Query 017895
Match_columns 364
No_of_seqs 196 out of 658
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 04:22:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017895hhsearch_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 1.3E-30 2.8E-35 199.2 4.6 59 127-187 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 1.6E-30 3.5E-35 199.0 2.9 59 127-188 1-59 (60)
3 PF04500 FLYWCH: FLYWCH zinc f 93.4 0.051 1.1E-06 39.7 1.9 52 126-187 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 32.2 34 0.00073 26.9 2.0 29 159-188 60-88 (91)
5 PF02268 TFIIA_gamma_N: Transc 28.7 1.1E+02 0.0024 23.0 4.1 36 19-57 11-46 (49)
6 PF08289 Flu_M1_C: Influenza M 21.4 1.7E+02 0.0038 24.7 4.3 39 19-58 44-90 (95)
7 PF03859 CG-1: CG-1 domain; I 20.9 36 0.00077 30.1 0.2 8 128-135 52-59 (118)
8 COG1722 XseB Exonuclease VII s 17.4 2.4E+02 0.0051 23.2 4.3 22 11-32 34-55 (81)
9 cd00238 ERp29c ERp29 and ERp38 15.6 2.7E+02 0.0059 23.1 4.3 39 13-51 47-93 (93)
10 PF07216 LcrG: LcrG protein; 15.1 2E+02 0.0043 24.5 3.3 41 9-49 23-67 (93)
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=1.3e-30 Score=199.20 Aligned_cols=59 Identities=71% Similarity=1.236 Sum_probs=57.1
Q ss_pred cCCCccccccCccccCCCCCCccceeeccCCCCCCcccccccccCCCCCeEEEEeeccCCC
Q 017895 127 LDDGYCWRKYGQKDILGRNFPRGYYRCTHRHARGCLATKQVQRSDDDPSMFEVTYRGRHKC 187 (364)
Q Consensus 127 ~dDGy~WRKYGQK~I~gs~~PRsYYRCt~~~~~gC~A~KqVQr~~~dp~~~~vtY~G~Htc 187 (364)
++|||.|||||||.|+|+++||+|||||+ ++||+|+|+|||+++||.+++|||+|+|||
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=1.6e-30 Score=199.04 Aligned_cols=59 Identities=66% Similarity=1.222 Sum_probs=52.1
Q ss_pred cCCCccccccCccccCCCCCCccceeeccCCCCCCcccccccccCCCCCeEEEEeeccCCCC
Q 017895 127 LDDGYCWRKYGQKDILGRNFPRGYYRCTHRHARGCLATKQVQRSDDDPSMFEVTYRGRHKCS 188 (364)
Q Consensus 127 ~dDGy~WRKYGQK~I~gs~~PRsYYRCt~~~~~gC~A~KqVQr~~~dp~~~~vtY~G~Htc~ 188 (364)
++|||.|||||||.|+|++|||+|||||+. +|+|+|+|||+.+|+.+++|||+|+|||.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~---~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHP---GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECT---TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCCCchhhccCcccCCCceeeEeeecccc---ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 589999999999999999999999999994 99999999999999999999999999996
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=93.37 E-value=0.051 Score=39.66 Aligned_cols=52 Identities=25% Similarity=0.470 Sum_probs=28.8
Q ss_pred ccCCCccccccCccccCCCCCCccceeeccCCCCCCcccccccccCCCCCeEEEEeeccCCC
Q 017895 126 TLDDGYCWRKYGQKDILGRNFPRGYYRCTHRHARGCLATKQVQRSDDDPSMFEVTYRGRHKC 187 (364)
Q Consensus 126 ~~dDGy~WRKYGQK~I~gs~~PRsYYRCt~~~~~gC~A~KqVQr~~~dp~~~~vtY~G~Htc 187 (364)
.+-|||.-+++... ..+.|+||+.+...+|.|+=.+. + +...+ +...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~-~~~~~-~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--A-GDGRV-VRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TTEE-EE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--C-CCCEE-EECCCccCC
Confidence 46789877765554 35789999999888999998887 2 23344 333489987
No 4
>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=32.17 E-value=34 Score=26.92 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=25.6
Q ss_pred CCCcccccccccCCCCCeEEEEeeccCCCC
Q 017895 159 RGCLATKQVQRSDDDPSMFEVTYRGRHKCS 188 (364)
Q Consensus 159 ~gC~A~KqVQr~~~dp~~~~vtY~G~Htc~ 188 (364)
-||+|.=.|.+.. +..-.++.+..+|||.
