Query 036653
Match_columns 487
No_of_seqs 339 out of 1152
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 04:11:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036653.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036653hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03106 WRKY: WRKY DNA -bindi 100.0 1.7E-30 3.6E-35 205.9 2.8 59 348-406 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 2.3E-29 5.1E-34 199.1 5.2 58 348-405 1-59 (59)
3 PF03106 WRKY: WRKY DNA -bindi 100.0 3E-29 6.6E-34 198.7 4.8 59 173-231 1-60 (60)
4 smart00774 WRKY DNA binding do 99.9 3.2E-28 6.9E-33 192.7 4.6 57 173-229 1-59 (59)
5 PF04500 FLYWCH: FLYWCH zinc f 92.3 0.092 2E-06 39.8 2.0 49 347-405 11-62 (62)
6 PF04500 FLYWCH: FLYWCH zinc f 91.7 0.17 3.7E-06 38.3 2.9 48 173-229 12-62 (62)
7 PF03101 FAR1: FAR1 DNA-bindin 88.1 0.59 1.3E-05 38.5 3.6 29 203-231 61-89 (91)
8 PF03101 FAR1: FAR1 DNA-bindin 85.2 0.7 1.5E-05 38.1 2.5 30 377-407 60-89 (91)
9 PF09026 CENP-B_dimeris: Centr 74.5 0.98 2.1E-05 40.1 0.0 8 32-39 31-38 (101)
10 PTZ00415 transmission-blocking 60.8 3.1 6.6E-05 51.9 0.3 14 472-485 766-779 (2849)
11 KOG1832 HIV-1 Vpr-binding prot 55.2 4.7 0.0001 47.7 0.6 29 10-38 1399-1427(1516)
12 PF03859 CG-1: CG-1 domain; I 30.2 96 0.0021 28.6 4.7 75 327-401 30-116 (118)
13 cd07691 Ig_CD3_gamma_delta Imm 24.4 89 0.0019 26.3 3.2 29 174-203 16-54 (69)
14 PTZ00415 transmission-blocking 24.2 25 0.00054 44.6 -0.1 27 19-45 154-180 (2849)
15 PLN03097 FHY3 Protein FAR-RED 22.8 85 0.0018 37.3 3.8 34 199-232 156-189 (846)
16 PLN03097 FHY3 Protein FAR-RED 21.6 94 0.002 36.9 3.9 35 374-409 156-190 (846)
No 1
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=99.96 E-value=1.7e-30 Score=205.93 Aligned_cols=59 Identities=56% Similarity=1.216 Sum_probs=52.6
Q ss_pred cCCCcccccccccccCCCCCCCcccccccCCCCccceeeeccCCCCeEEEEEeeeccCC
Q 036653 348 SGDGYRWRKYGQKMVKGNPNPRNYYRCTSAGCPVRKHIETAVDNTSAVIITYKGVHDHD 406 (487)
Q Consensus 348 ~dDGy~WRKYGQK~vkgn~~pRsYYrCt~~gC~arK~Ver~~~d~~~~~~tY~G~HnH~ 406 (487)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+|+|||+|.|||+
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 58999999999999999999999999999999999999999999999999999999996
No 2
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=99.95 E-value=2.3e-29 Score=199.12 Aligned_cols=58 Identities=55% Similarity=1.167 Sum_probs=56.5
Q ss_pred cCCCcccccccccccCCCCCCCccccccc-CCCCccceeeeccCCCCeEEEEEeeeccC
Q 036653 348 SGDGYRWRKYGQKMVKGNPNPRNYYRCTS-AGCPVRKHIETAVDNTSAVIITYKGVHDH 405 (487)
Q Consensus 348 ~dDGy~WRKYGQK~vkgn~~pRsYYrCt~-~gC~arK~Ver~~~d~~~~~~tY~G~HnH 405 (487)
++|||+|||||||.|+|+++||+||||++ +||+|+|+|||+.+|+.+++|||+|.|||
T Consensus 1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCcccccccCcEecCCCcCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 47999999999999999999999999999 89999999999999999999999999998
No 3
>PF03106 WRKY: WRKY DNA -binding domain; InterPro: IPR003657 The WRKY domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger- like motif. The WRKY domain is found in one or two copies in a superfamily of plant transcription factors involved in the regulation of various physiological programs that are unique to plants, including pathogen defence, senescence, trichome development and the biosynthesis of secondary metabolites. The WRKY domain binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core of the W box is essential for function and WRKY binding []. Some proteins known to contain a WRKY domain include Arabidopsis thaliana ZAP1 (Zinc-dependent Activator Protein-1) and AtWRKY44/TTG2, a protein involved in trichome development and anthocyanin pigmentation; and wild oat ABF1-2, two proteins involved in the gibberelic acid-induced expression of the alpha-Amy2 gene. Structural studies indicate that this domain is a four-stranded beta-sheet with a zinc binding pocket, forming a novel zinc and DNA binding structure []. The WRKYGQK residues correspond to the most N-terminal beta-strand, which enables extensive hydrophobic interactions, contributing to the structural stability of the beta-sheet.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2AYD_A 1WJ2_A 2LEX_A.
