Query 046286
Match_columns 188
No_of_seqs 141 out of 677
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 10:29:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046286.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046286hhsearch_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 2.6E-33 5.6E-38 196.9 3.4 59 109-167 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 5.2E-32 1.1E-36 190.6 5.1 58 109-166 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 93.7 0.032 7E-07 36.7 1.2 49 108-166 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 93.2 0.08 1.7E-06 37.9 2.6 30 138-168 60-89 (91)
5 KOG2675 Adenylate cyclase-asso 72.1 3 6.6E-05 40.2 2.6 22 5-26 235-256 (480)
6 KOG2495 NADH-dehydrogenase (ub 38.7 14 0.00031 35.9 1.0 18 13-30 84-101 (491)
7 PLN03097 FHY3 Protein FAR-RED 37.1 35 0.00077 35.2 3.5 34 135-169 156-189 (846)
8 PF10533 Plant_zn_clust: Plant 23.8 59 0.0013 22.4 1.7 26 74-99 16-42 (47)
9 PF03859 CG-1: CG-1 domain; I 23.5 1.1E+02 0.0024 24.7 3.4 10 108-117 50-59 (118)
10 KOG0673 Thymidylate synthase [ 23.1 32 0.00069 31.3 0.4 26 110-135 114-160 (293)
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=99.97 E-value=2.6e-33 Score=196.87 Aligned_cols=59 Identities=73% Similarity=1.292 Sum_probs=52.5
Q ss_pred CCCCcchhccCcccccCCCCCccceeccCCCcccccceeeecCCCCEEEEEEecccCCC
Q 046286 109 LDDGYRWRKYGQKAVKNSLYPRSYYRCTHHTCNVKKQVQRLSKDTSIVVTTYEGIHNHP 167 (188)
Q Consensus 109 ~~DGy~WRKYGQK~Ikgs~~PRsYYRCt~~gC~akKqVqr~~~D~~~~~ttY~G~HnH~ 167 (188)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHPGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECTTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccccChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 58999999999999999999999999999999999999999999999999999999996
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=99.97 E-value=5.2e-32 Score=190.57 Aligned_cols=58 Identities=66% Similarity=1.157 Sum_probs=56.4
Q ss_pred CCCCcchhccCcccccCCCCCccceeccC-CCcccccceeeecCCCCEEEEEEecccCC
Q 046286 109 LDDGYRWRKYGQKAVKNSLYPRSYYRCTH-HTCNVKKQVQRLSKDTSIVVTTYEGIHNH 166 (188)
Q Consensus 109 ~~DGy~WRKYGQK~Ikgs~~PRsYYRCt~-~gC~akKqVqr~~~D~~~~~ttY~G~HnH 166 (188)
++|||+|||||||.|+|+++||+||||++ .||+|+|+|||+++|+.+++|||+|+|||
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 89999999999988999999999999998
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=93.73 E-value=0.032 Score=36.69 Aligned_cols=49 Identities=27% Similarity=0.584 Sum_probs=23.8
Q ss_pred CCCCCcchhccCcccccCCCCCccceeccCC---CcccccceeeecCCCCEEEEEEecccCC
Q 046286 108 ILDDGYRWRKYGQKAVKNSLYPRSYYRCTHH---TCNVKKQVQRLSKDTSIVVTTYEGIHNH 166 (188)
Q Consensus 108 ~~~DGy~WRKYGQK~Ikgs~~PRsYYRCt~~---gC~akKqVqr~~~D~~~~~ttY~G~HnH 166 (188)
++-|||.-++.... ....|++|+.. +|.|+=.+. .+ .. .++...+.|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~-~~-~~~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AG-DG-RVVRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TT-EEEE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CC-CC-EEEECCCccCC
Confidence 34588876664443 45679999985 899977766 22 33 33334489998
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=93.16 E-value=0.08 Score=37.89 Aligned_cols=30 Identities=33% Similarity=0.502 Sum_probs=25.8
Q ss_pred CCcccccceeeecCCCCEEEEEEecccCCCC
Q 046286 138 HTCNVKKQVQRLSKDTSIVVTTYEGIHNHPC 168 (188)
Q Consensus 138 ~gC~akKqVqr~~~D~~~~~ttY~G~HnH~~ 168 (188)
.||+|+=.|-+.. |+...++.+..+|||+.