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~ 88 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHP 88 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCC
Confidence 5899999999877 7888889999999985
No 5
>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=28.73 E-value=1.1e+02 Score=23.04 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=25.5
Q ss_pred hHHHHHHHHHhhcCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 017895 19 QGKELAKRLRNHLNPSSSPETREFLVQEILSSYEKALSM 57 (364)
Q Consensus 19 ~G~ElA~QL~~~L~p~sS~e~~~~Lv~~IL~S~~kALsi 57 (364)
=|..|..-|.+++.... ....|+.+||.-|+|+|.-
T Consensus 11 lG~aL~dtLDeli~~~~---I~p~La~kVL~~FDksi~~ 46 (49)
T PF02268_consen 11 LGIALTDTLDELIQEGK---ITPQLAMKVLEQFDKSINE 46 (49)
T ss_dssp HHHHHHHHHHHHHHTTS---S-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHH
Confidence 47777777887776221 1246899999999999863
No 6
>PF08289 Flu_M1_C: Influenza Matrix protein (M1) C-terminal domain; InterPro: IPR013188 Matrix protein (M1) of Influenza virus is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of RNA-nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously. M1 is comprised of two domains connected by a linker sequence. The C-terminal domain contains alpha-helical structure and appears to be involved in growth and virulence of the virus [, ].; GO: 0003723 RNA binding, 0005198 structural molecule activity
Probab=21.41 E-value=1.7e+02 Score=24.68 Aligned_cols=39 Identities=26% Similarity=0.416 Sum_probs=24.5
Q ss_pred hHHHHHHHHHhhcC--------CCCCHHHHHHHHHHHHHHHHHHHHHh
Q 017895 19 QGKELAKRLRNHLN--------PSSSPETREFLVQEILSSYEKALSML 58 (364)
Q Consensus 19 ~G~ElA~QL~~~L~--------p~sS~e~~~~Lv~~IL~S~~kALsiL 58 (364)
..+|+|.||+..+. |.++...+++|+ +.|..|.+.+.++
T Consensus 44 e~~eiAsq~r~~i~amRsiGt~~~~~~Gl~dDll-e~Lq~yQk~MG~~ 90 (95)
T PF08289_consen 44 EAMEIASQARSMIQAMRSIGTHPKNSEGLADDLL-ENLQAYQKRMGAQ 90 (95)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCccchHHHHH-HHHHHHHHHHhHH
Confidence 45667777776554 445555666655 4567787777654
No 7
>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=20.92 E-value=36 Score=30.08 Aligned_cols=8 Identities=63% Similarity=1.244 Sum_probs=6.9
Q ss_pred CCCccccc
Q 017895 128 DDGYCWRK 135 (364)
Q Consensus 128 dDGy~WRK 135 (364)
.|||.|||
T Consensus 52 kDG~~WrK 59 (118)
T PF03859_consen 52 KDGHNWRK 59 (118)
T ss_pred cccceeEE
Confidence 49999995
No 8
>COG1722 XseB Exonuclease VII small subunit [DNA replication, recombination, and repair]
Probab=17.37 E-value=2.4e+02 Score=23.23 Aligned_cols=22 Identities=23% Similarity=0.362 Sum_probs=14.4
Q ss_pred HHHHHHHHhHHHHHHHHHhhcC
Q 017895 11 NILITELAQGKELAKRLRNHLN 32 (364)
Q Consensus 11 k~vi~EL~~G~ElA~QL~~~L~ 32 (364)
..+|.++-+|.+|+++.+..|.
T Consensus 34 e~sl~~~erG~~L~k~c~~~L~ 55 (81)
T COG1722 34 EEALKEFERGMALYKECQEKLQ 55 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666677777777776654
No 9
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=15.58 E-value=2.7e+02 Score=23.12 Aligned_cols=39 Identities=26% Similarity=0.514 Sum_probs=18.6
Q ss_pred HHHHHH-hHHHHH----HHHHhhcCCCC-CHHHHHHHH--HHHHHHH
Q 017895 13 LITELA-QGKELA----KRLRNHLNPSS-SPETREFLV--QEILSSY 51 (364)
Q Consensus 13 vi~EL~-~G~ElA----~QL~~~L~p~s-S~e~~~~Lv--~~IL~S~ 51 (364)
+|+-+. +|.+.+ ++|..+|.... +++..++|. ..||++|
T Consensus 47 vm~Ki~~kg~~yv~~E~~RL~~iL~~~~ls~~K~del~~R~NIL~~F 93 (93)
T cd00238 47 VMEKILEKGEDYVEKELARLERLLEKKGLAPEKADELTRRLNILRSF 93 (93)
T ss_pred HHHHHHHcchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHhcC
Confidence 444443 555554 33555555322 555555554 3345543
No 10
>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=15.08 E-value=2e+02 Score=24.55 Aligned_cols=41 Identities=32% Similarity=0.355 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhHHHHHHHHHhhcCCCCCHHH----HHHHHHHHHH
Q 017895 9 DQNILITELAQGKELAKRLRNHLNPSSSPET----REFLVQEILS 49 (364)
Q Consensus 9 e~k~vi~EL~~G~ElA~QL~~~L~p~sS~e~----~~~Lv~~IL~ 49 (364)
++..|++||.+|..+.-+--.+|-...+.+. -.+|+.+|-+
T Consensus 23 ~R~~llqEm~~gLg~~p~ag~lLf~~~~~~~~k~AEqELL~Ei~R 67 (93)
T PF07216_consen 23 HRNDLLQEMLEGLGLGPVAGELLFGGSSPELMKQAEQELLEEIQR 67 (93)
T ss_pred HHHHHHHHHHHhcCCChhHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 3456889999888888777777665545433 2467777765
Done!