Query 025175
Match_columns 256
No_of_seqs 214 out of 649
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 03:21:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025175.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025175hhsearch_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 2E-32 4.3E-37 200.8 5.1 59 91-149 1-59 (59)
2 PF03106 WRKY: WRKY DNA -bindi 100.0 8.1E-33 1.7E-37 202.6 2.7 59 91-150 1-59 (60)
3 PF04500 FLYWCH: FLYWCH zinc f 93.7 0.047 1E-06 37.6 2.1 52 88-149 9-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 93.0 0.098 2.1E-06 39.2 2.9 30 121-151 60-89 (91)
5 PF03859 CG-1: CG-1 domain; I 37.8 12 0.00027 31.5 0.3 9 91-99 51-59 (118)
6 PF11159 DUF2939: Protein of u 29.5 63 0.0014 24.9 3.0 40 208-247 34-79 (95)
7 KOG0673 Thymidylate synthase [ 26.2 28 0.0006 33.1 0.6 31 89-119 111-162 (293)
8 PLN03097 FHY3 Protein FAR-RED 25.5 68 0.0015 34.8 3.4 32 121-153 159-190 (846)
9 PF06534 RGM_C: Repulsive guid 19.2 78 0.0017 28.4 2.0 29 227-255 150-178 (179)
10 PF10929 DUF2811: Protein of u 18.6 1.2E+02 0.0027 22.6 2.6 36 214-249 5-42 (57)
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=2e-32 Score=200.80 Aligned_cols=59 Identities=59% Similarity=1.258 Sum_probs=57.1
Q ss_pred ccCCccccccCccccCCCCCCCcccccCCCCCCccccceeecCCCCCEEEEEeeccCCC
Q 025175 91 VKDGYQWRKYGQKVTRDNPSPRAYFKCSFAPSCPVKKKVQRSAEDPSILVATYEGEHNH 149 (256)
Q Consensus 91 ~~DGy~WRKYGQK~ikgn~~pRsYYRCs~~~~C~akKqVQrs~~D~~i~~vtY~GeHnH 149 (256)
++|||+|||||||.|+|+++||+||||++.++|+|+|+|||+++|+.+++|||+|+|||
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 47999999999999999999999999999789999999999999999999999999998
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=8.1e-33 Score=202.61 Aligned_cols=59 Identities=61% Similarity=1.294 Sum_probs=52.2
Q ss_pred ccCCccccccCccccCCCCCCCcccccCCCCCCccccceeecCCCCCEEEEEeeccCCCC
Q 025175 91 VKDGYQWRKYGQKVTRDNPSPRAYFKCSFAPSCPVKKKVQRSAEDPSILVATYEGEHNHP 150 (256)
Q Consensus 91 ~~DGy~WRKYGQK~ikgn~~pRsYYRCs~~~~C~akKqVQrs~~D~~i~~vtY~GeHnH~ 150 (256)
++|||+|||||||.|+|+++||+||||++. +|+|+|+|||+.+|+.+++|||+|+|||+
T Consensus 1 ~~Dgy~WRKYGqK~i~g~~~pRsYYrCt~~-~C~akK~Vqr~~~d~~~~~vtY~G~H~h~ 59 (60)
T PF03106_consen 1 LDDGYRWRKYGQKNIKGSPYPRSYYRCTHP-GCPAKKQVQRSADDPNIVIVTYEGEHNHP 59 (60)
T ss_dssp --SSS-EEEEEEEEETTTTCEEEEEEEECT-TEEEEEEEEEETTCCCEEEEEEES--SS-
T ss_pred CCCCCchhhccCcccCCCceeeEeeecccc-ChhheeeEEEecCCCCEEEEEEeeeeCCC
Confidence 589999999999999999999999999995 99999999999999999999999999997
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=93.73 E-value=0.047 Score=37.65 Aligned_cols=52 Identities=31% Similarity=0.564 Sum_probs=27.8
Q ss_pred cccccCCccccccCccccCCCCCCCcccccCCC--CCCccccceeecCCCCCEEEEEeeccCCC
Q 025175 88 TLIVKDGYQWRKYGQKVTRDNPSPRAYFKCSFA--PSCPVKKKVQRSAEDPSILVATYEGEHNH 149 (256)
Q Consensus 88 s~~~~DGy~WRKYGQK~ikgn~~pRsYYRCs~~--~~C~akKqVQrs~~D~~i~~vtY~GeHnH 149 (256)
..++-|||.-.++... ....|+||+.. .+|+|+=.+. .++. .++...++|||
T Consensus 9 ~~L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~--~~~~~~~~HnH 62 (62)
T PF04500_consen 9 PKLVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG--RVVRTNGEHNH 62 (62)
T ss_dssp EEEEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT--EEEE-S---SS
T ss_pred EEEEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC--EEEECCCccCC
Confidence 4567899987776555 34689999974 3799998887 3343 33344499998
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=92.96 E-value=0.098 Score=39.24 Aligned_cols=30 Identities=33% Similarity=0.565 Sum_probs=26.3
Q ss_pred CCCccccceeecCCCCCEEEEEeeccCCCCC
Q 025175 121 PSCPVKKKVQRSAEDPSILVATYEGEHNHPQ 151 (256)
Q Consensus 121 ~~C~akKqVQrs~~D~~i~~vtY~GeHnH~~ 151 (256)
.+|+|+=.|-+.. |....++.+..+|||+.
