Query 021896
Match_columns 306
No_of_seqs 168 out of 733
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 06:29:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021896.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021896hhsearch_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 7.6E-33 1.6E-37 207.1 1.9 60 128-188 1-60 (60)
2 smart00774 WRKY DNA binding do 100.0 3E-32 6.5E-37 204.3 4.9 58 129-186 2-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 94.3 0.015 3.3E-07 41.0 0.6 49 128-186 12-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 93.3 0.076 1.6E-06 40.7 2.7 30 158-188 60-89 (91)
5 PF10533 Plant_zn_clust: Plant 33.1 28 0.00061 25.9 1.5 20 104-124 21-40 (47)
6 PLN03097 FHY3 Protein FAR-RED 26.6 60 0.0013 36.0 3.3 33 154-188 156-188 (846)
7 PF03859 CG-1: CG-1 domain; I 24.2 77 0.0017 27.5 2.9 56 128-184 51-118 (118)
8 KOG0673 Thymidylate synthase [ 23.1 32 0.00069 33.5 0.4 25 130-154 115-160 (293)
9 cd07691 Ig_CD3_gamma_delta Imm 14.5 91 0.002 24.8 1.1 26 130-156 17-52 (69)
10 COG4283 Uncharacterized conser 13.8 78 0.0017 29.1 0.7 13 127-139 75-87 (170)
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=7.6e-33 Score=207.14 Aligned_cols=60 Identities=63% Similarity=1.185 Sum_probs=52.1
Q ss_pred CCCCccccccCcccCCCCCCCCCceecCCCCCCccccceeeccCCCCeEEEEeCcCCCCCC
Q 021896 128 ACDKWAWRKYGQKPIKGSPYPRSYYRCSSSKGCLARKQVERSSADPGVFIITYGAEHNHGH 188 (306)
Q Consensus 128 ~~DGY~WRKYGQK~IKGs~~PRsYYRCs~~~gC~AkK~Vers~~D~~~~~vtY~GeHnH~~ 188 (306)
++|||+|||||||.|+|+++||+||||++ .+|+|+|+|||+.+|+.+++|||+|+|||+.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~-~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k 60 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTH-PGCPAKKQVQRSADDPNIVIVTYEGEHNHPK 60 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEEC-TTEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred CCCCCchhhccCcccCCCceeeEeeeccc-cChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence 37999999999999999999999999998 6999999999999999999999999999973
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=3e-32 Score=204.27 Aligned_cols=58 Identities=64% Similarity=1.176 Sum_probs=56.5
Q ss_pred CCCccccccCcccCCCCCCCCCceecCCCCCCccccceeeccCCCCeEEEEeCcCCCC
Q 021896 129 CDKWAWRKYGQKPIKGSPYPRSYYRCSSSKGCLARKQVERSSADPGVFIITYGAEHNH 186 (306)
Q Consensus 129 ~DGY~WRKYGQK~IKGs~~PRsYYRCs~~~gC~AkK~Vers~~D~~~~~vtY~GeHnH 186 (306)
+|||+|||||||.|+|+++||+||||++.++|+|+|+|||+.+|+.+++|||+|+|||
T Consensus 2 ~DGy~WRKYGQK~ikgs~~pRsYYrCt~~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 2 DDGYQWRKYGQKVIKGSPFPRSYYRCTYSQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CCcccccccCcEecCCCcCcceEEeccccCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 7999999999999999999999999998689999999999999999999999999998
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=94.34 E-value=0.015 Score=41.02 Aligned_cols=49 Identities=29% Similarity=0.592 Sum_probs=25.2
Q ss_pred CCCCccccccCcccCCCCCCCCCceecCCC--CCCccccceeeccCCCCeEEEEeCcCCCC
Q 021896 128 ACDKWAWRKYGQKPIKGSPYPRSYYRCSSS--KGCLARKQVERSSADPGVFIITYGAEHNH 186 (306)
Q Consensus 128 ~~DGY~WRKYGQK~IKGs~~PRsYYRCs~~--~gC~AkK~Vers~~D~~~~~vtY~GeHnH 186 (306)
.-|||.-+++... ..+.|+||+.. .+|+|+-.+. . +... ++...++|||
T Consensus 12 ~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~-~~~~-~~~~~~~HnH 62 (62)
T PF04500_consen 12 VYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--A-GDGR-VVRTNGEHNH 62 (62)
T ss_dssp EETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE-----TTE-EEE-S---SS
T ss_pred EECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--C-CCCE-EEECCCccCC
Confidence 3589888877655 34679999962 3799988777 2 2333 3444599999
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=93.25 E-value=0.076 Score=40.73 Aligned_cols=30 Identities=37% Similarity=0.531 Sum_probs=26.3
Q ss_pred CCCccccceeeccCCCCeEEEEeCcCCCCCC
Q 021896 158 KGCLARKQVERSSADPGVFIITYGAEHNHGH 188 (306)
Q Consensus 158 ~gC~AkK~Vers~~D~~~~~vtY~GeHnH~~ 188 (306)
-+|+|+=.|.+.. ++...++.+..+|||+.
