Query 041468
Match_columns 124
No_of_seqs 111 out of 597
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 07:26:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041468hhsearch_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 1.2E-35 2.6E-40 193.9 3.5 60 25-87 1-60 (60)
2 smart00774 WRKY DNA binding do 100.0 4.5E-35 9.9E-40 191.0 5.5 59 25-85 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 96.0 0.0037 8E-08 38.5 1.5 50 26-85 13-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 87.5 0.59 1.3E-05 30.9 2.6 31 57-88 60-90 (91)
5 PF10533 Plant_zn_clust: Plant 81.6 1.1 2.5E-05 28.1 1.8 23 5-27 25-47 (47)
6 PF03859 CG-1: CG-1 domain; I 46.6 7.3 0.00016 28.7 0.3 9 25-33 51-59 (118)
7 PLN03097 FHY3 Protein FAR-RED 29.5 60 0.0013 31.0 3.4 32 58-90 160-191 (846)
8 KOG0673 Thymidylate synthase [ 25.1 30 0.00064 28.9 0.5 14 24-37 112-125 (293)
9 TIGR02256 ICE_VC0181 integrati 24.4 61 0.0013 24.0 2.0 14 77-90 73-87 (131)
10 PF13408 Zn_ribbon_recom: Reco 24.3 49 0.0011 19.7 1.3 18 45-62 23-42 (58)
11 PF06839 zf-GRF: GRF zinc fing 22.4 75 0.0016 18.8 1.8 20 41-60 18-37 (45)
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=100.00 E-value=1.2e-35 Score=193.88 Aligned_cols=60 Identities=45% Similarity=0.727 Sum_probs=52.6
Q ss_pred CCCCccccccCceeccCCCCCcceeeccccccccCcccccceeecCCCCEEEEEEceeccCCC
Q 041468 25 EDDGYTWRKYGQKEILGSKFPRIARGATTDIRMDALQGKKLQQLSDDPVSFEITYHGEHTCQL 87 (124)
Q Consensus 25 ~~Dgy~WRKYGQK~Ikgs~~pRsYYrCt~~~~~~C~akK~Vqr~~~Dp~~~~vtY~GeHth~~ 87 (124)
.+|||+|||||||.|+|+++|||||||++. +|+|+|+|||+.+||.+|+|||+|+|||+.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~---~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k 60 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHP---GCPAKKQVQRSADDPNIVIVTYEGEHNHPK 60 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECT---TEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred CCCCCchhhccCcccCCCceeeEeeecccc---ChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence 489999999999999999999999999998 999999999999999999999999999973
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=100.00 E-value=4.5e-35 Score=191.00 Aligned_cols=59 Identities=51% Similarity=0.795 Sum_probs=56.4
Q ss_pred CCCCccccccCceeccCCCCCcceeeccccccccCcccccceeecCCCCEEEEEEceeccC
Q 041468 25 EDDGYTWRKYGQKEILGSKFPRIARGATTDIRMDALQGKKLQQLSDDPVSFEITYHGEHTC 85 (124)
Q Consensus 25 ~~Dgy~WRKYGQK~Ikgs~~pRsYYrCt~~~~~~C~akK~Vqr~~~Dp~~~~vtY~GeHth 85 (124)
++|||.|||||||.|+|+++||+|||||+. +||+|+|+||++++||.+|+|||+|+|||
T Consensus 1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~--~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTYS--QGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCCcccccccCcEecCCCcCcceEEecccc--CCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 479999999999999999999999999992 49999999999999999999999999998
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=96.01 E-value=0.0037 Score=38.46 Aligned_cols=50 Identities=14% Similarity=0.123 Sum_probs=24.8
Q ss_pred CCCccccccCceeccCCCCCcceeeccccccccCcccccceeecCCCCEEEEEEceeccC
Q 041468 26 DDGYTWRKYGQKEILGSKFPRIARGATTDIRMDALQGKKLQQLSDDPVSFEITYHGEHTC 85 (124)
Q Consensus 26 ~Dgy~WRKYGQK~Ikgs~~pRsYYrCt~~~~~~C~akK~Vqr~~~Dp~~~~vtY~GeHth 85 (124)
-|||.-.+.... ....|++|+.....+|+|+=.+. .++. .+ +...++|||
T Consensus 13 ~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~-~~-~~~~~~HnH 62 (62)
T PF04500_consen 13 YDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG-RV-VRTNGEHNH 62 (62)
T ss_dssp ETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT-EE-EE-S---SS
T ss_pred ECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC-EE-EECCCccCC
Confidence 366666554433 45689999999878999976666 3333 33 444599998
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=87.47 E-value=0.59 Score=30.94 Aligned_cols=31 Identities=13% Similarity=0.039 Sum_probs=26.0
Q ss_pred ccCcccccceeecCCCCEEEEEEceeccCCCC
Q 041468 57 MDALQGKKLQQLSDDPVSFEITYHGEHTCQLS 88 (124)
Q Consensus 57 ~~C~akK~Vqr~~~Dp~~~~vtY~GeHth~~~ 88 (124)
.||+|+=.|.+.. ++.-.++.+..+|||+..
