Query psy17958
Match_columns 678
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 46136
Date Fri Aug 16 18:42:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17958.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17958hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09665 RE_Alw26IDE: Type II 3.6 4.7E+02 0.01 28.9 0.8 19 15-33 18-36 (511)
2 PF00197 Kunitz_legume: Trypsi 3.2 6.9E+02 0.015 22.7 1.5 47 12-59 49-96 (176)
3 KOG0436|consensus 3.2 9.3E+02 0.02 26.9 2.6 43 3-45 224-271 (578)
4 TIGR02986 restrict_Alw26I type 3.1 5.4E+02 0.012 27.9 0.8 19 15-33 18-36 (424)
5 PF08155 NOGCT: NOGCT (NUC087) 3.0 6.7E+02 0.015 20.7 1.0 22 9-30 6-27 (55)
6 KOG4149|consensus 2.5 8.6E+02 0.019 22.9 1.2 19 18-36 46-64 (129)
7 PF15097 Ig_J_chain: Immunoglo 2.3 1E+03 0.022 22.6 1.4 26 18-45 38-63 (134)
8 PF08415 NRPS: Nonribosomal pe 2.1 7.6E+02 0.016 18.6 0.3 12 12-23 19-30 (58)
9 PF06959 RecQ5: RecQ helicase 2.0 8.2E+02 0.018 24.4 0.3 16 3-20 23-38 (205)
10 PF03738 GSP_synth: Glutathion 1.9 8.9E+02 0.019 19.7 0.3 24 7-30 19-42 (97)
No 1
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=3.58 E-value=4.7e+02 Score=28.94 Aligned_cols=19 Identities=37% Similarity=0.868 Sum_probs=17.3
Q ss_pred cCCCcccCCCCCcccCCCc
Q psy17958 15 AGMPTVYSPPARLNWSTPC 33 (678)
Q Consensus 15 agmptvyspparlnwstpc 33 (678)
+|||-++..-.|++|..|=
T Consensus 18 ~GmP~~~~~dG~I~W~a~s 36 (511)
T PF09665_consen 18 AGMPDARKEDGRIQWEAPS 36 (511)
T ss_pred CCCCcccCCCCceEEEecC
Confidence 7999999999999998763
No 2
>PF00197 Kunitz_legume: Trypsin and protease inhibitor; InterPro: IPR002160 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The Kunitz-type soybean trypsin inhibitor (STI) family consists mainly of proteinase inhibitors from Leguminosae seeds []. They belong to MEROPS inhibitor family I3, clan IC. They exhibit proteinase inhibitory activity against serine proteinases; trypsin (MEROPS peptidase family S1, IPR001254 from INTERPRO) and subtilisin (MEROPS peptidase family S8, IPR000209 from INTERPRO), thiol proteinases (MEROPS peptidase family C1, IPR000668 from INTERPRO) and aspartic proteinases (MEROPS peptidase family A1, IPR001461 from INTERPRO) []. Inhibitors from cereals are active against subtilisin and endogenous alpha-amylases, while some also inhibit tissue plasminogen activator. The inhibitors are usually specific for either trypsin or chymotrypsin, and some are effective against both. They are thought to protect the seeds against consumption by animal predators, while at the same time existing as seed storage proteins themselves - all the actively inhibitory members contain 2 disulphide bridges. The existence of a member with no inhibitory activity, winged bean albumin 1, suggests that the inhibitors may have evolved from seed storage proteins. Proteins from the Kunitz family contain from 170 to 200 amino acid residues and one or two intra-chain disulphide bonds. The best conserved region is found in their N-terminal section. The crystal structures of soybean trypsin inhibitor (STI), trypsin inhibitor DE-3 from the Kaffir tree Erythrina caffra (ETI) [] and the bifunctional proteinase K/alpha-amylase inhibitor from wheat (PK13) have been solved, showing them to share the same 12-stranded beta-sheet structure as those of interleukin-1 and heparin-binding growth factors []. The beta-sheets are arranged in 3 similar lobes around a central axis, 6 strands forming an anti-parallel beta-barrel. Despite the structural similarity, STI shows no interleukin-1 bioactivity, presumably as a result of their primary sequence disparities. The active inhibitory site containing the scissile bond is located in the loop between beta-strands 4 and 5 in STI and ETI. The STIs belong to a superfamily that also contains the interleukin-1 proteins, heparin binding growth factors (HBGF) and histactophilin, all of which have very similar structures, but share no sequence similarity with the STI family.; GO: 0004866 endopeptidase inhibitor activity; PDB: 3TC2_B 3S8J_A 3S8K_A 1TIE_A 2GZB_A 3E8L_C 2IWT_B 3BX1_C 1AVA_D 3IIR_A ....
