcription factor E2F	0.544	0.114	0.440	5.5e-15

TAIR|locus:2100444 DEL1 "DP-E2F-like 1" [Arabidopsis thaliana (taxid:3702)]

 Score = 378 (138.1 bits), Expect = 6.5e-35, P = 6.5e-35
 Identities = 74/100 (74%), Positives = 90/100 (90%)

Query:    87 TMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVER 146
             ++P+SSS+ ++      H++YSRKQKSLGLLC+NFL+LYNR+G+E +GLDDAASKLGVER
Sbjct:    18 SIPESSSALQL------HHSYSRKQKSLGLLCTNFLALYNREGIEMVGLDDAASKLGVER 71

Query:   147 RRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELK 186
             RRIYDIVNVLESVGVLTRRAKN+YTWKGF AI GAL+EL+
Sbjct:    72 RRIYDIVNVLESVGVLTRRAKNQYTWKGFSAIPGALKELQ 111

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IDA

GO:0042023 "DNA endoreduplication" evidence=IMP

GO:0032876 "negative regulation of DNA endoreduplication" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

TAIR|locus:2100272 DEL3 "DP-E2F-like protein 3" [Arabidopsis thaliana (taxid:3702)]

 Score = 300 (110.7 bits), Expect = 1.2e-26, P = 1.2e-26
 Identities = 61/97 (62%), Positives = 74/97 (76%)

Query:    91 SSSSTKVQDPSSRHYA-YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRI 149
             SS+    QD  S     YSRK+KSLG+L SNFL LYNRD V+ IGLDDAA +LGVERRRI
Sbjct:     2 SSAIVVSQDAESLGLQIYSRKEKSLGVLVSNFLRLYNRDDVDLIGLDDAAGQLGVERRRI 61

Query:   150 YDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELK 186
             YD+VN+LES+G++ RR KN+Y+WKGF  I  +L ELK
Sbjct:    62 YDVVNILESIGIVARRGKNQYSWKGFGEIPRSLDELK 98

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005515 "protein binding" evidence=IPI

GO:0006261 "DNA-dependent DNA replication" evidence=RCA

TAIR|locus:2147865 DEL2 "DP-E2F-like 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 288 (106.4 bits), Expect = 2.2e-25, P = 2.2e-25
 Identities = 54/80 (67%), Positives = 67/80 (83%)

Query:   107 YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA 166
             YSRK KSLG+L +NFL+LYNR  V+  GLDDAA+KLGVERRRIYD+VN+LES+G++ R  
Sbjct:    11 YSRKDKSLGVLVANFLTLYNRPDVDLFGLDDAAAKLGVERRRIYDVVNILESIGLVARSG 70

Query:   167 KNKYTWKGFKAIRGALQELK 186
             KN+Y+WKGF A+  AL ELK
Sbjct:    71 KNQYSWKGFGAVPRALSELK 90

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

GO:0005634 "nucleus" evidence=ISM;IDA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IDA

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

GO:0009733 "response to auxin stimulus" evidence=IEP

GO:0005515 "protein binding" evidence=IPI

GO:0009410 "response to xenobiotic stimulus" evidence=RCA

GO:0048522 "positive regulation of cellular process" evidence=RCA

ZFIN|ZDB-GENE-030131-3527 e2f7 "E2F transcription factor 7" [Danio rerio (taxid:7955)]

 Score = 210 (79.0 bits), Expect = 5.4e-16, P = 5.4e-16
 Identities = 48/82 (58%), Positives = 58/82 (70%)

Query:   108 SRKQKSLGLLCSNFLSLYNR--DGVESIG--LDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRKQKSLGLLC  FL+LY    +  ESI   LD+ A+ LGVERRRIYDIVNVLES+ +++
Sbjct:   146 SRKQKSLGLLCQKFLALYPDYPESSESINISLDEVATCLGVERRRIYDIVNVLESLMLVS 205

Query:   164 RRAKNKYTWKGFKAIRGALQEL 185
             R+AKN Y W G   +   LQ L
Sbjct:   206 RKAKNMYVWHGRSRLPQTLQGL 227

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

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0001890 "placenta development" evidence=ISS

GO:0032466 "negative regulation of cytokinesis" evidence=ISS

GO:0060707 "trophoblast giant cell differentiation" evidence=ISS

GO:0071930 "negative regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=ISS

GO:0003714 "transcription corepressor activity" evidence=ISS

GO:0030330 "DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0001047 "core promoter binding" evidence=ISS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=ISS

GO:0032877 "positive regulation of DNA endoreduplication" evidence=ISS

GO:0060718 "chorionic trophoblast cell differentiation" evidence=ISS

GO:0070365 "hepatocyte differentiation" evidence=ISS

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=ISS

GO:0002040 "sprouting angiogenesis" evidence=IMP

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

GO:0003677 "DNA binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007049 "cell cycle" evidence=IEA

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

UNIPROTKB|H0YHW2 E2F7 "Transcription factor E2F7" [Homo sapiens (taxid:9606)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 45/85 (52%), Positives = 58/85 (68%)

Query:   108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct:    17 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 76

Query:   164 RRAKNKYTWKGFKAIRGALQELKVL 188
             R AKN+Y W G  ++   L+ L+ L
Sbjct:    77 RVAKNQYGWHGRHSLPKTLRNLQRL 101

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|H0YIF4 E2F7 "Transcription factor E2F7" [Homo sapiens (taxid:9606)]

 Score = 197 (74.4 bits), Expect = 9.8e-16, P = 9.8e-16
 Identities = 45/85 (52%), Positives = 58/85 (68%)

Query:   108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRKQKSLGLLC  FL+ Y    + +    I LD+ A  LGVERRRIYDIVNVLES+ +++
Sbjct:    19 SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVAVSLGVERRRIYDIVNVLESLHLVS 78

Query:   164 RRAKNKYTWKGFKAIRGALQELKVL 188
             R AKN+Y W G  ++   L+ L+ L
Sbjct:    79 RVAKNQYGWHGRHSLPKTLRNLQRL 103

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|F6YVB9 e2f7 "Transcription factor E2F7" [Xenopus (Silurana) tropicalis (taxid:8364)]

 Score = 208 (78.3 bits), Expect = 1.2e-15, P = 1.2e-15
 Identities = 46/83 (55%), Positives = 58/83 (69%)

Query:   108 SRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRKQKSLGLLC  FL+ Y    + +    I LD+AAS LGVERRRIYDIVNVLES+ +++
Sbjct:   139 SRKQKSLGLLCQKFLARYPSYPISTEKMTISLDEAASSLGVERRRIYDIVNVLESLHLVS 198

Query:   164 RRAKNKYTWKGFKAIRGALQELK 186
             R AKN+Y W G   +   L+ L+
Sbjct:   199 RVAKNQYCWHGQHNLNETLRNLQ 221

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0001047 "core promoter binding" evidence=ISS

GO:0001890 "placenta development" evidence=ISS

GO:0002040 "sprouting angiogenesis" evidence=ISS

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

GO:0003714 "transcription corepressor activity" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=ISS

GO:0030330 "DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0032466 "negative regulation of cytokinesis" evidence=ISS

GO:0032877 "positive regulation of DNA endoreduplication" evidence=ISS

GO:0060707 "trophoblast giant cell differentiation" evidence=ISS

GO:0060718 "chorionic trophoblast cell differentiation" evidence=ISS

GO:0070365 "hepatocyte differentiation" evidence=ISS

GO:0071930 "negative regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=ISS

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=ISS

UNIPROTKB|E9PP48 E2F8 "Transcription factor E2F8" [Homo sapiens (taxid:9606)]

 Score = 196 (74.1 bits), Expect = 3.3e-15, P = 3.3e-15
 Identities = 46/83 (55%), Positives = 57/83 (68%)

Query:   108 SRKQKSLGLLCSNFLSLY-N--RDGVES-IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRK+KSLGLLC  FL+ Y N     V + I LD+ A +L VERRRIYDIVNVLES+ +++
Sbjct:   112 SRKEKSLGLLCHKFLARYPNYPNPAVNNDICLDEVAEELNVERRRIYDIVNVLESLHMVS 171

Query:   164 RRAKNKYTWKGFKAIRGALQELK 186
             R AKN+YTW G   +   L  LK
Sbjct:   172 RLAKNRYTWHGRHNLNKTLGTLK 194

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|F1P135 F1P135 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 202 (76.2 bits), Expect = 4.8e-15, P = 4.8e-15
 Identities = 47/83 (56%), Positives = 57/83 (68%)

Query:   108 SRKQKSLGLLCSNFLSLYNR--DGVES--IGLDDAASKLGVERRRIYDIVNVLESVGVLT 163
             SRK+KSLGLLC  FL+ Y      VES  I LD+ A +L VERRRIYDIVNVLES+ +++
Sbjct:    86 SRKEKSLGLLCHKFLARYPDYPSAVESNYICLDEVAEELNVERRRIYDIVNVLESLHMVS 145

Query:   164 RRAKNKYTWKGFKAIRGALQELK 186
             R AKN+Y W G   +   LQ LK
Sbjct:   146 RLAKNRYIWHGRHNLAETLQTLK 168

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

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

UNIPROTKB|E1BE02 E2F7 "Transcription factor E2F7" [Bos taurus (taxid:9913)]

