Query 021011
Match_columns 318
No_of_seqs 232 out of 697
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:54:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021011hhsearch_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 100.0 9E-31 2E-35 197.2 4.9 59 250-308 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 2.4E-31 5.2E-36 200.2 1.4 60 250-310 1-60 (60)
3 PF10533 Plant_zn_clust: Plant 99.3 4E-12 8.6E-17 92.4 3.5 46 203-248 1-47 (47)
4 PF03101 FAR1: FAR1 DNA-bindin 91.8 0.14 3E-06 39.7 2.5 33 279-312 59-91 (91)
5 PF04500 FLYWCH: FLYWCH zinc f 91.2 0.088 1.9E-06 37.5 0.8 48 251-308 13-62 (62)
6 KOG4369 RTK signaling protein 50.2 76 0.0016 37.5 8.7 27 70-98 1797-1823(2131)
7 cd07691 Ig_CD3_gamma_delta Imm 30.5 66 0.0014 25.6 3.3 25 252-277 17-51 (69)
8 KOG1883 Cofactor required for 27.4 82 0.0018 36.9 4.5 9 130-138 1448-1456(1517)
9 PLN03097 FHY3 Protein FAR-RED 23.9 87 0.0019 35.1 4.0 37 276-314 156-192 (846)
10 COG4283 Uncharacterized conser 23.1 32 0.0007 31.6 0.4 14 248-261 74-87 (170)
11 PF06752 E_Pc_C: Enhancer of P 22.1 1E+02 0.0022 29.7 3.5 15 115-129 9-23 (230)
12 KOG4407 Predicted Rho GTPase-a 21.6 67 0.0014 38.2 2.5 18 133-151 368-385 (1973)
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=99.96 E-value=9e-31 Score=197.22 Aligned_cols=59 Identities=59% Similarity=1.198 Sum_probs=56.6
Q ss_pred CCCCccccccCCCCCCCCCCCccccccCCCCCCccccceeecCCCCcEEEEEEeccCCC
Q 021011 250 PPDDYSWRKYGQKPIKGSPHPRGYYKCSSMRGCPARKHVERCLEEPTMLIVTYEGEHNH 308 (318)
Q Consensus 250 ~~DGy~WRKYGQK~Ikgs~~pRsYYRCs~~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~H 308 (318)
++|||.|||||||.|+|+++||+||||++.+||+|+|+|||+.+|+.+++|||+|+|||
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 47999999999999999999999999996589999999999999999999999999998
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=99.96 E-value=2.4e-31 Score=200.24 Aligned_cols=60 Identities=63% Similarity=1.301 Sum_probs=52.0
Q ss_pred CCCCccccccCCCCCCCCCCCccccccCCCCCCccccceeecCCCCcEEEEEEeccCCCCC
Q 021011 250 PPDDYSWRKYGQKPIKGSPHPRGYYKCSSMRGCPARKHVERCLEEPTMLIVTYEGEHNHPR 310 (318)
Q Consensus 250 ~~DGy~WRKYGQK~Ikgs~~pRsYYRCs~~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~H~~ 310 (318)
++|||+|||||||.|+|+++||+||||++ .+|+|+|+|||+.+|+.+++|||+|+|||+.