Probab=3.24 E-value=6.9e+02 Score=22.70 Aligned_cols=47 Identities=28% Similarity=0.443 Sum_probs=29.0
Q ss_pred hhhcCCCcccCCCCCcccCCCc-ccCCcccceEeeccccCCCcccceEe
Q psy17958 12 EIQAGMPTVYSPPARLNWSTPC-LTSPRQTKLVYSTPCLTSPRQTKLVY 59 (678)
Q Consensus 12 eiqagmptvyspparlnwstpc-ltsprqtklvystpcltsprqtklvy 59 (678)
|.+.|.|+.++|+.+..-.+.. ....-..+....+.|.-+. .-+++-
T Consensus 49 ~~~~GlPv~Fs~~~~~~~~~~ir~st~l~I~F~~~~~c~~~~-~W~V~~ 96 (176)
T PF00197_consen 49 ELSRGLPVKFSPPYRNSFDTVIRESTDLNIEFSSPTSCACST-VWKVVK 96 (176)
T ss_dssp TTS-BSEEEEEESSSSSSTBCTBTTSEEEEEESSECTTSSSS-BEEEEE
T ss_pred CCCCceeEEEEeCCcccCCCeeEcceEEEEEEccCCCCCccC-EEEEee
Confidence 5678999999998866655554 2334445555566677666 444443
No 3
>KOG0436|consensus
Probab=3.20 E-value=9.3e+02 Score=26.90 Aligned_cols=43 Identities=35% Similarity=0.642 Sum_probs=32.8
Q ss_pred ccccchh---hhhhhcCCCcc--cCCCCCcccCCCcccCCcccceEee
Q psy17958 3 VYSSYFK---AKEIQAGMPTV--YSPPARLNWSTPCLTSPRQTKLVYS 45 (678)
Q Consensus 3 vyssyfk---akeiqagmptv--yspparlnwstpcltsprqtklvys 45 (678)
|.-+||. -+||..|+|-. --|-|||.|..|--..+.||-.|+-
T Consensus 224 vqPs~~~~qVl~~lktglpDlSISRpsarl~WGIPvP~ddsQtIYVWf 271 (578)
T KOG0436|consen 224 VQPSYFHNQVLSWLKTGLPDLSISRPSARLDWGIPVPGDDSQTIYVWF 271 (578)
T ss_pred cCchHHHHHHHHHHHcCCCcccccChhhhcccCCCCCCCCcceEEEeH
Confidence 4445665 36888999864 4567999999999999999887763
No 4
>TIGR02986 restrict_Alw26I type II restriction endonuclease, Alw26I/Eco31I/Esp3I family. Members of this family are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. Characterized specificities of three members are GGTCTC, CGTCTC, and the shared subsequence GTCTC.
Probab=3.14 E-value=5.4e+02 Score=27.91 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=17.2
Q ss_pred cCCCcccCCCCCcccCCCc
Q psy17958 15 AGMPTVYSPPARLNWSTPC 33 (678)
Q Consensus 15 agmptvyspparlnwstpc 33 (678)
+|||-++....|++|..|=
T Consensus 18 ~Gmp~~~~~dG~I~W~~~s 36 (424)
T TIGR02986 18 IGMPNAGGEDGRISWQVSS 36 (424)
T ss_pred CCCCcccCCCCceEEEecC
Confidence 7999999999999998763
No 5
>PF08155 NOGCT: NOGCT (NUC087) domain; InterPro: IPR012973 This C-terminal domain is found in the NOG subfamily of nucleolar GTP-binding proteins [].
Probab=2.96 E-value=6.7e+02 Score=20.68 Aligned_cols=22 Identities=23% Similarity=0.320 Sum_probs=18.0
Q ss_pred hhhhhhcCCCcccCCCCCcccC
Q psy17958 9 KAKEIQAGMPTVYSPPARLNWS 30 (678)
Q Consensus 9 kakeiqagmptvyspparlnws 30 (678)
+.-|.+.|++-||+...|-+|-
T Consensus 6 rd~e~e~Gg~gvy~~dlkk~y~ 27 (55)
T PF08155_consen 6 RDIEEENGGAGVYSVDLKKHYD 27 (55)
T ss_pred HHHHHHhCCCCccccchhhccc
Confidence 3456778999999999998885
No 6
>KOG4149|consensus
Probab=2.45 E-value=8.6e+02 Score=22.92 Aligned_cols=19 Identities=37% Similarity=0.948 Sum_probs=15.4
Q ss_pred CcccCCCCCcccCCCcccC
Q psy17958 18 PTVYSPPARLNWSTPCLTS 36 (678)
Q Consensus 18 ptvyspparlnwstpclts 36 (678)
|-.+-|...+||.-|||.+
T Consensus 46 ~g~~~PDG~INwdCpClg~ 64 (129)
T KOG4149|consen 46 PGPTNPDGTINWDCPCLGG 64 (129)
T ss_pred CCCcCCCCceeecCccccc
Confidence 4456788999999999984
No 7
>PF15097 Ig_J_chain: Immunoglobulin J chain
Probab=2.30 E-value=1e+03 Score=22.56 Aligned_cols=26 Identities=42% Similarity=0.531 Sum_probs=19.0
Q ss_pred CcccCCCCCcccCCCcccCCcccceEee
Q psy17958 18 PTVYSPPARLNWSTPCLTSPRQTKLVYS 45 (678)
Q Consensus 18 ptvyspparlnwstpcltsprqtklvys 45 (678)
-++----+|-|.|.| +||-.||+||.
