Query psy12800
Match_columns 134
No_of_seqs 37 out of 39
Neff 2.5
Searched_HMMs 46136
Date Fri Aug 16 19:58:40 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12800.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12800hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06119 NIDO: Nidogen-like; 99.7 6E-18 1.3E-22 118.1 4.0 56 64-121 35-90 (90)
2 smart00539 NIDO Extracellular 99.6 3E-16 6.4E-21 119.1 4.2 53 68-122 99-151 (152)
3 KOG4291|consensus 99.5 3.6E-15 7.9E-20 140.9 3.0 68 64-133 308-375 (1043)
4 COG1490 Dtd D-Tyr-tRNAtyr deac 41.9 18 0.00038 28.9 1.8 32 5-36 77-108 (145)
5 TIGR00256 D-tyrosyl-tRNA(Tyr) 36.7 31 0.00067 27.0 2.3 34 5-38 77-110 (145)
6 cd00563 Dtyr_deacylase D-Tyros 35.9 31 0.00067 27.0 2.3 34 5-38 77-110 (145)
7 PF02580 Tyr_Deacylase: D-Tyr- 35.6 39 0.00084 26.2 2.7 33 5-37 76-108 (145)
8 PRK05273 D-tyrosyl-tRNA(Tyr) d 33.2 37 0.00081 26.6 2.3 35 5-39 77-111 (147)
9 KOG4494|consensus 31.3 38 0.00082 30.4 2.3 39 83-125 292-336 (352)
10 PTZ00120 D-tyrosyl-tRNA(Tyr) d 29.9 45 0.00097 26.4 2.3 33 5-38 78-110 (154)
11 smart00279 HhH2 Helix-hairpin- 22.2 59 0.0013 19.6 1.3 16 22-37 21-36 (36)
12 PRK05382 chorismate synthase; 21.3 35 0.00077 30.2 0.3 53 55-108 215-270 (359)
No 1
>PF06119 NIDO: Nidogen-like; InterPro: IPR003886 The ~180-residue NIDO domain is an extracellular domain of unknown function, found in nidogen (entactin) and hypothetical proteins. The NIDO domain is found in association with other domains, such as nidogen G2 beta-barrel (IPR006605 from INTERPRO), thyroglobulin type-1 (IPR000716 from INTERPRO), LDLRB (IPR000033 from INTERPRO), AMOP (IPR005533 from INTERPRO), EGF-like (IPR000742 from INTERPRO), VWFD, IPT/TIG, or sushi/CCP/SCR (IPR000436 from INTERPRO) [, , , ]. Some proteins known to contain a NIDO domain are listed below: Vertebrate nidogen-1 (NID-1) or entactin, a sulphated glycoprotein widely distributed in basement membranes. Vertebrate nidogen-2 (NID-2) or osteonidogen, a cell adhesion glycoprotein which is widely distributed in basement membranes. Vertebrate alpha-tectorin. Mammalian mucin-4 (MUC4), a highly glycosylated membrane-bound protein. Xenopus ID14, a putative matrix protein. ; GO: 0007160 cell-matrix adhesion
Probab=99.71 E-value=6e-18 Score=118.12 Aligned_cols=56 Identities=39% Similarity=0.599 Sum_probs=51.7
Q ss_pred CCCCCCCCccceeeeeccCceeeEEeecCCCcccccccccccccCCCCcceEEeechh
Q psy12800 64 KGQSPEMHRRSFVGFNAGNGTRSYEYYPYSQRSTIRDLVGRGWANGFPGRHIFRIDEN 121 (134)
Q Consensus 64 ~g~~G~GGipAqvGFNaGnGt~~y~y~P~Sqt~~I~dL~~ts~~ng~PGRwvFRIDe~ 121 (134)
.+.+|++++||+||||+||+++||+ +|+|++..|++|...+|+ |+||||+||||++
T Consensus 35 ~~~~~~~~~~a~aGf~~gd~~~~~~-lp~s~t~~i~~l~~~sN~-g~~G~wifrid~~ 90 (90)
T PF06119_consen 35 GGYNGLGGVPAQAGFNSGDGTNYYN-LPGSGTDSIRNLDNSSNV-GVPGRWIFRIDSE 90 (90)
T ss_pred cccccceeeeeEEEEecCCCcceEE-ecCCCccceeehhhcCCC-CCCEEEEEEeCCC
Confidence 4568999999999999999999999 899999999999999855 6999999999975
No 2
>smart00539 NIDO Extracellular domain of unknown function in nidogen (entactin) and hypothetical proteins.
