Query 019404
Match_columns 341
No_of_seqs 228 out of 710
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 09:11:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019404.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019404hhsearch_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 2.3E-31 5.1E-36 201.9 4.8 59 262-320 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 7.7E-32 1.7E-36 204.7 1.8 60 262-322 1-60 (60)
3 PF10533 Plant_zn_clust: Plant 99.4 1.9E-13 4.2E-18 99.7 3.9 47 208-260 1-47 (47)
4 PF04500 FLYWCH: FLYWCH zinc f 91.5 0.074 1.6E-06 38.4 0.7 49 262-320 12-62 (62)
5 PF05344 DUF746: Domain of Unk 86.2 0.75 1.6E-05 36.3 2.9 52 29-81 2-61 (65)
6 PF03101 FAR1: FAR1 DNA-bindin 84.7 1.2 2.6E-05 34.9 3.5 31 292-323 60-90 (91)
7 cd07691 Ig_CD3_gamma_delta Imm 42.5 32 0.00069 27.5 3.3 25 264-289 17-51 (69)
8 cd00686 Terpene_cyclase_cis_tr 42.2 32 0.00069 35.2 4.1 24 17-40 257-280 (357)
9 PF09883 DUF2110: Uncharacteri 31.9 19 0.00041 34.6 0.6 12 62-73 173-184 (225)
10 PF03859 CG-1: CG-1 domain; I 22.5 91 0.002 27.4 3.1 54 263-317 52-117 (118)
11 PF08257 Sulfakinin: Sulfakini 21.9 35 0.00076 17.5 0.2 6 69-74 4-9 (9)
12 COG4044 Uncharacterized protei 21.3 39 0.00084 32.7 0.6 12 62-73 185-196 (247)
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=99.97 E-value=2.3e-31 Score=201.90 Aligned_cols=59 Identities=63% Similarity=1.265 Sum_probs=56.5
Q ss_pred CCCcccccccCCccCCCCCCCccccccCCCCCCCcccceeecCCCCCeEEEEEecCCCC
Q 019404 262 PPDEYSWRKYGQKPIKGSPYPRGYYKCSTMRGCPARKHVERAPDDPTMLIVTYEGEHRH 320 (341)
Q Consensus 262 ~~DGy~WRKYGQK~Ikgs~~pRsYYrCs~~~gC~A~K~Ver~~dDp~~~~vtY~G~HnH 320 (341)
++|||.|||||||.|+|+++||+||||++.+||+|+|+|||+++|+.+++|||+|+|||
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 47999999999999999999999999985589999999999999999999999999998
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=99.97 E-value=7.7e-32 Score=204.74 Aligned_cols=60 Identities=65% Similarity=1.315 Sum_probs=51.8
Q ss_pred CCCcccccccCCccCCCCCCCccccccCCCCCCCcccceeecCCCCCeEEEEEecCCCCCC
Q 019404 262 PPDEYSWRKYGQKPIKGSPYPRGYYKCSTMRGCPARKHVERAPDDPTMLIVTYEGEHRHSQ 322 (341)
Q Consensus 262 ~~DGy~WRKYGQK~Ikgs~~pRsYYrCs~~~gC~A~K~Ver~~dDp~~~~vtY~G~HnH~~ 322 (341)
++|||+|||||||.|+|++|||+||||+ ..+|+|+|+|||+.+|+.+++|||+|+|||+.
