Query 045032
Match_columns 354
No_of_seqs 182 out of 540
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 09:13:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045032.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045032hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00774 WRKY DNA binding do 99.9 2.4E-27 5.1E-32 180.7 5.6 57 110-168 3-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 99.9 3.8E-27 8.3E-32 179.8 4.0 57 110-169 3-59 (60)
3 PF04500 FLYWCH: FLYWCH zinc f 88.5 0.51 1.1E-05 34.1 3.1 38 127-168 25-62 (62)
4 PF02268 TFIIA_gamma_N: Transc 47.2 51 0.0011 24.8 4.8 37 18-62 10-46 (49)
5 PF03101 FAR1: FAR1 DNA-bindin 37.3 31 0.00066 27.0 2.5 30 140-170 60-89 (91)
6 KOG3463 Transcription initiati 28.0 1.9E+02 0.0041 25.2 5.9 44 12-63 5-48 (109)
7 PF07216 LcrG: LcrG protein; 23.3 1.3E+02 0.0028 25.6 3.9 44 9-55 23-68 (93)
8 COG0783 Dps DNA-binding ferrit 20.2 4E+02 0.0086 24.3 6.8 54 9-65 99-153 (156)
9 TIGR02573 LcrG_PcrG type III s 19.0 1.7E+02 0.0038 24.7 3.9 44 8-54 19-64 (90)
10 COG1722 XseB Exonuclease VII s 18.4 2.8E+02 0.0061 22.7 4.9 22 11-32 34-55 (81)
No 1
>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=2.4e-27 Score=180.74 Aligned_cols=57 Identities=63% Similarity=1.184 Sum_probs=54.5
Q ss_pred cccchhcccccccCCCCCCceeEEeeccCCCCCcccceeeecCCCCCEEEEEeeeeecC
Q 045032 110 SKKSWRKYGQKDILGAKYPRGYYRCTYRNGQGCLATKQVQRSDEDPTIFEITYRGNHTC 168 (354)
Q Consensus 110 ~kk~WRKYGQK~I~gs~~pRsYYrCt~~~~~gC~a~KqVQr~~~d~~~~~vtY~G~Htc 168 (354)
++++|||||||.|+|+++||+|||||+ ++||+|+|+|||+++|+.+++|||+|+|||
T Consensus 3 DGy~WRKYGQK~ikgs~~pRsYYrCt~--~~~C~a~K~Vq~~~~d~~~~~vtY~g~H~h 59 (59)
T smart00774 3 DGYQWRKYGQKVIKGSPFPRSYYRCTY--SQGCPAKKQVQRSDDDPSVVEVTYEGEHTH 59 (59)
T ss_pred CcccccccCcEecCCCcCcceEEeccc--cCCCCCcccEEEECCCCCEEEEEEeeEeCC
Confidence 367999999999999999999999998 589999999999999999999999999998
No 2
>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=99.93 E-value=3.8e-27 Score=179.84 Aligned_cols=57 Identities=58% Similarity=1.073 Sum_probs=50.9
Q ss_pred cccchhcccccccCCCCCCceeEEeeccCCCCCcccceeeecCCCCCEEEEEeeeeecCC
Q 045032 110 SKKSWRKYGQKDILGAKYPRGYYRCTYRNGQGCLATKQVQRSDEDPTIFEITYRGNHTCA 169 (354)
Q Consensus 110 ~kk~WRKYGQK~I~gs~~pRsYYrCt~~~~~gC~a~KqVQr~~~d~~~~~vtY~G~Htc~ 169 (354)
++++|||||||.|+|+++||+||||++ .+|+|+|+|||+.+|+.+++|||+|+|||+
T Consensus 3 Dgy~WRKYGqK~i~g~~~pRsYYrCt~---~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 3 DGYRWRKYGQKNIKGSPYPRSYYRCTH---PGCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp SSS-EEEEEEEEETTTTCEEEEEEEEC---TTEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCchhhccCcccCCCceeeEeeeccc---cChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 367999999999999999999999999 499999999999999999999999999996