 Score = 202 (76.2 bits), Expect = 5.5e-15, P = 5.5e-15
 Identities = 48/109 (44%), Positives = 67/109 (61%)

Query:    84 FTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGVES----IGLDDAA 139
             FT+++   +      D   +    SRKQKSLGLLC  FL+ Y    + +    I LD+ A
Sbjct:   117 FTDSLQLDAVDDSAVDEFEKQRP-SRKQKSLGLLCQKFLARYPSYPLSTEKTTISLDEVA 175

Query:   140 SKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGALQELKVL 188
               LGVERRRIYDIVNVLES+ +++R AKN+Y+W G  ++   L+ L+ L
Sbjct:   176 VSLGVERRRIYDIVNVLESLHLVSRVAKNQYSWHGRHSLPKTLRNLQRL 224

GO:0003714 "transcription corepressor activity" evidence=ISS

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

GO:0001047 "core promoter binding" evidence=ISS

GO:2000134 "negative regulation of G1/S transition of mitotic cell cycle" evidence=ISS

GO:0070365 "hepatocyte differentiation" evidence=ISS

GO:0060718 "chorionic trophoblast cell differentiation" evidence=ISS

GO:0060707 "trophoblast giant cell differentiation" evidence=ISS

GO:0032877 "positive regulation of DNA endoreduplication" evidence=ISS

GO:0032466 "negative regulation of cytokinesis" evidence=ISS

GO:0001890 "placenta development" evidence=ISS

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISS

GO:0002040 "sprouting angiogenesis" evidence=ISS

GO:0071930 "negative regulation of transcription involved in G1/S phase of mitotic cell cycle" evidence=ISS

GO:0030330 "DNA damage response, signal transduction by p53 class mediator" evidence=ISS

GO:0008285 "negative regulation of cell proliferation" evidence=ISS

GO:0042802 "identical protein binding" evidence=IEA

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

GO:0005667 "transcription factor complex" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	191
pfam02319	67	pfam02319, E2F_TDP, E2F/DP family winged-helix DNA	8e-25

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

 Score = 91.5 bits (228), Expect = 8e-25
 Identities = 31/67 (46%), Positives = 45/67 (67%), Gaps = 1/67 (1%)

Query: 109 RKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRRAK 167
           RK+KSLGLL   FL L  +       L++AA +L V ++RRIYDI NVLE +G++ +++K
Sbjct: 1   RKEKSLGLLTQKFLKLCEKSPDGITDLNEAAKELDVKQKRRIYDITNVLEGIGLIEKKSK 60

Query: 168 NKYTWKG 174
           N+  W G
Sbjct: 61  NEIRWIG 67

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	191
KOG2577	354	consensus Transcription factor E2F/dimerization pa	99.92
KOG2578	388	consensus Transcription factor E2F/dimerization pa	99.9
PF02319	71	E2F_TDP: E2F/DP family winged-helix DNA-binding do	99.9
KOG2578	388	consensus Transcription factor E2F/dimerization pa	99.77
KOG2829	326	consensus E2F-like protein [Transcription]	98.79
PF01978	68	TrmB: Sugar-specific transcriptional regulator Trm	95.02
cd00092	67	HTH_CRP helix_turn_helix, cAMP Regulatory protein	93.25
PF08279	55	HTH_11: HTH domain; InterPro: IPR013196 Winged hel	92.41
smart00346	91	HTH_ICLR helix_turn_helix isocitrate lyase regulat	92.08
smart00420	53	HTH_DEOR helix_turn_helix, Deoxyribose operon repr	91.92
smart00550	68	Zalpha Z-DNA-binding domain in adenosine deaminase	90.91
PF09339	52	HTH_IclR: IclR helix-turn-helix domain; InterPro:	90.89
smart00418	66	HTH_ARSR helix_turn_helix, Arsenical Resistance Op	88.49
PF02082	83	Rrf2: Transcriptional regulator; InterPro: IPR0009	87.6
TIGR02944	130	suf_reg_Xantho FeS assembly SUF system regulator,	87.19
cd00090	78	HTH_ARSR Arsenical Resistance Operon Repressor and	87.04
COG1378	247	Predicted transcriptional regulators [Transcriptio	86.92
PF13412	48	HTH_24: Winged helix-turn-helix DNA-binding; PDB:	86.57
PF12802	62	MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP	85.24
smart00419	48	HTH_CRP helix_turn_helix, cAMP Regulatory protein.	82.71
PF00392	64	GntR: Bacterial regulatory proteins, gntR family;	82.51
cd08768	87	Cdc6_C Winged-helix domain of essential DNA replic	82.44
PF09079	85	Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The	81.52
smart00345	60	HTH_GNTR helix_turn_helix gluconate operon transcr	81.34
PF13730	55	HTH_36: Helix-turn-helix domain	81.24
PRK10163	271	DNA-binding transcriptional repressor AllR; Provis	80.76

>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]

Probab=99.92  E-value=3.8e-25  Score=200.10  Aligned_cols=86  Identities=35%  Similarity=0.563  Sum_probs=77.6

Q ss_pred             CcCCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccch-----
Q 045382          104 HYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAI-----  178 (191)
Q Consensus       104 ~~~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I-----  178 (191)
                      .....|.++||++||+|||.+++.++++++||+.||+.|+|+|||||||+|||||||||+|++||.++|+|.+..     
T Consensus        63 ~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~~~  142 (354)
T KOG2577|consen   63 PSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTGGV  142 (354)
T ss_pred             CCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccccceeeehhhhhhcccceeeccccceeeecCCCcccccc
Confidence            356789999999999999999999999999999999999999999999999999999999999999999997654     


Q ss_pred             HHHHHHHHHHh
Q 045382          179 RGALQELKVLL  189 (191)
Q Consensus       179 ~~tLekLk~Ei  189 (191)
                      ...++.|++|+
T Consensus       143 ~e~~~~l~~e~  153 (354)
T KOG2577|consen  143 PERLNGLEAEV  153 (354)
T ss_pred             HHHHHHHHHHH
Confidence            35556666665

>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]

Probab=99.90  E-value=6e-25  Score=196.66  Aligned_cols=86  Identities=66%  Similarity=1.013  Sum_probs=83.0

Q ss_pred             CCcCCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccchHHHH
Q 045382          103 RHYAYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKAIRGAL  182 (191)
Q Consensus       103 ~~~~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~I~~tL  182 (191)
                      +.+.++||+||||.||++|+.++.......+.|+.+|.+|||+|||||||+||||+||+++|.+||+|.|.||++||.+|
T Consensus        15 ~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~aiPral   94 (388)
T KOG2578|consen   15 DLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGAIPRAL   94 (388)
T ss_pred             cchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhhhhHHH
Confidence            35789999999999999999999888888999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHHH
Q 045382          183 QELKVL  188 (191)
Q Consensus       183 ekLk~E  188 (191)
                      .+||+|
T Consensus        95 ~eLqeE  100 (388)
T KOG2578|consen   95 FELQEE  100 (388)
T ss_pred             HHHHHH
Confidence            999998

>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=99.90  E-value=1.2e-24  Score=156.28  Aligned_cols=66  Identities=48%  Similarity=0.896  Sum_probs=62.7

Q ss_pred             CCCCchHHHHHHHHHHHhhCCCceecHHHHHHHh---CC--eeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382          109 RKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKL---GV--ERRRIYDIVNVLESVGVLTRRAKNKYTWKG  174 (191)
Q Consensus       109 RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L---~V--~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G  174 (191)
                      |+++||+.+|++||++|...++..++++++|+.|   ++  ++||||||+|||||+|+|+|.+|+.|.|+|
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            7899999999999999999888999999999999   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 Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]

Probab=99.77  E-value=7.1e-20  Score=164.26  Aligned_cols=128  Identities=29%  Similarity=0.383  Sum_probs=100.1

Q ss_pred             cccCcccc-CCcCCCCceee-cCccceecccccccccccCCCCCCCCCCCCCC------CCCcCCCCCCCchHHHHHHHH
Q 045382           51 FRSVPTLA-GGVEGNGNEIR-VGSLYKVTYSSLKSFTETMPQSSSSTKVQDPS------SRHYAYSRKQKSLGLLCSNFL  122 (191)
Q Consensus        51 ~r~~~~l~-~g~~~~~~~~~-~~~~~~~~~~~~~~~~e~m~~~~~~~~~~~~~------~~~~~~~RkeKSL~~Lt~kFI  122 (191)
                      =|.|-||+ |||+|.|.++. ..++.++++.+... +...+.++..++.+.|.      ...+...|++|||++|||+||
T Consensus        91 Pral~eLqeEgvke~l~~~~~~~~~~m~s~e~~~e-e~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekSL~lL~qnFv  169 (388)
T KOG2578|consen   91 PRALFELQEEGVKEGLPERVLRVNSAMVSFEEESE-ERGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKSLWLLAQNFV  169 (388)
T ss_pred             hHHHHHHHHHHHhhcccceeeeccccccccccccc-ccCCccccCCCCCCCCCcchhcCCCCcccchhhhHHHHHHHHHH
Confidence            45678999 99999999986 66777777666554 32234444433332221      135788899999999999999


