Query psy15167
Match_columns 75
No_of_seqs 64 out of 66
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 22:16:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15167.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15167hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14753 DUF4475: Domain of un 72.1 4.2 9.1E-05 30.5 2.8 37 37-74 99-135 (196)
2 PF06827 zf-FPG_IleRS: Zinc fi 34.7 18 0.00039 18.5 0.5 10 57-66 1-10 (30)
3 PF13963 Transpos_assoc: Trans 31.1 15 0.00034 22.6 -0.1 40 20-67 10-49 (77)
4 PF12800 Fer4_4: 4Fe-4S bindin 29.9 34 0.00074 16.1 1.0 9 60-68 7-15 (17)
5 PF07945 Toxin_16: Janus-atrac 21.3 52 0.0011 19.0 0.9 16 55-70 5-20 (36)
6 TIGR03157 cas_Csc2 CRISPR-asso 20.3 33 0.00071 27.2 -0.1 38 3-42 19-58 (282)
7 PRK13945 formamidopyrimidine-D 19.4 55 0.0012 24.5 0.9 11 55-65 252-262 (282)
8 PRK14811 formamidopyrimidine-D 18.5 58 0.0012 24.3 0.9 12 55-66 233-244 (269)
9 PRK14810 formamidopyrimidine-D 18.3 59 0.0013 24.2 0.9 11 55-65 242-252 (272)
10 TIGR00577 fpg formamidopyrimid 18.2 60 0.0013 24.1 0.9 11 55-65 243-253 (272)
No 1
>PF14753 DUF4475: Domain of unknown function (DUF4475)
Probab=72.09 E-value=4.2 Score=30.52 Aligned_cols=37 Identities=22% Similarity=0.483 Sum_probs=26.2
Q ss_pred cccccccccccCcceecCCCCcccccCCCCCCCCcccC
Q psy15167 37 LSWTRPSLLEGHKLAHDLGAGSPCLQCKDNCPGLDLHF 74 (75)
Q Consensus 37 ~~~~Rre~~kq~~L~he~~~GaPClkCk~~CpGFeLHf 74 (75)
++|.=|=.=|-....|++.....|.+|. .|.||+.+|
T Consensus 99 Gs~~~rCrCKH~~~eH~~~~~~~C~k~~-~C~~F~S~f 135 (196)
T PF14753_consen 99 GSWPARCRCKHSHEEHSPKGPHKCKKCC-GCSGFESSF 135 (196)
T ss_pred CCccccccCCCCccccCCCCCccCCCCC-CCCCCCCCc
Confidence 3333333334456778888899999997 999999876
No 2
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=34.75 E-value=18 Score=18.54 Aligned_cols=10 Identities=30% Similarity=0.856 Sum_probs=5.4
Q ss_pred CcccccCCCC
Q psy15167 57 GSPCLQCKDN 66 (75)
Q Consensus 57 GaPClkCk~~ 66 (75)
|.||.+|+..
T Consensus 1 G~~C~rC~~~ 10 (30)
T PF06827_consen 1 GEKCPRCWNY 10 (30)
T ss_dssp TSB-TTT--B
T ss_pred CCcCccCCCc
Confidence 6789998753
No 3
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=31.05 E-value=15 Score=22.61 Aligned_cols=40 Identities=13% Similarity=0.238 Sum_probs=25.3
Q ss_pred ccccCCchhhhhhhhhhcccccccccccCcceecCCCCcccccCCCCC
Q psy15167 20 IGTRSGRWLSVSTMQRQLSWTRPSLLEGHKLAHDLGAGSPCLQCKDNC 67 (75)
Q Consensus 20 ~~~~~p~wls~le~~~~~~~~Rre~~kq~~L~he~~~GaPClkCk~~C 67 (75)
.+-.+++|+.++++|-+... +.....+ ..-=||.+|++.-
T Consensus 10 ~~r~s~ey~~Gv~~Fi~~A~-------~~~~~~~-~i~CPC~~C~N~~ 49 (77)
T PF13963_consen 10 KDRFSPEYIEGVEEFIDFAF-------SNPSNDN-MIRCPCRKCKNEK 49 (77)
T ss_pred CCCCCHHHHHHHHHHHHHHH-------hcccCCC-ceECCchhhccCc
Confidence 35578999999999875422 1111111 4467999998753
No 4
>PF12800 Fer4_4: 4Fe-4S binding domain; InterPro: IPR001450 This superfamily includes proteins containing domains which bind to iron-sulphur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Ferredoxins are iron-sulphur proteins that mediate electron transfer in a range of metabolic reactions; they fall into several subgroups according to the nature of their iron-sulphur cluster(s) [, ]. One group, originally found in bacteria, has been termed "bacterial-type", in which the active centre is a 4Fe-4S cluster. 4Fe-4S ferredoxins may in turn be subdivided into further groups, based on their sequence properties. Most contain at least one conserved domain, including four Cys residues that bind to a 4Fe-4S centre. ; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 1BD6_A 1BQX_A 1BWE_A 1BC6_A.