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=88.50 E-value=0.51 Score=34.15 Aligned_cols=38 Identities=26% Similarity=0.470 Sum_probs=18.4
Q ss_pred CCceeEEeeccCCCCCcccceeeecCCCCCEEEEEeeeeecC
Q 045032 127 YPRGYYRCTYRNGQGCLATKQVQRSDEDPTIFEITYRGNHTC 168 (354)
Q Consensus 127 ~pRsYYrCt~~~~~gC~a~KqVQr~~~d~~~~~vtY~G~Htc 168 (354)
....|+||+.....+|+|+=.+. . +...+... .++|||
T Consensus 25 ~~~~~WrC~~~~~~~C~a~~~~~--~-~~~~~~~~-~~~HnH 62 (62)
T PF04500_consen 25 DGKTYWRCSRRRSHGCRARLITD--A-GDGRVVRT-NGEHNH 62 (62)
T ss_dssp SS-EEEEEGGGTTS----EEEEE-----TTEEEE--S---SS
T ss_pred CCcEEEEeCCCCCCCCeEEEEEE--C-CCCEEEEC-CCccCC
Confidence 45689999998888999976665 2 22333333 389997
No 4
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=47.17 E-value=51 Score=24.77 Aligned_cols=37 Identities=14% Similarity=0.237 Sum_probs=27.1
Q ss_pred HhHHHHHHHHHHHhcccCCCCchhHHhhHHHHHHHHHHHHHHHHh
Q 045032 18 LQGRESAKQLQIQLNLRTSSSSHDQTRGIMLVQKIISSYEKALSM 62 (354)
Q Consensus 18 ~~GrElA~QL~~~L~~~~~~ss~e~~~e~~Lv~~ILsSf~~ALS~ 62 (354)
.-|..|..-|..++.. +.-++ .|+.+||.-|+++|.-
T Consensus 10 tlG~aL~dtLDeli~~--~~I~p------~La~kVL~~FDksi~~ 46 (49)
T PF02268_consen 10 TLGIALTDTLDELIQE--GKITP------QLAMKVLEQFDKSINE 46 (49)
T ss_dssp HHHHHHHHHHHHHHHT--TSS-H------HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHc--CCCCH------HHHHHHHHHHHHHHHH
Confidence 4578888888888773 22222 4999999999999863
No 5
>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=37.34 E-value=31 Score=27.04 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=25.6
Q ss_pred CCCcccceeeecCCCCCEEEEEeeeeecCCC
Q 045032 140 QGCLATKQVQRSDEDPTIFEITYRGNHTCAQ 170 (354)
Q Consensus 140 ~gC~a~KqVQr~~~d~~~~~vtY~G~Htc~~ 170 (354)
.||+|.=.|.+.. +....++.+..+|||.-
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 5999988888776 78888899999999963
No 6
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=27.99 E-value=1.9e+02 Score=25.22 Aligned_cols=44 Identities=16% Similarity=0.222 Sum_probs=33.3
Q ss_pred HHHHHHHhHHHHHHHHHHHhcccCCCCchhHHhhHHHHHHHHHHHHHHHHhh
Q 045032 12 SLINVLLQGRESAKQLQIQLNLRTSSSSHDQTRGIMLVQKIISSYEKALSML 63 (354)
Q Consensus 12 ~vi~EL~~GrElA~QL~~~L~~~~~~ss~e~~~e~~Lv~~ILsSf~~ALS~L 63 (354)
.+.+-..-|+-|.+-|..+++. +.-++ .|+.+||-.|+++|...
T Consensus 5 elYR~ttlG~~L~~tLDe~v~~--g~itp------~la~~VL~~FDKSi~~a 48 (109)
T KOG3463|consen 5 ELYRRTTLGNALQKTLDELVSD--GVITP------SLAKKVLEQFDKSINEA 48 (109)
T ss_pred HHHHHhhHHHHHHHHHHHHHHc--CCCCH------HHHHHHHHHHHHHHHHH
Confidence 4566777888888888887763 22233 49999999999999765
No 7
>PF07216 LcrG: LcrG protein; InterPro: IPR009863 This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops []. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the prot ein is believed to make a 1:1 complex with PcrV (LcrV) []. Mutations in LcrG cause premature secretion of effector proteins into the medium [].
