Query 024825
Match_columns 262
No_of_seqs 164 out of 631
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:41:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024825.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024825hhsearch_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 5.2E-32 1.1E-36 199.0 4.9 59 47-107 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 2.7E-32 5.9E-37 200.4 2.5 59 47-108 1-59 (60)
3 PF04500 FLYWCH: FLYWCH zinc f 94.0 0.031 6.7E-07 38.8 1.6 52 46-107 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 56.7 10 0.00022 28.4 2.5 30 79-109 60-89 (91)
5 PF03859 CG-1: CG-1 domain; I 31.8 15 0.00034 30.9 0.0 9 47-55 51-59 (118)
6 PF10533 Plant_zn_clust: Plant 23.8 50 0.0011 23.9 1.4 20 19-40 22-41 (47)
7 cd07691 Ig_CD3_gamma_delta Imm 23.5 75 0.0016 24.5 2.4 26 49-75 17-52 (69)
8 PF03193 DUF258: Protein of un 18.5 32 0.00069 30.0 -0.6 20 70-89 126-145 (161)
9 PF13408 Zn_ribbon_recom: Reco 17.5 68 0.0015 21.8 1.0 20 68-88 24-45 (58)
10 TIGR00157 ribosome small subun 16.8 45 0.00097 30.1 -0.1 20 70-89 210-229 (245)
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=99.97 E-value=5.2e-32 Score=199.01 Aligned_cols=59 Identities=69% Similarity=1.242 Sum_probs=56.8
Q ss_pred CCCCchhhccCCccccCCCCCCcccccccCcCCCCccccceeecCCCCCeEEEEeccccCC
Q 024825 47 FEDGYSWRKYGQKDILGAKYPRSYYRCTYRNTQNCWATKQVQRSDEDPSTFEVTYRGTHTC 107 (262)
Q Consensus 47 ~dDGy~WRKYGQK~Ikgs~~PRsYYRCt~~~~~gC~A~KqVQrs~~Dp~~~~vtY~G~Htc 107 (262)
++|||+|||||||.|+|+++||+|||||+ .+||+|+|+|||+++|+.+++|||+|+|||
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 47999999999999999999999999998 479999999999999999999999999998
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=99.97 E-value=2.7e-32 Score=200.45 Aligned_cols=59 Identities=61% Similarity=1.091 Sum_probs=52.3
Q ss_pred CCCCchhhccCCccccCCCCCCcccccccCcCCCCccccceeecCCCCCeEEEEeccccCCC
Q 024825 47 FEDGYSWRKYGQKDILGAKYPRSYYRCTYRNTQNCWATKQVQRSDEDPSTFEVTYRGTHTCF 108 (262)
Q Consensus 47 ~dDGy~WRKYGQK~Ikgs~~PRsYYRCt~~~~~gC~A~KqVQrs~~Dp~~~~vtY~G~Htc~ 108 (262)
++|||+|||||||.|+|+++||+||||++. +|+|+|+|||+.+|+.+++|||+|+|||+
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 589999999999999999999999999996 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=94.02 E-value=0.031 Score=38.79 Aligned_cols=52 Identities=23% Similarity=0.451 Sum_probs=26.9
Q ss_pred CCCCCchhhccCCccccCCCCCCcccccccCcCCCCccccceeecCCCCCeEEEEeccccCC
Q 024825 46 PFEDGYSWRKYGQKDILGAKYPRSYYRCTYRNTQNCWATKQVQRSDEDPSTFEVTYRGTHTC 107 (262)
Q Consensus 46 ~~dDGy~WRKYGQK~Ikgs~~PRsYYRCt~~~~~gC~A~KqVQrs~~Dp~~~~vtY~G~Htc 107 (262)
..-|||.-++...+ ..+.|+||+.+...+|+|+=.+. + +...+ +...++|||
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 35588877765554 34689999998778999976665 2 23333 334489997
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=56.66 E-value=10 Score=28.39 Aligned_cols=30 Identities=20% Similarity=0.138 Sum_probs=25.6
Q ss_pred CCCccccceeecCCCCCeEEEEeccccCCCC
Q 024825 79 QNCWATKQVQRSDEDPSTFEVTYRGTHTCFN 109 (262)
Q Consensus 79 ~gC~A~KqVQrs~~Dp~~~~vtY~G~Htc~~ 109 (262)
.||+|.=.|-+.. |....++.+..+|||+.
