Query 035138
Match_columns 72
No_of_seqs 101 out of 115
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 09:30:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035138.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035138hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08038 Tom7: TOM7 family; I 99.9 1.1E-23 2.4E-28 122.3 -0.3 40 30-69 1-42 (42)
2 KOG4449 Translocase of outer m 99.7 1E-17 2.2E-22 102.1 1.9 46 20-72 3-50 (53)
3 cd00495 Ribosomal_L25_TL5_CTC 41.1 9.5 0.00021 23.7 0.1 10 47-56 23-32 (91)
4 PRK05943 50S ribosomal protein 41.0 9.6 0.00021 24.1 0.1 9 47-55 24-32 (94)
5 PF01386 Ribosomal_L25p: Ribos 32.4 12 0.00027 23.3 -0.4 10 47-56 21-30 (88)
6 PF15049 DUF4534: Protein of u 25.6 3.1 6.6E-05 30.3 -4.5 24 34-57 120-143 (163)
7 TIGR03297 Ppyr-DeCO2ase phosph 20.9 44 0.00095 26.0 0.7 14 48-61 79-92 (361)
8 TIGR00731 ctc_TL5 ribosomal pr 19.6 39 0.00084 23.8 0.2 10 47-56 21-30 (176)
9 COG3571 Predicted hydrolase of 19.5 81 0.0018 23.9 1.8 29 18-46 25-53 (213)
10 PF04622 ERG2_Sigma1R: ERG2 an 19.4 37 0.00081 25.2 0.0 20 33-57 164-183 (216)
No 1
>PF08038 Tom7: TOM7 family; InterPro: IPR012621 This family consists of TOM7 family of mitochondrial import receptors. TOM7 forms part of the translocase of the outer mitochondrial membrane (TOM) complex and it appears to function as a modulator of the dynamics of the mitochondrial protein transport machinery by promoting the dissociation of subunits of the outer membrane translocase [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=99.87 E-value=1.1e-23 Score=122.27 Aligned_cols=40 Identities=55% Similarity=0.865 Sum_probs=37.6
Q ss_pred hhhheeeeeceEEEEEeehhhheeeccccC--CCCcceeccc
Q 035138 30 KEWSTWTMKKAKVVTHYGFIPLIIIIGMNS--DPKPQVYQLL 69 (72)
Q Consensus 30 kew~tw~~~~~k~~~HyGfIPlIIylG~~S--~PkPsL~~LL 69 (72)
|||.+|+++++|+++|||||||||||||++ ||+|||+|||
T Consensus 1 Keri~~v~~~~k~~~HyGfIP~IlylG~~~~~~p~Psl~~LL 42 (42)
T PF08038_consen 1 KERITKVLDVAKTVFHYGFIPLILYLGFRSGADPMPSLIQLL 42 (42)
T ss_pred ChHHHHHHHhheeeEEeeehHHHHHHhhccCCCCCCcHHhhC
Confidence 799999999999999999999999999964 7789999997
No 2
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.68 E-value=1e-17 Score=102.14 Aligned_cols=46 Identities=35% Similarity=0.601 Sum_probs=38.3
Q ss_pred hhhhhhhhhhhhhheeeeeceEEEEEeehhhheeeccc-c-CCCCcceeccccCC
Q 035138 20 SEEKSMVDSFKEWSTWTMKKAKVVTHYGFIPLIIIIGM-N-SDPKPQVYQLLSPV 72 (72)
Q Consensus 20 ~~~~s~~~~~kew~tw~~~~~k~~~HyGfIPlIIylG~-~-S~PkPsL~~LLsPl 72 (72)
.++++++|++|- ++++++++||||||||||||| + ++| |+. ++||+|
T Consensus 3 lS~esKerl~k~-----~~is~~vih~G~IP~VlyLG~a~~a~~-Pn~-~~lS~l 50 (53)
T KOG4449|consen 3 LSEESKERLVKV-----FNISKFVIHYGWIPLVLYLGFAFGARP-PNF-NTLSLL 50 (53)
T ss_pred cCHHHHHHHHHH-----eechheeeeechhhHHHHhhhhhcCCC-CCC-cchhhc
Confidence 478999999999 999999999999999999999 4 555 544 555553
No 3
>cd00495 Ribosomal_L25_TL5_CTC Ribosomal_L25_TL5_CTC: Ribosomal L25/TL5/CTC N-terminal 5S rRNA binding domain. L25 is a single-domain protein, homologous to the N-terminal domain of TL5 and CTC, which each contain two domains. CTC is a known stress protein, and proteins of this family are believed to have two functions, acting as both ribosomal and stress proteins. In Escherichia coli, cells deleted for L25 were found to be viable; however, these cells grew slowly and had impaired protein synthesis capability. In Bacillus subtilis, CTC is induced under stress conditions and located in the ribosome; it has been proposed that CTC may be necessary for accurate translation under stress conditions. Ribosomal_L25_TL5_CTC is found only in bacteria and some plastids. Due to its limited taxonomic diversity and the viability of cells deleted for L25, this protein is not believed to be necessary for ribosomal assembly. Eukaryotes contain a protein called L25, which is not homologous to bacterial L
Probab=41.12 E-value=9.5 Score=23.70 Aligned_cols=10 Identities=30% Similarity=0.454 Sum_probs=9.0
Q ss_pred ehhhheeecc
Q 035138 47 GFIPLIIIIG 56 (72)
Q Consensus 47 GfIPlIIylG 56 (72)
|+||.|||=.