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt-~~~C~akK~Vqr~~~d~~~~~vtY~G~H~h~k 60 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCT-HPGCPAKKQVQRSADDPNIVIVTYEGEHNHPK 60 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEE-CTTEEEEEEEEEETTCCCEEEEEEES--SS--
T ss_pred CCCCCchhhccCcccCCCceeeEeeecc-ccChhheeeEEEecCCCCEEEEEEeeeeCCCC
Confidence 4799999999999999999999999997 56999999999999999999999999999973
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=99.40 E-value=1.9e-13 Score=99.66 Aligned_cols=47 Identities=66% Similarity=1.093 Sum_probs=39.3
Q ss_pred CCCCCCCCCCCCCCCCcccCCCCCCCccccccccccccceEEEEecccCCccC
Q 019404 208 KKRCQDHKDHSDDLSGKFSGSTSGNNKCHCSKRRKNRVKKTIRVPAISSKIAD 260 (341)
Q Consensus 208 kr~c~~~~~~s~~~sgk~~g~~s~~~rch~sKrRk~r~kr~~rvp~~s~~~~d 260 (341)
|++|++++ +.+|+|.+ +++++|||+||||.|+||+|||||||++++|
T Consensus 1 krkC~~~~----~~~~~~~~--sssgrCHCsKkRK~RvKR~irVPAiS~K~AD 47 (47)
T PF10533_consen 1 KRKCHSHN----DSSGKCKC--SSSGRCHCSKKRKSRVKRTIRVPAISSKIAD 47 (47)
T ss_pred CCcccccC----cccCcccc--CCCCcccCCCcccccceeeEEeecccccccC
Confidence 68999873 34466543 6789999999999999999999999999875
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=91.48 E-value=0.074 Score=38.37 Aligned_cols=49 Identities=31% Similarity=0.552 Sum_probs=24.6
Q ss_pred CCCcccccccCCccCCCCCCCccccccCCC--CCCCcccceeecCCCCCeEEEEEecCCCC
Q 019404 262 PPDEYSWRKYGQKPIKGSPYPRGYYKCSTM--RGCPARKHVERAPDDPTMLIVTYEGEHRH 320 (341)
Q Consensus 262 ~~DGy~WRKYGQK~Ikgs~~pRsYYrCs~~--~gC~A~K~Ver~~dDp~~~~vtY~G~HnH 320 (341)
.-|||.-+++... ....|++|+.. .+|+|+=.+. .++ ..+ +...++|||
T Consensus 12 ~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~-~~~-~~~~~~HnH 62 (62)
T PF04500_consen 12 VYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGD-GRV-VRTNGEHNH 62 (62)
T ss_dssp EETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----T-TEE-EE-S---SS
T ss_pred EECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCC-CEE-EECCCccCC
Confidence 3588887765555 34589999852 3799988777 333 334 345699999
No 5
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=86.22 E-value=0.75 Score=36.27 Aligned_cols=52 Identities=29% Similarity=0.373 Sum_probs=37.8
Q ss_pred HHHHHHHHhcCCCCCC------CCcchhhHHHHHHhhhhhhhhccccCc--cccccCCCCC
Q 019404 29 SMEHLIRLMSHHQSSN------HVDCSDLTDLTVSKFKKVISLLNRTGH--ARFRRGPVHS 81 (341)
Q Consensus 29 S~e~li~lLSq~~~q~------q~d~~~itd~AVskFKkVISLL~RTGH--ARFRr~P~~~ 81 (341)
.+++||++||++-.-. ..| ..++..-|..|++-+=.||.+|| +|+|-|=.++
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~-~~~v~~wv~~fR~wll~LDPSG~~E~RVRLg~r~a 61 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTD-PGTVRRWVRMFRQWLLQLDPSGHWEARVRLGVRPA 61 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcC-HHHHHHHHHHHHHHHHHcCCCCChHHHhhcCCCCC
Confidence 4789999999873221 112 33456789999999999999998 7888765433
No 6
>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=84.68 E-value=1.2 Score=34.87 Aligned_cols=31 Identities=32% Similarity=0.540 Sum_probs=26.0
Q ss_pred CCCCcccceeecCCCCCeEEEEEecCCCCCCc
Q 019404 292 RGCPARKHVERAPDDPTMLIVTYEGEHRHSQA 323 (341)
Q Consensus 292 ~gC~A~K~Ver~~dDp~~~~vtY~G~HnH~~~ 323 (341)
.||+|+=.|.+.. |....++.+..+|||+-.
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 4899999998876 667777889999999853
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=42.53 E-value=32 Score=27.54 Aligned_cols=25 Identities=40% Similarity=0.987 Sum_probs=17.8
Q ss_pred CcccccccCCccCC--------CC--CCCccccccC
Q 019404 264 DEYSWRKYGQKPIK--------GS--PYPRGYYKCS 289 (341)
Q Consensus 264 DGy~WRKYGQK~Ik--------gs--~~pRsYYrCs 289 (341)
.-+.|-| |-..+. |+ .-||+-|+|.
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 4588988 764442 22 6799999994
No 8
>cd00686 Terpene_cyclase_cis_trans_C1 Cis, Trans, Terpene Cyclases, Class 1. This CD includes the terpenoid cyclase, trichodiene synthase, which catalyzes the cyclization of farnesyl diphosphate (FPP) to trichodiene using a cis-trans pathway, and is the first committed step in the biosynthesis of trichothecene toxins and antibiotics. As with other enzymes with the 'terpenoid synthase fold', this enzyme has two conserved metal binding motifs that coordinate Mg2+ ion-bridged binding of the diphosphate moiety of FPP. Metal-triggered substrate ionization initiates catalysis, and the alpha-barrel active site serves as a template to channel and stabilize the conformations of reactive carbocation intermediates through a complex cyclization cascade. These enzymes function as homodimers and are found in several genera of fungi.