Probab=99.62 E-value=3e-16 Score=119.15 Aligned_cols=53 Identities=38% Similarity=0.627 Sum_probs=47.8
Q ss_pred CCCCccceeeeeccCceeeEEeecCCCcccccccccccccCCCCcceEEeechhh
Q psy12800 68 PEMHRRSFVGFNAGNGTRSYEYYPYSQRSTIRDLVGRGWANGFPGRHIFRIDENI 122 (134)
Q Consensus 68 G~GGipAqvGFNaGnGt~~y~y~P~Sqt~~I~dL~~ts~~ng~PGRwvFRIDe~I 122 (134)
|..|++||||||+|||+.+|+ +|+|++..|++|...+|+ |+||||+||||+..
T Consensus 99 ~~~~~~a~aGF~~Gdg~~~~~-lp~S~~~~~~~L~~~sN~-g~~G~w~frid~~~ 151 (152)
T smart00539 99 GDDGVRARAGFNGGDGTFSYT-LPASGEENIKNLAEGSNV-GIPGRWMFRVDGAE 151 (152)
T ss_pred CCCCcceeEEEeccCCceeEE-CCCCCCcchhhhhhcCCC-CCceEEEEEeCCcc
Confidence 344899999999999999998 999999999999999954 79999999999853
No 3
>KOG4291|consensus
Probab=99.52 E-value=3.6e-15 Score=140.87 Aligned_cols=68 Identities=37% Similarity=0.535 Sum_probs=62.3
Q ss_pred CCCCCCCCccceeeeeccCceeeEEeecCCCcccccccccccccCCCCcceEEeechhhhhccccccccC
Q psy12800 64 KGQSPEMHRRSFVGFNAGNGTRSYEYYPYSQRSTIRDLVGRGWANGFPGRHIFRIDENIMLELTLGEIQL 133 (134)
Q Consensus 64 ~g~~G~GGipAqvGFNaGnGt~~y~y~P~Sqt~~I~dL~~ts~~ng~PGRwvFRIDe~I~~g~C~~d~~~ 133 (134)
.++.|+|+.+||||||+||+|+.|. +||||++.|.+|. +++++++||||+||+||.++..+|.+++..
T Consensus 308 ~~~~g~~~~~~qagfn~G~~t~~~~-~P~s~t~~i~~~~-sg~~v~~PGr~~frvd~~~~~~~c~~~~g~ 375 (1043)
T KOG4291|consen 308 DGRAGRCGVSAQAGFNAGNGTVDFS-LPYSQTPNILALR-SGTNVGDPGRWMFRVDEVVRSAGCTNDIGG 375 (1043)
T ss_pred CCcccceeeEEeeeecCCCcccccc-ccCCCCceeEecc-ccccccCCcccceecCCeecccccccCcCC
Confidence 3457999999999999999999999 6999999999999 777889999999999999887669999875
No 4
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=41.89 E-value=18 Score=28.93 Aligned_cols=32 Identities=31% Similarity=0.363 Sum_probs=27.5
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhh
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQ 36 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinq 36 (134)
||=-|-...+|-+||||..+..-.-|.+|.++
T Consensus 77 SQFTL~adt~kG~RPsFs~aa~p~~A~~lYe~ 108 (145)
T COG1490 77 SQFTLYADTKKGRRPSFSKAAKPDQAEELYEY 108 (145)
T ss_pred EEEEEeecccCCCCCCccccCChHHHHHHHHH
Confidence 56667778899999999999999999998765
No 5
>TIGR00256 D-tyrosyl-tRNA(Tyr) deacylase. This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterization with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader.