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 4999998888776 77888889999999974
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=31.83 E-value=15 Score=30.94 Aligned_cols=9 Identities=56% Similarity=1.114 Sum_probs=7.6
Q ss_pred CCCCchhhc
Q 024825 47 FEDGYSWRK 55 (262)
Q Consensus 47 ~dDGy~WRK 55 (262)
-.|||.|||
T Consensus 51 RkDG~~WrK 59 (118)
T PF03859_consen 51 RKDGHNWRK 59 (118)
T ss_pred hcccceeEE
Confidence 469999995
No 6
>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=23.76 E-value=50 Score=23.89 Aligned_cols=20 Identities=25% Similarity=0.165 Sum_probs=14.6
Q ss_pred cccCcccCCCCCeeeeeeeecc
Q 024825 19 TAKLGCRKTLPRRTDKVKVSFE 40 (262)
Q Consensus 19 ~~~skkRk~~~~~t~qvrv~~~ 40 (262)
...+||||.+.|++ |||...
T Consensus 22 CHCsKkRK~RvKR~--irVPAi 41 (47)
T PF10533_consen 22 CHCSKKRKSRVKRT--IRVPAI 41 (47)
T ss_pred ccCCCcccccceee--EEeecc
Confidence 35578899888766 888753
No 7
>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=23.52 E-value=75 Score=24.52 Aligned_cols=26 Identities=35% Similarity=0.854 Sum_probs=18.8
Q ss_pred CCchhhccCCccc--------cCC--CCCCccccccc
Q 024825 49 DGYSWRKYGQKDI--------LGA--KYPRSYYRCTY 75 (262)
Q Consensus 49 DGy~WRKYGQK~I--------kgs--~~PRsYYRCt~ 75 (262)
.-+.|-| |-..+ +|+ +-||+=|+|.-
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~~ 52 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCKE 52 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEecC
Confidence 4589999 86444 333 78999999964
No 8
>PF03193 DUF258: Protein of unknown function, DUF258; InterPro: IPR004881 This entry contains Escherichia coli (strain K12) RsgA, which may play a role in 30S ribosomal subunit biogenesis. RsgA is an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. It is dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96 fold increase in kcat) ribosomes []. The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin [] streptomycin and spectinomycin []. This inhibition is not due to competition for binding sites on the 30S or 70S ribosome []. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2YKR_W 2YV5_A 1T9H_A 2RCN_A 4A2I_V 1U0L_B.
Probab=18.55 E-value=32 Score=29.96 Aligned_cols=20 Identities=20% Similarity=0.444 Sum_probs=17.0
Q ss_pred ccccccCcCCCCccccceee
Q 024825 70 YYRCTYRNTQNCWATKQVQR 89 (262)
Q Consensus 70 YYRCt~~~~~gC~A~KqVQr 89 (262)
|.-|+|.+..||.+++-|+.
T Consensus 126 F~~C~H~~Ep~CaV~~av~~ 145 (161)
T PF03193_consen 126 FRDCTHIHEPGCAVKAAVEN 145 (161)
T ss_dssp STTTTSSSSTT-HHHHHHHT
T ss_pred ccCCCCCCCCCChHHHHHHC
Confidence 56899999999999999984
No 9
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=17.51 E-value=68 Score=21.84 Aligned_cols=20 Identities=30% Similarity=0.795 Sum_probs=14.1
Q ss_pred CcccccccCcCCC--Ccccccee
Q 024825 68 RSYYRCTYRNTQN--CWATKQVQ 88 (262)
Q Consensus 68 RsYYRCt~~~~~g--C~A~KqVQ 88 (262)
+.||+|..+...+ |+++ .+.
T Consensus 24 ~~yy~C~~~~~~~~~C~~~-~i~ 45 (58)
T PF13408_consen 24 YRYYRCSNRRRKGKGCPNK-SIR 45 (58)
T ss_pred ceEEEcCCCcCCCCCCCCC-EeC
Confidence 3899999876555 8865 443
No 10
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=16.80 E-value=45 Score=30.13 Aligned_cols=20 Identities=15% Similarity=0.487 Sum_probs=17.8
Q ss_pred ccccccCcCCCCccccceee
Q 024825 70 YYRCTYRNTQNCWATKQVQR 89 (262)
Q Consensus 70 YYRCt~~~~~gC~A~KqVQr 89 (262)
|--|+|.+.+||.+++.|+.
T Consensus 210 f~~C~H~~ep~C~v~~a~~~ 229 (245)
T TIGR00157 210 FRDCLHQSEPGCAVRQAVEQ 229 (245)
T ss_pred CCCCccCCCCCChHHHHHHc
Confidence 45799999999999999984
Done!