Probab=99.95 E-value=3e-29 Score=198.74 Aligned_cols=59 Identities=42% Similarity=0.847 Sum_probs=49.5
Q ss_pred CCCccccccccccccCCCCCCCceeeeeeCCeeeee-eEecCCCCcEEEEEeecCCCCCC
Q 036653 173 VSDGYNWRKYGQKQVKSPKGSRSYYKCTYSDCCAKK-IECSDHSGHVIEIVNKGMHSHDP 231 (487)
Q Consensus 173 ~~DGy~WRKYGQK~vkgs~~pRsYYrCt~~~C~akK-~~~~~~dg~~~~i~Y~G~HnH~~ 231 (487)
++|||+|||||||.|+|+++|||||||++.+|+|+| |++...|+.+++|+|+|+|||++
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k 60 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHPK 60 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence 589999999999999999999999999999999998 56666799999999999999974
No 4
>smart00774 WRKY DNA binding domain. The WRKY domain is a DNA binding domain found in one or two copies in a superfamily of plant transcription factors. These transcription factors are involved in the regulation of various physiological programs that are unique to plants, including pathogen defense, senescence and trichome development. The domain is a 60 amino acid region that is defined by the conserved amino acid sequence WRKYGQK at its N-terminal end, together with a novel zinc-finger-like motif. It binds specifically to the DNA sequence motif (T)(T)TGAC(C/T), which is known as the W box. The invariant TGAC core is essential for function and WRKY binding.
Probab=99.94 E-value=3.2e-28 Score=192.66 Aligned_cols=57 Identities=51% Similarity=0.987 Sum_probs=53.6
Q ss_pred CCCccccccccccccCCCCCCCceeeeee-CCeeeee-eEecCCCCcEEEEEeecCCCC
Q 036653 173 VSDGYNWRKYGQKQVKSPKGSRSYYKCTY-SDCCAKK-IECSDHSGHVIEIVNKGMHSH 229 (487)
Q Consensus 173 ~~DGy~WRKYGQK~vkgs~~pRsYYrCt~-~~C~akK-~~~~~~dg~~~~i~Y~G~HnH 229 (487)
++|||+|||||||.|+|+++||+|||||+ .+|+|+| |++.+.||.+++|+|+|+|||
T Consensus 1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCcccccccCcEecCCCcCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 48999999999999999999999999999 8999988 666667999999999999998
No 5
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=92.28 E-value=0.092 Score=39.79 Aligned_cols=49 Identities=27% Similarity=0.650 Sum_probs=26.2
Q ss_pred ccCCCcccccccccccCCCCCCCcccccccC---CCCccceeeeccCCCCeEEEEEeeeccC
Q 036653 347 ISGDGYRWRKYGQKMVKGNPNPRNYYRCTSA---GCPVRKHIETAVDNTSAVIITYKGVHDH 405 (487)
Q Consensus 347 ~~dDGy~WRKYGQK~vkgn~~pRsYYrCt~~---gC~arK~Ver~~~d~~~~~~tY~G~HnH 405 (487)
++-|||.-+++... ....|++|+.. +|+|+=.+. . +.. .++...+.|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~-~~~-~~~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--A-GDG-RVVRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TT-EEEE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--C-CCC-EEEECCCccCC
Confidence 44599998776555 45789999953 899999995 2 232 44555599999
No 6
>PF04500 FLYWCH: FLYWCH zinc finger domain; InterPro: IPR007588 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a potential FLYWCH Zn-finger domain found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH where X indicates any amino acid. This domain was first characterised in Drosophila Modifier of mdg4 proteins, Mod(mgd4), putative chromatin modulators involved in higher order chromatin domains. Mod(mdg4) proteins share a common N-terminal BTB/POZ domain, but differ in their C-terminal region, most containing C-terminal FLYWCH zinc finger motifs []. The FLYWCH domain in Mod(mdg4) proteins has a putative role in protein-protein interactions; for example, Mod(mdg4)-67.2 interacts with DNA-binding protein Su(Hw) via its FLYWCH domain. FLYWCH domains have been described in other proteins as well, including suppressor of killer of prune, Su(Kpn), which contains 4 terminal FLYWCH zinc finger motifs in a tandem array and a C-terminal glutathione SH-transferase (GST) domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2RPR_A.
