Query 030050
Match_columns 183
No_of_seqs 158 out of 668
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 07:44:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030050.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030050hhsearch_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 3.6E-34 7.8E-39 200.4 3.5 59 104-162 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 1E-32 2.3E-37 193.3 5.4 58 104-161 1-59 (59)
3 PF03101 FAR1: FAR1 DNA-bindin 95.0 0.024 5.2E-07 40.5 3.0 31 133-164 60-90 (91)
4 PF04500 FLYWCH: FLYWCH zinc f 93.3 0.058 1.3E-06 35.3 1.9 49 103-161 11-62 (62)
5 PLN03097 FHY3 Protein FAR-RED 55.4 15 0.00032 37.7 4.0 36 130-166 156-191 (846)
6 PF03859 CG-1: CG-1 domain; I 28.9 72 0.0016 25.6 3.3 56 103-158 50-117 (118)
7 KOG3277 Uncharacterized conser 23.1 89 0.0019 26.4 3.0 49 127-175 79-137 (165)
8 KOG0673 Thymidylate synthase [ 19.4 42 0.0009 30.4 0.3 26 106-131 115-161 (293)
9 PF04606 Ogr_Delta: Ogr/Delta- 15.3 85 0.0018 20.5 1.0 17 125-141 23-39 (47)
10 PF11732 Thoc2: Transcription- 12.3 64 0.0014 23.9 -0.3 19 159-181 6-24 (77)
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=3.6e-34 Score=200.43 Aligned_cols=59 Identities=69% Similarity=1.281 Sum_probs=52.6
Q ss_pred CCCCchhhccCceeccCCCCCCceeecccCCCCcccceeeecCCCCEEEEEEeccCCCC
Q 030050 104 LDDGYRWRKYGQKAVKDNKFPRSYYRCTHEGCNVKKQVQRLTNDEGIVVTTYEGMHNHR 162 (183)
Q Consensus 104 ~dDGy~WRKYGQK~ikgs~~pRsYYrCt~~gC~akKqVqr~~~D~~~~~ttY~G~HnHp 162 (183)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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=1e-32 Score=193.27 Aligned_cols=58 Identities=66% Similarity=1.213 Sum_probs=56.5
Q ss_pred CCCCchhhccCceeccCCCCCCceeeccc-CCCCcccceeeecCCCCEEEEEEeccCCC
Q 030050 104 LDDGYRWRKYGQKAVKDNKFPRSYYRCTH-EGCNVKKQVQRLTNDEGIVVTTYEGMHNH 161 (183)
Q Consensus 104 ~dDGy~WRKYGQK~ikgs~~pRsYYrCt~-~gC~akKqVqr~~~D~~~~~ttY~G~HnH 161 (183)
++|||.|||||||.|+|+++||+||||++ ++|+|+|+|||+++|+.+++|||+|+|||
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 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=94.99 E-value=0.024 Score=40.46 Aligned_cols=31 Identities=32% Similarity=0.491 Sum_probs=26.8
Q ss_pred CCCCcccceeeecCCCCEEEEEEeccCCCCCC
Q 030050 133 EGCNVKKQVQRLTNDEGIVVTTYEGMHNHRIE 164 (183)
Q Consensus 133 ~gC~akKqVqr~~~D~~~~~ttY~G~HnHp~~ 164 (183)
.||+|+=.|.+.. |....++.+..+|||+..
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 6999999998755 787888999999999964
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=93.31 E-value=0.058 Score=35.32 Aligned_cols=49 Identities=33% Similarity=0.678 Sum_probs=24.8
Q ss_pred cCCCCchhhccCceeccCCCCCCceeecccC---CCCcccceeeecCCCCEEEEEEeccCCC
Q 030050 103 ILDDGYRWRKYGQKAVKDNKFPRSYYRCTHE---GCNVKKQVQRLTNDEGIVVTTYEGMHNH 161 (183)
Q Consensus 103 ~~dDGy~WRKYGQK~ikgs~~pRsYYrCt~~---gC~akKqVqr~~~D~~~~~ttY~G~HnH 161 (183)
++-|||.-.+.... ....|++|+.. +|+|+=.+. .++. .+. ...++|||
T Consensus 11 L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~-~~~-~~~~~HnH 62 (62)
T PF04500_consen 11 LVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG-RVV-RTNGEHNH 62 (62)
T ss_dssp EEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT-EEE-E-S---SS
T ss_pred EEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC-EEE-ECCCccCC
Confidence 56689877664444 34689999973 899998876 2333 333 34499998
No 5
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=55.35 E-value=15 Score=37.74 Aligned_cols=36 Identities=25% Similarity=0.540 Sum_probs=30.2
Q ss_pred cccCCCCcccceeeecCCCCEEEEEEeccCCCCCCCC
Q 030050 130 CTHEGCNVKKQVQRLTNDEGIVVTTYEGMHNHRIEKP 166 (183)
Q Consensus 130 Ct~~gC~akKqVqr~~~D~~~~~ttY~G~HnHp~~~~ 166 (183)
|+-.||+|.=.|.+ ..|+.-+++-+..+||||..++
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 77789999999977 4566688899999999997654
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=28.93 E-value=72 Score=25.55 Aligned_cols=56 Identities=23% Similarity=0.421 Sum_probs=26.2
Q ss_pred cCCCCchhhc-cCceecc---------CCCCCCceeecccCCCCcccceeeecCCC--CEEEEEEecc
Q 030050 103 ILDDGYRWRK-YGQKAVK---------DNKFPRSYYRCTHEGCNVKKQVQRLTNDE--GIVVTTYEGM 158 (183)
Q Consensus 103 ~~dDGy~WRK-YGQK~ik---------gs~~pRsYYrCt~~gC~akKqVqr~~~D~--~~~~ttY~G~ 158 (183)
--.|||.||| =+-|.|+ |-...-+||-=+..+=.....+=+.-+.+ .+|.|-|...
