Query 018255
Match_columns 359
No_of_seqs 237 out of 726
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 07:27:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018255.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018255hhsearch_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 1.2E-30 2.5E-35 199.4 4.9 59 289-347 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 8.9E-31 1.9E-35 200.1 1.3 60 289-349 1-60 (60)
3 PF10533 Plant_zn_clust: Plant 99.3 1.4E-12 3.1E-17 96.0 3.6 46 241-287 1-47 (47)
4 PF04500 FLYWCH: FLYWCH zinc f 89.9 0.14 3E-06 37.1 0.9 49 289-347 12-62 (62)
5 PF03101 FAR1: FAR1 DNA-bindin 89.4 0.3 6.4E-06 38.5 2.5 32 318-350 59-90 (91)
6 PF05344 DUF746: Domain of Unk 65.1 3.8 8.2E-05 32.7 1.5 53 14-68 2-58 (65)
7 cd07691 Ig_CD3_gamma_delta Imm 32.9 53 0.0012 26.5 3.2 25 291-316 17-51 (69)
8 PF03859 CG-1: CG-1 domain; I 19.9 39 0.00084 29.9 0.3 8 290-297 52-59 (118)
9 KOG0673 Thymidylate synthase [ 15.7 58 0.0013 32.4 0.4 24 289-312 113-157 (293)
10 PF10083 DUF2321: Uncharacteri 15.3 40 0.00086 31.2 -0.8 50 10-59 83-136 (158)
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=1.2e-30 Score=199.45 Aligned_cols=59 Identities=61% Similarity=1.217 Sum_probs=56.8
Q ss_pred CCCCccccccCCCCCCCCCCCCccccccCCCCCCcccceeecCCCCceEEEEEeccCCC
Q 018255 289 PPDEYTWRKYGQKPIKGSPHPRGYYKCSSVRGCPARKHVERCPEEPSMLIVTYEGEHNH 347 (359)
Q Consensus 289 p~Dgy~WRKYGQK~Ikgs~~PRsYYRCs~~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~h 347 (359)
++|||.|||||||.|+|+++||+||||++..||+|+|+|||+++|+.+++|||+|+|||
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 47999999999999999999999999997689999999999999999999999999998
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=8.9e-31 Score=200.14 Aligned_cols=60 Identities=62% Similarity=1.267 Sum_probs=51.9
Q ss_pred CCCCccccccCCCCCCCCCCCCccccccCCCCCCcccceeecCCCCceEEEEEeccCCCCC
Q 018255 289 PPDEYTWRKYGQKPIKGSPHPRGYYKCSSVRGCPARKHVERCPEEPSMLIVTYEGEHNHSR 349 (359)
Q Consensus 289 p~Dgy~WRKYGQK~Ikgs~~PRsYYRCs~~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~h~~ 349 (359)
.+|||+|||||||.|+|+++||+||||++ .+|+|+|+|||+.+|+.+++|||+|+|||+.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~-~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k 60 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTH-PGCPAKKQVQRSADDPNIVIVTYEGEHNHPK 60 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEEC-TTEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccc-cChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence 37999999999999999999999999996 5999999999999999999999999999973
No 3
>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=99.31 E-value=1.4e-12 Score=96.03 Aligned_cols=46 Identities=63% Similarity=1.185 Sum_probs=36.5
Q ss_pred cccccCCCcCC-CCCcccCCCCcccCccccccccceeEeecccCCccC
Q 018255 241 KKRCFSSRAED-GSLKCSTSGKCHCSKRRKHRVKRSIKVPAISNKVAD 287 (359)
Q Consensus 241 ~~~c~~~~~~d-~~~~~~~~~rch~skrrK~r~kr~~~vpais~~~~d 287 (359)
+++|+. ++++ +..+|+++++|||+||||.|+||+|+||||+.+++|
T Consensus 1 krkC~~-~~~~~~~~~~sssgrCHCsKkRK~RvKR~irVPAiS~K~AD 47 (47)
T PF10533_consen 1 KRKCHS-HNDSSGKCKCSSSGRCHCSKKRKSRVKRTIRVPAISSKIAD 47 (47)
T ss_pred CCcccc-cCcccCccccCCCCcccCCCcccccceeeEEeecccccccC
Confidence 478943 3222 333367899999999999999999999999999875
No 4
>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=89.95 E-value=0.14 Score=37.14 Aligned_cols=49 Identities=31% Similarity=0.582 Sum_probs=24.1
Q ss_pred CCCCccccccCCCCCCCCCCCCccccccCC--CCCCcccceeecCCCCceEEEEEeccCCC
Q 018255 289 PPDEYTWRKYGQKPIKGSPHPRGYYKCSSV--RGCPARKHVERCPEEPSMLIVTYEGEHNH 347 (359)
Q Consensus 289 p~Dgy~WRKYGQK~Ikgs~~PRsYYRCs~~--~gC~ArK~Vqr~~dDp~~~~VtY~GeH~h 347 (359)
.-|||.-+++... ....|++|+.. .+|+|+=.+. .++..+ +...++|||
T Consensus 12 ~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~~~--~~~~~~HnH 62 (62)
T PF04500_consen 12 VYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDGRV--VRTNGEHNH 62 (62)
T ss_dssp EETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TTEE--EE-S---SS
T ss_pred EECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCCEE--EECCCccCC
Confidence 3588877665544 33589999962 3799987777 444433 345599998
No 5
>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=89.38 E-value=0.3 Score=38.55 Aligned_cols=32 Identities=31% Similarity=0.482 Sum_probs=26.7
Q ss_pred CCCCCcccceeecCCCCceEEEEEeccCCCCCC
Q 018255 318 VRGCPARKHVERCPEEPSMLIVTYEGEHNHSRI 350 (359)
Q Consensus 318 ~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~h~~~ 350 (359)
..||+|+=.|.+.. |....++.+..+|||+..