Probab=91.70 E-value=0.17 Score=38.33 Aligned_cols=48 Identities=27% Similarity=0.622 Sum_probs=24.9
Q ss_pred CCCccccccccccccCCCCCCCceeeeeeC---CeeeeeeEecCCCCcEEEEEeecCCCC
Q 036653 173 VSDGYNWRKYGQKQVKSPKGSRSYYKCTYS---DCCAKKIECSDHSGHVIEIVNKGMHSH 229 (487)
Q Consensus 173 ~~DGy~WRKYGQK~vkgs~~pRsYYrCt~~---~C~akK~~~~~~dg~~~~i~Y~G~HnH 229 (487)
.-|||.-+++... ..+.|+||+.. +|.|+=+.. ..++ .+ +...++|||
T Consensus 12 ~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~-~~~~-~~-~~~~~~HnH 62 (62)
T PF04500_consen 12 VYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD-AGDG-RV-VRTNGEHNH 62 (62)
T ss_dssp EETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE---TT-EE-EE-S---SS
T ss_pred EECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE-CCCC-EE-EECCCccCC
Confidence 4688887776655 66789999987 799986554 3333 33 344599999
No 7
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=88.10 E-value=0.59 Score=38.51 Aligned_cols=29 Identities=17% Similarity=0.029 Sum_probs=23.0
Q ss_pred CeeeeeeEecCCCCcEEEEEeecCCCCCC
Q 036653 203 DCCAKKIECSDHSGHVIEIVNKGMHSHDP 231 (487)
Q Consensus 203 ~C~akK~~~~~~dg~~~~i~Y~G~HnH~~ 231 (487)
+|+|+=.+....+|....+.+..+|||+.
T Consensus 61 gC~a~i~v~~~~~~~w~v~~~~~~HNH~L 89 (91)
T PF03101_consen 61 GCKARINVKRRKDGKWRVTSFVLEHNHPL 89 (91)
T ss_pred CCCEEEEEEEccCCEEEEEECcCCcCCCC
Confidence 79987544444489988899999999974
No 8
>PF03101 FAR1: FAR1 DNA-binding domain; InterPro: IPR004330 Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. It has been found that the proteins governing this response, which include FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), are a pair of homologous proteins sharing significant sequence homology to mutator-like transposases. These proteins appear to be novel transcription factors, which are essential for activating the expression of FHY1 and FHL (for FHY1-like) and related genes, whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses in plants. The FRS (FAR1 Related Sequences) family of proteins share a similar domain structure to mutator-like transposases, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). It seems plausible that the FRS family represent transcription factors derived from mutator-like transposases [, ]. This entry represents a domain found in FAR1 and FRS proteins. It contains a WRKY like fold and is therefore most likely a zinc binding DNA-binding domain.
