Query 030457
Match_columns 177
No_of_seqs 122 out of 619
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 14:00:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030457.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030457hhsearch_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 8.3E-19 1.8E-23 118.0 2.6 40 112-151 5-44 (44)
2 TIGR01030 rpmH_bact ribosomal 99.7 1.9E-18 4.1E-23 116.0 2.8 40 112-151 5-44 (44)
3 PRK00399 rpmH 50S ribosomal pr 99.7 2.7E-18 5.9E-23 115.2 2.6 40 112-151 5-44 (44)
4 CHL00115 rpl34 ribosomal prote 99.7 3.7E-18 7.9E-23 115.6 3.0 40 112-151 6-45 (46)
5 PF00468 Ribosomal_L34: Riboso 99.7 4.4E-18 9.5E-23 114.1 1.4 40 112-151 5-44 (44)
6 KOG4612 Mitochondrial ribosoma 99.4 6E-14 1.3E-18 108.1 2.6 43 108-150 62-104 (105)
7 PF11520 Cren7: Chromatin prot 32.4 23 0.0005 25.7 0.9 20 144-166 32-51 (60)
8 PF09671 Spore_GerQ: Spore coa 22.1 62 0.0013 24.7 1.7 20 143-168 45-64 (81)
9 TIGR02728 spore_gerQ spore coa 19.6 76 0.0016 24.3 1.7 20 143-168 43-62 (82)
10 PF13916 Phostensin_N: PP1-reg 16.4 86 0.0019 24.0 1.4 11 135-145 14-24 (82)
No 1
>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.74 E-value=8.3e-19 Score=118.05 Aligned_cols=40 Identities=50% Similarity=0.748 Sum_probs=37.8
Q ss_pred CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD 151 (177)
Q Consensus 112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~ 151 (177)
||||++||||+|||++||+|++||+||++||+|||++|++
T Consensus 5 yQPs~~kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~ 44 (44)
T COG0230 5 YQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV 44 (44)
T ss_pred cCCcchhhhhhhhHHHHhcccchHHHHHHHHHcCCcccCC
Confidence 4788889999999999999999999999999999999985
No 2
>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=1.9e-18 Score=116.00 Aligned_cols=40 Identities=50% Similarity=0.715 Sum_probs=37.8
Q ss_pred CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD 151 (177)
Q Consensus 112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~ 151 (177)
+||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus 5 ~qps~~kRkr~hGFraRm~T~~GR~vl~rRr~KGRk~Ls~ 44 (44)
T TIGR01030 5 YQPSNLKRKRTHGFRARMATKNGRKVLRRRRAKGRHKLTV 44 (44)
T ss_pred CCCcceeechhhcHHHHccChhhHHHHHHHHHcCCccccC
Confidence 4688889999999999999999999999999999999985
No 3
>PRK00399 rpmH 50S ribosomal protein L34; Reviewed
Probab=99.71 E-value=2.7e-18 Score=115.24 Aligned_cols=40 Identities=50% Similarity=0.770 Sum_probs=37.7
Q ss_pred CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD 151 (177)
Q Consensus 112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~ 151 (177)
+||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus 5 ~qps~~kr~r~hGFraRm~T~~GRkvl~rRR~KGR~~Lt~ 44 (44)
T PRK00399 5 YQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSA 44 (44)
T ss_pred CCCcceeechhhhHHHHccCcccHHHHHHHHHcCCccccC
Confidence 4677889999999999999999999999999999999985
No 4
>CHL00115 rpl34 ribosomal protein L34; Reviewed
Probab=99.71 E-value=3.7e-18 Score=115.63 Aligned_cols=40 Identities=40% Similarity=0.625 Sum_probs=37.9
Q ss_pred CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD 151 (177)
Q Consensus 112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~ 151 (177)
+||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus 6 ~qps~~krkr~hGFraRm~T~~GRkvl~rRR~KGRk~L~v 45 (46)
T CHL00115 6 LSGTKRKKVRKSGFRARMATAAGRKILNARRRKGRKKLAL 45 (46)
T ss_pred cCCcceeecccccHHHHcCCcchHHHHHHHHHcCCceeec
Confidence 4677889999999999999999999999999999999997
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=99.69 E-value=4.4e-18 Score=114.10 Aligned_cols=40 Identities=50% Similarity=0.742 Sum_probs=36.4
Q ss_pred CCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEec
Q 030457 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVFD 151 (177)
Q Consensus 112 r~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls~ 151 (177)
+||++++|+|+|||++||+|++||+||++||+|||++|++
T Consensus 5 ~qps~~kr~r~hGFr~Rm~T~~GRkvl~rRr~KGR~~Ls~ 44 (44)
T PF00468_consen 5 YQPSNRKRKRKHGFRARMSTKNGRKVLKRRRAKGRKRLSV 44 (44)
T ss_dssp S-S-HHHHHHHCSHHHHHCSHHHHHHHHHHHCHTSSTSSC
T ss_pred CCCceeeeeccccchhhhcchhHHHHHHHHHHcCCeeccC
Confidence 5788899999999999999999999999999999999985
No 6
>KOG4612 consensus Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.42 E-value=6e-14 Score=108.13 Aligned_cols=43 Identities=33% Similarity=0.474 Sum_probs=40.9
Q ss_pred ccccCCCcccchhhhhhhhhhcCChhHHHHHHHHHHcCCceEe
Q 030457 108 CQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGREVVF 150 (177)
Q Consensus 108 ~~Tkr~~Sr~kRkRkHGFraRM~Tk~GRkIL~RRR~KGRk~Ls 150 (177)
.+.+||||++||||+|||++|.+|++|++||+||+.|||+.|+
T Consensus 62 rGNeYQPSn~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~LS 104 (105)
T KOG4612|consen 62 RGNEYQPSNLKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFLS 104 (105)
T ss_pred cCCccCchhhhhhhhhhhhhhhcccchhHHHHHHHhccccccc
Confidence 3578999999999999999999999999999999999999986
No 7
>PF11520 Cren7: Chromatin protein Cren7; InterPro: IPR020906 Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo. Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. Its binding to double-stranded DNA is without sequence specificity. There is approximately 1 Cren7 molecule for 12 bp of DNA. The function of Cren7 has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea [].; GO: 0003690 double-stranded DNA binding, 0005737 cytoplasm; PDB: 3KXT_A 3LWH_A 3LWI_A 2JTM_A.
Probab=32.40 E-value=23 Score=25.74 Aligned_cols=20 Identities=40% Similarity=0.767 Sum_probs=11.2
Q ss_pred cCCceEeccccccccCCCCCCcc
Q 030457 144 KGREVVFDSLLGIFQRPSSGNKY 166 (177)
Q Consensus 144 KGRk~Ls~sl~~~~~~~~sgk~~ 166 (177)
|||+-.-. |++.+|++||++
T Consensus 32 kGrkGV~i---gLFk~P~tGk~f 51 (60)
T PF11520_consen 32 KGRKGVKI---GLFKDPETGKYF 51 (60)
T ss_dssp TTS--EEE---EEEE-TTT--EE
T ss_pred CCCCceEE---EEEeCCCCCcch
Confidence 56666655 778999999976
No 8
>PF09671 Spore_GerQ: Spore coat protein (Spore_GerQ); InterPro: IPR014099 Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=22.05 E-value=62 Score=24.75 Aligned_cols=20 Identities=30% Similarity=0.684 Sum_probs=16.6
Q ss_pred HcCCceEeccccccccCCCCCCccee
Q 030457 143 AKGREVVFDSLLGIFQRPSSGNKYVS 168 (177)
Q Consensus 143 ~KGRk~Ls~sl~~~~~~~~sgk~~~~ 168 (177)
+-||-.+.. ++|++||+|+-
T Consensus 45 ~aGRDhiii------sDp~tg~ryLl 64 (81)
T PF09671_consen 45 AAGRDHIII------SDPKTGKRYLL 64 (81)
T ss_pred hcCcceEEE------eCCCCCcEEEE
Confidence 568888877 99999999863
No 9
>TIGR02728 spore_gerQ spore coat protein GerQ. Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Probab=19.58 E-value=76 Score=24.33 Aligned_cols=20 Identities=30% Similarity=0.587 Sum_probs=16.8
Q ss_pred HcCCceEeccccccccCCCCCCccee
Q 030457 143 AKGREVVFDSLLGIFQRPSSGNKYVS 168 (177)
Q Consensus 143 ~KGRk~Ls~sl~~~~~~~~sgk~~~~ 168 (177)
+-||-.+.. ++|+||++|+-
T Consensus 43 ~AGRDhiii------sdp~tg~RyLl 62 (82)
T TIGR02728 43 NAGRDHIVI------SDPQSGMRYLL 62 (82)
T ss_pred hcCcceEEE------cCCCCCcEEEe
Confidence 568888877 99999999863
No 10
>PF13916 Phostensin_N: PP1-regulatory protein, Phostensin N-terminal
Probab=16.39 E-value=86 Score=24.03 Aligned_cols=11 Identities=73% Similarity=0.884 Sum_probs=9.7
Q ss_pred HHHHHHHHHcC
Q 030457 135 RAILKRRRAKG 145 (177)
Q Consensus 135 RkIL~RRR~KG 145 (177)
|.||.|||+|.
T Consensus 14 ReiLERrRAKl 24 (82)
T PF13916_consen 14 REILERRRAKL 24 (82)
T ss_pred HHHHHHHHHHh
Confidence 68999999985
Done!