Probab=36.69 E-value=31 Score=26.97 Aligned_cols=34 Identities=32% Similarity=0.382 Sum_probs=28.6
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhhhc
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQHF 38 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinqhl 38 (134)
||-.|-+..+|-+||+|..+-.-.-|..|-++-+
T Consensus 77 SQFTL~a~~~KG~rPsF~~a~~~~~A~~ly~~fv 110 (145)
T TIGR00256 77 SQFTLAADTKKGMRPSFSKGASPDRAEELYEYFV 110 (145)
T ss_pred ECCcccccCCCCCCCCccccCCHHHHHHHHHHHH
Confidence 6778888889999999998888888888877643
No 6
>cd00563 Dtyr_deacylase D-Tyrosyl-tRNAtyr deacylases; a class of tRNA-dependent hydrolases which are capable of hydrolyzing the ester bond of D-Tyrosyl-tRNA reducing the level of cellular D-Tyrosine while recycling the peptidyl-tRNA; found in bacteria and in eukaryotes but not in archea; beta barrel-like fold structure; forms homodimers in which two surface cavities serve as the active site for tRNA binding
Probab=35.93 E-value=31 Score=26.95 Aligned_cols=34 Identities=29% Similarity=0.359 Sum_probs=28.9
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhhhc
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQHF 38 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinqhl 38 (134)
||-.|-+..+|-+||+|..+.+-.-|..|-++-+
T Consensus 77 sQFTL~~~~~KG~rP~F~~a~~~e~A~~ly~~fv 110 (145)
T cd00563 77 SQFTLYADTKKGRRPSFSAAAPPDKAEPLYESFV 110 (145)
T ss_pred EccccccccCCCCCCCccccCCHHHHHHHHHHHH
Confidence 6778888888999999999888888988877644
No 7
>PF02580 Tyr_Deacylase: D-Tyr-tRNA(Tyr) deacylase; InterPro: IPR003732 This homodimeric enzyme appears able to cleave any D-amino acid (and glycine, which does not have distinct D/L forms) from charged tRNA. The name reflects characterisation with respect to D-Tyr on tRNA(Tyr) as established in the literature, but substrate specificity seems much broader. ; GO: 0016788 hydrolase activity, acting on ester bonds, 0019478 D-amino acid catabolic process, 0005737 cytoplasm; PDB: 3LMU_F 3LMT_B 3KNF_B 3KOC_C 3KNP_D 3KO9_F 3KO3_B 3KO5_C 3KOB_D 3LMV_E ....
Probab=35.61 E-value=39 Score=26.21 Aligned_cols=33 Identities=27% Similarity=0.342 Sum_probs=26.1
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhhh
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQH 37 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinqh 37 (134)
||-.|-+..+|-+||+|.-..+-.-|..|-++-
T Consensus 76 sQFTL~g~~~kG~rp~f~~a~~~~~a~~ly~~f 108 (145)
T PF02580_consen 76 SQFTLYGDTKKGNRPSFHNAAPPEEAEELYERF 108 (145)
T ss_dssp E-GGGGSBCSSSSSEBGTTB--HHHHHHHHHHH
T ss_pred EeeeeeeeccCCCCccccccCCHHHHHHHHHHH
Confidence 788999999999999998888888888887654
No 8
>PRK05273 D-tyrosyl-tRNA(Tyr) deacylase; Provisional
Probab=33.21 E-value=37 Score=26.61 Aligned_cols=35 Identities=26% Similarity=0.338 Sum_probs=29.3
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhhhcC
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQHFP 39 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinqhlf 39 (134)
||-.|-+..+|-+||+|..+-+-.-|..|-++-+=
T Consensus 77 sQFTL~a~~~KG~rP~F~~a~~~~~A~~ly~~f~~ 111 (147)
T PRK05273 77 SQFTLYADTRKGRRPSFSAAAPPEEAEPLYDYFVE 111 (147)
T ss_pred EcccccccCCCCCCCCccccCCHHHHHHHHHHHHH
Confidence 67788888889999999999888899888876543
No 9
>KOG4494|consensus
Probab=31.34 E-value=38 Score=30.37 Aligned_cols=39 Identities=26% Similarity=0.601 Sum_probs=32.4
Q ss_pred ceeeEEeecCCCcccccccccccccCCCCcc------eEEeechhhhhc
Q psy12800 83 GTRSYEYYPYSQRSTIRDLVGRGWANGFPGR------HIFRIDENIMLE 125 (134)
Q Consensus 83 Gt~~y~y~P~Sqt~~I~dL~~ts~~ng~PGR------wvFRIDe~I~~g 125 (134)
|--.|.|+|+-...-|+-|+..- +||+ .+|+||-.+|+.
