Query 035165
Match_columns 71
No_of_seqs 101 out of 123
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 09:44:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035165hhsearch_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 99.8 4.1E-22 9E-27 115.3 2.4 39 30-68 2-42 (42)
2 KOG4449 Translocase of outer m 99.8 1.6E-20 3.5E-25 114.0 3.3 47 18-71 2-50 (53)
3 smart00496 IENR2 Intron-encode 49.5 17 0.00036 19.2 1.9 16 16-31 2-17 (26)
4 PRK05943 50S ribosomal protein 35.8 8.5 0.00018 24.3 -0.7 9 46-54 24-32 (94)
5 cd00495 Ribosomal_L25_TL5_CTC 35.5 8.6 0.00019 23.8 -0.7 11 45-55 22-32 (91)
6 PF15049 DUF4534: Protein of u 31.1 6.7 0.00014 28.5 -2.0 24 33-56 120-143 (163)
7 PF01386 Ribosomal_L25p: Ribos 26.7 11 0.00024 23.4 -1.3 10 46-55 21-30 (88)
8 TIGR00842 bcct choline/carniti 24.7 21 0.00045 28.9 -0.4 35 37-71 86-129 (453)
9 PF09574 DUF2374: Protein of 23.9 30 0.00066 20.3 0.3 15 42-56 11-25 (42)
10 PRK09950 putative transporter; 21.3 21 0.00045 29.3 -1.0 35 37-71 132-176 (506)
11 TIGR02808 short_TIGR02808 cons 20.8 36 0.00078 20.0 0.2 15 42-56 11-25 (42)
12 PF14959 GSAP-16: gamma-Secret 20.5 27 0.00058 23.7 -0.5 42 22-68 44-85 (115)
13 PF07460 NUMOD3: NUMOD3 motif 20.5 80 0.0017 17.1 1.5 14 16-29 2-15 (37)
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=99.85 E-value=4.1e-22 Score=115.34 Aligned_cols=39 Identities=49% Similarity=0.848 Sum_probs=33.0
Q ss_pred HhhhhhhhheeeeeEeehhhhhhhhccc--CCCcccccccc
Q 035165 30 EWSTWAMKKAKVITHYGFIPLVIIIGMN--SDPKPQLHQLL 68 (71)
Q Consensus 30 ~~~~w~~~~~k~v~HyGfIPlVIylG~~--s~PkPsl~~LL 68 (71)
|+.+|.++++|+++|||||||||||||+ +||+|||+|||
T Consensus 2 eri~~v~~~~k~~~HyGfIP~IlylG~~~~~~p~Psl~~LL 42 (42)
T PF08038_consen 2 ERITKVLDVAKTVFHYGFIPLILYLGFRSGADPMPSLIQLL 42 (42)
T ss_pred hHHHHHHHhheeeEEeeehHHHHHHhhccCCCCCCcHHhhC
Confidence 3344444999999999999999999996 47889999997
No 2
>KOG4449 consensus Translocase of outer mitochondrial membrane complex, subunit TOM7 [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.81 E-value=1.6e-20 Score=114.01 Aligned_cols=47 Identities=38% Similarity=0.698 Sum_probs=39.5
Q ss_pred cCcHHHHHHHHHHhhhhhhhheeeeeEeehhhhhhhhcc-c-CCCcccccccccCC
Q 035165 18 KDSEKSRADCLKEWSTWAMKKAKVITHYGFIPLVIIIGM-N-SDPKPQLHQLLSPV 71 (71)
Q Consensus 18 ~~se~sk~R~~k~~~~w~~~~~k~v~HyGfIPlVIylG~-~-s~PkPsl~~LLsPl 71 (71)
+.|||+|||++|++ +++++++||||||||||||| + ++| |+. ++||+|
T Consensus 2 klS~esKerl~k~~-----~is~~vih~G~IP~VlyLG~a~~a~~-Pn~-~~lS~l 50 (53)
T KOG4449|consen 2 KLSEESKERLVKVF-----NISKFVIHYGWIPLVLYLGFAFGARP-PNF-NTLSLL 50 (53)
T ss_pred ccCHHHHHHHHHHe-----echheeeeechhhHHHHhhhhhcCCC-CCC-cchhhc
Confidence 57999999999999 99999999999999999999 3 555 444 555543
No 3
>smart00496 IENR2 Intron-encoded nuclease repeat 2. Short helical motif of unknown function (unpublished results).
