Query 016623
Match_columns 386
No_of_seqs 300 out of 795
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 08:31:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016623hhsearch_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 4.2E-32 9E-37 208.7 2.4 60 127-187 1-60 (60)
2 smart00774 WRKY DNA binding do 100.0 1.2E-31 2.6E-36 206.5 4.4 59 127-185 1-59 (59)
3 PF03101 FAR1: FAR1 DNA-bindin 93.8 0.04 8.7E-07 43.6 2.2 32 157-189 60-91 (91)
4 PF04500 FLYWCH: FLYWCH zinc f 93.8 0.028 6.2E-07 40.9 1.1 50 126-185 11-62 (62)
5 PLN03097 FHY3 Protein FAR-RED 24.7 70 0.0015 36.7 3.5 36 153-190 156-191 (846)
6 PF03859 CG-1: CG-1 domain; I 24.4 23 0.0005 31.6 -0.2 9 127-135 51-59 (118)
7 KOG0673 Thymidylate synthase [ 19.6 38 0.00082 34.0 0.2 28 127-154 113-161 (293)
8 COG4391 Uncharacterized protei 13.4 75 0.0016 25.7 0.4 13 3-15 37-49 (62)
9 cd07691 Ig_CD3_gamma_delta Imm 11.7 98 0.0021 25.4 0.6 27 129-156 17-53 (69)
10 PF08731 AFT: Transcription fa 10.6 2.9E+02 0.0063 24.6 3.2 31 157-187 81-111 (111)
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=4.2e-32 Score=208.74 Aligned_cols=60 Identities=65% Similarity=1.255 Sum_probs=52.2
Q ss_pred CCccchhhhccccccCCCCCCCccccccccCCcccccceeeecCCCcEEEEEeccCCCCCC
Q 016623 127 ITDGCQWRKYGQKMAKGNPCPRAYYRCTMAVGCPVRKQVQRCAEDRTILITTYEGNHNHPL 187 (386)
Q Consensus 127 ~~DGy~WRKYGQK~IKGsp~PRsYYRCT~~~gC~arKqVQR~~dD~~il~tTYeG~HnH~~ 187 (386)
++|||+|||||||.|+|+++||+||||++. +|+|+|+|||+.+|+.+++|||+|+|||+.
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 579999999999999999999999999995 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=99.97 E-value=1.2e-31 Score=206.50 Aligned_cols=59 Identities=59% Similarity=1.203 Sum_probs=57.1
Q ss_pred CCccchhhhccccccCCCCCCCccccccccCCcccccceeeecCCCcEEEEEeccCCCC
Q 016623 127 ITDGCQWRKYGQKMAKGNPCPRAYYRCTMAVGCPVRKQVQRCAEDRTILITTYEGNHNH 185 (386)
Q Consensus 127 ~~DGy~WRKYGQK~IKGsp~PRsYYRCT~~~gC~arKqVQR~~dD~~il~tTYeG~HnH 185 (386)
++|||+|||||||.|||+++||+||||++.++|+|+|+|||+++|+.+++|||+|+|||
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 47999999999999999999999999999779999999999999999999999999998
No 3
>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=93.85 E-value=0.04 Score=43.60 Aligned_cols=32 Identities=41% Similarity=0.692 Sum_probs=27.0
Q ss_pred CCcccccceeeecCCCcEEEEEeccCCCCCCCh
Q 016623 157 VGCPVRKQVQRCAEDRTILITTYEGNHNHPLPP 189 (386)
Q Consensus 157 ~gC~arKqVQR~~dD~~il~tTYeG~HnH~~P~ 189 (386)
.||+|+=.|.+.. |....++.+..+|||++-|
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPLCP 91 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCCCC
Confidence 5999999998776 6777888999999999743
No 4
>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=93.80 E-value=0.028 Score=40.87 Aligned_cols=50 Identities=28% Similarity=0.575 Sum_probs=26.3
Q ss_pred CCCccchhhhccccccCCCCCCCcccccccc--CCcccccceeeecCCCcEEEEEeccCCCC
Q 016623 126 MITDGCQWRKYGQKMAKGNPCPRAYYRCTMA--VGCPVRKQVQRCAEDRTILITTYEGNHNH 185 (386)
Q Consensus 126 ~~~DGy~WRKYGQK~IKGsp~PRsYYRCT~~--~gC~arKqVQR~~dD~~il~tTYeG~HnH 185 (386)
++-|||.-+++... ..+.|+||+.. .+|+|+=.+. .++. .++...++|||
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 45699988876655 34589999985 3799987776 3344 23344499998
No 5
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=24.68 E-value=70 Score=36.65 Aligned_cols=36 Identities=31% Similarity=0.612 Sum_probs=28.6
Q ss_pred ccccCCcccccceeeecCCCcEEEEEeccCCCCCCChh
