Query 020291
Match_columns 328
No_of_seqs 208 out of 649
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:34:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020291.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020291hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00774 WRKY DNA binding do 100.0 9.4E-31 2E-35 197.0 2.9 59 140-200 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 1E-30 2.2E-35 197.3 0.7 59 140-201 1-59 (60)
3 PF04500 FLYWCH: FLYWCH zinc f 90.5 0.068 1.5E-06 38.5 -0.3 52 139-200 11-62 (62)
4 PF10533 Plant_zn_clust: Plant 32.5 25 0.00054 25.9 1.1 21 117-137 19-39 (47)
5 PF09966 DUF2200: Uncharacteri 32.2 30 0.00064 29.7 1.7 18 22-39 94-111 (111)
6 PF02268 TFIIA_gamma_N: Transc 22.9 1.6E+02 0.0035 21.8 4.0 35 30-74 11-45 (49)
7 PF07216 LcrG: LcrG protein; 22.5 82 0.0018 26.3 2.6 45 19-67 22-67 (93)
8 PF04699 P16-Arc: ARP2/3 compl 20.0 1.4E+02 0.0031 26.7 3.9 52 19-71 37-88 (152)
9 PF03101 FAR1: FAR1 DNA-bindin 19.9 43 0.00093 25.9 0.5 30 172-202 60-89 (91)
10 COG0783 Dps DNA-binding ferrit 18.9 3.5E+02 0.0076 24.3 6.1 54 20-78 99-153 (156)
No 1
>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=99.96 E-value=9.4e-31 Score=196.96 Aligned_cols=59 Identities=58% Similarity=1.044 Sum_probs=57.2
Q ss_pred CCCChhhhhhccccccCCCCCcccccccCCCCcCChhhhhhhhhcCCCCeEEEEEeccCCC
Q 020291 140 TDDGHAWRKYGQKVILNARFPRNYFRCTHKFDQGCQASKQVQRIQEEPPLHRTTYYGRHTC 200 (328)
Q Consensus 140 ~~Dg~~WRKYGQK~I~~s~~pRsYyrCt~~~~~gC~A~KqVqr~~~dp~~~~vtY~G~Htc 200 (328)
++|||.|||||||.|+|+++||+|||||+ ++||+|+|+|||+.+||.++.|||+|+|||
T Consensus 1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~--~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTY--SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCcccccccCcEecCCCcCcceEEeccc--cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 47999999999999999999999999999 689999999999999999999999999998
No 2
>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=1e-30 Score=197.28 Aligned_cols=59 Identities=53% Similarity=0.988 Sum_probs=52.1
Q ss_pred CCCChhhhhhccccccCCCCCcccccccCCCCcCChhhhhhhhhcCCCCeEEEEEeccCCCC
Q 020291 140 TDDGHAWRKYGQKVILNARFPRNYFRCTHKFDQGCQASKQVQRIQEEPPLHRTTYYGRHTCK 201 (328)
Q Consensus 140 ~~Dg~~WRKYGQK~I~~s~~pRsYyrCt~~~~~gC~A~KqVqr~~~dp~~~~vtY~G~Htc~ 201 (328)
++|||+|||||||.|+|++|||+||||++ .+|+|+|+|||+.+||.++.|||+|+|||.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~---~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTH---PGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEEC---TTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccc---cChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 48999999999999999999999999999 599999999999999999999999999996
No 3
>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=90.49 E-value=0.068 Score=38.46 Aligned_cols=52 Identities=21% Similarity=0.402 Sum_probs=27.3
Q ss_pred cCCCChhhhhhccccccCCCCCcccccccCCCCcCChhhhhhhhhcCCCCeEEEEEeccCCC
Q 020291 139 LTDDGHAWRKYGQKVILNARFPRNYFRCTHKFDQGCQASKQVQRIQEEPPLHRTTYYGRHTC 200 (328)
Q Consensus 139 ~~~Dg~~WRKYGQK~I~~s~~pRsYyrCt~~~~~gC~A~KqVqr~~~dp~~~~vtY~G~Htc 200 (328)
+.-|||.-+++... ..+.|+||+.+...+|+|+-.+. .++. ..+...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 45688877665544 34689999998878999987776 3333 33444488987
No 4
>PF10533 Plant_zn_clust: Plant zinc cluster domain; InterPro: IPR018872 This zinc binding domain is found associated with the WRKY domain IPR003657 from INTERPRO [].
Probab=32.46 E-value=25 Score=25.90 Aligned_cols=21 Identities=29% Similarity=0.329 Sum_probs=16.5
Q ss_pred cCccccccccccCcceeeccc
Q 020291 117 KDRRGCYKRRKCAESWTEHSS 137 (328)
Q Consensus 117 k~r~~~~krrk~~~~~~~~t~ 137 (328)
..|++|.||||....++...+
T Consensus 19 sgrCHCsKkRK~RvKR~irVP 39 (47)
T PF10533_consen 19 SGRCHCSKKRKSRVKRTIRVP 39 (47)
T ss_pred CCcccCCCcccccceeeEEee
Confidence 568999999999888765443
No 5
>PF09966 DUF2200: Uncharacterized protein conserved in bacteria (DUF2200); InterPro: IPR014580 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3C9P_A.