Probab=85.17 E-value=0.7 Score=38.08 Aligned_cols=30 Identities=17% Similarity=0.410 Sum_probs=25.8
Q ss_pred CCCCccceeeeccCCCCeEEEEEeeeccCCC
Q 036653 377 AGCPVRKHIETAVDNTSAVIITYKGVHDHDM 407 (487)
Q Consensus 377 ~gC~arK~Ver~~~d~~~~~~tY~G~HnH~~ 407 (487)
.||+|+=.|-+.. +..-.++.+...|||++
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L 89 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPL 89 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCC
Confidence 6999999998876 55678889999999975
No 9
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=74.55 E-value=0.98 Score=40.09 Aligned_cols=8 Identities=50% Similarity=0.593 Sum_probs=0.0
Q ss_pred ccChhhhh
Q 036653 32 ILDDEEED 39 (487)
Q Consensus 32 ~~~~~~~~ 39 (487)
|+||++|+
T Consensus 31 Dddddee~ 38 (101)
T PF09026_consen 31 DDDDDEEE 38 (101)
T ss_dssp --------
T ss_pred cccccccc
Confidence 33333333
No 10
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=60.82 E-value=3.1 Score=51.86 Aligned_cols=14 Identities=36% Similarity=0.562 Sum_probs=8.0
Q ss_pred hhhhhhhhcceeec
Q 036653 472 ESARTLLSIGFEIK 485 (487)
Q Consensus 472 esartl~si~~~~~ 485 (487)
.|.+.+++|-|-|-
T Consensus 766 ~s~~d~~~l~fqvP 779 (2849)
T PTZ00415 766 GSDEDLFSLQFQIP 779 (2849)
T ss_pred CCCCCeEEEEEecC
Confidence 45566666666553
No 11
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=55.23 E-value=4.7 Score=47.69 Aligned_cols=29 Identities=34% Similarity=0.633 Sum_probs=15.5
Q ss_pred hhhccCCCCCchhhhhhhhhhhccChhhh
Q 036653 10 RKRHENPQNDEFEEEEEEEDEEILDDEEE 38 (487)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (487)
|.|-..+.||+++++|+|+.+||+|+|++
T Consensus 1399 R~r~~~dd~DeeeD~e~Ed~dEddd~edd 1427 (1516)
T KOG1832|consen 1399 RRRPTDDDSDEEEDDETEDEDEDDDEEDD 1427 (1516)
T ss_pred ccCCCccccCccccchhhccccccccccc
Confidence 44444566666666555555554444443
No 12
>PF03859 CG-1: CG-1 domain; InterPro: IPR005559 CG-1 domains are highly conserved domains of about 130 amino-acid residues containing a predicted bipartite NLS and named after a partial cDNA clone isolated from parsley encoding a sequence-specific DNA-binding protein []. CG-1 domains are associated with CAMTA proteins (for CAlModulin -binding Transcription Activator) that are transcription factors containing a calmodulin-binding domain and ankyrins [].; GO: 0005516 calmodulin binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=30.16 E-value=96 Score=28.62 Aligned_cols=75 Identities=20% Similarity=0.241 Sum_probs=37.0
Q ss_pred CCCCCCCCCceEEeecCCccccCCCccccc-cccccc---------CCCCCCCcccccccCCCCccceeeeccCCC--Ce
Q 036653 327 SFLKPGKKPKFVVHAAGDVGISGDGYRWRK-YGQKMV---------KGNPNPRNYYRCTSAGCPVRKHIETAVDNT--SA 394 (487)
Q Consensus 327 ~~~k~~~~~~~vv~t~sd~~~~dDGy~WRK-YGQK~v---------kgn~~pRsYYrCt~~gC~arK~Ver~~~d~--~~ 394 (487)
++.+|..+.-++.-..-....-.|||.||| =+-|.| .|....-+||-=+..+=.+...+=+--+.+ .+
T Consensus 30 ~~~rP~sGslfLf~Rk~~r~fRkDG~~WrKkkdgktvRE~HekLKv~~~e~l~~~Yah~~~~~~F~RR~Ywll~~~~~~i 109 (118)
T PF03859_consen 30 PPNRPPSGSLFLFNRKVVRFFRKDGHNWRKKKDGKTVREDHEKLKVGGVEVLNCYYAHSEDNPTFHRRCYWLLDPPYEHI 109 (118)
T ss_pred CCCCCCCceEEEEEchHhhhhhcccceeEEcCCCCchhhhhhhhccCceeeeEEEEEeeccCCCeeeEEEEccCCCCceE
Confidence 345555555555544333335689999995 233322 333444455543333333333333334433 46
Q ss_pred EEEEEee
Q 036653 395 VIITYKG 401 (487)
Q Consensus 395 ~~~tY~G 401 (487)
+.|.|.-
T Consensus 110 VLVHY~~ 116 (118)
T PF03859_consen 110 VLVHYLD 116 (118)
T ss_pred EEEEeee
Confidence 6666643
No 13
>cd07691 Ig_CD3_gamma_delta Immunoglobulin (Ig)-like domain of CD3 gamma and delta chains. Ig_CD3_gamma_delta; immunoglobulin (Ig)-like domain of CD3 gamma and delta chains. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signalling once the TCR has bound an MHC/antigen complex.