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 37999999999999999999999999995 7999999999999999999999999999974
No 3
>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=99.26 E-value=4e-12 Score=92.41 Aligned_cols=46 Identities=65% Similarity=1.189 Sum_probs=38.1
Q ss_pred ccccCCCCCC-CCCccCCCCcccccccccccccceEEeecccCCCCC
Q 021011 203 KRKCSGRGED-GSVKCGSNGRCHCSKKRKHRVKKSIKVPAISNKLAD 248 (318)
Q Consensus 203 kr~c~~~g~~-~~~k~~~~~r~~~sKrrK~r~kr~i~vpa~s~~~~d 248 (318)
+++|.+.+++ +..+++++++|||+||||.|+||+|+|||||++++|
T Consensus 1 krkC~~~~~~~~~~~~sssgrCHCsKkRK~RvKR~irVPAiS~K~AD 47 (47)
T PF10533_consen 1 KRKCHSHNDSSGKCKCSSSGRCHCSKKRKSRVKRTIRVPAISSKIAD 47 (47)
T ss_pred CCcccccCcccCccccCCCCcccCCCcccccceeeEEeecccccccC
Confidence 5788876543 333467899999999999999999999999999875
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=91.79 E-value=0.14 Score=39.72 Aligned_cols=33 Identities=36% Similarity=0.600 Sum_probs=27.2
Q ss_pred CCCCccccceeecCCCCcEEEEEEeccCCCCCCC
Q 021011 279 MRGCPARKHVERCLEEPTMLIVTYEGEHNHPRLP 312 (318)
Q Consensus 279 ~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~H~~~~ 312 (318)
..||+|+=.|.+.. |....++.+..+|||+-.|
T Consensus 59 ktgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 59 KTGCKARINVKRRK-DGKWRVTSFVLEHNHPLCP 91 (91)
T ss_pred ccCCCEEEEEEEcc-CCEEEEEECcCCcCCCCCC
Confidence 35899998888776 7777778899999998754
No 5
>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=91.21 E-value=0.088 Score=37.48 Aligned_cols=48 Identities=31% Similarity=0.605 Sum_probs=23.9
Q ss_pred CCCccccccCCCCCCCCCCCccccccCCC--CCCccccceeecCCCCcEEEEEEeccCCC
Q 021011 251 PDDYSWRKYGQKPIKGSPHPRGYYKCSSM--RGCPARKHVERCLEEPTMLIVTYEGEHNH 308 (318)
Q Consensus 251 ~DGy~WRKYGQK~Ikgs~~pRsYYRCs~~--~gC~ArK~Vqr~~dDp~~~~VtY~GeH~H 308 (318)
-|||.-.++... ....|++|+.. .+|+|+=.+. .++.. + +...++|||
T Consensus 13 ~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~~-~-~~~~~~HnH 62 (62)
T PF04500_consen 13 YDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDGR-V-VRTNGEHNH 62 (62)
T ss_dssp ETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TTE-E-EE-S---SS
T ss_pred ECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCCE-E-EECCCccCC
Confidence 588877765544 33589999962 3799987777 34443 3 335699998
No 6
>KOG4369 consensus RTK signaling protein MASK/UNC-44 [Signal transduction mechanisms]
Probab=50.23 E-value=76 Score=37.52 Aligned_cols=27 Identities=30% Similarity=0.198 Sum_probs=15.5
Q ss_pred hhcccccccccccCCCcccccccCCCccc
Q 021011 70 QEMGSLAKSSLTLGNPSLELISNGKQHLQ 98 (318)
Q Consensus 70 ~~~~~~~~~~~~~~~~~~~l~~~~~~~~~ 98 (318)
.+.+.-+.++..+|-.+++|.. ++|..
T Consensus 1797 ~~v~qps~~~~~~g~ss~~~~~--~~p~s 1823 (2131)
T KOG4369|consen 1797 APVQQPSTSSVTTGLSSLELKG--WMPAS 1823 (2131)
T ss_pred cccCCCccccccccccchhhcC--CCCcc
Confidence 3444444566667777777765 44433
No 7
>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=30.51 E-value=66 Score=25.57 Aligned_cols=25 Identities=36% Similarity=0.915 Sum_probs=17.7
Q ss_pred CCccccccCCCCCCC--------C--CCCccccccC
Q 021011 252 DDYSWRKYGQKPIKG--------S--PHPRGYYKCS 277 (318)
Q Consensus 252 DGy~WRKYGQK~Ikg--------s--~~pRsYYRCs 277 (318)
.-+.|-| |-..+.- + .-||+-|+|.