T Consensus 38 RiiVpL~~ReNISDP--tSp~RT~FVY~ 63 (134)
T PF15097_consen 38 RIIVPLNNRENISDP--TSPLRTKFVYH 63 (134)
T ss_pred EEEEEcccccccCCC--CCccceeeeeh
Confidence 344444678898888 78888888885
No 8
>PF08415 NRPS: Nonribosomal peptide synthase; InterPro: IPR013624 This domain is found in bacterial non-ribosomal peptide synthetases (NRPS). NRPS are megaenzymes organised as iterative modules, one for each amino acid to be built into the peptide product []. NRPS modules are involved in epothilone biosynthesis (EpoB), myxothiazol biosynthesis (MtaC and MtaD), and other functions []. The NRPS domain tends to be found together with the condensation domain (IPR001242 from INTERPRO) and the phosphopantetheine binding domain (IPR006163 from INTERPRO).
Probab=2.13 E-value=7.6e+02 Score=18.64 Aligned_cols=12 Identities=33% Similarity=0.501 Sum_probs=8.8
Q ss_pred hhhcCCCcccCC
Q psy17958 12 EIQAGMPTVYSP 23 (678)
Q Consensus 12 eiqagmptvysp 23 (678)
.-.+.||+||.-
T Consensus 19 ~~~~~~PVVFTS 30 (58)
T PF08415_consen 19 GRAAVMPVVFTS 30 (58)
T ss_pred CCCCcCCEEEeC
Confidence 456789999864
No 9
>PF06959 RecQ5: RecQ helicase protein-like 5 (RecQ5); InterPro: IPR010716 This family represents a conserved region approximately 200 residues long within eukaryotic RecQ helicase protein-like 5 (RecQ5). The RecQ helicases have been implicated in DNA repair and recombination, and RecQ5 may have an important role in DNA metabolism [].
Probab=1.97 E-value=8.2e+02 Score=24.45 Aligned_cols=16 Identities=50% Similarity=0.825 Sum_probs=11.5
Q ss_pred ccccchhhhhhhcCCCcc
Q psy17958 3 VYSSYFKAKEIQAGMPTV 20 (678)
Q Consensus 3 vyssyfkakeiqagmptv 20 (678)
||| ||.|.+-||+|.-
T Consensus 23 vYS--lKpKRVGAGfpkg 38 (205)
T PF06959_consen 23 VYS--LKPKRVGAGFPKG 38 (205)
T ss_pred ccc--ccccccccCCCCC
Confidence 454 7888888888753
No 10
>PF03738 GSP_synth: Glutathionylspermidine synthase preATP-grasp; InterPro: IPR005494 This region contains the Glutathionylspermidine synthase enzymatic activity 6.3.1.8 from EC. This is the C-terminal region in bienzymes such as P43675 from SWISSPROT. Glutathionylspermidine (GSP) synthetases of Trypanosomatidae and Escherichia coli couple hydrolysis of ATP (to ADP and Pi) with formation of an amide bond between spermidine and the glycine carboxylate of glutathione (gamma-Glu-Cys-Gly). In the pathogenic trypanosomatids, this reaction is the penultimate step in the biosynthesis of the antioxidant metabolite, trypanothione (N1,N8-bis-(glutathionyl)spermidine), and is a target for drug design [].; PDB: 2VPM_B 2VOB_B 2VPS_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B 3O98_B.
Probab=1.86 E-value=8.9e+02 Score=19.66 Aligned_cols=24 Identities=33% Similarity=0.656 Sum_probs=0.0
Q ss_pred chhhhhhhcCCCcccCCCCCcccC
Q psy17958 7 YFKAKEIQAGMPTVYSPPARLNWS 30 (678)
Q Consensus 7 yfkakeiqagmptvyspparlnws 30 (678)
|+..--.|||..+.+-+...|.|.
T Consensus 19 yL~~~a~qaG~~~~~~~i~~l~~~ 42 (97)
T PF03738_consen 19 YLMDTARQAGLDTRFIPIEDLGWD 42 (97)
T ss_dssp HHHHHHHHTT-EEEEETTTTEEE-
T ss_pred HHHHHHHHCCCCeEEechHheEEC
Done!