T Consensus 23 G~iPavvYG~ 32 (91)
T cd00495 23 GKVPAVIYGK 32 (91)
T ss_pred CCCCEEEECC
Confidence 9999999974
No 4
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=41.03 E-value=9.6 Score=24.14 Aligned_cols=9 Identities=44% Similarity=0.501 Sum_probs=8.4
Q ss_pred ehhhheeec
Q 035138 47 GFIPLIIII 55 (72)
Q Consensus 47 GfIPlIIyl 55 (72)
|+||.|||=
T Consensus 24 G~vPaViYG 32 (94)
T PRK05943 24 GKFPAIIYG 32 (94)
T ss_pred CCCCEEEEC
Confidence 999999995
No 5
>PF01386 Ribosomal_L25p: Ribosomal L25p family; InterPro: IPR020055 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry models the short-form of the ribosomal L25 protein. The long-form has homology to the general stress protein Ctc of Bacillus subtilis, a mesophile, and ribosomal protein TL5 of Thermus thermophilus, a thermophile. Ribosomal protein L25 of Escherichia coli and Haemophilus influenzae appear to be orthologous but consist only of the N-terminal half of Ctc and TL5. Both short (L25-like) and full-length (CTC-like) members of this family bind the E-loop of bacterial 5S rRNA.; GO: 0003735 structural constituent of ribosome, 0008097 5S rRNA binding, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2HGQ_Y 2HGJ_Y 2Y19_Z 2WRL_Z 3KIT_Z 2WH2_Z 2WDN_Z 3V25_Z 3HUZ_Z 3KIY_Z ....
Probab=32.36 E-value=12 Score=23.29 Aligned_cols=10 Identities=40% Similarity=0.484 Sum_probs=8.7
Q ss_pred ehhhheeecc
Q 035138 47 GFIPLIIIIG 56 (72)
Q Consensus 47 GfIPlIIylG 56 (72)
|+||.|||=+
T Consensus 21 G~iPaviYG~ 30 (88)
T PF01386_consen 21 GKIPAVIYGK 30 (88)
T ss_dssp TEEEEEEEES
T ss_pred CCceEEEECC
Confidence 9999999954
No 6
>PF15049 DUF4534: Protein of unknown function (DUF4534)
Probab=25.58 E-value=3.1 Score=30.27 Aligned_cols=24 Identities=17% Similarity=0.557 Sum_probs=21.4
Q ss_pred eeeeeceEEEEEeehhhheeeccc
Q 035138 34 TWTMKKAKVVTHYGFIPLIIIIGM 57 (72)
Q Consensus 34 tw~~~~~k~~~HyGfIPlIIylG~ 57 (72)
.|...++|...|+.|+|+|+--++
T Consensus 120 ~w~g~iSRm~lH~f~Lpfvi~~ay 143 (163)
T PF15049_consen 120 RWFGQISRMLLHFFWLPFVIKYAY 143 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477889999999999999997776
No 7
>TIGR03297 Ppyr-DeCO2ase phosphonopyruvate decarboxylase. This family consists of examples of phosphonopyruvate an decarboxylase enzyme that produces phosphonoacetaldehyde (Pald), the second step in the biosynthesis phosphonate-containing compounds. Since the preceding enzymate step, PEP phosphomutase (AepX, TIGR02320) favors the substrate PEP energetically, the decarboxylase is required to drive the reaction in the direction of phosphonate production. Pald is a precursor of natural products including antibiotics like bialaphos and phosphonothricin in Streptomyces species, phosphonate-modified molecules such as the polysaccharide B of Bacteroides fragilis, the phosphonolipids of Tetrahymena pyroformis, the glycosylinositolphospholipids of Trypanosoma cruzi. This gene generally occurs in prokaryotic organisms adjacent to the gene for AepX. Most often an aminotansferase (aepZ) is also present which leads to the production of the most common phosphonate compound, 2-aminoethylphosphonate (A
Probab=20.86 E-value=44 Score=25.99 Aligned_cols=14 Identities=43% Similarity=0.961 Sum_probs=12.0
Q ss_pred hhhheeeccccCCC
Q 035138 48 FIPLIIIIGMNSDP 61 (72)
Q Consensus 48 fIPlIIylG~~S~P 61 (72)
=||+++.+|||.+|
T Consensus 79 ~iP~l~~i~~RG~~ 92 (361)
T TIGR03297 79 DIPLLLIVGWRGEP 92 (361)
T ss_pred CcCeeEEEecCCCC
Confidence 48999999999665
No 8
>TIGR00731 ctc_TL5 ribosomal protein L25, Ctc-form. The C-terminal domain of sll1824, an apparent L25 of Synechocystis PCC6803, matches the N-terminal domain of this family. Examples of L25 and Ctc are not separated by a UPGMA tree built on the region of shared homology.
