Query 026950
Match_columns 230
No_of_seqs 157 out of 677
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 02:55:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026950.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026950hhsearch_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 3.9E-33 8.5E-38 201.3 3.2 59 152-210 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 4.5E-32 9.8E-37 196.3 5.2 58 152-209 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 92.1 0.063 1.4E-06 36.3 0.8 49 151-209 11-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 75.6 2.9 6.2E-05 30.6 2.7 31 181-212 60-90 (91)
5 PLN03097 FHY3 Protein FAR-RED 23.7 94 0.002 33.2 4.0 35 178-213 156-190 (846)
6 KOG0673 Thymidylate synthase [ 16.1 52 0.0011 30.9 0.2 26 153-178 114-160 (293)
7 PF03859 CG-1: CG-1 domain; I 16.0 1.5E+02 0.0033 24.7 2.8 10 197-206 108-117 (118)
8 PF04606 Ogr_Delta: Ogr/Delta- 14.1 79 0.0017 21.5 0.6 16 173-188 23-38 (47)
9 PF03119 DNA_ligase_ZBD: NAD-d 13.3 79 0.0017 19.7 0.4 13 173-185 15-28 (28)
10 cd07691 Ig_CD3_gamma_delta Imm 13.2 1.9E+02 0.0042 22.0 2.5 28 154-182 17-54 (69)
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=3.9e-33 Score=201.32 Aligned_cols=59 Identities=63% Similarity=1.192 Sum_probs=52.6
Q ss_pred CCCCchhhhccceecCCCCCCCcccccCCCCCccccceeeecCCCCEEEEEEeeccCCC
Q 026950 152 LDDGYKWRKYGQKVVKNTQHPRSYYRCTQDNCRVKKRVERLAEDPRMVITTYEGRHVHS 210 (230)
Q Consensus 152 ~~DGy~WRKYGQK~IkGs~~PRsYYRCt~~gC~AkK~Vqr~~~Dp~~~~vTY~G~HnH~ 210 (230)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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 48999999999999999999999999999999999999999999999999999999996
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=4.5e-32 Score=196.28 Aligned_cols=58 Identities=62% Similarity=1.190 Sum_probs=56.5
Q ss_pred CCCCchhhhccceecCCCCCCCcccccCC-CCCccccceeeecCCCCEEEEEEeeccCC
Q 026950 152 LDDGYKWRKYGQKVVKNTQHPRSYYRCTQ-DNCRVKKRVERLAEDPRMVITTYEGRHVH 209 (230)
Q Consensus 152 ~~DGy~WRKYGQK~IkGs~~PRsYYRCt~-~gC~AkK~Vqr~~~Dp~~~~vTY~G~HnH 209 (230)
++|||.|||||||.|+|+++||+||||++ +||+|+|+|||+++|+.+++|||+|+|||
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 89999999999999999999999999998
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=92.05 E-value=0.063 Score=36.28 Aligned_cols=49 Identities=29% Similarity=0.649 Sum_probs=23.6
Q ss_pred cCCCCchhhhccceecCCCCCCCcccccCCC---CCccccceeeecCCCCEEEEEEeeccCC
Q 026950 151 VLDDGYKWRKYGQKVVKNTQHPRSYYRCTQD---NCRVKKRVERLAEDPRMVITTYEGRHVH 209 (230)
Q Consensus 151 ~~~DGy~WRKYGQK~IkGs~~PRsYYRCt~~---gC~AkK~Vqr~~~Dp~~~~vTY~G~HnH 209 (230)
++-|||.-.+.... ....|++|+.. +|+|+=.+. .++ ..+ +...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~-~~~-~~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGD-GRV-VRTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----T-TEE-EE-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCC-CEE-EECCCccCC
Confidence 34578776654443 44689999974 899987766 223 333 334499998
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=75.59 E-value=2.9 Score=30.64 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=26.1
Q ss_pred CCCccccceeeecCCCCEEEEEEeeccCCCCC
Q 026950 181 DNCRVKKRVERLAEDPRMVITTYEGRHVHSPS 212 (230)
Q Consensus 181 ~gC~AkK~Vqr~~~Dp~~~~vTY~G~HnH~ps 212 (230)
-+|+|+=.|.+.. |....++.+..+|||+-.