Q 016623 153 CTMAVGCPVRKQVQRCAEDRTILITTYEGNHNHPLPPA 190 (386)
Q Consensus 153 CT~~~gC~arKqVQR~~dD~~il~tTYeG~HnH~~P~a 190 (386)
|+- .||+|+=.|.+..+ ..-.++-++.+|||++-++
T Consensus 156 ~tR-tGC~A~m~Vk~~~~-gkW~V~~fv~eHNH~L~p~ 191 (846)
T PLN03097 156 CAK-TDCKASMHVKRRPD-GKWVIHSFVKEHNHELLPA 191 (846)
T ss_pred ccC-CCCceEEEEEEcCC-CeEEEEEEecCCCCCCCCc
Confidence 554 59999999987544 4578889999999998654
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=24.37 E-value=23 Score=31.62 Aligned_cols=9 Identities=56% Similarity=1.129 Sum_probs=7.5
Q ss_pred CCccchhhh
Q 016623 127 ITDGCQWRK 135 (386)
Q Consensus 127 ~~DGy~WRK 135 (386)
-.|||.|||
T Consensus 51 RkDG~~WrK 59 (118)
T PF03859_consen 51 RKDGHNWRK 59 (118)
T ss_pred hcccceeEE
Confidence 369999996
No 7
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=19.63 E-value=38 Score=34.02 Aligned_cols=28 Identities=32% Similarity=0.565 Sum_probs=20.2
Q ss_pred CCccchhhhcccc---------------------ccCCCCCCCcccccc
Q 016623 127 ITDGCQWRKYGQK---------------------MAKGNPCPRAYYRCT 154 (386)
Q Consensus 127 ~~DGy~WRKYGQK---------------------~IKGsp~PRsYYRCT 154 (386)
+-=|++||-+|-| .||.||+-|----|.
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 3469999999977 567888877544443
No 8
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=13.38 E-value=75 Score=25.73 Aligned_cols=13 Identities=38% Similarity=0.864 Sum_probs=11.0
Q ss_pred CcccccCCCCCcc
Q 016623 3 PRQFIGLGPSAET 15 (386)
Q Consensus 3 prqf~~lg~~~~~ 15 (386)
||-|||+|..+|.
T Consensus 37 PrV~L~mg~~gev 49 (62)
T COG4391 37 PRVFLDMGDEGEV 49 (62)
T ss_pred CEEEEEcCCCCcE
Confidence 8999999888764
No 9
>cd07691 Ig_CD3_gamma_delta Immunoglobulin (Ig)-like domain of CD3 gamma and delta chains. Ig_CD3_gamma_delta; immunoglobulin (Ig)-like domain of CD3 gamma and delta chains. CD3 is a T cell surface receptor that is associated with alpha/beta T cell receptors (TCRs). The CD3 complex consists of one gamma, one delta, two epsilon, and two zeta chains. The CD3 subunits form heterodimers as gamma/epsilon, delta/epsilon, and zeta/zeta. The gamma, delta, and epsilon chains each contain an extracellular Ig domain, whereas the extracellular domains of the zeta chains are very small and have unknown structure. The CD3 domain participates in intracellular signalling once the TCR has bound an MHC/antigen complex.
Probab=11.74 E-value=98 Score=25.39 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=19.6
Q ss_pred ccchhhhccccccCCC----------CCCCcccccccc
Q 016623 129 DGCQWRKYGQKMAKGN----------PCPRAYYRCTMA 156 (386)
Q Consensus 129 DGy~WRKYGQK~IKGs----------p~PRsYYRCT~~ 156 (386)
.-+.|-| |-..+.-+ .-||+-|+|.-.
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~~s 53 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCKES 53 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEecCc
Confidence 5588999 86544332 789999999753
No 10
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=10.57 E-value=2.9e+02 Score=24.59 Aligned_cols=31 Identities=26% Similarity=0.572 Sum_probs=19.4
Q ss_pred CCcccccceeeecCCCcEEEEEeccCCCCCC
Q 016623 157 VGCPVRKQVQRCAEDRTILITTYEGNHNHPL 187 (386)
Q Consensus 157 ~gC~arKqVQR~~dD~~il~tTYeG~HnH~~ 187 (386)
-+||.+-.---+..+..=-+++-.++|+|++
T Consensus 81 ~~CPFriRA~yS~k~k~W~lvvvnn~HnH~l 111 (111)
T PF08731_consen 81 NTCPFRIRANYSKKNKKWTLVVVNNEHNHPL 111 (111)
T ss_pred cCCCeEEEEEEEecCCeEEEEEecCCcCCCC
Confidence 3667654443334444445778899999985
Done!