Q ss_pred             HHHhhCCCc-eecHHHHHHHh----------CCeeeEeeehhhHhhhhcceeec-----CCCceEEecccchH
Q 045382          123 SLYNRDGVE-SIGLDDAASKL----------GVERRRIYDIVNVLESVGVLTRR-----AKNKYTWKGFKAIR  179 (191)
Q Consensus       123 ~l~~~~~~~-~i~L~~aA~~L----------~V~rRRIYDIiNVLEslgLI~K~-----~Kn~y~W~G~~~I~  179 (191)
                      ++|.+++.. .|+|+.||..|          ..+.||||||.|||.+||||+|+     .|+.|+|.|-..+.
T Consensus       170 klflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG~~~~~  242 (388)
T KOG2578|consen  170 KLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLGSKPIQ  242 (388)
T ss_pred             HheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeCCCccc
Confidence            999988876 89999999887          34789999999999999999995     68999999977654

>KOG2829 consensus E2F-like protein [Transcription]

Probab=98.79  E-value=3e-09  Score=95.40  Aligned_cols=90  Identities=20%  Similarity=0.312  Sum_probs=65.9

Q ss_pred             eecCccceecccccccccccCCCCCCCCCCCCCCCCCcCCCCCCCchHHHHHHHHHHHhhCCC-ceecHHHHHHHhCCee
Q 045382           68 IRVGSLYKVTYSSLKSFTETMPQSSSSTKVQDPSSRHYAYSRKQKSLGLLCSNFLSLYNRDGV-ESIGLDDAASKLGVER  146 (191)
Q Consensus        68 ~~~~~~~~~~~~~~~~~~e~m~~~~~~~~~~~~~~~~~~~~RkeKSL~~Lt~kFI~l~~~~~~-~~i~L~~aA~~L~V~r  146 (191)
                      |.+..|+||   +.++.+.|                           .+.+...|..|..... .-|..++-+--....|
T Consensus        49 fs~kVCeKv---e~Kg~TtY---------------------------neVADelVaef~~~n~~~~i~~n~~~yd~KNIR   98 (326)
T KOG2829|consen   49 FSMKVCEKV---ERKGTTTY---------------------------NEVADELVAEFAGANNYSHICPNEQEYDQKNIR   98 (326)
T ss_pred             hhHHHHHHH---HhcCCccH---------------------------HHHHHHHHHHHhccccccccCccccccchHHHH
Confidence            679999999   77776666                           6677777776654432 2455555554556679


Q ss_pred             eEeeehhhHhhhhcceeecCCCceEEeccc-chHHHHHHHHHH
Q 045382          147 RRIYDIVNVLESVGVLTRRAKNKYTWKGFK-AIRGALQELKVL  188 (191)
Q Consensus       147 RRIYDIiNVLEslgLI~K~~Kn~y~W~G~~-~I~~tLekLk~E  188 (191)
                      ||+||.+|||.+|.+|.|. |..|+|+|+. +-.+.+++|++|
T Consensus        99 RRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~ss~dv~~le~E  140 (326)
T KOG2829|consen   99 RRVYDALNVLMAMNIISKD-KKEIRWIGLPATSSQDVSELEEE  140 (326)
T ss_pred             HHHHHHHHHHHHHHHHhcc-cceeeeeccCccchHHHHHHHHH
Confidence            9999999999999999999 5579999986 233455555544

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

Probab=95.02  E-value=0.019  Score=39.69  Aligned_cols=43  Identities=21%  Similarity=0.459  Sum_probs=38.3

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWK  173 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~  173 (191)
                      +..+..++|+.+++.+..+|+++|-|+..|+|++...+.+.|.
T Consensus        21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~   63 (68)
T PF01978_consen   21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYR   63 (68)
T ss_dssp             CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence            4699999999999999999999999999999999876666553

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.

>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family

Probab=93.25  E-value=0.13  Score=34.48  Aligned_cols=54  Identities=30%  Similarity=0.422  Sum_probs=42.1

Q ss_pred             HHHHHHHHHhhC-----CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382          117 LCSNFLSLYNRD-----GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY  170 (191)
Q Consensus       117 Lt~kFI~l~~~~-----~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y  170 (191)
                      ++.-|+.++...     ....++..++|+.+|+.+.-++.+++.|+.-|+|.+...+.|
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            344455554432     345689999999999999999999999999999998864444

>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=92.41  E-value=0.15  Score=33.66  Aligned_cols=41  Identities=29%  Similarity=0.358  Sum_probs=34.3

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhc
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVG  160 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslg  160 (191)
                      .+.+.++.++++. ++..++|+.|+|.+|=|+--++.|+..|
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            3567777555554 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 ....

>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation

Probab=92.08  E-value=0.21  Score=35.49  Aligned_cols=55  Identities=18%  Similarity=0.325  Sum_probs=43.0

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG  174 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G  174 (191)
                      ...++++.+.+ ..+++.++|+.+++.+.-+|-+++.|+..|++.+...+.....|
T Consensus         8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~   62 (91)
T smart00346        8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNGRYRLG   62 (91)
T ss_pred             HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCCceeec
Confidence            44566666553 36999999999999999999999999999999987443333344

>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor

Probab=91.92  E-value=0.17  Score=31.98  Aligned_cols=46  Identities=33%  Similarity=0.475  Sum_probs=38.4

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK  167 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K  167 (191)
                      .++.++..++  .+++.++++.+++.++-+|..++-|+..|+|.+..+
T Consensus         4 ~il~~l~~~~--~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~   49 (53)
T smart00420        4 QILELLAQQG--KVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG   49 (53)
T ss_pred             HHHHHHHHcC--CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence            3555665543  489999999999999999999999999999987644

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

Probab=90.91  E-value=0.29  Score=34.53  Aligned_cols=56  Identities=20%  Similarity=0.369  Sum_probs=46.0

Q ss_pred             HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382          117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW  172 (191)
Q Consensus       117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W  172 (191)
                      .-++.++++...++..+...++|+.||+.++-+.-++.-|+.-|+|.+.+.+.=.|
T Consensus         7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W   62 (68)
T smart00550        7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW   62 (68)
T ss_pred             HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence            34677888887765459999999999999999999999999999999976432345

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

>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities

Probab=90.89  E-value=0.21  Score=33.05  Aligned_cols=45  Identities=20%  Similarity=0.376  Sum_probs=37.4

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..++++..++. .+++.++|+++|+.|=-+|-+++.|+..|++++.
T Consensus         7 ~iL~~l~~~~~-~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d   51 (52)
T PF09339_consen    7 RILEALAESGG-PLTLSEIARALGLPKSTVHRLLQTLVEEGYVERD   51 (52)
T ss_dssp             HHHHCHHCTBS-CEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHcCCC-CCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence            45566666654 3799999999999999999999999999999875

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.

>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor

Probab=88.49  E-value=0.71  Score=29.44  Aligned_cols=37  Identities=16%  Similarity=0.314  Sum_probs=33.4

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK  167 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K  167 (191)
                      ..+++.+++..+++.+.-++++++.|+.-|++....+
T Consensus         9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~   45 (66)
T smart00418        9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE   45 (66)
T ss_pred             CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence            4579999999999999999999999999999987653

>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=87.60  E-value=0.67  Score=33.35  Aligned_cols=59  Identities=14%  Similarity=0.191  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHhhCCCc-eecHHHHHHHhCCeeeEeeehhhHhhhhcceeec-CCCceEEec
Q 045382          116 LLCSNFLSLYNRDGVE-SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR-AKNKYTWKG  174 (191)
Q Consensus       116 ~Lt~kFI~l~~~~~~~-~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~-~Kn~y~W~G  174 (191)
                      ..+-+++-++...++. .+++.++|+.+++..+.+..|++-|+.-|+|+.. +++-=.|..
T Consensus         8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~   68 (83)
T PF02082_consen    8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLA   68 (83)
T ss_dssp             HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEES
T ss_pred             HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeec
Confidence            4455666776655543 4999999999999999999999999999999754 333333333

(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.

>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial

Probab=87.19  E-value=0.72  Score=35.51  Aligned_cols=48  Identities=15%  Similarity=0.306  Sum_probs=40.7

Q ss_pred             HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      +-+.+.++...++..+++.++|+++++.+..++.+++.|+.-|+|...
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            344556666566678999999999999999999999999999999864

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.

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

Probab=87.04  E-value=1.7  Score=28.25  Aligned_cols=46  Identities=20%  Similarity=0.364  Sum_probs=37.7

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK  167 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K  167 (191)
                      ..++.++...+   ++..++++.+++.+.-++-++|.|+.-|+|.+...
T Consensus        10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~   55 (78)
T cd00090          10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE   55 (78)
T ss_pred             HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence            44555555543   89999999999999999999999999999987543

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.

>COG1378 Predicted transcriptional regulators [Transcription]

Probab=86.92  E-value=0.9  Score=39.76  Aligned_cols=36  Identities=22%  Similarity=0.415  Sum_probs=32.5

Q ss_pred             eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382          132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK  167 (191)
Q Consensus       132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K  167 (191)
                      ..+-.++|+..||++=|+|||++-||.=|+++.+..
T Consensus        30 ~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g   65 (247)
T COG1378          30 EATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEG   65 (247)
T ss_pred             CccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCC
Confidence            467889999999999999999999999999988633

>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=86.57  E-value=0.83  Score=29.37  Aligned_cols=43  Identities=23%  Similarity=0.404  Sum_probs=36.3

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhccee
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT  163 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~  163 (191)
                      .+.+.++.+++.  ++..++|+.+|+.+..++.+++-|+.-|+|+
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            567778878755  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=85.24  E-value=0.87  Score=30.13  Aligned_cols=46  Identities=26%  Similarity=0.417  Sum_probs=38.9

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..+.++...++..+.+.++|+.+++.+=.+--+++-|+.-|+|++.
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            3455566776667999999999999999999999999999999986

...