Probab=19.58 E-value=39 Score=23.77 Aligned_cols=10 Identities=30% Similarity=0.457 Sum_probs=8.8
Q ss_pred ehhhheeecc
Q 035138 47 GFIPLIIIIG 56 (72)
Q Consensus 47 GfIPlIIylG 56 (72)
|+||.|||=.
T Consensus 21 G~VPaVvYG~ 30 (176)
T TIGR00731 21 GRIPAVVYGK 30 (176)
T ss_pred CCccEEEECC
Confidence 9999999964
No 9
>COG3571 Predicted hydrolase of the alpha/beta-hydrolase fold [General function prediction only]
Probab=19.50 E-value=81 Score=23.94 Aligned_cols=29 Identities=14% Similarity=0.063 Sum_probs=24.8
Q ss_pred cchhhhhhhhhhhhhheeeeeceEEEEEe
Q 035138 18 KASEEKSMVDSFKEWSTWTMKKAKVVTHY 46 (72)
Q Consensus 18 ~~~~~~s~~~~~kew~tw~~~~~k~~~Hy 46 (72)
++.+.-+..++.++|.+-.+.++|+-|||
T Consensus 25 asmdSt~m~~~a~~la~~G~~vaRfefpY 53 (213)
T COG3571 25 ASMDSTSMTAVAAALARRGWLVARFEFPY 53 (213)
T ss_pred CCCCCHHHHHHHHHHHhCceeEEEeecch
Confidence 44455678999999999999999999997
No 10
>PF04622 ERG2_Sigma1R: ERG2 and Sigma1 receptor like protein; InterPro: IPR006716 This family consists of the fungal C-8 sterol isomerase and mammalian sigma1 receptor. C-8 sterol isomerase (delta-8--delta-7 sterol isomerase), catalyses a reaction in ergosterol biosynthesis, which results in unsaturation at C-7 in the B ring of sterols []. Sigma 1 receptor is a low molecular mass mammalian protein located in the endoplasmic reticulum [], which interacts with endogenous steroid hormones, such as progesterone and testosterone []. It also binds the sigma ligands, which are a set of chemically unrelated drugs including haloperidol, pentazocine, and ditolylguanidine []. Sigma1 effectors are not well understood, but sigma1 agonists have been observed to affect NMDA receptor function, the alpha-adrenergic system and opioid analgesia.; GO: 0000247 C-8 sterol isomerase activity, 0006696 ergosterol biosynthetic process, 0005783 endoplasmic reticulum
Probab=19.39 E-value=37 Score=25.23 Aligned_cols=20 Identities=30% Similarity=0.906 Sum_probs=18.1
Q ss_pred heeeeeceEEEEEeehhhheeeccc
Q 035138 33 STWTMKKAKVVTHYGFIPLIIIIGM 57 (72)
Q Consensus 33 ~tw~~~~~k~~~HyGfIPlIIylG~ 57 (72)
.+|+++.+| ||||..+-.|+
T Consensus 164 ~tw~LEY~R-----G~IP~~lpf~~ 183 (216)
T PF04622_consen 164 GTWALEYGR-----GWIPSMLPFGF 183 (216)
T ss_pred CeEEEEecC-----CchhhhhHHHH
Confidence 589999998 99999999997
Done!