Query 023784
Match_columns 277
No_of_seqs 62 out of 64
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 06:38:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02817 E3_binding: e3 bindin 23.8 52 0.0011 22.7 1.5 17 208-224 21-37 (39)
2 PF08756 YfkB: YfkB-like domai 21.1 43 0.00094 29.8 0.8 20 13-33 29-48 (153)
3 PF06744 DUF1215: Protein of u 11.5 1.4E+02 0.003 24.4 1.4 20 205-228 55-74 (125)
4 cd04412 NDPk7B Nucleoside diph 10.2 1.5E+02 0.0033 24.7 1.2 23 207-230 4-26 (134)
5 PF03785 Peptidase_C25_C: Pept 9.2 1.8E+02 0.0039 23.5 1.3 24 251-274 46-69 (81)
6 TIGR00214 lipB lipoate-protein 8.9 1.6E+02 0.0035 26.5 1.0 20 206-225 142-163 (184)
7 PF03471 CorC_HlyC: Transporte 8.6 1.9E+02 0.0041 21.6 1.1 17 215-231 10-26 (81)
8 PF00312 Ribosomal_S15: Riboso 8.5 1E+02 0.0022 24.0 -0.3 10 56-65 55-64 (83)
9 COG3889 Predicted solute bindi 8.3 2.3E+02 0.005 31.4 2.0 30 197-228 483-513 (872)
10 COG0184 RpsO Ribosomal protein 8.3 1.2E+02 0.0025 24.7 -0.2 11 56-66 60-70 (89)
No 1
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=23.83 E-value=52 Score=22.66 Aligned_cols=17 Identities=35% Similarity=0.507 Sum_probs=15.6
Q ss_pred eeeccCCccCCcchHhH
Q 023784 208 AFIKPCGVHGDITLKDI 224 (277)
Q Consensus 208 ~~vKP~g~~gd~TL~DI 224 (277)
+-|++.|.+|-||..||
T Consensus 21 ~~v~gtG~~GrI~k~Dv 37 (39)
T PF02817_consen 21 SQVKGTGPGGRITKEDV 37 (39)
T ss_dssp GGSSSSSTTSBBCHHHH
T ss_pred ccccccCCCCcEeHHHh
Confidence 47899999999999998
No 2
>PF08756 YfkB: YfkB-like domain; InterPro: IPR014866 YfkB is adjacent to YfkA in Bacillus subtilis. In other bacterial species, it is fused to this protein. As YfkA contains a Radical SAM domain it suggests this domain is interacts with them.
Probab=21.05 E-value=43 Score=29.83 Aligned_cols=20 Identities=30% Similarity=0.413 Sum_probs=16.8
Q ss_pred CccccccccCCCCcccccCcc
Q 023784 13 GEDLSYMLDDETTPVKACGDL 33 (277)
Q Consensus 13 ~eD~s~~m~~~tTPvk~C~df 33 (277)
.+.+.||||| |-|+..|..-
T Consensus 29 Rd~~~WMLFG-TLPfy~Cs~~ 48 (153)
T PF08756_consen 29 RDPNVWMLFG-TLPFYPCSDD 48 (153)
T ss_pred cCCCeeEEec-ccccccCCCC
Confidence 4556899999 8899999876
No 3
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=11.52 E-value=1.4e+02 Score=24.38 Aligned_cols=20 Identities=30% Similarity=0.575 Sum_probs=15.5
Q ss_pred eeeeeeccCCccCCcchHhHHhhh
Q 023784 205 YPFAFIKPCGVHGDITLKDINQRI 228 (277)
Q Consensus 205 yPF~~vKP~g~~gd~TL~DIN~ri 228 (277)
|||+ -...-||+|.|+++-.