>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein

Probab=82.71  E-value=0.83  Score=28.51  Aligned_cols=38  Identities=21%  Similarity=0.420  Sum_probs=33.7

Q ss_pred             eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382          132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY  170 (191)
Q Consensus       132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y  170 (191)
                      .++..++|+.+++.+..+..+++.|+.-|++.+.. +.|
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            47889999999999999999999999999999874 444

>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=82.51  E-value=2.7  Score=28.67  Aligned_cols=50  Identities=18%  Similarity=0.293  Sum_probs=37.7

Q ss_pred             HHHHHHHHhh---CCCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC
Q 045382          118 CSNFLSLYNR---DGVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK  167 (191)
Q Consensus       118 t~kFI~l~~~---~~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K  167 (191)
                      ...+.+.+..   .++..+ +..++|++++|.+.=+.+.++.|+.-|+|++..+
T Consensus         6 ~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~   59 (64)
T PF00392_consen    6 YDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG   59 (64)
T ss_dssp             HHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred             HHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence            3444444433   356678 9999999999999999999999999999987644

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 ....

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

Probab=82.44  E-value=1.1  Score=31.75  Aligned_cols=43  Identities=28%  Similarity=0.474  Sum_probs=29.0

Q ss_pred             CchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          112 KSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       112 KSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      -+++.+-+.+-++|+.....           -...||++|++|-|+.+|+|.-.
T Consensus        23 ~~~~~vy~~Y~~~c~~~~~~-----------~l~~~~~~~~l~~L~~~gli~~~   65 (87)
T cd08768          23 ATTGEVYEVYEELCEEIGVD-----------PLTQRRISDLLSELEMLGLLETE   65 (87)
T ss_pred             ccHHHHHHHHHHHHHHcCCC-----------CCcHHHHHHHHHHHHHcCCeEEE
Confidence            34455555555555543211           13679999999999999999753

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

>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=81.52  E-value=0.42  Score=34.42  Aligned_cols=21  Identities=29%  Similarity=0.493  Sum_probs=18.2

Q ss_pred             eeeEeeehhhHhhhhcceeec
Q 045382          145 ERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       145 ~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..||++|++|-|+.+|+|...
T Consensus        38 s~~r~~~~l~eL~~~gli~~~   58 (85)
T PF09079_consen   38 SYRRFSDYLSELEMLGLIESE   58 (85)
T ss_dssp             -HHHHHHHHHHHHHTTSEEEE
T ss_pred             CHHHHHHHHHHHHhCCCeEEE
Confidence            579999999999999999654

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.

>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor

Probab=81.34  E-value=2  Score=27.61  Aligned_cols=40  Identities=25%  Similarity=0.446  Sum_probs=34.5

Q ss_pred             CCcee-cHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382          129 GVESI-GLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN  168 (191)
Q Consensus       129 ~~~~i-~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn  168 (191)
                      ++..+ +..++|+.+++.+=-+...++.|+.-|+|.+....
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            34456 89999999999999999999999999999876543

>PF13730 HTH_36: Helix-turn-helix domain

Probab=81.24  E-value=1.4  Score=28.84  Aligned_cols=30  Identities=30%  Similarity=0.487  Sum_probs=28.2

Q ss_pred             ecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382          133 IGLDDAASKLGVERRRIYDIVNVLESVGVL  162 (191)
Q Consensus       133 i~L~~aA~~L~V~rRRIYDIiNVLEslgLI  162 (191)
                      -+.+.+|+.+|+.+|.++-.++.|+..|+|
T Consensus        26 pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I   55 (55)
T PF13730_consen   26 PSQETLAKDLGVSRRTVQRAIKELEEKGLI   55 (55)
T ss_pred             cCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence            389999999999999999999999999986

>PRK10163 DNA-binding transcriptional repressor AllR; Provisional

Probab=80.76  E-value=4.1  Score=35.36  Aligned_cols=56  Identities=14%  Similarity=0.291  Sum_probs=43.6

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF  175 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~  175 (191)
                      -..+++|...+ ..+.+.++|+.+|+.|=.+|.+++-|+..|++.+.....-.+.|.
T Consensus        28 l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~   83 (271)
T PRK10163         28 IAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGL   83 (271)
T ss_pred             HHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence            34556665543 358999999999999999999999999999998865444444553

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	191
1cf7_A	76	Structural Basis Of Dna Recognition By The Heterodi		6e-11

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

Iteration: 1
 Score = 63.9 bits (154), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 35/71 (49%), Positives = 48/71 (67%), Gaps = 5/71 (7%)
Query: 108 SRKQKSLGLLCSNFLSLYN--RDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTR 164
           SR +KSLGLL + F+SL    +DGV  + L  AA  L V ++RRIYDI NVLE +G++ +
Sbjct: 6   SRHEKSLGLLTTKFVSLLQEAKDGVLDLKL--AADTLAVRQKRRIYDITNVLEGIGLIEK 63
Query: 165 RAKNKYTWKGF 175
           ++KN   WKG 
Sbjct: 64  KSKNSIQWKGV 74

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	191
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	1e-26
1cf7_B	95	Protein (transcription factor DP-2); E2F, winged-h	4e-04

>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 = 96.1 bits (239), Expect = 1e-26
 Identities = 32/70 (45%), Positives = 44/70 (62%), Gaps = 1/70 (1%)

Query: 107 YSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRR 165
            SR +KSLGLL + F+SL        + L  AA  L V ++RRIYDI NVLE +G++ ++
Sbjct: 5   PSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKK 64

Query: 166 AKNKYTWKGF 175
           +KN   WKG 
Sbjct: 65  SKNSIQWKGV 74

>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 Length = 95

 Score = 37.4 bits (86), Expect = 4e-04
 Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 1/30 (3%)

Query: 146 RRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175
           RRR+YD +NVL ++ ++++  K +  W G 
Sbjct: 61  RRRVYDALNVLMAMNIISKEKK-EIKWIGL 89

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	191
1cf7_A	76	Protein (transcription factor E2F-4); E2F, winged-	99.95
1cf7_B	95	Protein (transcription factor DP-2); E2F, winged-h	99.37
1qgp_A	77	Protein (double stranded RNA adenosine deaminase);	93.2
2heo_A	67	Z-DNA binding protein 1; protein DLM1-Z-DNA comple	92.39
1qbj_A	81	Protein (double-stranded RNA specific adenosine D	92.18
1oyi_A	82	Double-stranded RNA-binding protein; (alpha+beta)	91.86
2xvc_A	59	ESCRT-III, SSO0910; cell cycle, cell division, cyt	91.84
1u2w_A	122	CADC repressor, cadmium efflux system accessory pr	89.52
3r0a_A	123	Putative transcriptional regulator; structural gen	89.41
2htj_A	81	P fimbrial regulatory protein KS71A; winged helix-	89.25
3cuo_A	99	Uncharacterized HTH-type transcriptional regulato;	88.02
1r1u_A	106	CZRA, repressor protein; zinc, DNA binding, transc	87.69
3pqk_A	102	Biofilm growth-associated repressor; helix-turn-he	87.47
2y75_A	129	HTH-type transcriptional regulator CYMR; DNA bindi	86.95
2kko_A	108	Possible transcriptional regulatory protein (possi	86.65
3jth_A	98	Transcription activator HLYU; transcription factor	86.59
3qph_A	342	TRMB, A global transcription regulator; transcript	86.46
2d1h_A	109	ST1889, 109AA long hypothetical transcriptional re	84.71
1r1t_A	122	Transcriptional repressor SMTB; zinc, transcriptio	84.55
1sfx_A	109	Conserved hypothetical protein AF2008; structural	83.82
2lkp_A	119	Transcriptional regulator, ARSR family; symmetric	82.88
2oqg_A	114	Possible transcriptional regulator, ARSR family P;	82.24
3mq0_A	275	Transcriptional repressor of the blcabc operon; he	81.46
1ub9_A	100	Hypothetical protein PH1061; helix-turn-helix moti	81.35
1y0u_A	96	Arsenical resistance operon repressor, putative; s	81.25
1ku9_A	152	Hypothetical protein MJ223; putative transcription	80.91
3bro_A	141	Transcriptional regulator; helix_TURN_helix, multi	80.19
3eco_A	139	MEPR; mutlidrug efflux pump regulator winged helix	80.05

>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=99.95  E-value=9.1e-29  Score=180.02  Aligned_cols=72  Identities=44%  Similarity=0.737  Sum_probs=65.4