Probab=24.41 E-value=89 Score=26.32 Aligned_cols=29 Identities=24% Similarity=0.642 Sum_probs=20.3
Q ss_pred CCccccccccccccC--------C--CCCCCceeeeeeCC
Q 036653 174 SDGYNWRKYGQKQVK--------S--PKGSRSYYKCTYSD 203 (487)
Q Consensus 174 ~DGy~WRKYGQK~vk--------g--s~~pRsYYrCt~~~ 203 (487)
+.-+.|-| |-..+. | ..-||+-|+|.-.+
T Consensus 16 ~tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~~s~ 54 (69)
T cd07691 16 ATNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCKESE 54 (69)
T ss_pred CCcEEEec-CcccccccccEEeccCcccCCCcceEecCcc
Confidence 35589999 764442 2 27899999995543
No 14
>PTZ00415 transmission-blocking target antigen s230; Provisional
Probab=24.19 E-value=25 Score=44.60 Aligned_cols=27 Identities=41% Similarity=0.735 Sum_probs=11.3
Q ss_pred CchhhhhhhhhhhccChhhhhhcccCC
Q 036653 19 DEFEEEEEEEDEEILDDEEEDEGASQL 45 (487)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 45 (487)
|+++++|+|++++++|||||+|++.|+
T Consensus 154 d~~~~~~~~~~~~~~~~~e~~~~~~~~ 180 (2849)
T PTZ00415 154 DDDDEDEDEDDDDEEDDEEEEEEEEEI 180 (2849)
T ss_pred CCccccccccccccccccccccccccc
Confidence 444444444444444444444444433
No 15
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=22.85 E-value=85 Score=37.26 Aligned_cols=34 Identities=21% Similarity=0.226 Sum_probs=28.8
Q ss_pred eeeCCeeeeeeEecCCCCcEEEEEeecCCCCCCC
Q 036653 199 CTYSDCCAKKIECSDHSGHVIEIVNKGMHSHDPP 232 (487)
Q Consensus 199 Ct~~~C~akK~~~~~~dg~~~~i~Y~G~HnH~~p 232 (487)
|+.-+|+|+=.+....+|....+-+..+|||+.-
T Consensus 156 ~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~ 189 (846)
T PLN03097 156 CAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELL 189 (846)
T ss_pred ccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCC
Confidence 7888999987666678899988999999999853
No 16
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=21.63 E-value=94 Score=36.91 Aligned_cols=35 Identities=23% Similarity=0.504 Sum_probs=29.4
Q ss_pred cccCCCCccceeeeccCCCCeEEEEEeeeccCCCCC
Q 036653 374 CTSAGCPVRKHIETAVDNTSAVIITYKGVHDHDMPV 409 (487)
Q Consensus 374 Ct~~gC~arK~Ver~~~d~~~~~~tY~G~HnH~~P~ 409 (487)
|+..||+|+=.|.+..+ ..-+++-+...|||+.-+
T Consensus 156 ~tRtGC~A~m~Vk~~~~-gkW~V~~fv~eHNH~L~p 190 (846)
T PLN03097 156 CAKTDCKASMHVKRRPD-GKWVIHSFVKEHNHELLP 190 (846)
T ss_pred ccCCCCceEEEEEEcCC-CeEEEEEEecCCCCCCCC
Confidence 78889999999988554 468899999999998743
Done!