T Consensus 50 fRkDG~~WrKkkdgktvRE~HekLKv~~~e~l~~~Yah~~~~~~F~RR~Ywll~~~~~~iVLVHY~~v 117 (118)
T PF03859_consen 50 FRKDGHNWRKKKDGKTVREDHEKLKVGGVEVLNCYYAHSEDNPTFHRRCYWLLDPPYEHIVLVHYLDV 117 (118)
T ss_pred hhcccceeEEcCCCCchhhhhhhhccCceeeeEEEEEeeccCCCeeeEEEEccCCCCceEEEEEeeec
Confidence 3569999995 2333333 33333345532222222222232332323 4777777644
No 7
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.15 E-value=89 Score=26.44 Aligned_cols=49 Identities=27% Similarity=0.489 Sum_probs=29.7
Q ss_pred eeecccCCCCcccceeeecCCCCEEEEEEeccCCCCC----------CCCCCCHHHHhh
Q 030050 127 YYRCTHEGCNVKKQVQRLTNDEGIVVTTYEGMHNHRI----------EKPTDNFEHILN 175 (183)
Q Consensus 127 YYrCt~~gC~akKqVqr~~~D~~~~~ttY~G~HnHp~----------~~~t~n~~~~l~ 175 (183)
-|.|.-=+=.-.|.+-..+=..++|+|+..|.++|.. .+.+.|.|.||.
T Consensus 79 ~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~~nied~l~ 137 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGKRNIEDILA 137 (165)
T ss_pred EEEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhcccccccccccHHHHHH
Confidence 4666542222334444444446799999999999853 345556777664
No 8
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=19.35 E-value=42 Score=30.41 Aligned_cols=26 Identities=27% Similarity=0.671 Sum_probs=19.8
Q ss_pred CCchhhccCce---------------------eccCCCCCCceeecc
Q 030050 106 DGYRWRKYGQK---------------------AVKDNKFPRSYYRCT 131 (183)
Q Consensus 106 DGy~WRKYGQK---------------------~ikgs~~pRsYYrCt 131 (183)
=|++||-+|-+ .||+||.-|----|+
T Consensus 115 yGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIimsA 161 (293)
T KOG0673|consen 115 YGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMSA 161 (293)
T ss_pred cceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeeec
Confidence 57999999877 678888877655444
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=15.25 E-value=85 Score=20.47 Aligned_cols=17 Identities=24% Similarity=0.516 Sum_probs=14.2
Q ss_pred CceeecccCCCCcccce
Q 030050 125 RSYYRCTHEGCNVKKQV 141 (183)
Q Consensus 125 RsYYrCt~~gC~akKqV 141 (183)
..||.|++..|.++-..
T Consensus 23 ~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFVA 39 (47)
T ss_pred EEEEEECCCcCCCEEEE
Confidence 48999999999987654
No 10
>PF11732 Thoc2: Transcription- and export-related complex subunit; InterPro: IPR021726 The THO/TREX complex is the transcription- and export-related complex associated with spliceosomes that preferentially deal with spliced mRNAs as opposed to unspliced mRNAs. Thoc2 plays a role in RNA polymerase II (RNA pol II)-dependent transcription and is required for the stability of DNA repeats []. In humans, the TRE complex is comprised of the exon-junction-associated proteins Aly/REF and UAP56 together with the THO proteins THOC1 (hHpr1/p84), Thoc2 (hRlr1), THOC3 (hTex1), THOC5 (fSAP79), THOC6 (fSAP35), and THOC7 (fSAP24). Although much evidence indicates that the function of the TREX complex as an adaptor between the mRNA and components of the export machinery is conserved among eukaryotes, in Drosophila the majority of mRNAs can be exported from the nucleus independently of the THO complex []. This entry represents a conserved domain found towards the N terminus of these proteins.
Probab=12.27 E-value=64 Score=23.85 Aligned_cols=19 Identities=32% Similarity=0.613 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCHHHHhhhccccC
Q 030050 159 HNHRIEKPTDNFEHILNQLQIYT 181 (183)
Q Consensus 159 HnHp~~~~t~n~~~~l~~~~~~~ 181 (183)
|++|.. =|+.+|+|.|.|.
T Consensus 6 hsnP~~----vf~~il~Qie~Yd 24 (77)
T PF11732_consen 6 HSNPLI----VFDVILSQIESYD 24 (77)
T ss_pred ccCcHH----HHHHHHHHHHHhh
Confidence 555544 7999999999984
Done!