Q ss_pred             CCCCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCC-eeeEeeehhhHhhhhcceeecCCCceEEecccc
Q 045382          106 AYSRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKA  177 (191)
Q Consensus       106 ~~~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V-~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~  177 (191)
                      ..+|+++||+.||++||++|.+++++.++|+++|++|+| +|||||||+|||||||||+|.+||.|+|+|++.
T Consensus         4 ~~~R~~~SL~~lt~kFi~l~~~~~~~~i~l~~aa~~L~v~~kRRiYDI~NVLe~igli~K~~k~~~~W~G~~~   76 (76)
T 1cf7_A            4 TPSRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKSKNSIQWKGVGP   76 (76)
T ss_dssp             --CTTTTCHHHHHHHHHHHHHHSSTTEEEHHHHHHHTTTCCTHHHHHHHHHHHHHTSEEEEETTEEEEC----
T ss_pred             CCCCccCcHHHHHHHHHHHHHhCCCCcCcHHHHHHHhCCccceehhhHHHHHhHhcceeecCCCcEEEeCCCC
Confidence            578999999999999999999999999999999999999 999999999999999999999999999999863

>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=99.37  E-value=5.1e-14  Score=106.55  Aligned_cols=62  Identities=24%  Similarity=0.463  Sum_probs=47.7

Q ss_pred             chHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccc
Q 045382          113 SLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKA  177 (191)
Q Consensus       113 SL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~  177 (191)
                      ++.+++..+|..|.+.++.. ..+. .......|||+||++|||+++|||+| .++.|+|+|+++
T Consensus        30 ty~eVAdeLV~e~~~~~~~~-~~~~-~~d~~~~rRRvYD~~NVl~a~gii~K-~k~~i~W~g~~~   91 (95)
T 1cf7_B           30 SYNEVADELVSEFTNSNNHL-AADS-AYDQKNIRRRVYDALNVLMAMNIISK-EKKEIKWIGLPT   91 (95)
T ss_dssp             CHHHHHHHHHHHHHTCTTCC-GGGS-HHHHHHHHHHHHHHHHHHHHTTSBCC-CSSCEEBCCCC-
T ss_pred             cHHHHHHHHHHHHhcccccC-ccch-hcccccchhhHHHHHHHHHHhcceec-CCCEEEEecCCc
Confidence            45888888888887765543 2221 22345589999999999999999999 699999999875

>1qgp_A Protein (double stranded RNA adenosine deaminase); Z-alpha-Z-DNA binding domain, RNA-editing, Z-DNA recognition, ADAR1, helix- turn-helix; NMR {Homo sapiens} SCOP: a.4.5.19

Probab=93.20  E-value=0.058  Score=37.90  Aligned_cols=54  Identities=22%  Similarity=0.386  Sum_probs=45.7

Q ss_pred             HHHHHHHhhCC-CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382          119 SNFLSLYNRDG-VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW  172 (191)
Q Consensus       119 ~kFI~l~~~~~-~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W  172 (191)
                      ++.+.++.+.+ +..++..++|++||+.++-+.-.+.-|+.-|+|.+.+.+.=.|
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            66777777665 5679999999999999999999999999999999976554556

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

Probab=92.39  E-value=0.087  Score=35.76  Aligned_cols=53  Identities=11%  Similarity=0.203  Sum_probs=43.0

Q ss_pred             HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382          117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY  170 (191)
Q Consensus       117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y  170 (191)
                      .-.+.++++.++ +..+++.++|+.|++.|--++-+++.|+.-|+|....+..|
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            345677777653 24699999999999999999999999999999987544444

>1qbj_A Protein (double-stranded RNA specific adenosine D (ADAR1)); protein-Z-DNA complex, hydrolase-DNA complex; HET: DNA; 2.10A {Homo sapiens} SCOP: a.4.5.19 PDB: 3f21_A* 3f22_A* 3f23_A* 3irr_A* 3irq_D* 2gxb_A 2acj_A 2l54_A

Probab=92.18  E-value=0.097  Score=37.42  Aligned_cols=56  Identities=23%  Similarity=0.373  Sum_probs=45.6

Q ss_pred             HHHHHHHHhhCC-CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382          118 CSNFLSLYNRDG-VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWK  173 (191)
Q Consensus       118 t~kFI~l~~~~~-~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~  173 (191)
                      -++.++++.+++ +..++..++|.+||+.|+-+.-.+.-|+.-|+|.+.+.+.=.|.
T Consensus        12 ~~~IL~~L~~~~pg~~~t~~eLA~~Lgvsr~tV~~~L~~Le~~G~I~~~g~~~~~W~   68 (81)
T 1qbj_A           12 EQRILKFLEELGEGKATTAHDLSGKLGTPKKEINRVLYSLAKKGKLQKEAGTPPLWK   68 (81)
T ss_dssp             HHHHHHHHHHHCTTCCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEESSSSCEEE
T ss_pred             HHHHHHHHHHcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCCeeE
Confidence            456777776554 56799999999999999999999999999999998765545663

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

Probab=91.86  E-value=0.15  Score=37.01  Aligned_cols=57  Identities=11%  Similarity=0.171  Sum_probs=50.0

Q ss_pred             HHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382          115 GLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG  174 (191)
Q Consensus       115 ~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G  174 (191)
                      ..+.++.+.++..++   ++..++|.+||+.|.-++=.++-||.=|+|.+..-+--+|.=
T Consensus        16 ~~~~~~IL~lL~~~g---~sa~eLAk~LgiSk~aVr~~L~~Le~eG~I~~~~~~PP~W~~   72 (82)
T 1oyi_A           16 AEIVCEAIKTIGIEG---ATAAQLTRQLNMEKREVNKALYDLQRSAMVYSSDDIPPRWFM   72 (82)
T ss_dssp             HHHHHHHHHHHSSST---EEHHHHHHHSSSCHHHHHHHHHHHHHHTSSEECSSSSCEEES
T ss_pred             HHHHHHHHHHHHHcC---CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCccee
Confidence            677889999988543   999999999999988888888999999999999888899953

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

Probab=91.84  E-value=0.11  Score=36.05  Aligned_cols=44  Identities=14%  Similarity=0.368  Sum_probs=39.0

Q ss_pred             HHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhccee
Q 045382          119 SNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLT  163 (191)
Q Consensus       119 ~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~  163 (191)
                      ++.++++.++ ++.+++..++.++||.|--+||+++=|+.=|||.
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            5667777776 4689999999999999999999999999999986

>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=89.52  E-value=0.6  Score=34.38  Aligned_cols=67  Identities=21%  Similarity=0.118  Sum_probs=48.6

Q ss_pred             HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC--CceEEecccchHHHHHHHHHHh
Q 045382          121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK--NKYTWKGFKAIRGALQELKVLL  189 (191)
Q Consensus       121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K--n~y~W~G~~~I~~tLekLk~Ei  189 (191)
                      .+.++...  +.+++.++|+.||+.+--++-.++.|+..|+|.+...  ..+.......+...++.+.+.+
T Consensus        47 IL~~L~~~--~~~s~~eLa~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~~~~~~l~~~~  115 (122)
T 1u2w_A           47 ITYALCQD--EELCVCDIANILGVTIANASHHLRTLYKQGVVNFRKEGKLALYSLGDEHIRQIMMIALAHK  115 (122)
T ss_dssp             HHHHHHHS--SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEC----CCEEEESCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHC--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEECCEEEEEECHHHHHHHHHHHHHHh
Confidence            44455433  3589999999999999999999999999999976533  3455556666666666665544

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

Probab=89.41  E-value=0.38  Score=35.70  Aligned_cols=46  Identities=17%  Similarity=0.221  Sum_probs=38.2

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..+..+...+..-++..++|+.+++.+-.+|-.++.|+..|+|.+.
T Consensus        30 ~il~~L~~~~~~~~t~~eLa~~l~~s~sTV~r~L~~L~~~GlV~r~   75 (123)
T 3r0a_A           30 NVMKSFLNEPDRWIDTDALSKSLKLDVSTVQRSVKKLHEKEILQRS   75 (123)
T ss_dssp             HHHHHHHHSTTCCEEHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence            4555555554323999999999999999999999999999999885

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

Probab=89.25  E-value=0.4  Score=32.78  Aligned_cols=43  Identities=23%  Similarity=0.307  Sum_probs=36.5

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceee
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTR  164 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K  164 (191)
                      +.+.++...  ..++..++|+.+++.+.-++-.++.|+.-|+|.+
T Consensus         4 ~Il~~L~~~--~~~s~~eLa~~lgvs~~tv~r~L~~L~~~GlI~~   46 (81)
T 2htj_A            4 EILEFLNRH--NGGKTAEIAEALAVTDYQARYYLLLLEKAGMVQR   46 (81)
T ss_dssp             HHHHHHHHS--CCCCHHHHHHHHTSCHHHHHHHHHHHHHHTSEEE
T ss_pred             HHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence            455566554  3489999999999999999999999999999984

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

Probab=88.02  E-value=1.2  Score=30.35  Aligned_cols=64  Identities=9%  Similarity=0.143  Sum_probs=43.8

Q ss_pred             HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCc--eEEecccchHHHHHHHH
Q 045382          121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNK--YTWKGFKAIRGALQELK  186 (191)
Q Consensus       121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~--y~W~G~~~I~~tLekLk  186 (191)
                      .+.++..  +..+++.++|+.+++.+--++-.++.|+..|+|.+...+.  +...-...+...++.+.
T Consensus        29 il~~l~~--~~~~s~~ela~~l~is~~tvs~~l~~L~~~glv~~~~~~r~~~y~l~~~~~~~l~~~l~   94 (99)
T 3cuo_A           29 ILCMLSG--SPGTSAGELTRITGLSASATSQHLARMRDEGLIDSQRDAQRILYSIKNEAVNAIIATLK   94 (99)
T ss_dssp             HHHHHTT--CCSEEHHHHHHHHCCCHHHHHHHHHHHHHTTSEEEEECSSCEEEEECCHHHHHHHHHHH
T ss_pred             HHHHHHh--CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEChHHHHHHHHHHH
Confidence            4444433  3468999999999999999999999999999998754333  33333333444444433

