Query 020585
Match_columns 324
No_of_seqs 212 out of 749
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:34:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020585.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020585hhsearch_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 1.1E-30 2.3E-35 197.3 2.5 59 216-274 1-60 (60)
2 smart00774 WRKY DNA binding do 100.0 2.3E-29 4.9E-34 190.0 4.7 57 216-272 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 92.1 0.072 1.6E-06 38.1 1.2 50 214-272 10-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 88.6 0.31 6.8E-06 37.9 2.1 29 246-274 61-89 (91)
5 PF03859 CG-1: CG-1 domain; I 35.5 14 0.00029 32.2 0.2 10 215-224 50-59 (118)
6 PLN03097 FHY3 Protein FAR-RED 32.3 40 0.00087 37.7 3.2 36 242-277 156-191 (846)
7 PF03615 GCM: GCM motif protei 15.6 1.2E+02 0.0026 27.3 2.3 21 257-277 113-133 (143)
8 PF06364 DUF1068: Protein of u 12.0 56 0.0012 30.3 -0.8 20 44-63 52-71 (176)
9 COG4283 Uncharacterized conser 10.7 1.3E+02 0.0028 27.8 1.0 15 213-227 73-87 (170)
10 PF06753 Bradykinin: Bradykini 10.6 1.3E+02 0.0028 18.4 0.7 7 51-57 4-10 (19)
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=1.1e-30 Score=197.27 Aligned_cols=59 Identities=61% Similarity=1.230 Sum_probs=50.8
Q ss_pred CCCCccccccCCccCCCCCCCCccccccccccccccceeecC-CCCEEEEEEccccCCCC
Q 020585 216 SDDGYNWRKYGQKHVKGSEFPRSYYKCTHPNCEVKKLFERSH-DGQITEIIYKGTHDHPK 274 (324)
Q Consensus 216 ~~DGY~WRKYGQK~IkGs~~pRsYYrCt~~~C~akK~Vqrs~-Dg~i~~i~Y~G~HnH~~ 274 (324)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+. |+.+++|+|+|+|||++
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 489999999999999999999999999999999999999997 77899999999999985
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=189.98 Aligned_cols=57 Identities=58% Similarity=1.134 Sum_probs=54.9
Q ss_pred CCCCccccccCCccCCCCCCCCccccccc-cccccccceeecC-CCCEEEEEEccccCC
Q 020585 216 SDDGYNWRKYGQKHVKGSEFPRSYYKCTH-PNCEVKKLFERSH-DGQITEIIYKGTHDH 272 (324)
Q Consensus 216 ~~DGY~WRKYGQK~IkGs~~pRsYYrCt~-~~C~akK~Vqrs~-Dg~i~~i~Y~G~HnH 272 (324)
.+|||.|||||||.|+|+++||+||||++ ++|+|+|+|||+. |+.+++|+|+|+|||
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 8999999999996 789999999999998
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=92.07 E-value=0.072 Score=38.09 Aligned_cols=50 Identities=22% Similarity=0.556 Sum_probs=25.8
Q ss_pred CCCCCCccccccCCccCCCCCCCCcccccccc---ccccccceeecCCCCEEEEEEccccCC
Q 020585 214 MPSDDGYNWRKYGQKHVKGSEFPRSYYKCTHP---NCEVKKLFERSHDGQITEIIYKGTHDH 272 (324)
Q Consensus 214 ~~~~DGY~WRKYGQK~IkGs~~pRsYYrCt~~---~C~akK~Vqrs~Dg~i~~i~Y~G~HnH 272 (324)
.+.-|||.-+++..+ ..+.|++|+.. +|.|+=.+. ..++. .+...++|||
T Consensus 10 ~L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~-~~~~~--~~~~~~~HnH 62 (62)
T PF04500_consen 10 KLVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD-AGDGR--VVRTNGEHNH 62 (62)
T ss_dssp EEEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE---TTE--EEE-S---SS
T ss_pred EEEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE-CCCCE--EEECCCccCC
Confidence 456788887765544 45689999985 899977665 22333 3455699999
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=88.57 E-value=0.31 Score=37.88 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=24.4
Q ss_pred ccccccceeecCCCCEEEEEEccccCCCC
Q 020585 246 NCEVKKLFERSHDGQITEIIYKGTHDHPK 274 (324)
Q Consensus 246 ~C~akK~Vqrs~Dg~i~~i~Y~G~HnH~~ 274 (324)
+|+|+=.+-+..+|....+.+..+|||+.
