Query 026216
Match_columns 241
No_of_seqs 155 out of 665
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 05:09:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026216.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026216hhsearch_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 4.5E-32 9.7E-37 196.9 3.1 59 167-225 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 5.9E-31 1.3E-35 191.6 5.0 58 167-224 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 92.4 0.045 9.7E-07 37.2 0.3 49 166-224 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 88.9 0.36 7.8E-06 35.6 2.5 31 196-227 60-90 (91)
5 PF10533 Plant_zn_clust: Plant 72.8 1.9 4.2E-05 30.9 1.1 20 139-158 24-43 (47)
6 PLN03097 FHY3 Protein FAR-RED 29.9 52 0.0011 35.3 3.4 34 193-227 156-189 (846)
7 COG0319 Predicted metal-depend 23.7 76 0.0016 27.2 2.8 39 14-62 35-73 (153)
8 PF03859 CG-1: CG-1 domain; I 22.6 31 0.00068 28.9 0.2 10 166-175 50-59 (118)
9 KOG0612 Rho-associated, coiled 16.7 83 0.0018 35.5 1.8 31 28-60 182-212 (1317)
10 PF02130 UPF0054: Uncharacteri 16.5 1.4E+02 0.003 24.9 2.8 38 13-60 31-68 (145)
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=4.5e-32 Score=196.88 Aligned_cols=59 Identities=64% Similarity=1.173 Sum_probs=52.5
Q ss_pred CCCCccccccCcccccCCCCCcccccccCCCCccccceeeecCCCCeEEEEEeecCCCC
Q 026216 167 LDDGYKWRKYGQKIVKNSLHPRSYYRCTHNNCRVKKRVERLSEDCRMVITTYEGRHNHS 225 (241)
Q Consensus 167 ~dDGy~WRKYGQK~Ikgs~~PRsYYRCT~~gC~AkKqVQr~~~D~~~~~tTY~G~HnH~ 225 (241)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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 58999999999999999999999999999999999999999999999999999999997
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=5.9e-31 Score=191.59 Aligned_cols=58 Identities=60% Similarity=1.123 Sum_probs=56.5
Q ss_pred CCCCccccccCcccccCCCCCcccccccC-CCCccccceeeecCCCCeEEEEEeecCCC
Q 026216 167 LDDGYKWRKYGQKIVKNSLHPRSYYRCTH-NNCRVKKRVERLSEDCRMVITTYEGRHNH 224 (241)
Q Consensus 167 ~dDGy~WRKYGQK~Ikgs~~PRsYYRCT~-~gC~AkKqVQr~~~D~~~~~tTY~G~HnH 224 (241)
++|||.|||||||.|+|+++||+||||++ ++|+|+|+|||+++|+.+++|||+|+|||
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 48999999999999999999999999999 89999999999989999999999999998
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=92.36 E-value=0.045 Score=37.17 Aligned_cols=49 Identities=27% Similarity=0.668 Sum_probs=25.1
Q ss_pred cCCCCccccccCcccccCCCCCcccccccCC---CCccccceeeecCCCCeEEEEEeecCCC
Q 026216 166 VLDDGYKWRKYGQKIVKNSLHPRSYYRCTHN---NCRVKKRVERLSEDCRMVITTYEGRHNH 224 (241)
Q Consensus 166 ~~dDGy~WRKYGQK~Ikgs~~PRsYYRCT~~---gC~AkKqVQr~~~D~~~~~tTY~G~HnH 224 (241)
++-|||.-++.... ....|+||+.. +|+|+=.+. .++. .++...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 56788876654444 45689999984 899987666 2343 44445599998
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=88.90 E-value=0.36 Score=35.63 Aligned_cols=31 Identities=29% Similarity=0.618 Sum_probs=26.2
Q ss_pred CCCccccceeeecCCCCeEEEEEeecCCCCCC
Q 026216 196 NNCRVKKRVERLSEDCRMVITTYEGRHNHSPC 227 (241)
Q Consensus 196 ~gC~AkKqVQr~~~D~~~~~tTY~G~HnH~~~ 227 (241)
-+|+|+=.|.+.. |+...++.+..+|||+.+
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 4899998888755 788889999999999853
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=72.77 E-value=1.9 Score=30.91 Aligned_cols=20 Identities=25% Similarity=0.419 Sum_probs=17.2
Q ss_pred hhhhhhhhhhhcccCCceEE
Q 026216 139 SEKINKVKARRKLREPRFCF 158 (241)
Q Consensus 139 ~~K~~K~k~RR~~r~pr~~~ 158 (241)
+.|+||.+++|.+++|.+..
