Query 032623
Match_columns 137
No_of_seqs 139 out of 625
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 03:49:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032623.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032623hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00115 rpl34 ribosomal prote 99.9 6.2E-25 1.3E-29 143.5 3.4 45 93-137 1-45 (46)
2 COG0230 RpmH Ribosomal protein 99.9 2.1E-24 4.5E-29 140.1 3.5 44 94-137 1-44 (44)
3 TIGR01030 rpmH_bact ribosomal 99.9 4.6E-24 9.9E-29 138.3 3.6 44 94-137 1-44 (44)
4 PRK00399 rpmH 50S ribosomal pr 99.9 6.3E-24 1.4E-28 137.6 3.6 44 94-137 1-44 (44)
5 PF00468 Ribosomal_L34: Riboso 99.9 1.2E-23 2.5E-28 136.3 2.4 44 94-137 1-44 (44)
6 KOG4612 Mitochondrial ribosoma 99.6 1.4E-15 3E-20 113.2 2.7 42 95-136 63-104 (105)
7 PF13916 Phostensin_N: PP1-reg 16.7 90 0.0019 23.0 1.5 13 119-131 12-24 (82)
8 PF11073 NSs: Rift valley feve 12.6 79 0.0017 26.9 0.3 16 65-80 105-120 (238)
9 TIGR03317 ygfZ_signature folat 11.8 1.5E+02 0.0033 19.3 1.4 17 119-135 44-62 (67)
10 PF03723 Hemocyanin_C: Hemocya 9.4 90 0.002 26.0 -0.4 26 67-93 157-182 (250)
No 1
>CHL00115 rpl34 ribosomal protein L34; Reviewed
Probab=99.90 E-value=6.2e-25 Score=143.52 Aligned_cols=45 Identities=36% Similarity=0.609 Sum_probs=44.1
Q ss_pred CCCCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccCC
Q 032623 93 FPKRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRITA 137 (137)
Q Consensus 93 ~~KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt~ 137 (137)
|+|||||||++||+|+|||++||+|++||+||++||+|||++|+|
T Consensus 1 m~KrT~qps~~krkr~hGFraRm~T~~GRkvl~rRR~KGRk~L~v 45 (46)
T CHL00115 1 MTKRTLSGTKRKKVRKSGFRARMATAAGRKILNARRRKGRKKLAL 45 (46)
T ss_pred CCccccCCcceeecccccHHHHcCCcchHHHHHHHHHcCCceeec
Confidence 799999999999999999999999999999999999999999986
No 2
>COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=2.1e-24 Score=140.05 Aligned_cols=44 Identities=64% Similarity=0.949 Sum_probs=42.7
Q ss_pred CCCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccCC
Q 032623 94 PKRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRITA 137 (137)
Q Consensus 94 ~KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt~ 137 (137)
+|||||||++||+|+|||++||+|++||+||++||+|||++|++
T Consensus 1 mkrTyQPs~~kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~ 44 (44)
T COG0230 1 MKRTYQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV 44 (44)
T ss_pred CCcccCCcchhhhhhhhHHHHhcccchHHHHHHHHHcCCcccCC
Confidence 48999999999999999999999999999999999999999986
No 3
>TIGR01030 rpmH_bact ribosomal protein L34, bacterial type. This model describes the bacterial protein L34 and its equivalents in organelles.