Probab=32.20 E-value=30 Score=29.69 Aligned_cols=18 Identities=39% Similarity=0.632 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 020291 22 RRAIEELIKGQEMALQLR 39 (328)
Q Consensus 22 ~~vi~EL~rGrelA~QL~ 39 (328)
.++|+||++|+-+.+-||
T Consensus 94 DKLVDELAKGK~mekIlR 111 (111)
T PF09966_consen 94 DKLVDELAKGKAMEKILR 111 (111)
T ss_dssp HHHHHHHHTT--HHHHH-
T ss_pred HHHHHHHHcCCcHHhhcC
Confidence 489999999999988775
No 6
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=22.93 E-value=1.6e+02 Score=21.75 Aligned_cols=35 Identities=26% Similarity=0.426 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhccCCCCCCCchhhhHHHHHHHHHHHhHHHHHH
Q 020291 30 KGQEMALQLRNLIHTSTKKGEGSKAMIINQDLVANILSSFTNSLS 74 (328)
Q Consensus 30 rGrelA~QL~~lL~~~~~~~~~~~a~~~a~~Lv~~IL~Sfs~aLs 74 (328)
=|..|..-|.+++... ....+|+.+||..|++++.
T Consensus 11 lG~aL~dtLDeli~~~----------~I~p~La~kVL~~FDksi~ 45 (49)
T PF02268_consen 11 LGIALTDTLDELIQEG----------KITPQLAMKVLEQFDKSIN 45 (49)
T ss_dssp HHHHHHHHHHHHHHTT----------SS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcC----------CCCHHHHHHHHHHHHHHHH
Confidence 3777778888887642 1234799999999999986
No 7
>PF07216 LcrG: LcrG protein; InterPro: IPR009863 This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops []. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the prot ein is believed to make a 1:1 complex with PcrV (LcrV) []. Mutations in LcrG cause premature secretion of effector proteins into the medium [].
Probab=22.48 E-value=82 Score=26.27 Aligned_cols=45 Identities=18% Similarity=0.305 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCchhhhHH-HHHHHHHHH
Q 020291 19 SDRRRAIEELIKGQEMALQLRNLIHTSTKKGEGSKAMIIN-QDLVANILS 67 (328)
Q Consensus 19 s~~~~vi~EL~rGrelA~QL~~lL~~~~~~~~~~~a~~~a-~~Lv~~IL~ 67 (328)
.+|..+.+||..|..+.-+--.+|-...+.. ....| ++|+.+|-+
T Consensus 22 d~R~~llqEm~~gLg~~p~ag~lLf~~~~~~----~~k~AEqELL~Ei~R 67 (93)
T PF07216_consen 22 DHRNDLLQEMLEGLGLGPVAGELLFGGSSPE----LMKQAEQELLEEIQR 67 (93)
T ss_pred HHHHHHHHHHHHhcCCChhHHHHHhcCCCHH----HHHHHHHHHHHHHHH
Confidence 4566788999998888877777776542211 11222 367777755
No 8
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=20.00 E-value=1.4e+02 Score=26.69 Aligned_cols=52 Identities=12% Similarity=0.206 Sum_probs=34.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHhhccCCCCCCCchhhhHHHHHHHHHHHhHHH
Q 020291 19 SDRRRAIEELIKGQEMALQLRNLIHTSTKKGEGSKAMIINQDLVANILSSFTN 71 (328)
Q Consensus 19 s~~~~vi~EL~rGrelA~QL~~lL~~~~~~~~~~~a~~~a~~Lv~~IL~Sfs~ 71 (328)
..+..-|+-|+++-.++.-|+..|..+|-.... ..-..+..+|-++|.+|..
T Consensus 37 ~~~~~qvr~ll~~g~~~~ALk~aL~npP~~~k~-~~K~~~~~~Vl~vL~s~k~ 88 (152)
T PF04699_consen 37 QPKEQQVRQLLSSGDNEEALKAALENPPYGSKD-AVKDRALQLVLEVLTSIKS 88 (152)
T ss_dssp GGTHHHHHHHHHCT-HHHHHHHHTSS--TT-S--HHHHHHHHHHHHHHHCS-G
T ss_pred chhHHHHHHHHhCCCHHHHHHHhccCCCcCCCc-chHHHHHHHHHHHHHHccH
Confidence 456677888888779999999999877543322 3345567788888888755
No 9
>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=19.95 E-value=43 Score=25.92 Aligned_cols=30 Identities=23% Similarity=0.379 Sum_probs=24.2
Q ss_pred cCChhhhhhhhhcCCCCeEEEEEeccCCCCC
Q 020291 172 QGCQASKQVQRIQEEPPLHRTTYYGRHTCKS 202 (328)
Q Consensus 172 ~gC~A~KqVqr~~~dp~~~~vtY~G~Htc~~ 202 (328)
.||+|.=.|-+.. +.....+.+..+|+|.-
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 6999998888766 55567778999999974
No 10
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=18.86 E-value=3.5e+02 Score=24.30 Aligned_cols=54 Identities=24% Similarity=0.443 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHH-HHHHHHHhhccCCCCCCCchhhhHHHHHHHHHHHhHHHHHHHHcC
Q 020291 20 DRRRAIEELIKGQE-MALQLRNLIHTSTKKGEGSKAMIINQDLVANILSSFTNSLSILKN 78 (328)
Q Consensus 20 ~~~~vi~EL~rGre-lA~QL~~lL~~~~~~~~~~~a~~~a~~Lv~~IL~Sfs~aLsiL~~ 78 (328)
.-+..|++|+++.+ +++.+|..+.-....+ -....+|+.++++.+++.+=+|.+
T Consensus 99 ~~~~~l~~l~~~~~~l~~~~r~~~~~a~e~g-----D~~Tadl~~~~~~~~EK~~Wml~a 153 (156)
T COG0783 99 TAREMLKELVEDYEYLIKELRKGIELADEAG-----DEVTADLLTDIIRELEKTLWMLRA 153 (156)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC-----ChhHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999998874 5667888776543322 234568999999999999988863
Done!