Query 029110
Match_columns 199
No_of_seqs 117 out of 618
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 07:40:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029110.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029110hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0230 RpmH Ribosomal protein 99.7 1.1E-18 2.4E-23 119.1 2.7 44 103-151 1-44 (44)
2 CHL00115 rpl34 ribosomal prote 99.7 2.2E-18 4.8E-23 118.3 3.2 44 104-152 3-46 (46)
3 TIGR01030 rpmH_bact ribosomal 99.7 2.2E-18 4.8E-23 117.2 2.8 43 104-151 2-44 (44)
4 PRK00399 rpmH 50S ribosomal pr 99.7 2.6E-18 5.5E-23 117.0 2.7 43 104-151 2-44 (44)
5 PF00468 Ribosomal_L34: Riboso 99.7 7.9E-18 1.7E-22 114.4 0.9 43 104-151 2-44 (44)
6 KOG4612 Mitochondrial ribosoma 99.1 2.7E-11 5.8E-16 94.9 2.5 39 112-150 66-104 (105)
7 PF00533 BRCT: BRCA1 C Terminu 27.6 49 0.0011 21.3 1.8 26 158-183 2-29 (78)
8 PF10799 YliH: Biofilm formati 22.3 23 0.0005 29.3 -0.6 28 137-166 24-51 (127)
9 KOG2475 CDC45 (cell division c 19.2 75 0.0016 31.9 2.0 34 163-196 75-113 (587)
10 COG0338 Dam Site-specific DNA 12.9 1.5E+02 0.0033 26.5 2.2 30 167-196 157-186 (274)
No 1
>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.73 E-value=1.1e-18 Score=119.08 Aligned_cols=44 Identities=50% Similarity=0.730 Sum_probs=40.7
Q ss_pred cCcccccccCCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEee
Q 029110 103 GKAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVVE 151 (199)
Q Consensus 103 GKRtl~~TkR~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls~ 151 (199)
.|+||+|+++ ||||+|||++||+|++||+||++||+|||++|++
T Consensus 1 mkrTyQPs~~-----kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~ 44 (44)
T COG0230 1 MKRTYQPSKR-----KRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV 44 (44)
T ss_pred CCcccCCcch-----hhhhhhhHHHHhcccchHHHHHHHHHcCCcccCC
Confidence 3788888776 9999999999999999999999999999999985
No 2
>CHL00115 rpl34 ribosomal protein L34; Reviewed
Probab=99.72 E-value=2.2e-18 Score=118.28 Aligned_cols=44 Identities=48% Similarity=0.688 Sum_probs=40.6
Q ss_pred CcccccccCCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEeec
Q 029110 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVVEI 152 (199)
Q Consensus 104 KRtl~~TkR~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls~s 152 (199)
|+|++|+++ ||+|+|||++||+|++||+||++||+||||+|++.
T Consensus 3 KrT~qps~~-----krkr~hGFraRm~T~~GRkvl~rRR~KGRk~L~v~ 46 (46)
T CHL00115 3 KRTLSGTKR-----KKVRKSGFRARMATAAGRKILNARRRKGRKKLALR 46 (46)
T ss_pred ccccCCcce-----eecccccHHHHcCCcchHHHHHHHHHcCCceeecC
Confidence 678888766 89999999999999999999999999999999974
No 3
>TIGR01030 rpmH_bact ribosomal protein L34, bacterial type. This model describes the bacterial protein L34 and its equivalents in organelles.
