Query 015394
Match_columns 407
No_of_seqs 292 out of 1009
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:53:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015394.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015394hhsearch_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 99.9 3.5E-29 7.7E-34 194.2 1.2 59 216-274 1-60 (60)
2 smart00774 WRKY DNA binding do 99.9 3.9E-28 8.5E-33 188.0 4.2 57 216-272 1-59 (59)
3 PF03106 WRKY: WRKY DNA -bindi 99.7 1.8E-19 4E-24 140.0 0.8 29 379-407 1-29 (60)
4 smart00774 WRKY DNA binding do 99.7 8.4E-19 1.8E-23 136.1 2.1 29 379-407 1-29 (59)
5 PF04500 FLYWCH: FLYWCH zinc f 87.6 0.2 4.3E-06 37.1 0.4 49 215-272 11-62 (62)
6 PF03101 FAR1: FAR1 DNA-bindin 83.7 0.72 1.6E-05 37.2 1.9 30 245-274 60-89 (91)
7 KOG0673 Thymidylate synthase [ 31.1 19 0.00042 36.0 0.5 22 380-401 114-156 (293)
8 PLN03097 FHY3 Protein FAR-RED 25.8 67 0.0015 37.2 3.7 36 242-277 156-191 (846)
9 PF03859 CG-1: CG-1 domain; I 23.3 47 0.001 29.8 1.5 28 360-387 32-59 (118)
10 PF02756 GYR: GYR motif; Inte 20.5 41 0.00089 20.9 0.4 7 380-386 1-7 (18)
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=99.95 E-value=3.5e-29 Score=194.23 Aligned_cols=59 Identities=61% Similarity=1.230 Sum_probs=50.9
Q ss_pred CCCCcchhhcCcccCCCCCCCCCccccCCcccccccceeccc-CCceEEEEecccCCCCC
Q 015394 216 SDDGYNWRKYGQKHVKGSEFPRSYYKCTHPNCEVKKLFERSH-DGQITEIIYKGTHDHPK 274 (407)
Q Consensus 216 ~~DGy~WRKYGQK~ikgs~~pRsYYkCt~~~C~akK~Vqr~~-dg~i~~i~Y~G~HnH~~ 274 (407)
.+|||+|||||||.|+|+++||+||||++.+|+|+|+|||+. |+.+++|+|+|+|||++
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 479999999999999999999999999999999999999987 88999999999999985
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=99.94 E-value=3.9e-28 Score=187.99 Aligned_cols=57 Identities=58% Similarity=1.134 Sum_probs=54.8
Q ss_pred CCCCcchhhcCcccCCCCCCCCCccccCC-cccccccceeccc-CCceEEEEecccCCC
Q 015394 216 SDDGYNWRKYGQKHVKGSEFPRSYYKCTH-PNCEVKKLFERSH-DGQITEIIYKGTHDH 272 (407)
Q Consensus 216 ~~DGy~WRKYGQK~ikgs~~pRsYYkCt~-~~C~akK~Vqr~~-dg~i~~i~Y~G~HnH 272 (407)
.+|||.|||||||.|+|+++||+|||||+ ++|+|+|+|||+. |+++++|+|+|+|||
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 8999999999986 789999999999998
No 3
>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=99.75 E-value=1.8e-19 Score=139.98 Aligned_cols=29 Identities=59% Similarity=1.098 Sum_probs=25.4
Q ss_pred CCCccccccccccccCCCCCCCceeeccC
Q 015394 379 LDDGYRWRKYGQKVVRGNPNPRYVSNLMI 407 (407)
Q Consensus 379 ldDGyrWRKYGQK~VKGnp~PRsYYrCT~ 407 (407)
|||||+|||||||.||||+|||+|||||+
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~ 29 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTH 29 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEEC
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccc
Confidence 69999999999999999999999999985
No 4
>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=99.73 E-value=8.4e-19 Score=136.09 Aligned_cols=29 Identities=59% Similarity=1.123 Sum_probs=27.8
Q ss_pred CCCccccccccccccCCCCCCCceeeccC
Q 015394 379 LDDGYRWRKYGQKVVRGNPNPRYVSNLMI 407 (407)
Q Consensus 379 ldDGyrWRKYGQK~VKGnp~PRsYYrCT~ 407 (407)
++|||+|||||||.||||++||+|||||+
T Consensus 1 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~ 29 (59)
T smart00774 1 LDDGYQWRKYGQKVIKGSPFPRSYYRCTY 29 (59)
T ss_pred CCCcccccccCcEecCCCcCcceEEeccc
Confidence 58999999999999999999999999985
No 5
>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=87.59 E-value=0.2 Score=37.14 Aligned_cols=49 Identities=22% Similarity=0.611 Sum_probs=23.7
Q ss_pred CCCCCcchhhcCcccCCCCCCCCCccccCCc---ccccccceecccCCceEEEEecccCCC
Q 015394 215 PSDDGYNWRKYGQKHVKGSEFPRSYYKCTHP---NCEVKKLFERSHDGQITEIIYKGTHDH 272 (407)
Q Consensus 215 ~~~DGy~WRKYGQK~ikgs~~pRsYYkCt~~---~C~akK~Vqr~~dg~i~~i~Y~G~HnH 272 (407)
+.-|||.-+++... ..+.|++|+.. +|.|+=.+. ..++.+ +...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~-~~~~~~--~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD-AGDGRV--VRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE---TTEE--EE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE-CCCCEE--EECCCccCC
Confidence 44577775554433 45689999985 799987766 223333 445699999
No 6
>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=83.69 E-value=0.72 Score=37.19 Aligned_cols=30 Identities=23% Similarity=0.472 Sum_probs=25.6
Q ss_pred cccccccceecccCCceEEEEecccCCCCC
Q 015394 245 PNCEVKKLFERSHDGQITEIIYKGTHDHPK 274 (407)
Q Consensus 245 ~~C~akK~Vqr~~dg~i~~i~Y~G~HnH~~ 274 (407)
-+|+|+=.|.+..+|....+.+..+|||+.