T Consensus 17 tsi~W~k-G~~~~~~~~~tlnLGs~~~DPRG~Y~C~ 51 (69)
T cd07691 17 TNITWKK-GKEILEVSNTLLDLGSRINDPRGTYSCK 51 (69)
T ss_pred CcEEEec-CcccccccccEEeccCcccCCCcceEec
Confidence 4478888 7644433 2 6899999997
No 8
>KOG1883 consensus Cofactor required for Sp1 transcriptional activation, subunit 3 [Transcription]
Probab=27.38 E-value=82 Score=36.86 Aligned_cols=9 Identities=22% Similarity=0.350 Sum_probs=4.5
Q ss_pred HHHHHHHHH
Q 021011 130 QQHHMKLQA 138 (318)
Q Consensus 130 ~q~~~~~q~ 138 (318)
+|||++||.
T Consensus 1448 ~qqqlqhq~ 1456 (1517)
T KOG1883|consen 1448 TQQQLQHQI 1456 (1517)
T ss_pred HHHHHHHhc
Confidence 445555554
No 9
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=23.93 E-value=87 Score=35.10 Aligned_cols=37 Identities=38% Similarity=0.661 Sum_probs=29.2
Q ss_pred cCCCCCCccccceeecCCCCcEEEEEEeccCCCCCCCCC
Q 021011 276 CSSMRGCPARKHVERCLEEPTMLIVTYEGEHNHPRLPSQ 314 (318)
Q Consensus 276 Cs~~~gC~ArK~Vqr~~dDp~~~~VtY~GeH~H~~~~~~ 314 (318)
|+ .-||+|.=.|.+.. |..-.++-+..+|||+-.|+.
T Consensus 156 ~t-RtGC~A~m~Vk~~~-~gkW~V~~fv~eHNH~L~p~~ 192 (846)
T PLN03097 156 CA-KTDCKASMHVKRRP-DGKWVIHSFVKEHNHELLPAQ 192 (846)
T ss_pred cc-CCCCceEEEEEEcC-CCeEEEEEEecCCCCCCCCcc
Confidence 66 46999999998854 455777889999999987653
No 10
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=23.12 E-value=32 Score=31.56 Aligned_cols=14 Identities=29% Similarity=0.805 Sum_probs=12.0
Q ss_pred CCCCCCccccccCC
Q 021011 248 DIPPDDYSWRKYGQ 261 (318)
Q Consensus 248 di~~DGy~WRKYGQ 261 (318)
-+|.+||.|+.||.
T Consensus 74 f~Ps~~ykWn~~ge 87 (170)
T COG4283 74 FTPSPGYKWNNLGE 87 (170)
T ss_pred CCCCCCCcccccHH
Confidence 57789999999994
No 11
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=22.12 E-value=1e+02 Score=29.67 Aligned_cols=15 Identities=40% Similarity=0.384 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHhHHH
Q 021011 115 QQQLQQRLLHQQQQQ 129 (318)
Q Consensus 115 ~~~~~~~~~~~~q~~ 129 (318)
+||||--+||.||+-
T Consensus 9 qHQqQL~~MQkQQLa 23 (230)
T PF06752_consen 9 QHQQQLVLMQKQQLA 23 (230)
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333456655543
No 12
>KOG4407 consensus Predicted Rho GTPase-activating protein [General function prediction only]
Probab=21.57 E-value=67 Score=38.17 Aligned_cols=18 Identities=22% Similarity=0.301 Sum_probs=11.9
Q ss_pred HHHHHHHHhhhcCCCCcee
Q 021011 133 HMKLQAEKMFRKSNSGVSL 151 (318)
Q Consensus 133 ~~~~q~~~~~~r~~~g~~l 151 (318)
|+++|+ +.|.|-+.--++
T Consensus 368 ~qq~QH-~q~~~~nq~~n~ 385 (1973)
T KOG4407|consen 368 QQQQQH-HQFMRANQPPNL 385 (1973)
T ss_pred hhHHHH-HHHHhccCCcch
Confidence 566666 577787666554
Done!