Query 032690
Match_columns 135
No_of_seqs 124 out of 631
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:42:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032690.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032690hhsearch_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 9.6E-36 2.1E-40 197.5 1.2 60 30-89 1-60 (60)
2 smart00774 WRKY DNA binding do 100.0 1.4E-34 3.1E-39 191.7 2.6 58 30-87 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 92.3 0.051 1.1E-06 33.8 0.5 49 29-87 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 89.4 0.14 3.1E-06 34.6 0.6 30 60-90 61-90 (91)
5 PF03859 CG-1: CG-1 domain; I 47.5 6.9 0.00015 29.4 0.3 9 30-38 51-59 (118)
6 COG4283 Uncharacterized conser 32.0 23 0.0005 28.1 1.0 18 24-41 70-87 (170)
7 KOG0673 Thymidylate synthase [ 27.9 25 0.00053 29.9 0.6 16 26-42 110-125 (293)
8 PLN03097 FHY3 Protein FAR-RED 23.7 50 0.0011 32.1 1.8 35 56-91 156-190 (846)
9 PF11776 DUF3315: Domain of un 20.3 38 0.00082 21.4 0.2 22 23-44 19-40 (52)
10 PF03119 DNA_ligase_ZBD: NAD-d 19.5 43 0.00093 18.7 0.3 12 52-63 16-28 (28)
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=9.6e-36 Score=197.48 Aligned_cols=60 Identities=43% Similarity=0.861 Sum_probs=52.6
Q ss_pred CCCCccccccccccccCCCCCccccccccccchhhhhhhhhcCCCCeEEEEEecCCCCCC
Q 032690 30 PEDGYEWKKYGQKFIKNIRKFRSYFKCQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTH 89 (135)
Q Consensus 30 ~~DGy~WRKYGQK~ikg~~~pRsYyrCt~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~ 89 (135)
++|||.|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+|+|||+|+|||+.
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 479999999999999999999999999999999999999999999999999999999973
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=1.4e-34 Score=191.73 Aligned_cols=58 Identities=45% Similarity=0.912 Sum_probs=56.4
Q ss_pred CCCCccccccccccccCCCCCcccccccc-ccchhhhhhhhhcCCCCeEEEEEecCCCC
Q 032690 30 PEDGYEWKKYGQKFIKNIRKFRSYFKCQE-SSCMAKKRAEWCTSDPTNVRIVYDGVHSH 87 (135)
Q Consensus 30 ~~DGy~WRKYGQK~ikg~~~pRsYyrCt~-~~C~akK~Vqr~~~d~~~~~vtY~G~H~h 87 (135)
++|||.|||||||.|+|+++||+||||++ ++|+|+|+||++++|+.+|+|||+|+|||
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=92.28 E-value=0.051 Score=33.81 Aligned_cols=49 Identities=22% Similarity=0.503 Sum_probs=24.7
Q ss_pred CCCCCccccccccccccCCCCCccccccccc---cchhhhhhhhhcCCCCeEEEEEecCCCC
Q 032690 29 LPEDGYEWKKYGQKFIKNIRKFRSYFKCQES---SCMAKKRAEWCTSDPTNVRIVYDGVHSH 87 (135)
Q Consensus 29 ~~~DGy~WRKYGQK~ikg~~~pRsYyrCt~~---~C~akK~Vqr~~~d~~~~~vtY~G~H~h 87 (135)
+.-|||.-.+.... ....|++|+.. +|+|+=.+. .+... .+...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~---~~~~~-~~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD---AGDGR-VVRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TTE-EEE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE---CCCCE-EEECCCccCC
Confidence 45678887765554 44689999986 699977666 22233 3444489998
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=89.43 E-value=0.14 Score=34.56 Aligned_cols=30 Identities=17% Similarity=0.126 Sum_probs=24.3
Q ss_pred cchhhhhhhhhcCCCCeEEEEEecCCCCCCC
Q 032690 60 SCMAKKRAEWCTSDPTNVRIVYDGVHSHTHH 90 (135)
Q Consensus 60 ~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p 90 (135)
+|+|+=.|-+.. ++...++.+..+|||+.-
T Consensus 61 gC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~ 90 (91)
T PF03101_consen 61 GCKARINVKRRK-DGKWRVTSFVLEHNHPLC 90 (91)
T ss_pred CCCEEEEEEEcc-CCEEEEEECcCCcCCCCC
Confidence 499987777754 777888899999999863
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=47.53 E-value=6.9 Score=29.37 Aligned_cols=9 Identities=44% Similarity=1.125 Sum_probs=7.6
Q ss_pred CCCCccccc
Q 032690 30 PEDGYEWKK 38 (135)
Q Consensus 30 ~~DGy~WRK 38 (135)
-.|||.|||
T Consensus 51 RkDG~~WrK 59 (118)
T PF03859_consen 51 RKDGHNWRK 59 (118)
T ss_pred hcccceeEE
Confidence 479999995
No 6
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=32.00 E-value=23 Score=28.14 Aligned_cols=18 Identities=28% Similarity=0.831 Sum_probs=14.4
Q ss_pred ccccCCCCCCcccccccc
Q 032690 24 VHRLVLPEDGYEWKKYGQ 41 (135)
Q Consensus 24 ~~~~~~~~DGy~WRKYGQ 41 (135)
+-..-+|.+||.|+.||.
