Query 031298
Match_columns 162
No_of_seqs 160 out of 688
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 12:07:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031298hhsearch_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-34 9.8E-39 196.0 3.5 59 85-143 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 1.1E-32 2.3E-37 189.3 4.9 58 85-142 1-59 (59)
3 PF03101 FAR1: FAR1 DNA-bindin 93.2 0.089 1.9E-06 36.8 2.8 31 114-145 60-90 (91)
4 PF04500 FLYWCH: FLYWCH zinc f 92.4 0.082 1.8E-06 34.0 1.6 50 83-142 10-62 (62)
5 PLN03097 FHY3 Protein FAR-RED 40.0 36 0.00077 34.3 3.9 36 111-147 156-191 (846)
6 KOG0673 Thymidylate synthase [ 27.5 25 0.00054 31.0 0.5 27 86-112 114-161 (293)
7 PF03859 CG-1: CG-1 domain; I 23.0 99 0.0022 24.2 3.1 10 84-93 50-59 (118)
8 cd07691 Ig_CD3_gamma_delta Imm 21.2 1.1E+02 0.0024 21.7 2.8 27 87-114 17-53 (69)
9 PF04606 Ogr_Delta: Ogr/Delta- 15.8 61 0.0013 20.6 0.4 18 105-122 22-39 (47)
10 PRK09678 DNA-binding transcrip 12.5 91 0.002 22.2 0.6 16 105-120 24-39 (72)
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=100.00 E-value=4.5e-34 Score=195.98 Aligned_cols=59 Identities=69% Similarity=1.303 Sum_probs=52.6
Q ss_pred CCCCccccccCceeccCCCCCcccccccccCcccccceeeecCCCCEEEEEEeccCCCC
Q 031298 85 LDDGYRWRKYGQKVVKNSKFPRSYYKCTHKGCNVKKQVQRNTKDEEIVVTTYEGLHTHP 143 (162)
Q Consensus 85 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~gC~akK~Vqr~~~D~~~~~ttY~G~H~h~ 143 (162)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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=99.97 E-value=1.1e-32 Score=189.27 Aligned_cols=58 Identities=69% Similarity=1.241 Sum_probs=56.5
Q ss_pred CCCCccccccCceeccCCCCCcccccccc-cCcccccceeeecCCCCEEEEEEeccCCC
Q 031298 85 LDDGYRWRKYGQKVVKNSKFPRSYYKCTH-KGCNVKKQVQRNTKDEEIVVTTYEGLHTH 142 (162)
Q Consensus 85 ~~DGy~WRKYGQK~ikgs~~pRsYYrCt~-~gC~akK~Vqr~~~D~~~~~ttY~G~H~h 142 (162)
++|||.|||||||.|+|+++||+||||++ ++|+|+|+|||+++|+.+++|||+|+|||
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 99999999999989999999999999998
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=93.19 E-value=0.089 Score=36.78 Aligned_cols=31 Identities=32% Similarity=0.603 Sum_probs=26.5
Q ss_pred cCcccccceeeecCCCCEEEEEEeccCCCCCC
Q 031298 114 KGCNVKKQVQRNTKDEEIVVTTYEGLHTHPIG 145 (162)
Q Consensus 114 ~gC~akK~Vqr~~~D~~~~~ttY~G~H~h~~~ 145 (162)
-+|+|+=.|-+.. |+...++.+..+|||+.-
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 5999998888755 888899999999999863
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=92.44 E-value=0.082 Score=33.96 Aligned_cols=50 Identities=26% Similarity=0.610 Sum_probs=24.7
Q ss_pred ccCCCCccccccCceeccCCCCCccccccccc---CcccccceeeecCCCCEEEEEEeccCCC
Q 031298 83 DILDDGYRWRKYGQKVVKNSKFPRSYYKCTHK---GCNVKKQVQRNTKDEEIVVTTYEGLHTH 142 (162)
Q Consensus 83 ~~~~DGy~WRKYGQK~ikgs~~pRsYYrCt~~---gC~akK~Vqr~~~D~~~~~ttY~G~H~h 142 (162)
.++-|||.-.+.... ....|++|+.. +|+|+=.+. .++. .+ +...++|||
T Consensus 10 ~L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~-~~-~~~~~~HnH 62 (62)
T PF04500_consen 10 KLVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG-RV-VRTNGEHNH 62 (62)
T ss_dssp EEEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT-EE-EE-S---SS