T Consensus 24 CsKkRK~RvKR~irVPAiS~ 43 (47)
T PF10533_consen 24 CSKKRKSRVKRTIRVPAISS 43 (47)
T ss_pred CCCcccccceeeEEeecccc
Confidence 56889999999999998764
No 6
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=29.88 E-value=52 Score=35.29 Aligned_cols=34 Identities=29% Similarity=0.641 Sum_probs=29.5
Q ss_pred ccCCCCccccceeeecCCCCeEEEEEeecCCCCCC
Q 026216 193 CTHNNCRVKKRVERLSEDCRMVITTYEGRHNHSPC 227 (241)
Q Consensus 193 CT~~gC~AkKqVQr~~~D~~~~~tTY~G~HnH~~~ 227 (241)
|+.-||+|.=.|.+ ..|+.-.++-+..+|||+..
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 56778889999999999875
No 7
>COG0319 Predicted metal-dependent hydrolase [General function prediction only]
Probab=23.67 E-value=76 Score=27.24 Aligned_cols=39 Identities=15% Similarity=0.190 Sum_probs=30.3
Q ss_pred CCCceEEEeeecHHHHHHHHHHHHhccCCccccccccccccEeEeccCC
Q 026216 14 IPNYEVQASFTTAEAEAAAAAAAAQGMGSFVHDFDENHEHQVLSFMGAP 62 (241)
Q Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~ 62 (241)
++.+||-|.|+..+. |++++ ......+.-+.||||=.-+
T Consensus 35 ~~~~elsv~~vdd~e--------i~eLN--~~yR~kD~pTDVLSFp~~e 73 (153)
T COG0319 35 ISTAELSVVLVDDAE--------IRELN--LEYRGKDKPTDVLSFPYNE 73 (153)
T ss_pred CCCceEEEEEeCHHH--------HHHHH--HHHcCCCCCCceEEecCCC
Confidence 678999999998877 89998 2244566788999996533
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=22.63 E-value=31 Score=28.89 Aligned_cols=10 Identities=50% Similarity=1.013 Sum_probs=8.2
Q ss_pred cCCCCccccc
Q 026216 166 VLDDGYKWRK 175 (241)
Q Consensus 166 ~~dDGy~WRK 175 (241)
.-.|||.|||
T Consensus 50 fRkDG~~WrK 59 (118)
T PF03859_consen 50 FRKDGHNWRK 59 (118)
T ss_pred hhcccceeEE
Confidence 4579999995
No 9
>KOG0612 consensus Rho-associated, coiled-coil containing protein kinase [Signal transduction mechanisms]
Probab=16.66 E-value=83 Score=35.50 Aligned_cols=31 Identities=32% Similarity=0.473 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhccCCccccccccccccEeEecc
Q 026216 28 AEAAAAAAAAQGMGSFVHDFDENHEHQVLSFMG 60 (241)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 60 (241)
||-..|..+||.|| |||. +-..+|..|.--+
T Consensus 182 aEiVlAldslH~mg-yVHR-DiKPDNvLld~~G 212 (1317)
T KOG0612|consen 182 AEIVLALDSLHSMG-YVHR-DIKPDNVLLDKSG 212 (1317)
T ss_pred HHHHHHHHHHHhcc-ceec-cCCcceeEecccC
Confidence 67788899999999 9975 4456788887644
No 10
>PF02130 UPF0054: Uncharacterized protein family UPF0054; InterPro: IPR002036 These, as yet, uncharacterised proteins are of 17 to 21 kDa. They contain a conserved region with three histidines at the C terminus. The protein family is represented by a single member sequence only in nearly every bacterium. The crystal structure of the protein from the hyperthermophilic bacteria Aquifex aeolicus has been determined. The overall fold consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis reveals a good resemblance to the metal-dependent proteinases such as collagenases and gelatinases. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions [].; GO: 0046872 metal ion binding; PDB: 1TVI_A 1OZ9_A 1XM5_A 1XAX_A.
Probab=16.52 E-value=1.4e+02 Score=24.85 Aligned_cols=38 Identities=21% Similarity=0.337 Sum_probs=25.7
Q ss_pred CCCCceEEEeeecHHHHHHHHHHHHhccCCccccccccccccEeEecc
Q 026216 13 GIPNYEVQASFTTAEAEAAAAAAAAQGMGSFVHDFDENHEHQVLSFMG 60 (241)
Q Consensus 13 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~ 60 (241)
.++.+||-+.|.+.+. |++|+. - -...+.-+.||||=.
T Consensus 31 ~~~~~el~i~fv~~~~--------i~~LN~-~-yr~~d~pTDVLSFp~ 68 (145)
T PF02130_consen 31 KVPDFELSIVFVDDEE--------IRELNK-Q-YRGKDYPTDVLSFPY 68 (145)
T ss_dssp CSCCCEEEEEEE-HHH--------HHHHHH-H-HHS-SSS-SEEEEE-
T ss_pred CCCCCeEEEEEECHHH--------HHHHHH-H-HcCCCCCCeEEeECC
Confidence 4566799999998888 899982 1 234456789999954
Done!