Probab=23.26 E-value=1.3e+02 Score=25.60 Aligned_cols=44 Identities=20% Similarity=0.163 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhcccCCCCchhH--HhhHHHHHHHHHH
Q 045032 9 EKNSLINVLLQGRESAKQLQIQLNLRTSSSSHDQ--TRGIMLVQKIISS 55 (354)
Q Consensus 9 e~~~vi~EL~~GrElA~QL~~~L~~~~~~ss~e~--~~e~~Lv~~ILsS 55 (354)
++..|++||.+|..+.-+--.+|-. .+++++ .+|.+|+.+|-+-
T Consensus 23 ~R~~llqEm~~gLg~~p~ag~lLf~---~~~~~~~k~AEqELL~Ei~Rr 68 (93)
T PF07216_consen 23 HRNDLLQEMLEGLGLGPVAGELLFG---GSSPELMKQAEQELLEEIQRR 68 (93)
T ss_pred HHHHHHHHHHHhcCCChhHHHHHhc---CCCHHHHHHHHHHHHHHHHHH
Confidence 4556999999999888888777763 334443 2335799998664
No 8
>COG0783 Dps DNA-binding ferritin-like protein (oxidative damage protectant) [Inorganic ion transport and metabolism]
Probab=20.15 E-value=4e+02 Score=24.30 Aligned_cols=54 Identities=26% Similarity=0.327 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhHHH-HHHHHHHHhcccCCCCchhHHhhHHHHHHHHHHHHHHHHhhhc
Q 045032 9 EKNSLINVLLQGRE-SAKQLQIQLNLRTSSSSHDQTRGIMLVQKIISSYEKALSMLNF 65 (354)
Q Consensus 9 e~~~vi~EL~~GrE-lA~QL~~~L~~~~~~ss~e~~~e~~Lv~~ILsSf~~ALS~L~~ 65 (354)
.-+..|.+|+++.+ +.+.+|..+.......... ++ .|+.++++..+|.+=||.+
T Consensus 99 ~~~~~l~~l~~~~~~l~~~~r~~~~~a~e~gD~~-Ta--dl~~~~~~~~EK~~Wml~a 153 (156)
T COG0783 99 TAREMLKELVEDYEYLIKELRKGIELADEAGDEV-TA--DLLTDIIRELEKTLWMLRA 153 (156)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCChh-HH--HHHHHHHHHHHHHHHHHHH
Confidence 34567888887766 4566666665311111222 44 5999999999999998864
No 9
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=19.04 E-value=1.7e+02 Score=24.67 Aligned_cols=44 Identities=16% Similarity=0.074 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHhHHHHHHHHHHHhcccCCCCchhH--HhhHHHHHHHHH
Q 045032 8 WEKNSLINVLLQGRESAKQLQIQLNLRTSSSSHDQ--TRGIMLVQKIIS 54 (354)
Q Consensus 8 ~e~~~vi~EL~~GrElA~QL~~~L~~~~~~ss~e~--~~e~~Lv~~ILs 54 (354)
.++..+++|+.+|..+.-+--.+|-. ..++++ .+|.+|+.+|=+
T Consensus 19 d~R~~llqEm~~gLgl~p~ag~~Lf~---~~~~e~~~~AEqELL~EiqR 64 (90)
T TIGR02573 19 DERNDLLQEMWQGLGLGPVAGEVLFG---GLNAELMQHAEQELLEEVQR 64 (90)
T ss_pred HHHHHHHHHHHHHcCCChHHHHHHHc---CCCHHHHHHHHHHHHHHHHH
Confidence 45567999999999999888887773 233442 233478888855
No 10
>COG1722 XseB Exonuclease VII small subunit [DNA replication, recombination, and repair]
Probab=18.37 E-value=2.8e+02 Score=22.70 Aligned_cols=22 Identities=18% Similarity=0.191 Sum_probs=19.1
Q ss_pred HHHHHHHHhHHHHHHHHHHHhc
Q 045032 11 NSLINVLLQGRESAKQLQIQLN 32 (354)
Q Consensus 11 ~~vi~EL~~GrElA~QL~~~L~ 32 (354)
..+|.++-+|.+|+++.+..|.
T Consensus 34 e~sl~~~erG~~L~k~c~~~L~ 55 (81)
T COG1722 34 EEALKEFERGMALYKECQEKLQ 55 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888899999999998887
Done!