Query 035432
Match_columns 60
No_of_seqs 111 out of 198
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:56:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035432.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035432hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00190 60S ribosomal protein 100.0 3.8E-40 8.2E-45 202.9 0.9 53 1-53 1-54 (70)
2 PF01779 Ribosomal_L29e: Ribos 100.0 3.2E-35 7E-40 165.2 2.4 40 3-42 1-40 (40)
3 KOG3504 60S ribosomal protein 100.0 3.4E-33 7.4E-38 176.5 1.2 54 1-54 1-54 (84)
4 KOG3725 SH3 domain protein SH3 46.2 14 0.00031 28.7 1.8 21 31-55 346-366 (375)
5 PF11795 DUF3322: Uncharacteri 29.8 37 0.00081 23.0 1.6 16 28-43 165-180 (190)
6 PF04208 MtrA: Tetrahydrometha 22.3 60 0.0013 23.1 1.6 38 4-44 78-115 (176)
7 cd01737 LSm16_N LSm16 belongs 18.5 38 0.00083 20.6 -0.1 13 14-26 37-49 (62)
8 PF00846 Hanta_nucleocap: Hant 18.0 41 0.00089 27.0 0.0 17 17-34 167-183 (428)
9 cd06416 GH25_Lys1-like Lys-1 i 17.9 1.2E+02 0.0026 20.0 2.2 33 20-52 22-54 (196)
10 PF13980 UPF0370: Uncharacteri 17.1 15 0.00033 22.5 -2.1 12 31-42 25-37 (63)
No 1
>PTZ00190 60S ribosomal protein L29; Provisional
Probab=100.00 E-value=3.8e-40 Score=202.92 Aligned_cols=53 Identities=57% Similarity=0.688 Sum_probs=51.7
Q ss_pred CCCCccccchhhhHHhhhcCCCCCC-CCCCCCCCCCCHHHHHHHHHHHhhcCCC
Q 035432 1 MAKSKNHTAHNQSYKAHKNGIKKPK-KHRHTSTKGMDPKFLRNQRYARKHNKSN 53 (60)
Q Consensus 1 MaKsKNHT~HNQs~K~HRNGIKKp~-~~ry~slKGvdpKFLRN~rfAkK~nkk~ 53 (60)
||||||||+||||+||||||||||+ ++||+||+||||+||||||||+++++++
T Consensus 1 MAKSKNHT~HNQs~K~HRNGIKKp~~~~ry~S~kG~d~kflrN~r~akk~n~k~ 54 (70)
T PTZ00190 1 MAKSKNHTNHNQSSKNHRNGIKGPLPLHLHNSKRGSWLPALVNARRVRKHNQKA 54 (70)
T ss_pred CCCcccccccccchhhhccCcCCCccccccchhcccChHHHHHHHHHHhhCHHH
Confidence 9999999999999999999999999 4999999999999999999999999987
No 2
>PF01779 Ribosomal_L29e: Ribosomal L29e protein family; InterPro: IPR002673 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 L29e forms part of the 60S ribosomal subunit []. This family is found in eukaryotes. There are there are 20 to 22 copies of the L29 gene in Rattus norvegicus (Rat). Rat L29 is related to yeast ribosomal protein YL43 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_d 4A18_T 4A1B_T 4A1D_T 4A19_T 3IZR_d.
Probab=100.00 E-value=3.2e-35 Score=165.16 Aligned_cols=40 Identities=75% Similarity=1.043 Sum_probs=19.8
Q ss_pred CCccccchhhhHHhhhcCCCCCCCCCCCCCCCCCHHHHHH
Q 035432 3 KSKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRN 42 (60)
Q Consensus 3 KsKNHT~HNQs~K~HRNGIKKp~~~ry~slKGvdpKFLRN 42 (60)
||||||+||||+||||||||||+++||+||+||||+||||
T Consensus 1 KsKNhT~hNqs~K~HRNGIKKp~~~r~~SlKGvdpKflrN 40 (40)
T PF01779_consen 1 KSKNHTTHNQSRKWHRNGIKKPKSQRYESLKGVDPKFLRN 40 (40)
T ss_dssp -------TTHHHHHHTT--------SS---TT--HHHHHH
T ss_pred CCccccccchhhhhhccCcCCCcccccccccCcCchhhcC
Confidence 7999999999999999999999999999999999999998
No 3
>KOG3504 consensus 60S ribosomal protein L29 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.4e-33 Score=176.45 Aligned_cols=54 Identities=67% Similarity=0.937 Sum_probs=51.8
Q ss_pred CCCCccccchhhhHHhhhcCCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCC
Q 035432 1 MAKSKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRNQRYARKHNKSNG 54 (60)
Q Consensus 1 MaKsKNHT~HNQs~K~HRNGIKKp~~~ry~slKGvdpKFLRN~rfAkK~nkk~~ 54 (60)
||||||||+|||+.|||||||+||+++||.||+||||+||+||+||++++++..
