Query 045509
Match_columns 291
No_of_seqs 208 out of 715
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 02:50:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045509.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045509hhsearch_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 1.7E-31 3.7E-36 198.7 2.4 59 142-200 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 1.7E-30 3.7E-35 193.6 4.4 58 142-199 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 90.0 0.16 3.4E-06 35.6 1.2 48 142-199 12-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 84.7 0.66 1.4E-05 35.3 2.0 30 172-202 61-90 (91)
5 COG3280 TreY Maltooligosyl tre 31.7 17 0.00036 40.0 0.2 15 275-289 80-94 (889)
6 PF03859 CG-1: CG-1 domain; I 24.2 23 0.00051 30.4 -0.2 8 143-150 52-59 (118)
7 PF10533 Plant_zn_clust: Plant 18.1 1.3E+02 0.0028 22.3 2.5 21 112-132 21-42 (47)
8 PLN03097 FHY3 Protein FAR-RED 14.1 2E+02 0.0043 32.0 3.9 35 168-203 156-190 (846)
9 KOG0673 Thymidylate synthase [ 12.9 70 0.0015 31.0 0.1 28 142-169 113-161 (293)
10 PF04606 Ogr_Delta: Ogr/Delta- 12.7 90 0.002 22.0 0.6 16 163-178 23-38 (47)
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=99.96 E-value=1.7e-31 Score=198.74 Aligned_cols=59 Identities=68% Similarity=1.322 Sum_probs=52.6
Q ss_pred CCccchhhhcCccccCCCCCCcccccccCCccccccceecccCCCCEEEEEEecccCCC
Q 045509 142 LEDGYRWRKYGQKAVKNSPFPRSYYRCTNSKCTVKKRVERSSEDPTIVITTYEGQHCHH 200 (291)
Q Consensus 142 ~~DGy~WRKYGQK~Ikgs~~pRsYYRCt~~~C~akKqVqrs~~Dp~~~~~tY~G~H~H~ 200 (291)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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 47999999999999999999999999999999999999999999999999999999996
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=99.96 E-value=1.7e-30 Score=193.64 Aligned_cols=58 Identities=66% Similarity=1.296 Sum_probs=56.3
Q ss_pred CCccchhhhcCccccCCCCCCcccccccC-CccccccceecccCCCCEEEEEEecccCC
Q 045509 142 LEDGYRWRKYGQKAVKNSPFPRSYYRCTN-SKCTVKKRVERSSEDPTIVITTYEGQHCH 199 (291)
Q Consensus 142 ~~DGy~WRKYGQK~Ikgs~~pRsYYRCt~-~~C~akKqVqrs~~Dp~~~~~tY~G~H~H 199 (291)
++|||.|||||||.|+|+++||+|||||+ ++|+|+|+|||+.+|+.+++|||+|+|||
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 89999999999999999999999999998
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=89.96 E-value=0.16 Score=35.62 Aligned_cols=48 Identities=25% Similarity=0.573 Sum_probs=23.8
Q ss_pred CCccchhhhcCccccCCCCCCcccccccCC---ccccccceecccCCCCEEEEEEecccCC
Q 045509 142 LEDGYRWRKYGQKAVKNSPFPRSYYRCTNS---KCTVKKRVERSSEDPTIVITTYEGQHCH 199 (291)
Q Consensus 142 ~~DGy~WRKYGQK~Ikgs~~pRsYYRCt~~---~C~akKqVqrs~~Dp~~~~~tY~G~H~H 199 (291)
.-|||.-+++... ....|+||+.. +|.|+=.+. .++. .++...++|||
T Consensus 12 ~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 12 VYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp EETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred EECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 4578886654444 45689999985 799977666 3344 34445599998
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=84.72 E-value=0.66 Score=35.32 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=25.5
Q ss_pred ccccccceecccCCCCEEEEEEecccCCCCC
Q 045509 172 KCTVKKRVERSSEDPTIVITTYEGQHCHHTV 202 (291)
Q Consensus 172 ~C~akKqVqrs~~Dp~~~~~tY~G~H~H~~~ 202 (291)
+|+|+=.|.+.. ++...++.+..+|||+..
