Query 043122
Match_columns 106
No_of_seqs 132 out of 631
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 13:05:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043122.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043122hhsearch_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 2.8E-36 6E-41 192.5 3.9 59 27-85 1-59 (60)
2 smart00774 WRKY DNA binding do 100.0 7.9E-35 1.7E-39 185.8 4.5 58 27-84 1-59 (59)
3 PF04500 FLYWCH: FLYWCH zinc f 95.0 0.021 4.5E-07 34.1 2.3 50 25-84 10-62 (62)
4 PF03101 FAR1: FAR1 DNA-bindin 92.8 0.11 2.4E-06 33.6 2.6 32 56-88 60-91 (91)
5 PLN03097 FHY3 Protein FAR-RED 58.1 13 0.00028 34.4 3.8 36 53-89 156-191 (846)
6 PF03859 CG-1: CG-1 domain; I 52.1 6.2 0.00013 28.5 0.6 10 26-35 50-59 (118)
7 KOG0673 Thymidylate synthase [ 30.3 24 0.00053 28.8 0.9 22 28-49 114-156 (293)
8 PF04606 Ogr_Delta: Ogr/Delta- 24.2 31 0.00068 20.3 0.4 17 48-64 23-39 (47)
9 PF03615 GCM: GCM motif protei 22.8 69 0.0015 23.8 2.0 22 70-91 114-135 (143)
10 COG4283 Uncharacterized conser 22.7 35 0.00075 26.1 0.5 15 24-38 73-87 (170)
11 PF03119 DNA_ligase_ZBD: NAD-d 20.6 35 0.00075 18.3 0.1 12 49-60 16-28 (28)
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=2.8e-36 Score=192.45 Aligned_cols=59 Identities=68% Similarity=1.301 Sum_probs=52.6
Q ss_pred cCCCcceeecCcccccCCCCCCccccccccccccccceeeecCCCCEEEEeEeccCCCC
Q 043122 27 LDDGYRWRKYGQKAVKNNKFPRSYYRCTHQGCNVKKQVQRLTKDEGVVVTTYEGMHSHP 85 (106)
Q Consensus 27 ~~DGy~WRKYGQK~ikg~~~pRsYyrCt~~~C~akK~Vqr~~~D~~~~~~tY~G~H~h~ 85 (106)
++|||+|||||||.|+|+++||+||||++.+|+|+|+|||+.+|+.+++|||+|+|||+
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=100.00 E-value=7.9e-35 Score=185.79 Aligned_cols=58 Identities=69% Similarity=1.218 Sum_probs=56.6
Q ss_pred cCCCcceeecCcccccCCCCCCccccccc-cccccccceeeecCCCCEEEEeEeccCCC
Q 043122 27 LDDGYRWRKYGQKAVKNNKFPRSYYRCTH-QGCNVKKQVQRLTKDEGVVVTTYEGMHSH 84 (106)
Q Consensus 27 ~~DGy~WRKYGQK~ikg~~~pRsYyrCt~-~~C~akK~Vqr~~~D~~~~~~tY~G~H~h 84 (106)
++|||.|||||||.|+|+++||+||||++ ++|+|+|+||++++|+.+++|||+|+|||
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 48999999999999999999999999999 99999999999999999999999999998
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=95.04 E-value=0.021 Score=34.05 Aligned_cols=50 Identities=30% Similarity=0.649 Sum_probs=24.9
Q ss_pred cccCCCcceeecCcccccCCCCCCcccccccc---ccccccceeeecCCCCEEEEeEeccCCC
Q 043122 25 DILDDGYRWRKYGQKAVKNNKFPRSYYRCTHQ---GCNVKKQVQRLTKDEGVVVTTYEGMHSH 84 (106)
Q Consensus 25 ~~~~DGy~WRKYGQK~ikg~~~pRsYyrCt~~---~C~akK~Vqr~~~D~~~~~~tY~G~H~h 84 (106)
.++-|||.-.+.... ....|++|+.. +|+|+=.+. ++++ .+. ...++|||
T Consensus 10 ~L~~~Gy~y~~~~~~------~~~~~WrC~~~~~~~C~a~~~~~--~~~~-~~~-~~~~~HnH 62 (62)