>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=87.69  E-value=0.55  Score=33.53  Aligned_cols=66  Identities=9%  Similarity=0.129  Sum_probs=47.5

Q ss_pred             HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCc--eEEecccchHHHHHHHHHHh
Q 045382          121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNK--YTWKGFKAIRGALQELKVLL  189 (191)
Q Consensus       121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~--y~W~G~~~I~~tLekLk~Ei  189 (191)
                      .+.++..   ..+++.++|+.+++.+--++-.++.|+..|+|.+...+.  |.-.....+...++.+...+
T Consensus        31 IL~~L~~---~~~~~~ela~~l~is~stvs~~L~~L~~~Glv~~~~~gr~~~y~l~~~~~~~~~~~l~~~~   98 (106)
T 1r1u_A           31 IMELLSV---SEASVGHISHQLNLSQSNVSHQLKLLKSVHLVKAKRQGQSMIYSLDDIHVATMLKQAIHHA   98 (106)
T ss_dssp             HHHHHHH---CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHHHHHHH
T ss_pred             HHHHHHh---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHHHHH
Confidence            4444442   347999999999999999999999999999998654433  33344555666666665544

>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=87.47  E-value=1.5  Score=30.76  Aligned_cols=57  Identities=11%  Similarity=0.235  Sum_probs=43.2

Q ss_pred             eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC--CceEEecccchHHHHHHHHHH
Q 045382          132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK--NKYTWKGFKAIRGALQELKVL  188 (191)
Q Consensus       132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K--n~y~W~G~~~I~~tLekLk~E  188 (191)
                      ..++.++|+.+|+.+--++--++.|+..|+|.+...  ..|.-.....+...++.+.+.
T Consensus        36 ~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~~~~~l~~~   94 (102)
T 3pqk_A           36 EFSVGELEQQIGIGQPTLSQQLGVLRESGIVETRRNIKQIFYRLTEAKAAQLVNALYTI   94 (102)
T ss_dssp             CBCHHHHHHHHTCCTTHHHHHHHHHHHTTSEEEECSSSCCEEEECSSTHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECcHHHHHHHHHHHHH
Confidence            489999999999999999999999999999976533  333334445566666655543

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

Probab=86.95  E-value=0.72  Score=33.94  Aligned_cols=49  Identities=12%  Similarity=0.189  Sum_probs=39.7

Q ss_pred             HHHHHHHHHhhC-CCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          117 LCSNFLSLYNRD-GVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       117 Lt~kFI~l~~~~-~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      .+-+.+.++... ++..++..++|+.+++.++-++.|++.|+..|+|+..
T Consensus        10 ~al~iL~~la~~~~~~~~s~~ela~~~~i~~~~v~~il~~L~~~Glv~~~   59 (129)
T 2y75_A           10 YGLTIMIELAKKHGEGPTSLKSIAQTNNLSEHYLEQLVSPLRNAGLVKSI   59 (129)
T ss_dssp             HHHHHHHHHHHTTTSCCBCHHHHHHHTTSCHHHHHHHHHHHHHTTSEEEC
T ss_pred             HHHHHHHHHHhCCCCCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCceEec
Confidence            344455555443 3567999999999999999999999999999999876

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

Probab=86.65  E-value=0.99  Score=32.48  Aligned_cols=55  Identities=11%  Similarity=0.143  Sum_probs=40.5

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE--ecccchHHHHHHH
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW--KGFKAIRGALQEL  185 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W--~G~~~I~~tLekL  185 (191)
                      +.+++.++|+.+++.+.-++-.++.|+..|+|++...+...+  .....+...++.|
T Consensus        37 ~~~s~~eLa~~lgis~stvs~~L~~L~~~GlV~~~~~gr~~~y~l~~~~~~~l~~~l   93 (108)
T 2kko_A           37 GERAVEAIATATGMNLTTASANLQALKSGGLVEARREGTRQYYRIAGEDVARLFALV   93 (108)
T ss_dssp             CCEEHHHHHHHHTCCHHHHHHHHHHHHHHTSEEEEEETTEEEEEESCHHHHHHHHHH
T ss_pred             CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHH
Confidence            458999999999999999999999999999998654443333  3333444444433

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

Probab=86.59  E-value=1.2  Score=30.93  Aligned_cols=57  Identities=14%  Similarity=0.258  Sum_probs=42.8

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCC--CceEEecccchHHHHHHHHH
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAK--NKYTWKGFKAIRGALQELKV  187 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~K--n~y~W~G~~~I~~tLekLk~  187 (191)
                      +.+++.++|+.+|+.+--++--++.|+..|+|.+...  ..|.......+...++.+.+
T Consensus        35 ~~~~~~ela~~l~is~~tvs~~L~~L~~~Glv~~~~~g~~~~y~l~~~~~~~l~~~l~~   93 (98)
T 3jth_A           35 QELSVGELCAKLQLSQSALSQHLAWLRRDGLVTTRKEAQTVYYTLKSEEVKAMIKLLHS   93 (98)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEECCTTCCEEEECCHHHHHHHHHHHH
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEECHHHHHHHHHHHHH
Confidence            4699999999999999999999999999999976543  33444444555555544443

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

Probab=86.46  E-value=0.18  Score=44.23  Aligned_cols=43  Identities=19%  Similarity=0.341  Sum_probs=36.3

Q ss_pred             eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEec
Q 045382          132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKG  174 (191)
Q Consensus       132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G  174 (191)
                      ..+..++|+.+|+.+.++|++++.|+..|+|.+...+...|.=
T Consensus        32 ~~t~~eia~~~gv~~~~Vy~~L~~L~~~GlV~~~~g~p~~y~a   74 (342)
T 3qph_A           32 PSTAKEISTKSGIPYNRVYDTISSLKLRGFVTEIEGTPKVYAA   74 (342)
T ss_dssp             HHHHSCCSSSTTSSSCSCCHHHHHHHHHTSEEEECCTTCEEEE
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceeEEEE
Confidence            4677889999999999999999999999999887555555653

>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=84.71  E-value=0.63  Score=31.90  Aligned_cols=36  Identities=14%  Similarity=0.297  Sum_probs=33.2

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecC
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRA  166 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~  166 (191)
                      ..++..++|+.+++.+--++-+++.|+.-|+|.+..
T Consensus        35 ~~~t~~ela~~l~is~~tv~~~l~~L~~~g~v~~~~   70 (109)
T 2d1h_A           35 KPITSEELADIFKLSKTTVENSLKKLIELGLVVRTK   70 (109)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence            358999999999999999999999999999998763

>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=84.55  E-value=1.2  Score=32.96  Aligned_cols=59  Identities=17%  Similarity=0.201  Sum_probs=46.6

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec--CCCceEEecccchHHHHHHHHHHh
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR--AKNKYTWKGFKAIRGALQELKVLL  189 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~--~Kn~y~W~G~~~I~~tLekLk~Ei  189 (191)
                      +..++.++|+.|++.+--++-.++.|+..|+|.+.  ++..|.......+...++.+.+.+
T Consensus        58 ~~~s~~ela~~lgis~stvs~~L~~Le~~Glv~~~~~gr~~~y~l~~~~l~~~~~~l~~~~  118 (122)
T 1r1t_A           58 SELCVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHL  118 (122)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEEETTEEEEEESSHHHHHHHHHHHHHT
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEeCCEEEEEEChHHHHHHHHHHHHHH
Confidence            35899999999999999999999999999999764  333455556666777777776654

>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=83.82  E-value=0.76  Score=31.37  Aligned_cols=44  Identities=23%  Similarity=0.324  Sum_probs=36.7

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..+.++...  ..++..++|+.+++.+--+|.+++.|+.-|+|.+.
T Consensus        24 ~il~~l~~~--~~~s~~ela~~l~is~~tv~~~l~~L~~~glv~~~   67 (109)
T 1sfx_A           24 RIYSLLLER--GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             HHHHHHHHH--CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHHc--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence            344555443  34899999999999999999999999999999885

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

Probab=82.88  E-value=1.5  Score=31.33  Aligned_cols=57  Identities=16%  Similarity=0.249  Sum_probs=40.6

Q ss_pred             eecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCc-eEE-ecccchHHHHHHHHHH
Q 045382          132 SIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNK-YTW-KGFKAIRGALQELKVL  188 (191)
Q Consensus       132 ~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~-y~W-~G~~~I~~tLekLk~E  188 (191)
                      ..++.++|+.|++.+--++-.++.||..|+|.+...+. +.+ ..-..+...++.+...
T Consensus        45 ~~s~~ela~~l~is~stvsr~l~~Le~~Glv~~~~~~r~~~~~~~~~~~~~~~~~~~~~  103 (119)
T 2lkp_A           45 PLPVTDLAEAIGMEQSAVSHQLRVLRNLGLVVGDRAGRSIVYSLYDTHVAQLLDEAIYH  103 (119)
T ss_dssp             CCCHHHHHHHHSSCHHHHHHHHHHHHHHCSEEEEEETTEEEEEESCHHHHHHHHHHHHH
T ss_pred             CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEecCCEEEEEEchHHHHHHHHHHHHH
Confidence            48999999999999999999999999999997653332 222 2223444455544443