Probab=99.89 E-value=4.6e-24 Score=138.29 Aligned_cols=44 Identities=61% Similarity=0.959 Sum_probs=42.7
Q ss_pred CCCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccCC
Q 032623 94 PKRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRITA 137 (137)
Q Consensus 94 ~KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt~ 137 (137)
+|||||||+++|+|+|||++||+|++||+||++||+|||++|+|
T Consensus 1 mkrT~qps~~kRkr~hGFraRm~T~~GR~vl~rRr~KGRk~Ls~ 44 (44)
T TIGR01030 1 MKRTYQPSNLKRKRTHGFRARMATKNGRKVLRRRRAKGRHKLTV 44 (44)
T ss_pred CCCCCCCcceeechhhcHHHHccChhhHHHHHHHHHcCCccccC
Confidence 48999999999999999999999999999999999999999986
No 4
>PRK00399 rpmH 50S ribosomal protein L34; Reviewed
Probab=99.89 E-value=6.3e-24 Score=137.64 Aligned_cols=44 Identities=66% Similarity=0.967 Sum_probs=42.8
Q ss_pred CCCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccCC
Q 032623 94 PKRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRITA 137 (137)
Q Consensus 94 ~KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt~ 137 (137)
+|||||||++||+|+|||++||+|++||+||++||+|||++|+|
T Consensus 1 mKrT~qps~~kr~r~hGFraRm~T~~GRkvl~rRR~KGR~~Lt~ 44 (44)
T PRK00399 1 MKRTYQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSA 44 (44)
T ss_pred CCCCCCCcceeechhhhHHHHccCcccHHHHHHHHHcCCccccC
Confidence 58999999999999999999999999999999999999999986
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=99.88 E-value=1.2e-23 Score=136.30 Aligned_cols=44 Identities=59% Similarity=0.924 Sum_probs=38.5
Q ss_pred CCCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccCC
Q 032623 94 PKRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRITA 137 (137)
Q Consensus 94 ~KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt~ 137 (137)
+|||||||+++|+|+|||++||+|++||+||++||+|||++|++
T Consensus 1 mkrT~qps~~kr~r~hGFr~Rm~T~~GRkvl~rRr~KGR~~Ls~ 44 (44)
T PF00468_consen 1 MKRTYQPSNRKRKRKHGFRARMSTKNGRKVLKRRRAKGRKRLSV 44 (44)
T ss_dssp ---SS-S-HHHHHHHCSHHHHHCSHHHHHHHHHHHCHTSSTSSC
T ss_pred CCCCCCCceeeeeccccchhhhcchhHHHHHHHHHHcCCeeccC
Confidence 58999999999999999999999999999999999999999986
No 6
>KOG4612 consensus Mitochondrial ribosomal protein L34 [Translation, ribosomal structure and biogenesis]
Probab=99.56 E-value=1.4e-15 Score=113.18 Aligned_cols=42 Identities=45% Similarity=0.801 Sum_probs=40.3
Q ss_pred CCCCCCCccchhhhhhhhhhcCChhhHHHHHHHHHhCccccC
Q 032623 95 KRTFQPSTIRRKRNHGFFARKATKGGRRVIARRIAKGRSRIT 136 (137)
Q Consensus 95 KrT~qPs~~kRkR~hGFraRm~T~~GRkVL~rRR~KGRk~Lt 136 (137)
.++|||||+||||+|||++|.+|++|++||++|+.|||+.|+
T Consensus 63 GNeYQPSn~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~LS 104 (105)
T KOG4612|consen 63 GNEYQPSNLKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFLS 104 (105)
T ss_pred CCccCchhhhhhhhhhhhhhhcccchhHHHHHHHhccccccc
Confidence 379999999999999999999999999999999999999986
No 7
>PF13916 Phostensin_N: PP1-regulatory protein, Phostensin N-terminal
Probab=16.71 E-value=90 Score=22.99 Aligned_cols=13 Identities=38% Similarity=0.363 Sum_probs=10.6
Q ss_pred hhHHHHHHHHHhC
Q 032623 119 GGRRVIARRIAKG 131 (137)
Q Consensus 119 ~GRkVL~rRR~KG 131 (137)
.=|.||.|||+|.
T Consensus 12 WKReiLERrRAKl 24 (82)
T PF13916_consen 12 WKREILERRRAKL 24 (82)
T ss_pred HHHHHHHHHHHHh
Confidence 3478999999984
No 8
>PF11073 NSs: Rift valley fever virus non structural protein (NSs) like ; InterPro: IPR024376 This family contains several Phlebovirus non structural proteins which act as a major determinant of virulence by antagonising interferon beta gene expression [].