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L 89 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPL 89 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCC
Confidence 4899999998877 78888899999999985
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=33.06 E-value=28 Score=25.87 Aligned_cols=20 Identities=30% Similarity=0.333 Sum_probs=16.2
Q ss_pred CCCCCCCCcccCceEEEeecc
Q 021896 104 PAAQPKGGKNQHKRVVQRVTA 124 (306)
Q Consensus 104 ~~~rsKRRk~~~k~vv~~v~~ 124 (306)
.=-.+||||...+++|. |++
T Consensus 21 rCHCsKkRK~RvKR~ir-VPA 40 (47)
T PF10533_consen 21 RCHCSKKRKSRVKRTIR-VPA 40 (47)
T ss_pred cccCCCcccccceeeEE-eec
Confidence 44578999999999998 765
No 6
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=26.60 E-value=60 Score=36.05 Aligned_cols=33 Identities=33% Similarity=0.552 Sum_probs=27.8
Q ss_pred cCCCCCCccccceeeccCCCCeEEEEeCcCCCCCC
Q 021896 154 CSSSKGCLARKQVERSSADPGVFIITYGAEHNHGH 188 (306)
Q Consensus 154 Cs~~~gC~AkK~Vers~~D~~~~~vtY~GeHnH~~ 188 (306)
|+- -||+|+=.|.+. .++.-.++-+..+|||+.
T Consensus 156 ~tR-tGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L 188 (846)
T PLN03097 156 CAK-TDCKASMHVKRR-PDGKWVIHSFVKEHNHEL 188 (846)
T ss_pred ccC-CCCceEEEEEEc-CCCeEEEEEEecCCCCCC
Confidence 664 699999999885 467788999999999986
No 7
>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=24.19 E-value=77 Score=27.52 Aligned_cols=56 Identities=20% Similarity=0.303 Sum_probs=28.7
Q ss_pred CCCCccccc-cCcccC---------CCCCCCCCceecCCCCCCccccceeeccCCC--CeEEEEeCcCC
Q 021896 128 ACDKWAWRK-YGQKPI---------KGSPYPRSYYRCSSSKGCLARKQVERSSADP--GVFIITYGAEH 184 (306)
Q Consensus 128 ~~DGY~WRK-YGQK~I---------KGs~~PRsYYRCs~~~gC~AkK~Vers~~D~--~~~~vtY~GeH 184 (306)
-.|||.||| =+-|.| .|-...-+||-=+....| ....+=+..+.+ .|+.|.|...|
T Consensus 51 RkDG~~WrKkkdgktvRE~HekLKv~~~e~l~~~Yah~~~~~~-F~RR~Ywll~~~~~~iVLVHY~~v~ 118 (118)
T PF03859_consen 51 RKDGHNWRKKKDGKTVREDHEKLKVGGVEVLNCYYAHSEDNPT-FHRRCYWLLDPPYEHIVLVHYLDVK 118 (118)
T ss_pred hcccceeEEcCCCCchhhhhhhhccCceeeeEEEEEeeccCCC-eeeEEEEccCCCCceEEEEEeeecC
Confidence 369999994 333333 333433456654432222 222233334333 58888886543
No 8
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=23.14 E-value=32 Score=33.52 Aligned_cols=25 Identities=28% Similarity=0.623 Sum_probs=18.6
Q ss_pred CCccccccCcc---------------------cCCCCCCCCCceec
Q 021896 130 DKWAWRKYGQK---------------------PIKGSPYPRSYYRC 154 (306)
Q Consensus 130 DGY~WRKYGQK---------------------~IKGs~~PRsYYRC 154 (306)
=|++||-+|-| .||++|+-|----|
T Consensus 115 yGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIims 160 (293)
T KOG0673|consen 115 YGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMS 160 (293)
T ss_pred cceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeee
Confidence 58999999977 56888877754433
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=14.46 E-value=91 Score=24.75 Aligned_cols=26 Identities=35% Similarity=0.842 Sum_probs=19.1
Q ss_pred CCccccccCcccCC--------CC--CCCCCceecCC
Q 021896 130 DKWAWRKYGQKPIK--------GS--PYPRSYYRCSS 156 (306)
Q Consensus 130 DGY~WRKYGQK~IK--------Gs--~~PRsYYRCs~ 156 (306)
.-+.|-| |-..+. |+ .-||+=|+|.-
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~~ 52 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCKE 52 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEecC
Confidence 4589999 864442 22 78999999974
No 10
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=13.84 E-value=78 Score=29.07 Aligned_cols=13 Identities=15% Similarity=0.631 Sum_probs=10.8
Q ss_pred CCCCCccccccCc
Q 021896 127 LACDKWAWRKYGQ 139 (306)
Q Consensus 127 l~~DGY~WRKYGQ 139 (306)
++.+||.|+.||.
T Consensus 75 ~Ps~~ykWn~~ge 87 (170)
T COG4283 75 TPSPGYKWNNLGE 87 (170)
T ss_pred CCCCCCcccccHH
Confidence 4579999999993
Done!