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 79998888777677777779999999985
No 5
>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=35.50 E-value=14 Score=32.22 Aligned_cols=10 Identities=60% Similarity=1.049 Sum_probs=8.1
Q ss_pred CCCCCccccc
Q 020585 215 PSDDGYNWRK 224 (324)
Q Consensus 215 ~~~DGY~WRK 224 (324)
--.|||+|||
T Consensus 50 fRkDG~~WrK 59 (118)
T PF03859_consen 50 FRKDGHNWRK 59 (118)
T ss_pred hhcccceeEE
Confidence 3479999995
No 6
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=32.29 E-value=40 Score=37.75 Aligned_cols=36 Identities=19% Similarity=0.406 Sum_probs=30.6
Q ss_pred ccccccccccceeecCCCCEEEEEEccccCCCCCCC
Q 020585 242 CTHPNCEVKKLFERSHDGQITEIIYKGTHDHPKPQL 277 (324)
Q Consensus 242 Ct~~~C~akK~Vqrs~Dg~i~~i~Y~G~HnH~~P~~ 277 (324)
|+--||.|+=.|.+..||....+-+..+|||+.-.+
T Consensus 156 ~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~ 191 (846)
T PLN03097 156 CAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPA 191 (846)
T ss_pred ccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCc
Confidence 666799999999887788877789999999998544
No 7
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=15.57 E-value=1.2e+02 Score=27.26 Aligned_cols=21 Identities=48% Similarity=0.865 Sum_probs=7.1
Q ss_pred CCCCEEEEEEccccCCCCCCC
Q 020585 257 HDGQITEIIYKGTHDHPKPQL 277 (324)
Q Consensus 257 ~Dg~i~~i~Y~G~HnH~~P~~ 277 (324)
++|......-+|.|.|++|..
T Consensus 113 ~~~~~IfFQaKG~HDHpRPe~ 133 (143)
T PF03615_consen 113 HDGNAIFFQAKGVHDHPRPEA 133 (143)
T ss_dssp E-SSBEEEEEE----S-----
T ss_pred cCCCEEEEEcccccCCCCCCc
Confidence 455544567799999999974
No 8
>PF06364 DUF1068: Protein of unknown function (DUF1068); InterPro: IPR010471 This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=12.00 E-value=56 Score=30.26 Aligned_cols=20 Identities=50% Similarity=0.823 Sum_probs=14.9
Q ss_pred CCCCCccCCCCCCCCCccCC
Q 020585 44 SRSPCIMIPPGLSPSSFLES 63 (324)
Q Consensus 44 S~SpyftIPPGLSPt~lLdS 63 (324)
++.|+++||+||+=..|.|.
T Consensus 52 s~~~ll~ip~gl~N~S~~DC 71 (176)
T PF06364_consen 52 SSQPLLSIPPGLSNLSFTDC 71 (176)
T ss_pred CCHHHHHhcccccccchHhh
Confidence 45568999999887766664
No 9
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=10.67 E-value=1.3e+02 Score=27.85 Aligned_cols=15 Identities=27% Similarity=0.882 Sum_probs=12.1
Q ss_pred CCCCCCCccccccCC
Q 020585 213 SMPSDDGYNWRKYGQ 227 (324)
Q Consensus 213 ~~~~~DGY~WRKYGQ 227 (324)
...+.+||+|+.||.
T Consensus 73 ~f~Ps~~ykWn~~ge 87 (170)
T COG4283 73 VFTPSPGYKWNNLGE 87 (170)
T ss_pred CCCCCCCCcccccHH
Confidence 446788999999994
No 10
>PF06753 Bradykinin: Bradykinin; InterPro: IPR009608 This family consists of several bradykinin sequences. The skins of anuran amphibians, in addition to mucus glands, contain highly specialised poison glands, which, in reaction to stress or attack, exude a complex noxious cocktail of biologically active molecules. These secretions often contain a plethora of peptides among which bradykinin or structural variants have been identified [].; GO: 0005179 hormone activity, 0006950 response to stress, 0005576 extracellular region
Probab=10.64 E-value=1.3e+02 Score=18.42 Aligned_cols=7 Identities=57% Similarity=1.450 Sum_probs=4.5
Q ss_pred CCCCCCC
Q 020585 51 IPPGLSP 57 (324)
Q Consensus 51 IPPGLSP 57 (324)
.||||+|
T Consensus 4 ~p~gftp 10 (19)
T PF06753_consen 4 RPPGFTP 10 (19)
T ss_pred cCCCCCc
Confidence 4667765
Done!