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

Probab=82.24  E-value=1.1  Score=31.52  Aligned_cols=46  Identities=22%  Similarity=0.323  Sum_probs=37.0

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCC
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKN  168 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn  168 (191)
                      +.+.++..   +.+++.++|+.+++.+--++-.++.|+.-|+|.+...+
T Consensus        25 ~IL~~L~~---~~~~~~ela~~l~is~~tv~~~l~~L~~~gli~~~~~g   70 (114)
T 2oqg_A           25 EILTELGR---ADQSASSLATRLPVSRQAIAKHLNALQACGLVESVKVG   70 (114)
T ss_dssp             HHHHHHHH---SCBCHHHHHHHSSSCHHHHHHHHHHHHHTTSEEEEEET
T ss_pred             HHHHHHHc---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeEEecC
Confidence            34555532   24899999999999999999999999999999875333

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

Probab=81.46  E-value=1.8  Score=36.28  Aligned_cols=54  Identities=15%  Similarity=0.228  Sum_probs=41.5

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF  175 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~  175 (191)
                      ..+++|...+ ..+++.++|+.+|+.|=-+|-+++.|+..|++.+.....| ..|.
T Consensus        34 ~IL~~l~~~~-~~ltl~eia~~lgl~ksTv~RlL~tL~~~G~v~~~~~~~Y-~LG~   87 (275)
T 3mq0_A           34 RILDLVAGSP-RDLTAAELTRFLDLPKSSAHGLLAVMTELDLLARSADGTL-RIGP   87 (275)
T ss_dssp             HHHHHHHHCS-SCEEHHHHHHHHTCC--CHHHHHHHHHHTTSEEECTTSEE-EECT
T ss_pred             HHHHHHhhCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCcE-EehH
Confidence            3556666654 4699999999999999999999999999999999864444 3564

>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=81.35  E-value=1  Score=30.68  Aligned_cols=43  Identities=12%  Similarity=0.169  Sum_probs=35.9

Q ss_pred             HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      .+.++...  +.+++.++|+.+++.+--++-.++.|+.-|+|++.
T Consensus        21 iL~~L~~~--~~~~~~ela~~l~is~~tvs~~l~~L~~~gli~~~   63 (100)
T 1ub9_A           21 IMIFLLPR--RKAPFSQIQKVLDLTPGNLDSHIRVLERNGLVKTY   63 (100)
T ss_dssp             HHHHHHHH--SEEEHHHHHHHTTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHhc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            44444433  35899999999999999999999999999999864

>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=81.25  E-value=0.64  Score=32.49  Aligned_cols=48  Identities=13%  Similarity=0.242  Sum_probs=39.1

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEE
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTW  172 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W  172 (191)
                      +.+.++ .   ..+++.++|+.+++.+--++-.++.|+..|+|.+.. +.|..
T Consensus        35 ~Il~~L-~---~~~~~~eLa~~l~is~~tv~~~L~~L~~~Glv~~~~-g~y~l   82 (96)
T 1y0u_A           35 KILRML-D---KGRSEEEIMQTLSLSKKQLDYHLKVLEAGFCIERVG-ERWVV   82 (96)
T ss_dssp             HHHHHH-H---TTCCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEET-TEEEE
T ss_pred             HHHHHH-c---CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEC-CEEEE
Confidence            344555 3   348999999999999999999999999999999876 55544

>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=80.91  E-value=3.1  Score=29.66  Aligned_cols=35  Identities=14%  Similarity=0.338  Sum_probs=33.0

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      +.+++.++|+.+++.+=-++.+++.|+.-|+|++.
T Consensus        40 ~~~t~~ela~~l~~~~stvs~~l~~L~~~G~v~r~   74 (152)
T 1ku9_A           40 KPLTISDIMEELKISKGNVSMSLKKLEELGFVRKV   74 (152)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence            45999999999999999999999999999999985

>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=80.19  E-value=1  Score=32.29  Aligned_cols=45  Identities=13%  Similarity=0.230  Sum_probs=38.3

Q ss_pred             HHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          121 FLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       121 FI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ++.++...++..+++.++|+.+++.+--+.-+++-|+.-|+|++.
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            445555555446999999999999999999999999999999886

>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=80.05  E-value=1  Score=32.33  Aligned_cols=46  Identities=15%  Similarity=0.189  Sum_probs=39.3

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..+.++...++..+++.++|+.+++.+=-+.-+++-|+.-|+|++.
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            3445555665567999999999999999999999999999999986

---

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	191
d1cf7a_	67	a.4.5.17 (A:) Cell cycle transcription factor E2F-	2e-26
d1cf7b_	82	a.4.5.17 (B:) Cell cycle transcription factor DP-2	1e-04

>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 = 93.7 bits (233), Expect = 2e-26
 Identities = 31/67 (46%), Positives = 43/67 (64%), Gaps = 1/67 (1%)

Query: 108 SRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRRA 166
           SR +KSLGLL + F+SL        + L  AA  L V ++RRIYDI NVLE +G++ +++
Sbjct: 1   SRHEKSLGLLTTKFVSLLQEAKDGVLDLKLAADTLAVRQKRRIYDITNVLEGIGLIEKKS 60

Query: 167 KNKYTWK 173
           KN   WK
Sbjct: 61  KNSIQWK 67

>d1cf7b_ a.4.5.17 (B:) Cell cycle transcription factor DP-2 {Human (Homo sapiens) [TaxId: 9606]} Length = 82

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]

 Score = 37.4 bits (87), Expect = 1e-04
 Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 1/30 (3%)

Query: 146 RRRIYDIVNVLESVGVLTRRAKNKYTWKGF 175
           RRR+YD +NVL ++ ++++  K +  W G 
Sbjct: 53  RRRVYDALNVLMAMNIISKEKK-EIKWIGL 81

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	191
d1cf7a_	67	Cell cycle transcription factor E2F-4 {Human (Homo	99.95
d1cf7b_	82	Cell cycle transcription factor DP-2 {Human (Homo	98.98
d1sfxa_	109	Hypothetical protein AF2008 {Archaeoglobus fulgidu	94.6
d1mkma1	75	Transcriptional regulator IclR, N-terminal domain	91.72
d1j5ya1	65	Putative transcriptional regulator TM1602, N-termi	90.8
d1tw3a1	85	Carminomycin 4-O-methyltransferase {Streptomyces p	86.31
d1biaa1	63	Biotin repressor, N-terminal domain {Escherichia c	86.26
d1qzza1	92	Aclacinomycin-10-hydroxylase RdmB {Streptomyces pu	85.94
d1lvaa3	64	C-terminal fragment of elongation factor SelB {Moo	85.12
d1ku9a_	151	DNA-binding protein Mj223 {Archaeon Methanococcus	84.9
d1jhfa1	71	LexA repressor, N-terminal DNA-binding domain {Esc	81.63
d2d1ha1	109	Hypothetical transcriptional regulator ST1889 {Sul	80.78

>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=99.95  E-value=7.9e-29  Score=175.54  Aligned_cols=66  Identities=47%  Similarity=0.786  Sum_probs=64.5

Q ss_pred             CCCCCchHHHHHHHHHHHhhCCCceecHHHHHHHhCC-eeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382          108 SRKQKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGV-ERRRIYDIVNVLESVGVLTRRAKNKYTWK  173 (191)
Q Consensus       108 ~RkeKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V-~rRRIYDIiNVLEslgLI~K~~Kn~y~W~  173 (191)
                      +|+|+||++||++|+.+|.++|++.++|+++|++|+| +|||||||+|||||||+|+|.+||.|+|.
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            5999999999999999999999999999999999999 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=98.98  E-value=4.8e-11  Score=86.43  Aligned_cols=62  Identities=24%  Similarity=0.492  Sum_probs=43.6

Q ss_pred             CCchHHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecc
Q 045382          111 QKSLGLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGF  175 (191)
Q Consensus       111 eKSL~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~  175 (191)
                      ..+..++++.++..|.+.... ..-+.. ..-...|||+||.+|||.++|+|+|. |..++|+|+
T Consensus        20 ~TtY~eVAdeLv~e~~~~~~~-~~~~~~-~d~KNIRRRVYDALNVLmA~~II~K~-kK~I~W~Gl   81 (82)
T d1cf7b_          20 TTSYNEVADELVSEFTNSNNH-LAADSA-YDQKNIRRRVYDALNVLMAMNIISKE-KKEIKWIGL   81 (82)
T ss_dssp             EECHHHHHHHHHHHHHTCTTC-CGGGSH-HHHHHHHHHHHHHHHHHHHTTSBCCC-SSCEEBCCC
T ss_pred             cCcHHHHHHHHHHHHHhhccC-CCcchh-hcchhhhHHHHHHHHHHHHHhhhhhc-CceeEeecC
Confidence            346677777777777654332 111111 12344699999999999999999999 556999997