T Consensus 1 maksknht~hNq~~KahRngIkkp~~~r~~sl~g~dpKf~rn~~~a~kg~~~~q 54 (84)
T KOG3504|consen 1 MAKSKNHTTHNQNKKAHRNGIKKPRKQRYESLRGVDPKFLRNMRPARKGSKKQQ 54 (84)
T ss_pred CCcccccccccccHHHHHhhccchhhhhhhhhcCCCHHHHHhcchhhcccHHHH
Confidence 999999999999999999999999999999999999999999999998887663
No 4
>KOG3725 consensus SH3 domain protein SH3GLB [Signal transduction mechanisms]
Probab=46.19 E-value=14 Score=28.71 Aligned_cols=21 Identities=33% Similarity=0.468 Sum_probs=17.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCC
Q 035432 31 STKGMDPKFLRNQRYARKHNKSNGG 55 (60)
Q Consensus 31 slKGvdpKFLRN~rfAkK~nkk~~~ 55 (60)
||.||||.|| .+.++|++|.+
T Consensus 346 slpGMD~dwl----mgErGnkkGKv 366 (375)
T KOG3725|consen 346 SLPGMDADWL----MGERGNKKGKV 366 (375)
T ss_pred ecCCCChHHh----hhhhcCCCCCc
Confidence 7899999998 46788888743
No 5
>PF11795 DUF3322: Uncharacterized protein conserved in bacteria N-term (DUF3322); InterPro: IPR024537 This domain, found in various hypothetical bacterial proteins, has no known function. The family represents just the N terminus.
Probab=29.77 E-value=37 Score=22.96 Aligned_cols=16 Identities=31% Similarity=0.661 Sum_probs=13.0
Q ss_pred CCCCCCCCCHHHHHHH
Q 035432 28 RHTSTKGMDPKFLRNQ 43 (60)
Q Consensus 28 ry~slKGvdpKFLRN~ 43 (60)
|-.++.|||.||+-+-
T Consensus 165 Rqlpi~GvDTKfiE~h 180 (190)
T PF11795_consen 165 RQLPIPGVDTKFIERH 180 (190)
T ss_pred hhCCcCCcchHHHHHH
Confidence 4478999999999753
No 6
>PF04208 MtrA: Tetrahydromethanopterin S-methyltransferase, subunit A ; InterPro: IPR013340 This domain is mostly found in N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit A (MtrA) in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive sodium-ion pump. 5-methyl-5,6,7,8-tetrahydromethanopterin + 2-mercaptoethanesulphonate = 5,6,7,8-tetrahydromethanopterin + 2-(methylthio)ethanesulphonate. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase (encoded by subunit A) is involved in the transfer of 'methyl' group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of methyl-coenzyme M by another enzyme, methyl-coenzyme M reductase. In some organisms this domain is found at the N-terminal region of what appears to be a fusion of the MtrA and MtrF proteins [, ]. The function of these proteins is unknown, though it is likely that they are involved in C1 metabolism. ; GO: 0008168 methyltransferase activity, 0030269 tetrahydromethanopterin S-methyltransferase activity
Probab=22.31 E-value=60 Score=23.14 Aligned_cols=38 Identities=34% Similarity=0.469 Sum_probs=22.3
Q ss_pred CccccchhhhHHhhhcCCCCCCCCCCCCCCCCCHHHHHHHH
Q 035432 4 SKNHTAHNQSYKAHKNGIKKPKKHRHTSTKGMDPKFLRNQR 44 (60)
Q Consensus 4 sKNHT~HNQs~K~HRNGIKKp~~~ry~slKGvdpKFLRN~r 44 (60)
|+-|-+=---..-|+|||-.-. |----+|-.| ||+|+-
T Consensus 78 v~GH~~Gqsl~aLh~NGid~~g--rIiGa~GaiP-fleNi~ 115 (176)
T PF04208_consen 78 VKGHLTGQSLLALHENGIDEDG--RIIGAKGAIP-FLENIP 115 (176)
T ss_pred cCCCcchHHHHHHHHcCCCCCC--CCccCCCCcc-hhhcCC
Confidence 3444444233445999995433 3445677765 888853
No 7
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=18.48 E-value=38 Score=20.65 Aligned_cols=13 Identities=23% Similarity=0.120 Sum_probs=9.6
Q ss_pred HHhhhcCCCCCCC
Q 035432 14 YKAHKNGIKKPKK 26 (60)
Q Consensus 14 ~K~HRNGIKKp~~ 26 (60)
.+..|||||++-.