Probab=29.91 E-value=34 Score=16.08 Aligned_cols=9 Identities=56% Similarity=1.431 Sum_probs=7.2
Q ss_pred cccCCCCCC
Q psy15167 60 CLQCKDNCP 68 (75)
Q Consensus 60 ClkCk~~Cp 68 (75)
|..|.+.||
T Consensus 7 C~~C~~~Cp 15 (17)
T PF12800_consen 7 CGSCVDVCP 15 (17)
T ss_dssp SSSSTTTST
T ss_pred CchHHhhcc
Confidence 777888887
No 5
>PF07945 Toxin_16: Janus-atracotoxin; InterPro: IPR012499 This family includes three peptides secreted by the spider Hadronyche versuta (Blue mountains funnel-web spider) (P82226 from SWISSPROT, P82227 from SWISSPROT, P82228 from SWISSPROT). These are insect-selective, excitatory neurotoxins that may function by antagonising muscle acetylcholine receptors, or acetylcholine receptor subtypes present in other invertebrate neurons []. Janus atracotoxin-Hv1c (J-ACTX-Hv1c, P82228 from SWISSPROT) is organised into a disulphide-rich globular core (residues 3-19) and a beta-hairpin (residues 20-34). There are 4 disulphide bridges, one of which is a vicinal disulphide bridge; this is known to be unimportant in the maintenance of structure but critical for insecticidal activity []. ; GO: 0009405 pathogenesis, 0005576 extracellular region; PDB: 1DL0_A.
Probab=21.25 E-value=52 Score=19.03 Aligned_cols=16 Identities=50% Similarity=1.190 Sum_probs=6.7
Q ss_pred CCCcccccCCCCCCCC
Q psy15167 55 GAGSPCLQCKDNCPGL 70 (75)
Q Consensus 55 ~~GaPClkCk~~CpGF 70 (75)
++..||..|-.-|||-
T Consensus 5 gadrpcaaccpccpgt 20 (36)
T PF07945_consen 5 GADRPCAACCPCCPGT 20 (36)
T ss_dssp -TTSB--SS----TTE
T ss_pred CCCCCcccccCCCCCc
Confidence 5567898887778874
No 6
>TIGR03157 cas_Csc2 CRISPR-associated protein Csc2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2.
Probab=20.26 E-value=33 Score=27.20 Aligned_cols=38 Identities=21% Similarity=0.248 Sum_probs=26.2
Q ss_pred cccCCCCCCCcchhhccccccCCchhhhhhhhh--hcccccc
Q psy15167 3 MFTHPGGPDTNHVQRSQIGTRSGRWLSVSTMQR--QLSWTRP 42 (75)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~p~wls~le~~~--~~~~~Rr 42 (75)
+|+|-|+| ....+.|+|.....-++.+-|++ +..+.|+
T Consensus 19 if~TdG~~--~n~~~~~~G~~~~~~~s~~vmfkRKq~~~eR~ 58 (282)
T TIGR03157 19 LFRTEGEP--ENSSLVRAGDEGKTEISPLIMFKRKQSAPERR 58 (282)
T ss_pred eEecCCCc--cceeeeeeccCCCcceeeEEEEecccccHHHH
Confidence 68999987 34678899988776677666654 3444444
No 7
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=19.40 E-value=55 Score=24.48 Aligned_cols=11 Identities=36% Similarity=1.063 Sum_probs=8.8
Q ss_pred CCCcccccCCC
Q psy15167 55 GAGSPCLQCKD 65 (75)
Q Consensus 55 ~~GaPClkCk~ 65 (75)
-.|+||.+|+.
T Consensus 252 R~g~pC~~Cg~ 262 (282)
T PRK13945 252 RTGKPCRKCGT 262 (282)
T ss_pred CCcCCCCcCCC
Confidence 35899999975
No 8
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=18.49 E-value=58 Score=24.31 Aligned_cols=12 Identities=33% Similarity=0.933 Sum_probs=9.3
Q ss_pred CCCcccccCCCC
Q psy15167 55 GAGSPCLQCKDN 66 (75)
Q Consensus 55 ~~GaPClkCk~~ 66 (75)
-.|.||..|+..
T Consensus 233 R~g~pC~~Cg~~ 244 (269)
T PRK14811 233 REGQPCPRCGTP 244 (269)
T ss_pred CCcCCCCcCCCe
Confidence 458999999753
No 9
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=18.25 E-value=59 Score=24.21 Aligned_cols=11 Identities=55% Similarity=1.358 Sum_probs=8.9
Q ss_pred CCCcccccCCC
Q psy15167 55 GAGSPCLQCKD 65 (75)
Q Consensus 55 ~~GaPClkCk~ 65 (75)
-.|.||.+|+.
T Consensus 242 R~g~pCprCG~ 252 (272)
T PRK14810 242 RTGEPCLNCKT 252 (272)
T ss_pred CCCCcCCCCCC
Confidence 34899999975
No 10
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=18.17 E-value=60 Score=24.12 Aligned_cols=11 Identities=36% Similarity=1.035 Sum_probs=8.9
Q ss_pred CCCcccccCCC
Q psy15167 55 GAGSPCLQCKD 65 (75)
Q Consensus 55 ~~GaPClkCk~ 65 (75)
-.|.||.+|+.
T Consensus 243 r~g~pC~~Cg~ 253 (272)
T TIGR00577 243 RKGEPCRRCGT 253 (272)
T ss_pred CCCCCCCCCCC
Confidence 45899999975
Done!