T PF04500_consen 10 KLVYDGYRYYFNKRN------DGKTYWRCSRRRSHGCRARLITD--AGDG-RVV-RTNGEHNH 62 (62)
T ss_dssp EEEETTEEEEEEEE-------SS-EEEEEGGGTTS----EEEEE----TT-EEE-E-S---SS
T ss_pred EEEECCeEEECcCCC------CCcEEEEeCCCCCCCCeEEEEEE--CCCC-EEE-ECCCccCC
Confidence 367789886664444 34589999983 899977765 2333 333 33489998
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=92.78 E-value=0.11 Score=33.58 Aligned_cols=32 Identities=31% Similarity=0.517 Sum_probs=26.8
Q ss_pred cccccccceeeecCCCCEEEEeEeccCCCCCCC
Q 043122 56 QGCNVKKQVQRLTKDEGVVVTTYEGMHSHPIER 88 (106)
Q Consensus 56 ~~C~akK~Vqr~~~D~~~~~~tY~G~H~h~~~~ 88 (106)
.+|+|+=.|-+.. |+...++.+..+|||+..+
T Consensus 60 tgC~a~i~v~~~~-~~~w~v~~~~~~HNH~L~P 91 (91)
T PF03101_consen 60 TGCKARINVKRRK-DGKWRVTSFVLEHNHPLCP 91 (91)
T ss_pred cCCCEEEEEEEcc-CCEEEEEECcCCcCCCCCC
Confidence 6999998887755 7888889999999999743
No 5
>PLN03097 FHY3 Protein FAR-RED ELONGATED HYPOCOTYL 3; Provisional
Probab=58.12 E-value=13 Score=34.43 Aligned_cols=36 Identities=22% Similarity=0.505 Sum_probs=29.7
Q ss_pred ccccccccccceeeecCCCCEEEEeEeccCCCCCCCC
Q 043122 53 CTHQGCNVKKQVQRLTKDEGVVVTTYEGMHSHPIERS 89 (106)
Q Consensus 53 Ct~~~C~akK~Vqr~~~D~~~~~~tY~G~H~h~~~~s 89 (106)
|+-.||+|.=.|.+ ..|+.-.++-+..+|||+.-++
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 67789999999977 4566788899999999997554
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=52.07 E-value=6.2 Score=28.45 Aligned_cols=10 Identities=50% Similarity=1.026 Sum_probs=8.5
Q ss_pred ccCCCcceee
Q 043122 26 ILDDGYRWRK 35 (106)
Q Consensus 26 ~~~DGy~WRK 35 (106)
--.|||.|||
T Consensus 50 fRkDG~~WrK 59 (118)
T PF03859_consen 50 FRKDGHNWRK 59 (118)
T ss_pred hhcccceeEE
Confidence 5689999995
No 7
>KOG0673 consensus Thymidylate synthase [Nucleotide transport and metabolism]
Probab=30.34 E-value=24 Score=28.75 Aligned_cols=22 Identities=36% Similarity=0.809 Sum_probs=17.3
Q ss_pred CCCcceeecCcc---------------------cccCCCCCCc
Q 043122 28 DDGYRWRKYGQK---------------------AVKNNKFPRS 49 (106)
Q Consensus 28 ~DGy~WRKYGQK---------------------~ikg~~~pRs 49 (106)
-=|++||-+|-+ .||+||+.|-
T Consensus 114 vyGfqWrHfgA~Y~~~~~dy~gqgvdQL~~vI~~ik~NP~drR 156 (293)
T KOG0673|consen 114 VYGFQWRHFGARYEDCDSDYTGQGVDQLADVINKIKNNPDDRR 156 (293)
T ss_pred ccceeeeecCccccccccccccccHHHHHHHHHHHhcCCccce
Confidence 447999999976 5788888774
No 8
>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=24.25 E-value=31 Score=20.26 Aligned_cols=17 Identities=24% Similarity=0.522 Sum_probs=13.6
Q ss_pred Cccccccccccccccce
Q 043122 48 RSYYRCTHQGCNVKKQV 64 (106)
Q Consensus 48 RsYyrCt~~~C~akK~V 64 (106)
..||.|++..|.++-..