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 4899998888755 78888999999999985
No 5
>KOG2675 consensus Adenylate cyclase-associated protein (CAP/Srv2p) [Cytoskeleton; Signal transduction mechanisms]
Probab=72.08 E-value=3 Score=40.19 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCCCceecCCCC
Q 046286 5 EPHPVSSPMSPQPNYLFTPSIP 26 (188)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~ 26 (188)
.|||||++|+|++.|++++...
T Consensus 235 ~PPPPPP~PPp~~~~~~~~~~~ 256 (480)
T KOG2675|consen 235 APPPPPPAPPPAPFFADSNPPS 256 (480)
T ss_pred CCCCCCCCCCCcccccccCCCC
Confidence 3555555677777777766544
No 6
>KOG2495 consensus NADH-dehydrogenase (ubiquinone) [Energy production and conversion]
Probab=38.70 E-value=14 Score=35.86 Aligned_cols=18 Identities=44% Similarity=0.960 Sum_probs=15.0
Q ss_pred CCCCCCceecCCCCCCCC
Q 046286 13 MSPQPNYLFTPSIPSSSM 30 (188)
Q Consensus 13 ~~~~~~~~~~~~~~s~s~ 30 (188)
-||.+-|||||.|||-.+
T Consensus 84 VSPRnyFlFTPLLpS~~v 101 (491)
T KOG2495|consen 84 VSPRNYFLFTPLLPSTTV 101 (491)
T ss_pred eccccceEEeeccCCccc
Confidence 478889999999998653
No 7
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=37.12 E-value=35 Score=35.23 Aligned_cols=34 Identities=26% Similarity=0.525 Sum_probs=29.0
Q ss_pred ccCCCcccccceeeecCCCCEEEEEEecccCCCCc
Q 046286 135 CTHHTCNVKKQVQRLSKDTSIVVTTYEGIHNHPCE 169 (188)
Q Consensus 135 Ct~~gC~akKqVqr~~~D~~~~~ttY~G~HnH~~~ 169 (188)
|+-.||.|.=.|.+ ..|+.-.++-+..+|||+.-
T Consensus 156 ~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~ 189 (846)
T PLN03097 156 CAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELL 189 (846)
T ss_pred ccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCC
Confidence 77789999999987 45677889999999999864
No 8
>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=23.84 E-value=59 Score=22.39 Aligned_cols=26 Identities=27% Similarity=0.531 Sum_probs=18.7
Q ss_pred CCcccccccccccccccccccC-CeeE
Q 046286 74 DQQDQGCKENKRKGSRMKKATR-PRFA 99 (188)
Q Consensus 74 ~~~~~~~k~~~~~~~~~k~~~~-pr~~ 99 (188)
+...+.+++.|+++.|+|++.+ |.|.
T Consensus 16 ~sssgrCHCsKkRK~RvKR~irVPAiS 42 (47)
T PF10533_consen 16 CSSSGRCHCSKKRKSRVKRTIRVPAIS 42 (47)
T ss_pred cCCCCcccCCCcccccceeeEEeeccc
Confidence 4556788888887888877765 6554
No 9
>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=23.53 E-value=1.1e+02 Score=24.69 Aligned_cols=10 Identities=50% Similarity=1.026 Sum_probs=8.3
Q ss_pred CCCCCcchhc
Q 046286 108 ILDDGYRWRK 117 (188)
Q Consensus 108 ~~~DGy~WRK 117 (188)
--.|||.|||
T Consensus 50 fRkDG~~WrK 59 (118)
T PF03859_consen 50 FRKDGHNWRK 59 (118)
T ss_pred hhcccceeEE
Confidence 4679999995
No 10
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=23.13 E-value=32 Score=31.26 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=19.1
Q ss_pred CCCcchhccCcc---------------------cccCCCCCccceec
Q 046286 110 DDGYRWRKYGQK---------------------AVKNSLYPRSYYRC 135 (188)
Q Consensus 110 ~DGy~WRKYGQK---------------------~Ikgs~~PRsYYRC 135 (188)
-=||+||-+|-| .||+|++.|----|
T Consensus 114 vyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIims 160 (293)
T KOG0673|consen 114 VYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMS 160 (293)
T ss_pred ccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeee
Confidence 358999999877 57888888744333
Done!