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 5999999998876 66788899999999987
No 5
>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=37.85 E-value=12 Score=31.48 Aligned_cols=9 Identities=67% Similarity=1.224 Sum_probs=7.6
Q ss_pred ccCCccccc
Q 025175 91 VKDGYQWRK 99 (256)
Q Consensus 91 ~~DGy~WRK 99 (256)
-.|||.|||
T Consensus 51 RkDG~~WrK 59 (118)
T PF03859_consen 51 RKDGHNWRK 59 (118)
T ss_pred hcccceeEE
Confidence 469999995
No 6
>PF11159 DUF2939: Protein of unknown function (DUF2939); InterPro: IPR021330 This bacterial family of proteins has no known function.
Probab=29.49 E-value=63 Score=24.93 Aligned_cols=40 Identities=25% Similarity=0.374 Sum_probs=28.5
Q ss_pred cccCChHHHHHHHHHHHHhhhC------CCChHHHHHHHHhccccc
Q 025175 208 QQIEAPAIHQILVQQMASNLTK------DPNFTAALAAAISGRFAD 247 (256)
Q Consensus 208 ~~~~~p~~~~~lveqma~slt~------DPnFtaALaaAis~~i~~ 247 (256)
..++.|.+|..|.+|+...+.+ +++.-++|..++.+.+.+
T Consensus 34 ~~VD~~avr~slk~ql~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~ 79 (95)
T PF11159_consen 34 RYVDFPAVRASLKDQLNAELVSRIGPEVADDPLAALGAMLAPGLVD 79 (95)
T ss_pred HHcCHHHHHHHHHHHHHHHHHhhcCccccCCHHHHHHHHHHHHHHH
Confidence 3467789999999998887654 356666777777755544
No 7
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=26.22 E-value=28 Score=33.12 Aligned_cols=31 Identities=29% Similarity=0.677 Sum_probs=21.7
Q ss_pred ccccCCccccccCcc---------------------ccCCCCCCCcccccCC
Q 025175 89 LIVKDGYQWRKYGQK---------------------VTRDNPSPRAYFKCSF 119 (256)
Q Consensus 89 ~~~~DGy~WRKYGQK---------------------~ikgn~~pRsYYRCs~ 119 (256)
+-+-=|++||-+|-| .||+||+-|----|.+
T Consensus 111 lgpvyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drRIimsAw 162 (293)
T KOG0673|consen 111 LGPVYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRRIIMSAW 162 (293)
T ss_pred cccccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccceeeeecc
Confidence 344568999999977 4678887776544443
No 8
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=25.50 E-value=68 Score=34.84 Aligned_cols=32 Identities=22% Similarity=0.447 Sum_probs=26.7
Q ss_pred CCCccccceeecCCCCCEEEEEeeccCCCCCCC
Q 025175 121 PSCPVKKKVQRSAEDPSILVATYEGEHNHPQPT 153 (256)
Q Consensus 121 ~~C~akKqVQrs~~D~~i~~vtY~GeHnH~~p~ 153 (256)
.||+|.=.|.+..+ ..-.++-+..+|||+.-+
T Consensus 159 tGC~A~m~Vk~~~~-gkW~V~~fv~eHNH~L~p 190 (846)
T PLN03097 159 TDCKASMHVKRRPD-GKWVIHSFVKEHNHELLP 190 (846)
T ss_pred CCCceEEEEEEcCC-CeEEEEEEecCCCCCCCC
Confidence 59999999988544 458899999999999943
No 9
>PF06534 RGM_C: Repulsive guidance molecule (RGM) C-terminus; InterPro: IPR009496 This entry contains of several mammalian and one bird sequence from Gallus gallus (Chicken) and represents the C-terminal region of several sequences, but in others it represents the full protein. All of the mammalian proteins are hypothetical and have no known function, but Q8JG54 from SWISSPROT from the chicken is annotated as being a repulsive guidance molecule (RGM). RGM is a GPI-linked axon guidance molecule of the retinotectal system. RGM is repulsive for a subset of axons, those from the temporal half of the retina. Temporal retinal axons invade the anterior optic tectum in a superficial layer, and encounter RGM expressed in a gradient with increasing concentration along the anterior-posterior axis. Temporal axons are able to receive posterior-dependent information by sensing gradients or concentrations of guidance cues. Thus, RGM is likely to provide positional information for temporal axons invading the optic tectum in the stratum opticum [].
Probab=19.21 E-value=78 Score=28.41 Aligned_cols=29 Identities=38% Similarity=0.475 Sum_probs=22.1
Q ss_pred hhCCCChHHHHHHHHhcccccccccccCC
Q 025175 227 LTKDPNFTAALAAAISGRFADQARTQRWS 255 (256)
Q Consensus 227 lt~DPnFtaALaaAis~~i~~~~~~~~~~ 255 (256)
.|-|+||++|-.+|+...-.-+....||-
T Consensus 150 TTGD~nft~aA~~AleD~~~l~p~~~~~h 178 (179)
T PF06534_consen 150 TTGDANFTAAAYSALEDVKALHPDPERWH 178 (179)
T ss_pred ecCCccHHHHHHHHHHHHHHhcCchhccc
Confidence 48999999999999877655555555653
No 10
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=18.56 E-value=1.2e+02 Score=22.64 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhhhCCCChH--HHHHHHHhccccccc
Q 025175 214 AIHQILVQQMASNLTKDPNFT--AALAAAISGRFADQA 249 (256)
Q Consensus 214 ~~~~~lveqma~slt~DPnFt--aALaaAis~~i~~~~ 249 (256)
+++..|.+.|..=|-..|++- --+.|||+|.+++..
T Consensus 5 eiPe~L~~~m~~fie~hP~WDQ~Rl~~aALa~FL~QnG 42 (57)
T PF10929_consen 5 EIPEDLHQAMKDFIETHPNWDQYRLFQAALAGFLLQNG 42 (57)
T ss_pred cccHHHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcC
Confidence 567889999999999999974 457788888887654
Done!