T Consensus 59 ktgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~ 90 (91)
T PF03101_consen 59 KTGCKARINVKRRK-DGKWRVTSFVLEHNHPLC 90 (91)
T ss_pred ccCCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence 35899998888877 777778889999999865
No 6
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=65.13 E-value=3.8 Score=32.70 Aligned_cols=53 Identities=23% Similarity=0.152 Sum_probs=35.4
Q ss_pred HHHHHHHHhcCCCCCcchhhhccchhh-hhHHHHHhcccceeeeccC-Cc--cceeecc
Q 018255 14 SCYRVLNLLSQHNKDPLQVHHQYRNLA-LETDEVVFKFKRVVSLLSH-GT--TRVRKLR 68 (359)
Q Consensus 14 Sc~rvL~LLSq~~~~~~~~~~~~~~~~-~~TdeAVsKFKKViSLL~r-GH--ARfRr~~ 68 (359)
.+..+|+||||+- .-.+.... ..+. .....-|.+|++-+=.|+- || ||+|-+-
T Consensus 2 ~~~~fIrlLs~~~-s~~~Aa~~-lG~~~~~v~~wv~~fR~wll~LDPSG~~E~RVRLg~ 58 (65)
T PF05344_consen 2 KARAFIRLLSQQI-SVAQAADR-LGTDPGTVRRWVRMFRQWLLQLDPSGHWEARVRLGV 58 (65)
T ss_pred cHHHHHHHhcccc-cHHHHHHH-HCcCHHHHHHHHHHHHHHHHHcCCCCChHHHhhcCC
Confidence 4678999999974 21111111 1111 3356778999999999998 87 8888874
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=32.87 E-value=53 Score=26.53 Aligned_cols=25 Identities=40% Similarity=0.911 Sum_probs=17.5
Q ss_pred CCccccccCCCCCCC--------C--CCCCcccccc
Q 018255 291 DEYTWRKYGQKPIKG--------S--PHPRGYYKCS 316 (359)
Q Consensus 291 Dgy~WRKYGQK~Ikg--------s--~~PRsYYRCs 316 (359)
.-+.|-| |-..+.- + .-|||-|+|.
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~ 51 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCK 51 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEec
Confidence 4478888 7543332 2 6899999997
No 8
>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=19.93 E-value=39 Score=29.91 Aligned_cols=8 Identities=50% Similarity=0.987 Sum_probs=7.0
Q ss_pred CCCccccc
Q 018255 290 PDEYTWRK 297 (359)
Q Consensus 290 ~Dgy~WRK 297 (359)
.|||.|||
T Consensus 52 kDG~~WrK 59 (118)
T PF03859_consen 52 KDGHNWRK 59 (118)
T ss_pred cccceeEE
Confidence 59999995
No 9
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=15.66 E-value=58 Score=32.39 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=18.5
Q ss_pred CCCCccccccCCC---------------------CCCCCCCCCcc
Q 018255 289 PPDEYTWRKYGQK---------------------PIKGSPHPRGY 312 (359)
Q Consensus 289 p~Dgy~WRKYGQK---------------------~Ikgs~~PRsY 312 (359)
|--|++||-+|.| .||++|+.|--
T Consensus 113 pvyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRI 157 (293)
T KOG0673|consen 113 PVYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRI 157 (293)
T ss_pred cccceeeeecCccccccccccccccHHHHHHHHHHHhcCCcccee
Confidence 3468999999988 57778877743
No 10
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=15.27 E-value=40 Score=31.23 Aligned_cols=50 Identities=18% Similarity=0.231 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhcCCCCCcc-hhhhccchhhh---hHHHHHhcccceeeeccC
Q 018255 10 IAVESCYRVLNLLSQHNKDPL-QVHHQYRNLAL---ETDEVVFKFKRVVSLLSH 59 (359)
Q Consensus 10 aavESc~rvL~LLSq~~~~~~-~~~~~~~~~~~---~TdeAVsKFKKViSLL~r 59 (359)
.+|++...|+..+..=..+.. +......+|.. .|-.||.||||+++.++.
T Consensus 83 ~~L~aa~el~ee~eeLs~deke~~~~sl~dL~~d~PkT~vA~~rfKk~~~K~g~ 136 (158)
T PF10083_consen 83 NALEAANELIEEDEELSPDEKEQFKESLPDLTKDTPKTKVAATRFKKILSKAGS 136 (158)
T ss_pred HHHHHHHHHHHHhhcCCHHHHHHHHhhhHHHhhcCCccHHHHHHHHHHHHHHhH
Confidence 456666666665543221111 11111233333 389999999999987654
Done!