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 4899998888776 778888999999999753
No 5
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=23.67 E-value=94 Score=33.24 Aligned_cols=35 Identities=26% Similarity=0.538 Sum_probs=29.1
Q ss_pred cCCCCCccccceeeecCCCCEEEEEEeeccCCCCCC
Q 026950 178 CTQDNCRVKKRVERLAEDPRMVITTYEGRHVHSPSH 213 (230)
Q Consensus 178 Ct~~gC~AkK~Vqr~~~Dp~~~~vTY~G~HnH~ps~ 213 (230)
|+--||+|.=.|.+. .|+.-+++-++.+|||+...
T Consensus 156 ~tRtGC~A~m~Vk~~-~~gkW~V~~fv~eHNH~L~p 190 (846)
T PLN03097 156 CAKTDCKASMHVKRR-PDGKWVIHSFVKEHNHELLP 190 (846)
T ss_pred ccCCCCceEEEEEEc-CCCeEEEEEEecCCCCCCCC
Confidence 677799999999875 46678889999999997654
No 6
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=16.07 E-value=52 Score=30.94 Aligned_cols=26 Identities=27% Similarity=0.655 Sum_probs=19.3
Q ss_pred CCCchhhhccce---------------------ecCCCCCCCccccc
Q 026950 153 DDGYKWRKYGQK---------------------VVKNTQHPRSYYRC 178 (230)
Q Consensus 153 ~DGy~WRKYGQK---------------------~IkGs~~PRsYYRC 178 (230)
-=|++||-+|-| .||+||+-|----|
T Consensus 114 vyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIims 160 (293)
T KOG0673|consen 114 VYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMS 160 (293)
T ss_pred ccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeee
Confidence 368999999977 57888888754333
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=16.05 E-value=1.5e+02 Score=24.72 Aligned_cols=10 Identities=20% Similarity=0.404 Sum_probs=7.1
Q ss_pred CEEEEEEeec
Q 026950 197 RMVITTYEGR 206 (230)
Q Consensus 197 ~~~~vTY~G~ 206 (230)
.++.|.|...
T Consensus 108 ~iVLVHY~~v 117 (118)
T PF03859_consen 108 HIVLVHYLDV 117 (118)
T ss_pred eEEEEEeeec
Confidence 5788888654
No 8
>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=14.10 E-value=79 Score=21.48 Aligned_cols=16 Identities=25% Similarity=0.528 Sum_probs=12.9
Q ss_pred CcccccCCCCCccccc
Q 026950 173 RSYYRCTQDNCRVKKR 188 (230)
Q Consensus 173 RsYYRCt~~gC~AkK~ 188 (230)
..||.|++..|..+-.
T Consensus 23 ~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFV 38 (47)
T ss_pred EEEEEECCCcCCCEEE
Confidence 4799999999987543
No 9
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=13.34 E-value=79 Score=19.72 Aligned_cols=13 Identities=23% Similarity=0.611 Sum_probs=7.4
Q ss_pred CcccccCCC-CCcc
Q 026950 173 RSYYRCTQD-NCRV 185 (230)
Q Consensus 173 RsYYRCt~~-gC~A 185 (230)
...|||.+. .|+|
T Consensus 15 ev~~~C~N~l~CpA 28 (28)
T PF03119_consen 15 EVDIRCPNPLSCPA 28 (28)
T ss_dssp TTCEEE--CGC-HH
T ss_pred CEeEECCCCCcCCC
Confidence 357899987 8876
No 10
>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=13.18 E-value=1.9e+02 Score=21.98 Aligned_cols=28 Identities=25% Similarity=0.811 Sum_probs=19.0
Q ss_pred CCchhhhccceec--------CCC--CCCCcccccCCCC
Q 026950 154 DGYKWRKYGQKVV--------KNT--QHPRSYYRCTQDN 182 (230)
Q Consensus 154 DGy~WRKYGQK~I--------kGs--~~PRsYYRCt~~g 182 (230)
.-+.|-| |-..+ .|+ .-||+-|+|.-.+
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~~s~ 54 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCKESE 54 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEecCcc
Confidence 4588988 76443 233 7899999995543
Done!