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 899998888776 777888999999999853
No 5
>COG3280 TreY Maltooligosyl trehalose synthase [Carbohydrate transport and metabolism]
Probab=31.73 E-value=17 Score=40.00 Aligned_cols=15 Identities=47% Similarity=0.629 Sum_probs=13.1
Q ss_pred CCCCcccCCCCCCCC
Q 045509 275 TDEGLLGDIVPPGMR 289 (291)
Q Consensus 275 ~d~GLL~Divp~~mr 289 (291)
.-.||+.||||.||=
T Consensus 80 ~GlGlI~DIVPNHMa 94 (889)
T COG3280 80 RGLGLIVDIVPNHMA 94 (889)
T ss_pred cCCceEEEecccchh
Confidence 467999999999994
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=24.18 E-value=23 Score=30.40 Aligned_cols=8 Identities=63% Similarity=1.361 Sum_probs=7.0
Q ss_pred Cccchhhh
Q 045509 143 EDGYRWRK 150 (291)
Q Consensus 143 ~DGy~WRK 150 (291)
.|||.|||
T Consensus 52 kDG~~WrK 59 (118)
T PF03859_consen 52 KDGHNWRK 59 (118)
T ss_pred cccceeEE
Confidence 59999995
No 7
>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=18.08 E-value=1.3e+02 Score=22.28 Aligned_cols=21 Identities=43% Similarity=0.406 Sum_probs=15.0
Q ss_pred CCCCchhhccCCCc-eecceeE
Q 045509 112 PEIPSKARKKGQKR-IRQPRFA 132 (291)
Q Consensus 112 ~~~~sK~rk~~~Kr-~~~~r~~ 132 (291)
...++|+||...|| ++.|++.
T Consensus 21 rCHCsKkRK~RvKR~irVPAiS 42 (47)
T PF10533_consen 21 RCHCSKKRKSRVKRTIRVPAIS 42 (47)
T ss_pred cccCCCcccccceeeEEeeccc
Confidence 46788888877776 6667654
No 8
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=14.09 E-value=2e+02 Score=32.00 Aligned_cols=35 Identities=26% Similarity=0.560 Sum_probs=29.1
Q ss_pred ccCCccccccceecccCCCCEEEEEEecccCCCCCC
Q 045509 168 CTNSKCTVKKRVERSSEDPTIVITTYEGQHCHHTVG 203 (291)
Q Consensus 168 Ct~~~C~akKqVqrs~~Dp~~~~~tY~G~H~H~~~~ 203 (291)
|+--||.|.=.|.+.. ++.-.++.+..+|||+...
T Consensus 156 ~tRtGC~A~m~Vk~~~-~gkW~V~~fv~eHNH~L~p 190 (846)
T PLN03097 156 CAKTDCKASMHVKRRP-DGKWVIHSFVKEHNHELLP 190 (846)
T ss_pred ccCCCCceEEEEEEcC-CCeEEEEEEecCCCCCCCC
Confidence 6777999999998754 5678899999999998753
No 9
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=12.94 E-value=70 Score=31.04 Aligned_cols=28 Identities=29% Similarity=0.655 Sum_probs=20.3
Q ss_pred CCccchhhhcCcc---------------------ccCCCCCCccccccc
Q 045509 142 LEDGYRWRKYGQK---------------------AVKNSPFPRSYYRCT 169 (291)
Q Consensus 142 ~~DGy~WRKYGQK---------------------~Ikgs~~pRsYYRCt 169 (291)
+-=||+||-+|-| .||++|+.|----|+
T Consensus 113 pvyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIimsA 161 (293)
T KOG0673|consen 113 PVYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMSA 161 (293)
T ss_pred cccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeeec
Confidence 4568999999977 578888877544333
No 10
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=12.65 E-value=90 Score=21.96 Aligned_cols=16 Identities=31% Similarity=0.619 Sum_probs=13.3
Q ss_pred cccccccCCccccccc
Q 045509 163 RSYYRCTNSKCTVKKR 178 (291)
Q Consensus 163 RsYYRCt~~~C~akKq 178 (291)
..||.|++..|..+-.
T Consensus 23 ~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEEECCCcCCCEEE
Confidence 4899999999988653
Done!