Probab=49.54 E-value=17 Score=19.18 Aligned_cols=16 Identities=25% Similarity=0.329 Sum_probs=13.1
Q ss_pred CCcCcHHHHHHHHHHh
Q 035165 16 GAKDSEKSRADCLKEW 31 (71)
Q Consensus 16 ~~~~se~sk~R~~k~~ 31 (71)
|++.|||+|+++.+.-
T Consensus 2 GkkhSEETK~KMSea~ 17 (26)
T smart00496 2 GKKHSEETKKKMSEAA 17 (26)
T ss_pred CCCCCHHHHHHHHHhh
Confidence 4678999999998763
No 4
>PRK05943 50S ribosomal protein L25; Reviewed
Probab=35.81 E-value=8.5 Score=24.32 Aligned_cols=9 Identities=33% Similarity=0.467 Sum_probs=8.1
Q ss_pred ehhhhhhhh
Q 035165 46 GFIPLVIII 54 (71)
Q Consensus 46 GfIPlVIyl 54 (71)
|+||.|||=
T Consensus 24 G~vPaViYG 32 (94)
T PRK05943 24 GKFPAIIYG 32 (94)
T ss_pred CCCCEEEEC
Confidence 899999995
No 5
>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=35.46 E-value=8.6 Score=23.85 Aligned_cols=11 Identities=36% Similarity=0.356 Sum_probs=9.2
Q ss_pred eehhhhhhhhc
Q 035165 45 YGFIPLVIIIG 55 (71)
Q Consensus 45 yGfIPlVIylG 55 (71)
=|+||.|||=.
T Consensus 22 ~G~iPavvYG~ 32 (91)
T cd00495 22 AGKVPAVIYGK 32 (91)
T ss_pred CCCCCEEEECC
Confidence 38999999974
No 6
>PF15049 DUF4534: Protein of unknown function (DUF4534)
Probab=31.07 E-value=6.7 Score=28.45 Aligned_cols=24 Identities=21% Similarity=0.574 Sum_probs=21.6
Q ss_pred hhhhhheeeeeEeehhhhhhhhcc
Q 035165 33 TWAMKKAKVITHYGFIPLVIIIGM 56 (71)
Q Consensus 33 ~w~~~~~k~v~HyGfIPlVIylG~ 56 (71)
.|...++|...|..|+|||+--++
T Consensus 120 ~w~g~iSRm~lH~f~Lpfvi~~ay 143 (163)
T PF15049_consen 120 RWFGQISRMLLHFFWLPFVIKYAY 143 (163)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999998777
No 7
>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=26.70 E-value=11 Score=23.43 Aligned_cols=10 Identities=50% Similarity=0.494 Sum_probs=8.1
Q ss_pred ehhhhhhhhc
Q 035165 46 GFIPLVIIIG 55 (71)
Q Consensus 46 GfIPlVIylG 55 (71)
|+||.|||=+
T Consensus 21 G~iPaviYG~ 30 (88)
T PF01386_consen 21 GKIPAVIYGK 30 (88)
T ss_dssp TEEEEEEEES
T ss_pred CCceEEEECC
Confidence 7899999854
No 8
>TIGR00842 bcct choline/carnitine/betaine transport. properties inherent to their polypeptide chains.
Probab=24.66 E-value=21 Score=28.90 Aligned_cols=35 Identities=20% Similarity=0.323 Sum_probs=22.6
Q ss_pred hheeeeeEeehhhhhhh------hc---ccCCCcccccccccCC
Q 035165 37 KKAKVITHYGFIPLVII------IG---MNSDPKPQLHQLLSPV 71 (71)
Q Consensus 37 ~~~k~v~HyGfIPlVIy------lG---~~s~PkPsl~~LLsPl 71 (71)
..+.+.+|||+.|--+| +| +|-+++.++-+.+.|+
T Consensus 86 A~~~~~fHWG~~aWaiY~l~ala~aY~~~rk~~~~~iss~~~pl 129 (453)
T TIGR00842 86 ALAYTLFHWGIHAWAIYALVGLALAYFHVRKGLPLRLSSALVPL 129 (453)
T ss_pred HHHHHHHHhCHHHHHHHHHHHHHHHHhheecCCCCchhhhhhcc
Confidence 44567899999998765 23 3455555666666553
No 9
>PF09574 DUF2374: Protein of unknown function (Duf2374); InterPro: IPR014175 This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC 7966.