Probab=12.61 E-value=79 Score=26.90 Aligned_cols=16 Identities=44% Similarity=0.933 Sum_probs=14.4
Q ss_pred CCcccCCCCCCccccc
Q 032623 65 QGFLYPSGLPSLEFYL 80 (137)
Q Consensus 65 ~~~l~p~glpsl~~~~ 80 (137)
+++.-|.|.|||.||-
T Consensus 105 ~ALsWPlG~Psl~Ff~ 120 (238)
T PF11073_consen 105 KALSWPLGYPSLEFFE 120 (238)
T ss_pred HHhcCCCCCCCchhhe
Confidence 7899999999999873
No 9
>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=11.82 E-value=1.5e+02 Score=19.30 Aligned_cols=17 Identities=35% Similarity=0.628 Sum_probs=12.7
Q ss_pred hhHHHHHHHHHhC--cccc
Q 032623 119 GGRRVIARRIAKG--RSRI 135 (137)
Q Consensus 119 ~GRkVL~rRR~KG--Rk~L 135 (137)
-|+.++.|.+.+| +++|
T Consensus 44 iGqe~l~r~~~~g~~~~~l 62 (67)
T TIGR03317 44 VGQEVVARMHYRGKVKRRL 62 (67)
T ss_pred cCHHHHHHHHHcCCCceeE
Confidence 3888998888888 4554
No 10
>PF03723 Hemocyanin_C: Hemocyanin, ig-like domain; InterPro: IPR005203 Haemocyanins are copper-containing oxygen transport proteins found in the haemolymph of many invertebrates. They are divided into 2 main groups, arthropodan and molluscan. These have structurally similar oxygen-binding centres, which are similar to the oxygen-binding centre of tyrosinases [], but their quaternary structures are arranged differently. The arthropodan proteins exist as hexamers comprising 3 heterogeneous subunits (a, b and c) and possess 1 oxygen-binding centre per subunit; and the molluscan proteins exist as cylindrical oligomers of 10 to 20 subunits and possess 7 or 8 oxygen-binding centres per subunit []. Although the proteins have similar amino acid compositions, the only real similarity in their primary sequences is in the region corresponding to the second copper-binding domain, which also shows similarity to the copper-binding domain of tyrosinases []. Larval storage proteins (LSP) [] are proteins from the hemolymph of insects, which may serve as a store of amino acids for synthesis of adult proteins. There are two classes of LSP's, arylphorins, which are rich in aromatic amino acids, and methionine-rich LSP's. LSP's forms hexameric complexes. LSP's are structurally related to arthropods hemocyanins.; PDB: 3HHS_A 1HCY_A 1HC1_C 1LL1_A 1NOL_A 1LLA_A 1OXY_A 3IXV_E 3IXW_L 3GWJ_F ....
Probab=9.39 E-value=90 Score=25.97 Aligned_cols=26 Identities=31% Similarity=0.611 Sum_probs=16.7
Q ss_pred cccCCCCCCcccccCCCCCCCcccccC
Q 032623 67 FLYPSGLPSLEFYLPNGNLSDEPMLLF 93 (137)
Q Consensus 67 ~l~p~glpsl~~~~p~~~~~~~~~~~~ 93 (137)
--.-||||. ++.+|.|...+.++.++
T Consensus 157 ~~~~cG~P~-rLLLPkG~~~Gm~f~lf 182 (250)
T PF03723_consen 157 SECSCGFPD-RLLLPKGTPEGMPFQLF 182 (250)
T ss_dssp SSTTTSEEG-GGSS---BTT-EEEEEE
T ss_pred cccCCCCCC-cccccCCCCCCeeEEEE
Confidence 347899998 69999998887776553
Done!