Probab=99.72 E-value=2.2e-18 Score=117.24 Aligned_cols=43 Identities=47% Similarity=0.733 Sum_probs=40.2
Q ss_pred CcccccccCCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEee
Q 029110 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVVE 151 (199)
Q Consensus 104 KRtl~~TkR~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls~ 151 (199)
|+|++|+++ ||+|+|||++||+|++||+||++||+||||+|++
T Consensus 2 krT~qps~~-----kRkr~hGFraRm~T~~GR~vl~rRr~KGRk~Ls~ 44 (44)
T TIGR01030 2 KRTYQPSNL-----KRKRTHGFRARMATKNGRKVLRRRRAKGRHKLTV 44 (44)
T ss_pred CCCCCCcce-----eechhhcHHHHccChhhHHHHHHHHHcCCccccC
Confidence 678888766 9999999999999999999999999999999985
No 4
>PRK00399 rpmH 50S ribosomal protein L34; Reviewed
Probab=99.72 E-value=2.6e-18 Score=116.96 Aligned_cols=43 Identities=51% Similarity=0.788 Sum_probs=40.1
Q ss_pred CcccccccCCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEee
Q 029110 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVVE 151 (199)
Q Consensus 104 KRtl~~TkR~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls~ 151 (199)
|+|++|+++ ||+|+|||++||+|++||+||++||+||||+|++
T Consensus 2 KrT~qps~~-----kr~r~hGFraRm~T~~GRkvl~rRR~KGR~~Lt~ 44 (44)
T PRK00399 2 KRTYQPSKR-----KRKRTHGFRARMATKNGRKVLARRRAKGRKRLSA 44 (44)
T ss_pred CCCCCCcce-----eechhhhHHHHccCcccHHHHHHHHHcCCccccC
Confidence 688888766 9999999999999999999999999999999985
No 5
>PF00468 Ribosomal_L34: Ribosomal protein L34; InterPro: IPR000271 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 L34 is one of the proteins from the large subunit of the prokaryotic ribosome. It is a small basic protein of 44 to 51 amino-acid residues []. L34 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Eubacterial L34, Red algal chloroplast L34 and Cyanelle L34.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBO_4 3PIO_2 3PIP_2 3SGF_6 2AW4_2 2AWB_2 2VHM_2 3OFZ_2 3UOS_6 2QOX_2 ....
Probab=99.67 E-value=7.9e-18 Score=114.43 Aligned_cols=43 Identities=49% Similarity=0.767 Sum_probs=36.6
Q ss_pred CcccccccCCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEee
Q 029110 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVVE 151 (199)
Q Consensus 104 KRtl~~TkR~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls~ 151 (199)
|+|++|+++ +|+|+|||++||+|++||+||++||+|||++|++
T Consensus 2 krT~qps~~-----kr~r~hGFr~Rm~T~~GRkvl~rRr~KGR~~Ls~ 44 (44)
T PF00468_consen 2 KRTYQPSNR-----KRKRKHGFRARMSTKNGRKVLKRRRAKGRKRLSV 44 (44)
T ss_dssp --SS-S-HH-----HHHHHCSHHHHHCSHHHHHHHHHHHCHTSSTSSC
T ss_pred CCCCCCcee-----eeeccccchhhhcchhHHHHHHHHHHcCCeeccC
Confidence 677777665 9999999999999999999999999999999985
No 6
>KOG4612 consensus Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.12 E-value=2.7e-11 Score=94.86 Aligned_cols=39 Identities=36% Similarity=0.520 Sum_probs=35.4
Q ss_pred CCccccchhhhhhhhhhcCChhhHHHHHHHHhcCCceEe
Q 029110 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRDQVV 150 (199)
Q Consensus 112 R~~sr~kRkRkHGFraRM~Tk~GRkVL~RRR~KGRk~Ls 150 (199)
.+.+++||||+|||++|.+|++|++||++|+.||||.|+
T Consensus 66 YQPSn~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~LS 104 (105)
T KOG4612|consen 66 YQPSNLKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFLS 104 (105)
T ss_pred cCchhhhhhhhhhhhhhhcccchhHHHHHHHhccccccc
Confidence 344556999999999999999999999999999999986
No 7
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=27.56 E-value=49 Score=21.33 Aligned_cols=26 Identities=19% Similarity=0.583 Sum_probs=16.3
Q ss_pred cccccCCcceee--ehhhhHHHHHHhhh
Q 029110 158 RNHLFNGCNIAV--INEARNCLLRRIAK 183 (199)
Q Consensus 158 ~~~~~~~~~~~~--~~~~~~~~~~~~~~ 183 (199)
+..+|.||.+.+ ..+...--|.++.+
T Consensus 2 ~~~~F~g~~f~i~~~~~~~~~~l~~~i~ 29 (78)
T PF00533_consen 2 KPKIFEGCTFCISGFDSDEREELEQLIK 29 (78)
T ss_dssp STTTTTTEEEEESSTSSSHHHHHHHHHH
T ss_pred CCCCCCCEEEEEccCCCCCHHHHHHHHH
Confidence 457999999999 33333333455444
No 8
>PF10799 YliH: Biofilm formation protein (YliH/bssR); InterPro: IPR020359 This entry represents Biofilm regulator, BssR (from the gene also known as yliH). It represses Escherichia coli biofilm formation in M9C glu and LB glu media but not in M9C and LB media. It may act as a global regulator of several genes involved in catabolite repression and stress response and regulation of the uptake and export of signalling pathways. It could also be involved the regulation of indole as well as uptake and export of AI-2 through a cAMP-dependent pathway [].