T Consensus 70 G~~~f~Ps~~ykWn~~ge 87 (170)
T COG4283 70 GLKVFTPSPGYKWNNLGE 87 (170)
T ss_pred CCcCCCCCCCCcccccHH
Confidence 444677889999999995
No 7
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=27.91 E-value=25 Score=29.87 Aligned_cols=16 Identities=25% Similarity=0.806 Sum_probs=11.5
Q ss_pred ccCCCCCCccccccccc
Q 032690 26 RLVLPEDGYEWKKYGQK 42 (135)
Q Consensus 26 ~~~~~~DGy~WRKYGQK 42 (135)
.+.+.. ||+||-+|-|
T Consensus 110 Dlgpvy-GfqWrHfgA~ 125 (293)
T KOG0673|consen 110 DLGPVY-GFQWRHFGAR 125 (293)
T ss_pred Cccccc-ceeeeecCcc
Confidence 334333 8999999977
No 8
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=23.70 E-value=50 Score=32.09 Aligned_cols=35 Identities=20% Similarity=0.270 Sum_probs=28.9
Q ss_pred cccccchhhhhhhhhcCCCCeEEEEEecCCCCCCCC
Q 032690 56 CQESSCMAKKRAEWCTSDPTNVRIVYDGVHSHTHHG 91 (135)
Q Consensus 56 Ct~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~~p~ 91 (135)
|+--+|+|.=.|.+. .|+.-.++-++.+|||+.-+
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p 190 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLP 190 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCC
Confidence 677789999998774 56678899999999999753
No 9
>PF11776 DUF3315: Domain of unknown function (DUF3315); InterPro: IPR024572 This is a bacterial family of uncharacterised proteins, which include YohN from Escherichia coli K12.; PDB: 2L1S_A.
Probab=20.31 E-value=38 Score=21.45 Aligned_cols=22 Identities=32% Similarity=0.765 Sum_probs=12.2
Q ss_pred cccccCCCCCCccccccccccc
Q 032690 23 RVHRLVLPEDGYEWKKYGQKFI 44 (135)
Q Consensus 23 ~~~~~~~~~DGy~WRKYGQK~i 44 (135)
....+..+..||.|.+.|.+-+
T Consensus 19 ~~~~L~~Pp~G~~Wvrv~~dyv 40 (52)
T PF11776_consen 19 RRYGLPAPPRGYHWVRVGGDYV 40 (52)
T ss_dssp TTSS-----TTEEEEE-SSEEE
T ss_pred HHCCCCcCCCCCEeEEECCeEE
Confidence 4456778899999999887655
No 10
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=19.45 E-value=43 Score=18.68 Aligned_cols=12 Identities=33% Similarity=0.728 Sum_probs=7.3
Q ss_pred cccccccc-cchh
Q 032690 52 SYFKCQES-SCMA 63 (135)
Q Consensus 52 sYyrCt~~-~C~a 63 (135)
..+||++. .|+|
T Consensus 16 v~~~C~N~l~CpA 28 (28)
T PF03119_consen 16 VDIRCPNPLSCPA 28 (28)
T ss_dssp TCEEE--CGC-HH
T ss_pred EeEECCCCCcCCC
Confidence 47899998 8987
Done!