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~ 90 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPLC 90 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence 4999988888766 778888899999999864
No 5
>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=81.59 E-value=1.1 Score=28.08 Aligned_cols=23 Identities=26% Similarity=0.215 Sum_probs=17.7
Q ss_pred CCCcccccccEEEecCCCCCCCC
Q 041468 5 PYSIVQKSQRTVRVDAPQIPEDD 27 (124)
Q Consensus 5 ~~~~~~k~k~~~~v~~~~~~~~D 27 (124)
.++...|.||+|+|+|++.-..|
T Consensus 25 sKkRK~RvKR~irVPAiS~K~AD 47 (47)
T PF10533_consen 25 SKKRKSRVKRTIRVPAISSKIAD 47 (47)
T ss_pred CCcccccceeeEEeecccccccC
Confidence 35677889999999999855444
No 6
>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=46.56 E-value=7.3 Score=28.74 Aligned_cols=9 Identities=56% Similarity=1.206 Sum_probs=7.4
Q ss_pred CCCCccccc
Q 041468 25 EDDGYTWRK 33 (124)
Q Consensus 25 ~~Dgy~WRK 33 (124)
-.|||.|||
T Consensus 51 RkDG~~WrK 59 (118)
T PF03859_consen 51 RKDGHNWRK 59 (118)
T ss_pred hcccceeEE
Confidence 369999995
No 7
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=29.48 E-value=60 Score=31.04 Aligned_cols=32 Identities=16% Similarity=0.131 Sum_probs=26.9
Q ss_pred cCcccccceeecCCCCEEEEEEceeccCCCCCC
Q 041468 58 DALQGKKLQQLSDDPVSFEITYHGEHTCQLSLE 90 (124)
Q Consensus 58 ~C~akK~Vqr~~~Dp~~~~vtY~GeHth~~~~~ 90 (124)
||+|.=.|.+.. |+.-.++-+..+|||+...+
T Consensus 160 GC~A~m~Vk~~~-~gkW~V~~fv~eHNH~L~p~ 191 (846)
T PLN03097 160 DCKASMHVKRRP-DGKWVIHSFVKEHNHELLPA 191 (846)
T ss_pred CCceEEEEEEcC-CCeEEEEEEecCCCCCCCCc
Confidence 999998888754 56788899999999998754
No 8
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=25.10 E-value=30 Score=28.89 Aligned_cols=14 Identities=29% Similarity=0.895 Sum_probs=10.9
Q ss_pred CCCCCccccccCce
Q 041468 24 PEDDGYTWRKYGQK 37 (124)
Q Consensus 24 ~~~Dgy~WRKYGQK 37 (124)
.+-=||+||-+|-+
T Consensus 112 gpvyGfqWrHfgA~ 125 (293)
T KOG0673|consen 112 GPVYGFQWRHFGAR 125 (293)
T ss_pred ccccceeeeecCcc
Confidence 34468999999977
No 9
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=24.39 E-value=61 Score=24.01 Aligned_cols=14 Identities=43% Similarity=0.416 Sum_probs=11.8
Q ss_pred EEEcee-ccCCCCCC
Q 041468 77 ITYHGE-HTCQLSLE 90 (124)
Q Consensus 77 vtY~Ge-Hth~~~~~ 90 (124)
+.|.|+ |||+....
T Consensus 73 ~~ylGeWHtHP~~~p 87 (131)
T TIGR02256 73 DTYLGEWHTHPEDQP 87 (131)
T ss_pred eEEEEecCcCCCCCC
Confidence 789999 99987755
No 10
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=24.27 E-value=49 Score=19.68 Aligned_cols=18 Identities=6% Similarity=-0.160 Sum_probs=12.8
Q ss_pred Ccceeecccccccc--Cccc
Q 041468 45 PRIARGATTDIRMD--ALQG 62 (124)
Q Consensus 45 pRsYYrCt~~~~~~--C~ak 62 (124)
.+.||+|......+ |+++
T Consensus 23 ~~~yy~C~~~~~~~~~C~~~ 42 (58)
T PF13408_consen 23 KYRYYRCSNRRRKGKGCPNK 42 (58)
T ss_pred CceEEEcCCCcCCCCCCCCC
Confidence 34899999875544 7764
No 11
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=22.35 E-value=75 Score=18.79 Aligned_cols=20 Identities=10% Similarity=-0.137 Sum_probs=13.9
Q ss_pred CCCCCcceeeccccccccCc
Q 041468 41 GSKFPRIARGATTDIRMDAL 60 (124)
Q Consensus 41 gs~~pRsYYrCt~~~~~~C~ 60 (124)
|.+.-|-||+|......+|.
T Consensus 18 ~~N~GR~Fy~C~~~~~~~C~ 37 (45)
T PF06839_consen 18 GPNPGRRFYKCPNYKDKGCN 37 (45)
T ss_pred CCCCCCcceECCCCCCCCcC
Confidence 44445889999988654564
Done!