Query 031306
Match_columns 161
No_of_seqs 124 out of 624
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 12:14:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031306.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031306hhsearch_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 5.8E-19 1.3E-23 117.4 2.8 43 104-151 2-44 (44)
2 CHL00115 rpl34 ribosomal prote 99.7 1.1E-18 2.5E-23 116.7 3.1 44 104-152 3-46 (46)
3 TIGR01030 rpmH_bact ribosomal 99.7 1.1E-18 2.4E-23 115.7 2.8 43 104-151 2-44 (44)
4 PRK00399 rpmH 50S ribosomal pr 99.7 1.4E-18 3E-23 115.3 2.7 43 104-151 2-44 (44)
5 PF00468 Ribosomal_L34: Riboso 99.7 3.7E-18 7.9E-23 113.1 1.0 43 104-151 2-44 (44)
6 KOG4612 Mitochondrial ribosoma 99.1 2E-11 4.4E-16 93.2 2.5 39 112-150 66-104 (105)
7 PF13916 Phostensin_N: PP1-reg 13.9 1.1E+02 0.0024 23.2 1.4 13 134-146 13-25 (82)
8 TIGR03317 ygfZ_signature folat 9.8 2.5E+02 0.0054 18.6 2.0 18 133-150 44-63 (67)
9 KOG4076 Regulator of ATP-sensi 9.0 2.2E+02 0.0048 22.8 1.7 25 125-149 39-63 (121)
10 PF08669 GCV_T_C: Glycine clea 6.9 3.9E+02 0.0085 18.2 2.0 17 134-150 5-23 (95)
No 1
>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=5.8e-19 Score=117.43 Aligned_cols=43 Identities=53% Similarity=0.742 Sum_probs=39.3
Q ss_pred ccccccccccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEec
Q 031306 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLCP 151 (161)
Q Consensus 104 kRtl~~TKR~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls~ 151 (161)
|+||+++++ ||+|+|||++||+|++||+||++||+|||++|++
T Consensus 2 krTyQPs~~-----kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~ 44 (44)
T COG0230 2 KRTYQPSKR-----KRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV 44 (44)
T ss_pred CcccCCcch-----hhhhhhhHHHHhcccchHHHHHHHHHcCCcccCC
Confidence 567777666 8999999999999999999999999999999985
No 2
>CHL00115 rpl34 ribosomal protein L34; Reviewed
Probab=99.74 E-value=1.1e-18 Score=116.71 Aligned_cols=44 Identities=50% Similarity=0.696 Sum_probs=39.0
Q ss_pred ccccccccccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEecc
Q 031306 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLCPK 152 (161)
Q Consensus 104 kRtl~~TKR~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls~s 152 (161)
|+||+++++ ||+|+|||++||+|++||+||++||+||||+|++.
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 456666655 88999999999999999999999999999999974
No 3
>TIGR01030 rpmH_bact ribosomal protein L34, bacterial type. This model describes the bacterial protein L34 and its equivalents in organelles.
Probab=99.73 E-value=1.1e-18 Score=115.73 Aligned_cols=43 Identities=49% Similarity=0.713 Sum_probs=39.3
Q ss_pred ccccccccccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEec
Q 031306 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLCP 151 (161)
Q Consensus 104 kRtl~~TKR~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls~ 151 (161)
|+||+++++ +|+|+|||++||+|++||+||++||+||||+|++
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 567777765 8999999999999999999999999999999986
No 4
>PRK00399 rpmH 50S ribosomal protein L34; Reviewed
Probab=99.73 E-value=1.4e-18 Score=115.28 Aligned_cols=43 Identities=53% Similarity=0.758 Sum_probs=39.3
Q ss_pred ccccccccccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEec
Q 031306 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLCP 151 (161)
Q Consensus 104 kRtl~~TKR~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls~ 151 (161)
|+||+++++ ||+|+|||++||+|++||+||++||+|||++|++
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 567777665 8999999999999999999999999999999985
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=3.7e-18 Score=113.15 Aligned_cols=43 Identities=51% Similarity=0.736 Sum_probs=35.8
Q ss_pred ccccccccccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEec
Q 031306 104 KAALCQTKRNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLCP 151 (161)
Q Consensus 104 kRtl~~TKR~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls~ 151 (161)
|+|++++++ +|+|+|||++||+|++||+||++||+|||++|++
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 455666554 8999999999999999999999999999999985
No 6
>KOG4612 consensus Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.14 E-value=2e-11 Score=93.17 Aligned_cols=39 Identities=41% Similarity=0.736 Sum_probs=35.1
Q ss_pred ccccccchhhhhhhhhhccChhhHHHHHHHHHcCCceEe
Q 031306 112 RNRSRKSLARTHGFRRRMRTTSGRAILKRRRAKGRWVLC 150 (161)
Q Consensus 112 R~~sr~kRkR~HGFraRM~T~~GRkVL~RRR~KGRk~Ls 150 (161)
.+.+++||||+|||++|.+|++|++||++|+.||||.|+
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 333456999999999999999999999999999999986
No 7
>PF13916 Phostensin_N: PP1-regulatory protein, Phostensin N-terminal
Probab=13.92 E-value=1.1e+02 Score=23.16 Aligned_cols=13 Identities=62% Similarity=0.695 Sum_probs=10.4
Q ss_pred hHHHHHHHHHcCC
Q 031306 134 GRAILKRRRAKGR 146 (161)
Q Consensus 134 GRkVL~RRR~KGR 146 (161)
=|.||.|||+|.=
T Consensus 13 KReiLERrRAKl~ 25 (82)
T PF13916_consen 13 KREILERRRAKLG 25 (82)
T ss_pred HHHHHHHHHHHhc
Confidence 3679999999853
No 8
>TIGR03317 ygfZ_signature folate-binding protein YgfZ. YgfZ is a protein from Escherichia coli, homologous to the glycine cleavage system T protein, or aminomethyltransferase, GcvT (TIGR00528). Homologs of YgfZ other than members of the GcvT family share a well-conserved signature region that includes the motif, KGCYxGQE. Elsewhere, sequence diverge and length variation are substantial. Members of this family are mostly bacterial, largely absent from the Firmicutes and otherwise usually present. A few eukaryotic examples are found among the Apicomplexa, and a few archaeal sequences are found. Two functions implicated for this folate-binding protein are RNA modification (a function likely to be conserved) and replication initiation (a function likely to be highly variable). Many members of this family are, at the time of construction of this model, misnamed as the glycine cleavage system T protein.
Probab=9.82 E-value=2.5e+02 Score=18.64 Aligned_cols=18 Identities=22% Similarity=0.471 Sum_probs=13.2
Q ss_pred hhHHHHHHHHHcC--CceEe
Q 031306 133 SGRAILKRRRAKG--RWVLC 150 (161)
Q Consensus 133 ~GRkVL~RRR~KG--Rk~Ls 150 (161)
-|+.+|.|.+.+| +++|.
T Consensus 44 iGqe~l~r~~~~g~~~~~lv 63 (67)
T TIGR03317 44 VGQEVVARMHYRGKVKRRLV 63 (67)
T ss_pred cCHHHHHHHHHcCCCceeEE
Confidence 3888888888888 55553
No 9
>KOG4076 consensus Regulator of ATP-sensitive K+ channels Alpha-endosulfine/ARPP-19 and related cAMP-regulated phosphoproteins [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=9.00 E-value=2.2e+02 Score=22.78 Aligned_cols=25 Identities=24% Similarity=0.418 Sum_probs=22.7
Q ss_pred hhhhccChhhHHHHHHHHHcCCceE
Q 031306 125 FRRRMRTTSGRAILKRRRAKGRWVL 149 (161)
Q Consensus 125 FraRM~T~~GRkVL~RRR~KGRk~L 149 (161)
|..=++=+.|..+|..|..||||+.
T Consensus 39 y~~~GklP~~sd~l~krlQkgrKyF 63 (121)
T KOG4076|consen 39 YPSYGKLPGGSDFLRKRLQKGRKYF 63 (121)
T ss_pred HHHhCCCCcccHHHHHHHHhccccc
Confidence 6777888999999999999999986
No 10
>PF08669 GCV_T_C: Glycine cleavage T-protein C-terminal barrel domain; InterPro: IPR013977 This entry shows glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase. ; PDB: 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 3GIR_A 1WOO_A 1WOS_A 1WOR_A ....
Probab=6.94 E-value=3.9e+02 Score=18.20 Aligned_cols=17 Identities=35% Similarity=0.587 Sum_probs=13.8
Q ss_pred hHHHHHHHHHcCC--ceEe
Q 031306 134 GRAILKRRRAKGR--WVLC 150 (161)
Q Consensus 134 GRkVL~RRR~KGR--k~Ls 150 (161)
||..|.+.+.+|. ++|.
T Consensus 5 G~eal~r~~~~g~~rr~lv 23 (95)
T PF08669_consen 5 GQEALARQKARGVKRRRLV 23 (95)
T ss_dssp THHHHHHHHHHTTS-EEEE
T ss_pred CHHHHHHHHhcCCCceEEE
Confidence 8999999999994 5554
Done!