Probab=42.21 E-value=32 Score=35.19 Aligned_cols=24 Identities=13% Similarity=0.358 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCC
Q 019404 17 TAIQEAATQGIKSMEHLIRLMSHH 40 (341)
Q Consensus 17 ~AvqEAA~agl~S~e~li~lLSq~ 40 (341)
.|+++...-.+++.+++..+|+..
T Consensus 257 eAL~~lt~dTv~~s~rv~~VLse~ 280 (357)
T cd00686 257 EALEKLTQDTLHSSKQMVAVFSDK 280 (357)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCC
Confidence 567777777899999999999864
No 9
>PF09883 DUF2110: Uncharacterized protein conserved in archaea (DUF2110); InterPro: IPR016757 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=31.88 E-value=19 Score=34.62 Aligned_cols=12 Identities=75% Similarity=0.988 Sum_probs=9.5
Q ss_pred hhhhccccCccc
Q 019404 62 VISLLNRTGHAR 73 (341)
Q Consensus 62 VISLL~RTGHAR 73 (341)
|=+.|+||||||
T Consensus 173 v~~alnrtGH~r 184 (225)
T PF09883_consen 173 VRAALNRTGHAR 184 (225)
T ss_pred HHHHHHhccccc
Confidence 445689999998
No 10
>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=22.54 E-value=91 Score=27.37 Aligned_cols=54 Identities=24% Similarity=0.359 Sum_probs=27.4
Q ss_pred CCcccccc-cCCccC---------CCCCCCccccccCCCCCCCcccceeecCCCC--CeEEEEEecC
Q 019404 263 PDEYSWRK-YGQKPI---------KGSPYPRGYYKCSTMRGCPARKHVERAPDDP--TMLIVTYEGE 317 (341)
Q Consensus 263 ~DGy~WRK-YGQK~I---------kgs~~pRsYYrCs~~~gC~A~K~Ver~~dDp--~~~~vtY~G~ 317 (341)
.|||.||| =+-|.| .|-..--+||-=+. .+=.....+=+..|.+ .++.|.|.-.
T Consensus 52 kDG~~WrKkkdgktvRE~HekLKv~~~e~l~~~Yah~~-~~~~F~RR~Ywll~~~~~~iVLVHY~~v 117 (118)
T PF03859_consen 52 KDGHNWRKKKDGKTVREDHEKLKVGGVEVLNCYYAHSE-DNPTFHRRCYWLLDPPYEHIVLVHYLDV 117 (118)
T ss_pred cccceeEEcCCCCchhhhhhhhccCceeeeEEEEEeec-cCCCeeeEEEEccCCCCceEEEEEeeec
Confidence 48999984 233333 33344446665431 2222333344445555 5666888653
No 11
>PF08257 Sulfakinin: Sulfakinin family; InterPro: IPR013259 The sulfakinin (SK) family of neuropeptides have only been identified in crustaceans and insects. For most species there is the potential for producing two sulfakinin peptides, one has a short sulfakinin sequence. The function of the sulfakinins is difficult to assess. For the Periplaneta americana (American cockroach), various forms of the endogenous sulfakinins have been shown to be active on the hindgut, and also on the heart. In Calliphora vomitoria (Blue blowfly) the peptides act as neurotransmitters or neuromodulators, linking the brain with all thoracic and abdominal ganglia. In adults of Penaeus monodon (Penoeid shrimp) they appear to be restricted to a few neurones in the brain with a neural pathway extending along to the ventral thoracic and abdominal ganglia [].
Probab=21.92 E-value=35 Score=17.53 Aligned_cols=6 Identities=67% Similarity=1.204 Sum_probs=4.9
Q ss_pred cCcccc
Q 019404 69 TGHARF 74 (341)
Q Consensus 69 TGHARF 74 (341)
-||-||
T Consensus 4 yghmrf 9 (9)
T PF08257_consen 4 YGHMRF 9 (9)
T ss_pred cccccC
Confidence 589887
No 12
>COG4044 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.33 E-value=39 Score=32.67 Aligned_cols=12 Identities=58% Similarity=0.883 Sum_probs=9.8
Q ss_pred hhhhccccCccc
Q 019404 62 VISLLNRTGHAR 73 (341)
Q Consensus 62 VISLL~RTGHAR 73 (341)
+=+.|+||||+|
T Consensus 185 i~ral~rtGh~R 196 (247)
T COG4044 185 IERALNRTGHGR 196 (247)
T ss_pred HHHHHHhccCCc
Confidence 445799999998
Done!