T ss_pred EEEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC-EE-EECCCccCC
Confidence 367789876555444 35689999983 899977765 2333 33 334499998
No 5
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=39.98 E-value=36 Score=34.30 Aligned_cols=36 Identities=22% Similarity=0.494 Sum_probs=30.2
Q ss_pred ccccCcccccceeeecCCCCEEEEEEeccCCCCCCCC
Q 031298 111 CTHKGCNVKKQVQRNTKDEEIVVTTYEGLHTHPIGKI 147 (162)
Q Consensus 111 Ct~~gC~akK~Vqr~~~D~~~~~ttY~G~H~h~~~~~ 147 (162)
|+--||+|.=.|.+ ..|+.-.++-+..+|||+.-++
T Consensus 156 ~tRtGC~A~m~Vk~-~~~gkW~V~~fv~eHNH~L~p~ 191 (846)
T PLN03097 156 CAKTDCKASMHVKR-RPDGKWVIHSFVKEHNHELLPA 191 (846)
T ss_pred ccCCCCceEEEEEE-cCCCeEEEEEEecCCCCCCCCc
Confidence 77789999999987 4667788999999999997644
No 6
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=27.46 E-value=25 Score=31.02 Aligned_cols=27 Identities=26% Similarity=0.582 Sum_probs=19.7
Q ss_pred CCCccccccCce---------------------eccCCCCCccccccc
Q 031298 86 DDGYRWRKYGQK---------------------VVKNSKFPRSYYKCT 112 (162)
Q Consensus 86 ~DGy~WRKYGQK---------------------~ikgs~~pRsYYrCt 112 (162)
-=||+||-+|-+ .||+||+.|----|.
T Consensus 114 vyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIimsA 161 (293)
T KOG0673|consen 114 VYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMSA 161 (293)
T ss_pred ccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeeec
Confidence 348999999977 578888887544443
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=22.98 E-value=99 Score=24.16 Aligned_cols=10 Identities=50% Similarity=1.026 Sum_probs=8.2
Q ss_pred cCCCCccccc
Q 031298 84 ILDDGYRWRK 93 (162)
Q Consensus 84 ~~~DGy~WRK 93 (162)
.-.|||.|||
T Consensus 50 fRkDG~~WrK 59 (118)
T PF03859_consen 50 FRKDGHNWRK 59 (118)
T ss_pred hhcccceeEE
Confidence 5689999994
No 8
>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=21.19 E-value=1.1e+02 Score=21.75 Aligned_cols=27 Identities=30% Similarity=0.799 Sum_probs=18.1
Q ss_pred CCccccccCceecc--------CC--CCCccccccccc
Q 031298 87 DGYRWRKYGQKVVK--------NS--KFPRSYYKCTHK 114 (162)
Q Consensus 87 DGy~WRKYGQK~ik--------gs--~~pRsYYrCt~~ 114 (162)
.-+.|-| |-..+. |+ .-||+=|+|.-.
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 4478888 754333 22 679999999543
No 9
>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=15.76 E-value=61 Score=20.63 Aligned_cols=18 Identities=22% Similarity=0.469 Sum_probs=13.9
Q ss_pred CcccccccccCcccccce
Q 031298 105 PRSYYKCTHKGCNVKKQV 122 (162)
Q Consensus 105 pRsYYrCt~~gC~akK~V 122 (162)
-..||.|++..|..+-..
T Consensus 22 ~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 22 RELYCQCTNPECGHTFVA 39 (47)
T ss_pred EEEEEEECCCcCCCEEEE
Confidence 347999999999886543
No 10
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=12.55 E-value=91 Score=22.18 Aligned_cols=16 Identities=19% Similarity=0.571 Sum_probs=13.4
Q ss_pred CcccccccccCccccc
Q 031298 105 PRSYYKCTHKGCNVKK 120 (162)
Q Consensus 105 pRsYYrCt~~gC~akK 120 (162)
.+.||.|++..|..+=
T Consensus 24 ~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 24 KERYHQCQNVNCSATF 39 (72)
T ss_pred heeeeecCCCCCCCEE
Confidence 6789999999998753
Done!