T Consensus 23 ~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 23 ELYCQCTNPECGHTFVA 39 (47)
T ss_pred EEEEEECCCcCCCEEEE
Confidence 47999999999986543
No 9
>PF03615 GCM: GCM motif protein; InterPro: IPR003902 GCM transcription factors are a family of proteins which contain a GCM motif. The GCM motif is a domain that has been identified in proteins belonging to a family of transcriptional regulators involved in fundamental developmental processes which comprise Drosophila melanogaster GCM and its mammalian homologs [, , , ]. IN GCM transcription factors the N-terminal moiety contains a DNA-binding domain of 150 residues. Sequence conservation is highest in this GCM domain. In contrast, the C-terminal moiety contains one or two transactivating regions and is only poorly conserved. The GCM motif has been shown to be a DNA binding domain that recognises preferentially the nonpalindromic octamer 5'-ATGCGGGT-3' [, , ]. The GCM motif contains many conserved basic amino acid residues, seven cysteine residues, and four histidine residues []. The conserved cysteines are involved in shaping the overall conformation of the domain, in the process of DNA binding and in the redox regulation of DNA binding []. The GCM domain as a new class of Zn-containing DNA-binding domain with no similarity to any other DNA-binding domain []. The GCM domain consists of a large and a small domain tethered together by one of the two Zn ions present in the structure. The large and the small domains comprise five- and three-stranded beta-sheets, respectively, with three small helical segments packed against the same side of the two beta-sheets. The GCM domain exercises a novel mode of sequence-specific DNA recognition, where the five-stranded beta-pleated sheet inserts into the major groove of the DNA. Residues protruding from the edge strand of the beta-pleated sheet and the following loop and strand contact the bases and backbone of both DNA strands, providing specificity for its DNA target site. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ODH_A.
Probab=22.83 E-value=69 Score=23.84 Aligned_cols=22 Identities=23% Similarity=0.484 Sum_probs=7.1
Q ss_pred CCCEEEEeEeccCCCCCCCCCC
Q 043122 70 DEGVVVTTYEGMHSHPIERSTD 91 (106)
Q Consensus 70 D~~~~~~tY~G~H~h~~~~st~ 91 (106)
++..+...=+|.|.||.|....
T Consensus 114 ~~~~IfFQaKG~HDHpRPe~K~ 135 (143)
T PF03615_consen 114 DGNAIFFQAKGVHDHPRPEAKS 135 (143)
T ss_dssp -SSBEEEEEE----S-----HH
T ss_pred CCCEEEEEcccccCCCCCCccc
Confidence 3444555678999999988543
No 10
>COG4283 Uncharacterized conserved protein [Function unknown]
Probab=22.69 E-value=35 Score=26.07 Aligned_cols=15 Identities=33% Similarity=0.811 Sum_probs=12.3
Q ss_pred ccccCCCcceeecCc
Q 043122 24 VDILDDGYRWRKYGQ 38 (106)
Q Consensus 24 ~~~~~DGy~WRKYGQ 38 (106)
+-++.+||.|+.||.
T Consensus 73 ~f~Ps~~ykWn~~ge 87 (170)
T COG4283 73 VFTPSPGYKWNNLGE 87 (170)
T ss_pred CCCCCCCCcccccHH
Confidence 446889999999994
No 11
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=20.62 E-value=35 Score=18.30 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=7.2
Q ss_pred cccccccc-cccc
Q 043122 49 SYYRCTHQ-GCNV 60 (106)
Q Consensus 49 sYyrCt~~-~C~a 60 (106)
..+||++. .|+|
T Consensus 16 v~~~C~N~l~CpA 28 (28)
T PF03119_consen 16 VDIRCPNPLSCPA 28 (28)
T ss_dssp TCEEE--CGC-HH
T ss_pred EeEECCCCCcCCC
Confidence 57899997 9986
Done!