T Consensus 292 GFSaFqFvPgT~d~iIVALKseE----~~gkp~At~itvF~idG~viL~ 336 (352)
T KOG4494|consen 292 GFSAFQFVPGTDDQIIVALKSEE----IPGKPVATYITVFDIDGTVILP 336 (352)
T ss_pred CceeeEecCCCCCeEEEEEeccc----cCCCcceEEEEEEEecCeEEcc
Confidence 33459999999999999999877 8888 689999876653
No 10
>PTZ00120 D-tyrosyl-tRNA(Tyr) deacylase; Provisional
Probab=29.95 E-value=45 Score=26.36 Aligned_cols=33 Identities=27% Similarity=0.244 Sum_probs=27.7
Q ss_pred chhhhccCCCCccCCccccCchhhhHHHHhhhhc
Q psy12800 5 SNESLESSGKKSRRPSFISGRSFASASRILNQHF 38 (134)
Q Consensus 5 s~esl~~~~~k~~r~~f~p~ks~asatriinqhl 38 (134)
||-.|- ..+|-+||+|..+-+-.-|..|-++-+
T Consensus 78 SQFTL~-~~~KG~RPsF~~aa~~~~A~~Ly~~f~ 110 (154)
T PTZ00120 78 SQFTLF-NVKKGNKPDFHLAMSPEDALPLYNKFV 110 (154)
T ss_pred Eccccc-cCCCCCCCCccccCCHHHHHHHHHHHH
Confidence 677787 788999999998888889998887654
No 11
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=22.19 E-value=59 Score=19.61 Aligned_cols=16 Identities=19% Similarity=0.351 Sum_probs=13.9
Q ss_pred ccCchhhhHHHHhhhh
Q psy12800 22 ISGRSFASASRILNQH 37 (134)
Q Consensus 22 ~p~ks~asatriinqh 37 (134)
+|+-+..+|.+||+++
T Consensus 21 v~giG~ktA~~ll~~~ 36 (36)
T smart00279 21 VKGIGPKTALKLLREF 36 (36)
T ss_pred CCcccHHHHHHHHHhC
Confidence 6788899999999985
No 12
>PRK05382 chorismate synthase; Validated
Probab=21.35 E-value=35 Score=30.24 Aligned_cols=53 Identities=15% Similarity=0.038 Sum_probs=41.4
Q ss_pred ccCccccccCCCCCCCCccceeeeeccCceeeEEeecCCCccccc---ccccccccC
Q psy12800 55 TLSADSLDSKGQSPEMHRRSFVGFNAGNGTRSYEYYPYSQRSTIR---DLVGRGWAN 108 (134)
Q Consensus 55 s~SaDSids~g~~G~GGipAqvGFNaGnGt~~y~y~P~Sqt~~I~---dL~~ts~~n 108 (134)
++--|+||++=..-+.+|||--||--|.|-..=. +++|+..+.. .+.+.+|.+
T Consensus 215 ~p~f~kLda~la~a~msIpAvKgvE~G~Gf~~a~-~~GSe~nD~~~~~~~~~~tN~~ 270 (359)
T PRK05382 215 EPVFDKLDADLAHALMSINAVKGVEIGDGFAAAR-LRGSEVNDEIYYTGIGRLTNHA 270 (359)
T ss_pred ccccccchHHHHHHhcCcCceeEEEECcchhhcc-ccCcccCceeecCCCeecccCC
Confidence 4445899988889999999999999999988666 9999997754 344445444
Done!