T Consensus 55 YPF~----~~s~~dv~l~Df~~fF 74 (125)
T PF06744_consen 55 YPFD----PDSSRDVSLADFARFF 74 (125)
T ss_pred CCCC----CCCcccCCHHHHHHHh
Confidence 9998 3456789999998654
No 4
>cd04412 NDPk7B Nucleoside diphosphate kinase 7 domain B (NDPk7B): The nm23-H7 class of nucleoside diphosphate kinase (NDPk7) consists of an N-terminal DM10 domain and two functional catalytic NDPk modules, NDPk7A and NDPk7B. The function of the DM10 domain, which also occurs in multiple copies in other proteins, is unknown. NDPk7 is predominantly expressed in testes, although appreciable amount are also found in liver, heart, brain, ovary, small intestine and spleen. The nm23-H7 gene is located in or near the hereditary prostrate cancer susceptibility locus. Nm23-H7 may be involved in the development of colon and gastric carcinoma, the latter possibly in a type-specific manner.
Probab=10.20 E-value=1.5e+02 Score=24.70 Aligned_cols=23 Identities=35% Similarity=0.430 Sum_probs=16.1
Q ss_pred eeeeccCCccCCcchHhHHhhhcC
Q 023784 207 FAFIKPCGVHGDITLKDINQRIHS 230 (277)
Q Consensus 207 F~~vKP~g~~gd~TL~DIN~ri~~ 230 (277)
|++|||+++.-. -+-.|-++|..
T Consensus 4 l~lIKPda~~~~-~~g~Ii~~i~~ 26 (134)
T cd04412 4 VCIIKPHAVSHG-LLGEILQQILD 26 (134)
T ss_pred EEEECchHhhcC-chHHHHHHHHH
Confidence 789999998654 23567666653
No 5
>PF03785 Peptidase_C25_C: Peptidase family C25, C terminal ig-like domain; InterPro: IPR005536 This domain is found in almost all members of MEROPS peptidase family C25, (clan CD). Peptidase family C25 is a protein family found in the bacteria Porphyromonas gingivalis (Bacteroides gingivalis) a Gram-negative anaerobic bacterial species strongly associated with adult periodontitis. One of its distinguishing characteristics and putative virulence properties is the ability to agglutinate erythrocytes []. It is a highly proteolytic organism which metabolises small peptides and amino acids. Indirect evidence suggests that the proteases produced by this microorganism constitute an important virulence factor []. Protease-encoding genes have been shown to contain multiple copies of repeated nucleotide sequences. These conserved sequences have also been found in haemagglutinin genes [].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 1CVR_A.
Probab=9.18 E-value=1.8e+02 Score=23.53 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=14.9
Q ss_pred CCCcceeeeeeeeCCCceeEEEEe
Q 023784 251 SGKPVVGKTKIRTEGGKGSITIMR 274 (277)
Q Consensus 251 SGK~Vv~~tri~T~gg~Gtiti~r 274 (277)
||++++.+++.-|+.|-=++||+|
T Consensus 46 sG~ati~l~~~it~~~~~tlTit~ 69 (81)
T PF03785_consen 46 SGNATINLTNPITDEGTLTLTITA 69 (81)
T ss_dssp TTEEEEE-SS--TT-SEEEEEEE-
T ss_pred CceEEEECCcccCCCceEEEEEEE
Confidence 999999999766754555666665
No 6
>TIGR00214 lipB lipoate-protein ligase B. Involved in lipoate biosynthesis as the main determinant of the lipoyl-protein ligase activity required for lipoylation of enzymes such as alpha-ketoacid dehydrogenases. Involved in activation and re-activation (following denaturation) of lipoyl-protein ligases (calcium ion-dependant process).