Probab=22.35 E-value=23 Score=29.31 Aligned_cols=28 Identities=36% Similarity=0.562 Sum_probs=22.9
Q ss_pred HHHHHHhcCCceEeecccccccccccCCcc
Q 029110 137 ILKRRRAKGRDQVVEISTFQLRNHLFNGCN 166 (199)
Q Consensus 137 VL~RRR~KGRk~Ls~ss~~r~~~~~~~~~~ 166 (199)
-|+-|++|| +.+|+.+..||..+|.=|+
T Consensus 24 YLQLRkAKG--YMSVSEsdhLRdn~FeLc~ 51 (127)
T PF10799_consen 24 YLQLRKAKG--YMSVSESDHLRDNLFELCR 51 (127)
T ss_pred HHHHHHHcC--ccccchhhhHHHHHHHHHH
Confidence 456688888 6788888899999998885
No 9
>KOG2475 consensus CDC45 (cell division cycle 45)-like protein [Replication, recombination and repair]
Probab=19.19 E-value=75 Score=31.94 Aligned_cols=34 Identities=35% Similarity=0.448 Sum_probs=21.9
Q ss_pred CCcceeeehhhhHHHHHHhh--hcce-eeeec--ccccc
Q 029110 163 NGCNIAVINEARNCLLRRIA--KQET-FMVCD--RPFHL 196 (199)
Q Consensus 163 ~~~~~~~~~~~~~~~~~~~~--~~~~-~~~~~--~~~~~ 196 (199)
+=|-|..||=.-+-=|.++- -+|. |.||| |||||
T Consensus 75 ~~~~iiLiNcG~~vDL~~~L~~P~e~~~fViDSHRP~nl 113 (587)
T KOG2475|consen 75 QIKYIILINCGATVDLTRLLQPPSEDVIFVIDSHRPFNL 113 (587)
T ss_pred CceEEEEecCCcchhHHHHhCCcccceEEEEeCCCCcch
Confidence 34566677654443344443 3666 99999 89997
No 10
>COG0338 Dam Site-specific DNA methylase [DNA replication, recombination, and repair]
Probab=12.94 E-value=1.5e+02 Score=26.52 Aligned_cols=30 Identities=20% Similarity=0.385 Sum_probs=20.5
Q ss_pred eeeehhhhHHHHHHhhhcceeeeecccccc
Q 029110 167 IAVINEARNCLLRRIAKQETFMVCDRPFHL 196 (199)
Q Consensus 167 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 196 (199)
+-++|.--.+++......++|+-||-|++.
T Consensus 157 ~~i~~~df~~v~~~a~~~~dfvY~DPPY~~ 186 (274)
T COG0338 157 ATIENGDFEEVLADADSGDDFVYCDPPYLP 186 (274)
T ss_pred CeEEcCCHHHHHhhccCCCcEEEeCCCCCc
Confidence 445555555566555555699999999875
Done!