>d1sfxa_ a.4.5.50 (A:) Hypothetical protein AF2008 {Archaeoglobus fulgidus [TaxId: 2234]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: "Winged helix" DNA-binding domain
family: TrmB-like
domain: Hypothetical protein AF2008
species: Archaeoglobus fulgidus [TaxId: 2234]

Probab=94.60  E-value=0.02  Score=40.25  Aligned_cols=35  Identities=23%  Similarity=0.363  Sum_probs=32.5

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      +..+..++|+.+++.+..+|++++-|+.-|+|.|.
T Consensus        33 g~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~r~   67 (109)
T d1sfxa_          33 GGMRVSEIARELDLSARFVRDRLKVLLKRGFVRRE   67 (109)
T ss_dssp             CCBCHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHhCCCcchHHHHHHHHHhCCCEEEE
Confidence            35899999999999999999999999999999875

>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=91.72  E-value=0.078  Score=35.20  Aligned_cols=56  Identities=20%  Similarity=0.399  Sum_probs=44.9

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEecccc
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWKGFKA  177 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~G~~~  177 (191)
                      +.++++..++ ..+++.++|+.+++.+=.+|-+++.|+..|++++...+. ...|..-
T Consensus         9 ~IL~~~a~~~-~~~s~~eia~~~~~~~st~~rll~tL~~~g~l~~~~~g~-y~lG~~l   64 (75)
T d1mkma1           9 EILDFIVKNP-GDVSVSEIAEKFNMSVSNAYKYMVVLEEKGFVLRKKDKR-YVPGYKL   64 (75)
T ss_dssp             HHHHHHHHCS-SCBCHHHHHHHTTCCHHHHHHHHHHHHHTTSEEECTTSC-EEECTHH
T ss_pred             HHHHHHHhCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEECCCCC-EeecHHH
Confidence            3456665554 469999999999999999999999999999999985444 5567553

>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=90.80  E-value=0.081  Score=34.24  Aligned_cols=53  Identities=23%  Similarity=0.391  Sum_probs=41.1

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcc-eeecCCCceEEec
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGV-LTRRAKNKYTWKG  174 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgL-I~K~~Kn~y~W~G  174 (191)
                      +.++++.++ ...++.+++|+.|+|.+|-||-=++-|+..|+ |....+ -|.+.|
T Consensus        11 ~Il~~L~~~-~~~vs~~~La~~l~VS~~TI~rdi~~L~~~G~~I~~~~g-GY~L~~   64 (65)
T d1j5ya1          11 SIVRILERS-KEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPR-GYVLAG   64 (65)
T ss_dssp             HHHHHHHHC-SSCBCHHHHHHHHTSCHHHHHHHHHHHHHHTCCCEEETT-EEECCT
T ss_pred             HHHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEEeCC-CEEeCC
Confidence            345566554 35799999999999999999999999999997 666543 576544

>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=86.31  E-value=0.13  Score=34.83  Aligned_cols=44  Identities=11%  Similarity=0.237  Sum_probs=38.6

Q ss_pred             CceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceEEe
Q 045382          130 VESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYTWK  173 (191)
Q Consensus       130 ~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~W~  173 (191)
                      ++.++++++|+++|+...++.-+...|.++|++++.+.+.|.=.
T Consensus        32 ~gp~s~~eLA~~~g~~~~~l~rlLr~l~a~gl~~e~~~~~y~lt   75 (85)
T d1tw3a1          32 AGARTVKALAARTDTRPEALLRLIRHLVAIGLLEEDAPGEFVPT   75 (85)
T ss_dssp             TTCCBHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEEETTEEEEC
T ss_pred             cCCCCHHHHHHHhCcChhHHHHHHHHHHHCCCeEecCCCeEecC
Confidence            34689999999999999999999999999999998877766543

>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=86.26  E-value=0.33  Score=31.20  Aligned_cols=43  Identities=21%  Similarity=0.226  Sum_probs=36.5

Q ss_pred             HHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcce
Q 045382          118 CSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVL  162 (191)
Q Consensus       118 t~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI  162 (191)
                      ..+.++++++  +..++..++|+.|+|.++-||-=++.|+..|++
T Consensus         7 ~~~iL~~L~~--~~~~s~~eLa~~l~vS~~ti~r~i~~L~~~G~~   49 (63)
T d1biaa1           7 PLKLIALLAN--GEFHSGEQLGETLGMSRAAINKHIQTLRDWGVD   49 (63)
T ss_dssp             HHHHHHHHTT--SSCBCHHHHHHHHTSCHHHHHHHHHHHHHTTCC
T ss_pred             HHHHHHHHHH--CCcCCHHHHHHHHCcCHHHHHHHHHHHHHCCCc
Confidence            3466777755  356999999999999999999999999999983

>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=85.94  E-value=0.13  Score=35.72  Aligned_cols=41  Identities=22%  Similarity=0.223  Sum_probs=36.1

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCceE
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKYT  171 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y~  171 (191)
                      +..++.++|.++++..++++-+...|.++|++++...+.+.
T Consensus        39 gp~t~~eLA~~~g~~~~~l~rLlr~L~a~gll~~~~d~~~~   79 (92)
T d1qzza1          39 GADTLAGLADRTDTHPQALSRLVRHLTVVGVLEGGEKQGRP   79 (92)
T ss_dssp             TCCSHHHHHHHHTCCHHHHHHHHHHHHHTTSEECCCC-CCC
T ss_pred             CCCCHHHHHHHHCcCchHHHHHHHHHHHCCCeeeecCCCce
Confidence            46899999999999999999999999999999998665443

>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=85.12  E-value=0.39  Score=31.10  Aligned_cols=56  Identities=14%  Similarity=0.263  Sum_probs=50.7

Q ss_pred             HHHHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeecCCCce
Q 045382          115 GLLCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRRAKNKY  170 (191)
Q Consensus       115 ~~Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~~Kn~y  170 (191)
                      ..+.++....|.+.+-.+-++.++|+.+|+.-..+=++++.|-..|.+.|...+.|
T Consensus         6 ~~l~~~I~~~~~~~g~~PP~vrdl~~~l~~~e~~~~~lL~~l~~~G~lvkI~~d~y   61 (64)
T d1lvaa3           6 KKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFY   61 (64)
T ss_dssp             HHHHHHHHHHHHHHTTSCCBHHHHHHHTTCCHHHHHHHHHHHHHTTSEEESSSSBE
T ss_pred             HHHHHHHHHHHHHcCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeccccc
Confidence            45678888889888888899999999999999999999999999999999988876

>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=84.90  E-value=0.3  Score=34.64  Aligned_cols=48  Identities=10%  Similarity=0.240  Sum_probs=39.0

Q ss_pred             HHHHHHHHHhhCCCceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          117 LCSNFLSLYNRDGVESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       117 Lt~kFI~l~~~~~~~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      ..-+.+.++..++ ..+++.++|+.+|+.|=.+|=+++.|+..|+|.+.
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            3444555554444 35999999999999999999999999999999865

>d1jhfa1 a.4.5.2 (A:2-72) LexA repressor, N-terminal DNA-binding domain {Escherichia coli [TaxId: 562]}

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

Probab=81.63  E-value=0.27  Score=32.41  Aligned_cols=47  Identities=13%  Similarity=0.106  Sum_probs=38.3

Q ss_pred             HHHHHHhhCCCceecHHHHHHHhCCe-eeEeeehhhHhhhhcceeecC
Q 045382          120 NFLSLYNRDGVESIGLDDAASKLGVE-RRRIYDIVNVLESVGVLTRRA  166 (191)
Q Consensus       120 kFI~l~~~~~~~~i~L~~aA~~L~V~-rRRIYDIiNVLEslgLI~K~~  166 (191)
                      .||.-+....+..-++.++|+.+|+. .--+++.++.||.-|+|++..
T Consensus        12 ~~I~~~~~~~G~~Ps~rei~~~~g~~S~stv~~~l~~Le~kG~I~r~~   59 (71)
T d1jhfa1          12 DLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVS   59 (71)
T ss_dssp             HHHHHHHHHHSSCCCHHHHHHHTTCSSHHHHHHHHHHHHHTTSEEECS
T ss_pred             HHHHHHHHHhCCCCCHHHHHHHcCCCCHHHHHHHHHHHHHCcCeecCC
Confidence            45555544456678999999999995 667999999999999999973

>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=80.78  E-value=1.4  Score=29.93  Aligned_cols=35  Identities=14%  Similarity=0.309  Sum_probs=32.6

Q ss_pred             ceecHHHHHHHhCCeeeEeeehhhHhhhhcceeec
Q 045382          131 ESIGLDDAASKLGVERRRIYDIVNVLESVGVLTRR  165 (191)
Q Consensus       131 ~~i~L~~aA~~L~V~rRRIYDIiNVLEslgLI~K~  165 (191)
                      +.+++.++|+.+++.+--+.-+++-|+.-|+|.+.
T Consensus        35 ~~~t~~eLa~~~~i~~~tvs~~l~~L~~~GlV~r~   69 (109)
T d2d1ha1          35 KPITSEELADIFKLSKTTVENSLKKLIELGLVVRT   69 (109)
T ss_dssp             SCEEHHHHHHHHTCCHHHHHHHHHHHHHTTSEEEE
T ss_pred             CCCCHHHHHHHHCccHhHHHHHHHHHHHCCCEEEe
Confidence            35899999999999999999999999999999765