Probab=8.94 E-value=1.6e+02 Score=26.50 Aligned_cols=20 Identities=40% Similarity=0.853 Sum_probs=16.6
Q ss_pred eeeeeccCCccCC--cchHhHH
Q 023784 206 PFAFIKPCGVHGD--ITLKDIN 225 (277)
Q Consensus 206 PF~~vKP~g~~gd--~TL~DIN 225 (277)
||..|.|||+.|- ++|++++
T Consensus 142 ~F~~I~PCGl~~~~vTSl~~~~ 163 (184)
T TIGR00214 142 PFSHINPCGYAGREMGSLNQFL 163 (184)
T ss_pred HhccEEcCCCCCCcEeeHHHHc
Confidence 6999999999985 5787764
No 7
>PF03471 CorC_HlyC: Transporter associated domain; InterPro: IPR005170 This small domain is found in a family of proteins with the CBS IPR002550 from INTERPRO domain and two CBS domains with this domain found at the C terminus of the proteins, the domain is also found at the C terminus of some Na+/H+ antiporters. This domain is also found in CorC that is involved in Magnesium and cobalt efflux. The function of this domain is uncertain but might be involved in modulating transport of ion substrates.; PDB: 3DED_F 2PLI_C 2R2Z_A 2P4P_A 2O3G_A 2P3H_A 3LLB_A 3LAE_A 2P13_B 2NQW_A ....
Probab=8.58 E-value=1.9e+02 Score=21.65 Aligned_cols=17 Identities=29% Similarity=0.466 Sum_probs=14.5
Q ss_pred ccCCcchHhHHhhhcCC
Q 023784 215 VHGDITLKDINQRIHSP 231 (277)
Q Consensus 215 ~~gd~TL~DIN~ri~~~ 231 (277)
+.|.++|.|+|+.+-..
T Consensus 10 v~G~~~l~~l~~~~~~~ 26 (81)
T PF03471_consen 10 VSGSTPLDDLNELLGLD 26 (81)
T ss_dssp EETTSBHHHHHHHHTS-
T ss_pred EEecCCHHHHHHHHCcC
Confidence 57999999999998876
No 8
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 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 [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=8.53 E-value=1e+02 Score=24.00 Aligned_cols=10 Identities=50% Similarity=0.913 Sum_probs=8.5
Q ss_pred Hhhhhhcccc
Q 023784 56 QIKRRRMLQF 65 (277)
Q Consensus 56 ~sKRRRmLqF 65 (277)
.+||||||.|
T Consensus 55 v~kRrrlL~Y 64 (83)
T PF00312_consen 55 VSKRRRLLKY 64 (83)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 3899999987
No 9
>COG3889 Predicted solute binding protein [General function prediction only]
Probab=8.33 E-value=2.3e+02 Score=31.44 Aligned_cols=30 Identities=43% Similarity=0.489 Sum_probs=24.6
Q ss_pred ccccceeeeeeeeeccCCccCC-cchHhHHhhh
Q 023784 197 TKLASSVAYPFAFIKPCGVHGD-ITLKDINQRI 228 (277)
Q Consensus 197 ~~~~~~vayPF~~vKP~g~~gd-~TL~DIN~ri 228 (277)
.|...+|.|||-.=| |.||- +||+||=.-|
T Consensus 483 ekAk~kV~~~~~~~k--WhDGq~itlaDil~~~ 513 (872)
T COG3889 483 EKAKIKVTYPFLDAK--WHDGQPITLADILKLI 513 (872)
T ss_pred CeeeeEEEEEecccc--ccCCCccCHHHHHHHH
Confidence 677889999987766 89996 9999996544
No 10
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=8.29 E-value=1.2e+02 Score=24.72 Aligned_cols=11 Identities=45% Similarity=0.709 Sum_probs=9.2
Q ss_pred Hhhhhhccccc
Q 023784 56 QIKRRRMLQFD 66 (277)
Q Consensus 56 ~sKRRRmLqF~ 66 (277)
.+||||+|-|=
T Consensus 60 vskrrrLl~Yl 70 (89)
T COG0184 60 VSKRRRLLKYL 70 (89)
T ss_pred HHHHHHHHHHH
Confidence 48999999884
Done!