Probab=23.92 E-value=30 Score=20.27 Aligned_cols=15 Identities=27% Similarity=0.769 Sum_probs=12.8
Q ss_pred eeEeehhhhhhhhcc
Q 035165 42 ITHYGFIPLVIIIGM 56 (71)
Q Consensus 42 v~HyGfIPlVIylG~ 56 (71)
+.-|+-+|+|+.-||
T Consensus 11 vLGY~AmPvI~L~GF 25 (42)
T PF09574_consen 11 VLGYAAMPVIILSGF 25 (42)
T ss_pred HhccccchHHHHhhH
Confidence 456899999999998
No 10
>PRK09950 putative transporter; Provisional
Probab=21.29 E-value=21 Score=29.34 Aligned_cols=35 Identities=9% Similarity=0.230 Sum_probs=22.9
Q ss_pred hheeeeeEeehhhhhhh------hcc----cCCCcccccccccCC
Q 035165 37 KKAKVITHYGFIPLVII------IGM----NSDPKPQLHQLLSPV 71 (71)
Q Consensus 37 ~~~k~v~HyGfIPlVIy------lG~----~s~PkPsl~~LLsPl 71 (71)
..+.+.+|||+.|--+| +|+ |-+++.++-+.+.|+
T Consensus 132 A~~~t~fHWG~~aWaiY~l~~l~iaY~~~~rk~~pl~iss~~~pl 176 (506)
T PRK09950 132 SVSYSFFHWGISAWATYALASLIMAYHFHVRKNKGLSLSGIIAAI 176 (506)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhcCCCCchHHhhHhh
Confidence 34557899999998776 344 445555665655553
No 11
>TIGR02808 short_TIGR02808 conserved hypothetical protein TIGR02808. This very small protein (about 46 amino acids) consists largely of a single predicted membrane-spanning region. It is found in Photobacterium profundum SS9 and in three species of Vibrio, always near periplasmic nitrate reductase genes, but far from the periplasmic nitrate reductase genes in Aeromonas hydrophila ATCC7966.
Probab=20.80 E-value=36 Score=19.96 Aligned_cols=15 Identities=33% Similarity=0.908 Sum_probs=12.6
Q ss_pred eeEeehhhhhhhhcc
Q 035165 42 ITHYGFIPLVIIIGM 56 (71)
Q Consensus 42 v~HyGfIPlVIylG~ 56 (71)
+.-|+-+|+||.-||
T Consensus 11 ilGY~AmPvIil~GF 25 (42)
T TIGR02808 11 VLGYGAMPFIILSGF 25 (42)
T ss_pred HhcccccchHHhhhh
Confidence 356899999999988
No 12
>PF14959 GSAP-16: gamma-Secretase-activating protein C-term
Probab=20.53 E-value=27 Score=23.67 Aligned_cols=42 Identities=12% Similarity=0.084 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhhhhhhheeeeeEeehhhhhhhhcccCCCcccccccc
Q 035165 22 KSRADCLKEWSTWAMKKAKVITHYGFIPLVIIIGMNSDPKPQLHQLL 68 (71)
Q Consensus 22 ~sk~R~~k~~~~w~~~~~k~v~HyGfIPlVIylG~~s~PkPsl~~LL 68 (71)
..-||+--.. +-...-+-=||-=+..|||++.-|.++++|.+
T Consensus 44 ~lmer~~~A~-----~~l~fPlP~GF~t~f~~LG~rcLp~~~FLqYi 85 (115)
T PF14959_consen 44 HLMERIYEAT-----ESLCFPLPPGFHTFFTYLGYRCLPLHTFLQYI 85 (115)
T ss_pred HHHHHHHHHH-----HHccCCCCccHHHHHHHHhHhhccHHHHHHHH
Confidence 4456666666 55566667799999999999999999988765
No 13
>PF07460 NUMOD3: NUMOD3 motif (2 copies); InterPro: IPR003611 This is a short helical motif of unknown function found in intron-associated nuclease 2, which is involved in intron homing.; GO: 0004519 endonuclease activity; PDB: 1I3J_A 1T2T_A.
Probab=20.47 E-value=80 Score=17.06 Aligned_cols=14 Identities=29% Similarity=0.456 Sum_probs=8.1
Q ss_pred CCcCcHHHHHHHHH
Q 035165 16 GAKDSEKSRADCLK 29 (71)
Q Consensus 16 ~~~~se~sk~R~~k 29 (71)
|.+.|||+|+++..
T Consensus 2 G~k~SeetK~kis~ 15 (37)
T PF07460_consen 2 GKKHSEETKKKISE 15 (37)
T ss_dssp T----HHHHHHHHH
T ss_pred CCcCCHHHHHHHHH
Confidence 45678999988876
Done!