T Consensus 60 tgC~a~i~v~~~~~~~w~v~~~~~~HNH~L 89 (91)
T PF03101_consen 60 TGCKARINVKRRKDGKWRVTSFVLEHNHPL 89 (91)
T ss_pred cCCCEEEEEEEccCCEEEEEECcCCcCCCC
Confidence 389999888776688888889999999986
No 7
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=31.11 E-value=19 Score=35.97 Aligned_cols=22 Identities=32% Similarity=0.931 Sum_probs=17.8
Q ss_pred CCcccccccccc---------------------ccCCCCCCCc
Q 015394 380 DDGYRWRKYGQK---------------------VVRGNPNPRY 401 (407)
Q Consensus 380 dDGyrWRKYGQK---------------------~VKGnp~PRs 401 (407)
-=||+||-+|-| .||.||+-|-
T Consensus 114 vyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drR 156 (293)
T KOG0673|consen 114 VYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRR 156 (293)
T ss_pred ccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccce
Confidence 359999999988 5788888774
No 8
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=25.76 E-value=67 Score=37.22 Aligned_cols=36 Identities=19% Similarity=0.406 Sum_probs=31.4
Q ss_pred cCCcccccccceecccCCceEEEEecccCCCCCCCc
Q 015394 242 CTHPNCEVKKLFERSHDGQITEIIYKGTHDHPKPQL 277 (407)
Q Consensus 242 Ct~~~C~akK~Vqr~~dg~i~~i~Y~G~HnH~~p~~ 277 (407)
|+--||+|.=.|.+..+|....+-+..+|||+.-.+
T Consensus 156 ~tRtGC~A~m~Vk~~~~gkW~V~~fv~eHNH~L~p~ 191 (846)
T PLN03097 156 CAKTDCKASMHVKRRPDGKWVIHSFVKEHNHELLPA 191 (846)
T ss_pred ccCCCCceEEEEEEcCCCeEEEEEEecCCCCCCCCc
Confidence 777899999999888889888889999999998644
No 9
>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=23.33 E-value=47 Score=29.77 Aligned_cols=28 Identities=21% Similarity=0.293 Sum_probs=16.9
Q ss_pred ccccccCeeEEecccccccCCCcccccc
Q 015394 360 VKPIREPRVVVQTLSEVDILDDGYRWRK 387 (407)
Q Consensus 360 ~~~~re~rvvvqt~se~dildDGyrWRK 387 (407)
.++....-+.+-..-...--.|||.|||
T Consensus 32 ~rP~sGslfLf~Rk~~r~fRkDG~~WrK 59 (118)
T PF03859_consen 32 NRPPSGSLFLFNRKVVRFFRKDGHNWRK 59 (118)
T ss_pred CCCCCceEEEEEchHhhhhhcccceeEE
Confidence 3444444454444444446689999998
No 10
>PF02756 GYR: GYR motif; InterPro: IPR004011 The GYR motif is found in several Drosophila melanogaster proteins, in either single or multiple copies. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases.
Probab=20.55 E-value=41 Score=20.88 Aligned_cols=7 Identities=71% Similarity=1.678 Sum_probs=5.8
Q ss_pred CCccccc
Q 015394 380 DDGYRWR 386 (407)
Q Consensus 380 dDGyrWR 386 (407)
||||+++
T Consensus 1 ddGYrYk 7 (18)
T PF02756_consen 1 DDGYRYK 7 (18)
T ss_pred CCcceee
Confidence 6999875
Done!