T Consensus 37 ~~~~~ngik~~~~ 49 (62)
T cd01737 37 AFPFHNGVKCLVP 49 (62)
T ss_pred eecccCCccccCc
Confidence 3567999988754
No 8
>PF00846 Hanta_nucleocap: Hantavirus nucleocapsid protein; InterPro: IPR002214 Hantaviruses are ssRNA negative-strand viruses. The nucleocapsid protein is an internal protein of the virus particle [, ].; GO: 0019013 viral nucleocapsid; PDB: 2IC9_A 2IC6_A 2K48_A 4FI5_A.
Probab=18.03 E-value=41 Score=26.96 Aligned_cols=17 Identities=47% Similarity=0.614 Sum_probs=0.0
Q ss_pred hhcCCCCCCCCCCCCCCC
Q 035432 17 HKNGIKKPKKHRHTSTKG 34 (60)
Q Consensus 17 HRNGIKKp~~~ry~slKG 34 (60)
-.|||+||+ +-|-||.-
T Consensus 167 ~~ngirkpk-hLYvSmP~ 183 (428)
T PF00846_consen 167 DVNGIRKPK-HLYVSMPT 183 (428)
T ss_dssp ------------------
T ss_pred ccccccccc-eEEEeCCC
Confidence 469999998 67877753
No 9
>cd06416 GH25_Lys1-like Lys-1 is a lysozyme encoded by the Caenorhabditis elegans lys-1 gene. This gene is one of a several lysozyme genes upregulated upon infection by the Gram-negative bacterial pathogen Serratia marcescens. Lys-1 contains a glycosyl hydrolase family 25 (GH25) catalytic domain. This family also includes Lys-5 from Caenorhabditis elegans.
Probab=17.90 E-value=1.2e+02 Score=19.96 Aligned_cols=33 Identities=24% Similarity=0.219 Sum_probs=22.2
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCC
Q 035432 20 GIKKPKKHRHTSTKGMDPKFLRNQRYARKHNKS 52 (60)
Q Consensus 20 GIKKp~~~ry~slKGvdpKFLRN~rfAkK~nkk 52 (60)
||.=.--+-++..-.+||.|..|..-|+..-..
T Consensus 22 g~~fv~ikateg~~~~D~~f~~n~~~A~~aGl~ 54 (196)
T cd06416 22 GYSFAIIRAYRSNGSFDPNSVTNIKNARAAGLS 54 (196)
T ss_pred CceEEEEEEEccCCccChHHHHHHHHHHHcCCc
Confidence 554333334455555999999999999876443
No 10
>PF13980 UPF0370: Uncharacterised protein family (UPF0370)
Probab=17.08 E-value=15 Score=22.48 Aligned_cols=12 Identities=42% Similarity=0.653 Sum_probs=6.8
Q ss_pred CCCCCCHH-HHHH
Q 035432 31 STKGMDPK-FLRN 42 (60)
Q Consensus 31 slKGvdpK-FLRN 42 (60)
.|..||+| ||-|
T Consensus 25 ~L~RvD~K~fL~n 37 (63)
T PF13980_consen 25 ELRRVDHKKFLDN 37 (63)
T ss_pred HHHhcCHHHHhcC
Confidence 45667764 5544
Done!