Query 537021.9.peg.374_1 Match_columns 42 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Tue May 24 20:48:13 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_374.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 TIGR01632 L11_bact ribosomal p 46.2 10 0.00026 20.2 1.3 14 5-18 66-79 (144) 2 KOG3009 consensus 20.4 86 0.0022 15.6 2.4 31 3-33 472-503 (614) 3 pfam02964 MeMO_Hyd_G Methane m 13.8 53 0.0013 16.6 0.0 12 17-28 115-126 (160) 4 COG0080 RplK Ribosomal protein 13.6 95 0.0024 15.4 1.3 14 5-18 66-79 (141) 5 cd04248 AAK_AK-Ectoine AAK_AK- 10.3 62 0.0016 16.3 -0.5 20 16-38 278-297 (304) 6 pfam10845 DUF2576 Protein of u 10.2 64 0.0016 16.2 -0.4 10 19-28 37-46 (48) 7 KOG3257 consensus 9.6 1.5E+02 0.0038 14.4 1.2 14 5-18 81-94 (168) 8 TIGR02787 codY_Gpos GTP-sensin 9.4 1.4E+02 0.0035 14.6 1.0 14 13-26 30-43 (255) 9 TIGR01605 PYST-D Plasmodium yo 8.9 1.2E+02 0.003 14.9 0.5 16 23-38 5-20 (55) 10 cd04244 AAK_AK-LysC-like AAK_A 8.1 83 0.0021 15.7 -0.6 19 16-37 272-290 (298) No 1 >TIGR01632 L11_bact ribosomal protein L11; InterPro: IPR006519 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 of 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 L11 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L11 is known to bind directly to the 23S rRNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, chloroplast, cyanelle, and most mitochondrial forms of ribosomal protein L11. L11 is a protein of 140 to 165 amino-acid residues. In E. coli, the C-terminal half of L11 has been shown to be in an extended and loosely folded conformation and is likely to be buried within the ribosomal structure. This entry represents the bacterial, chloroplast and mitochondrial forms. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome. Probab=46.24 E-value=10 Score=20.18 Aligned_cols=14 Identities=57% Similarity=1.037 Sum_probs=11.9 Q ss_pred EEEEECCCHHHHHH Q ss_conf 07998497443111 Q 537021.9.peg.3 5 SFIIITPPATVLLP 18 (42) Q Consensus 5 sfiiitppatvllp 18 (42) +|+.=|||+++||- T Consensus 66 ~F~~KtPPvs~lLK 79 (144) T TIGR01632 66 TFIVKTPPVSVLLK 79 (144) T ss_pred EEEECCCCHHHHHH T ss_conf 88844887689999 No 2 >KOG3009 consensus Probab=20.37 E-value=86 Score=15.60 Aligned_cols=31 Identities=29% Similarity=0.443 Sum_probs=23.5 Q ss_pred CCEEEEECCCHHHHH-HHHCCCEEECHHHHHH Q ss_conf 430799849744311-1013633433110134 Q 537021.9.peg.3 3 ESSFIIITPPATVLL-PMMDCNVFLDPIWIKN 33 (42) Q Consensus 3 essfiiitppatvll-pmmdcnvfldpiwikn 33 (42) +.+.-.|+|-+.-|| -|-+|+||.+|-|+.. T Consensus 472 v~~i~~i~PN~~Ell~a~k~~~v~~nps~~q~ 503 (614) T KOG3009 472 VGAITAISPNANELLKAAKLCHVSVNPSVIQT 503 (614) T ss_pred EEEEEEECCCHHHHHHHHHCCCEEECHHHHCC T ss_conf 03677518898999998645865547245311 No 3 >pfam02964 MeMO_Hyd_G Methane monooxygenase, hydrolase gamma chain. Probab=13.81 E-value=53 Score=16.64 Aligned_cols=12 Identities=58% Similarity=0.930 Sum_probs=9.7 Q ss_pred HHHHCCCEEECH Q ss_conf 110136334331 Q 537021.9.peg.3 17 LPMMDCNVFLDP 28 (42) Q Consensus 17 lpmmdcnvfldp 28 (42) -|||-.|+|++. T Consensus 115 PPvmPvN~Fl~t 126 (160) T pfam02964 115 PPVMPVNVFLDT 126 (160) T ss_pred CCCCCCHHCCHH T ss_conf 987760212210 No 4 >COG0080 RplK Ribosomal protein L11 [Translation, ribosomal structure and biogenesis] Probab=13.55 E-value=95 Score=15.39 Aligned_cols=14 Identities=57% Similarity=1.013 Sum_probs=9.8 Q ss_pred EEEEECCCHHHHHH Q ss_conf 07998497443111 Q 537021.9.peg.3 5 SFIIITPPATVLLP 18 (42) Q Consensus 5 sfiiitppatvllp 18 (42) +|++-|||++.||- T Consensus 66 tf~vktPPas~Llk 79 (141) T COG0080 66 TFIVKTPPASALLK 79 (141) T ss_pred EEEECCCCHHHHHH T ss_conf 99977998799999 No 5 >cd04248 AAK_AK-Ectoine AAK_AK-Ectoine: Amino Acid Kinase Superfamily (AAK), AK-Ectoine; this CD includes the N-terminal catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and other various halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinase and L-aspartate-semialdehyde dehydrogenase. The M. alcaliphilum and the V. cholerae aspartokinases are encoded on the ectABCask operon. Probab=10.28 E-value=62 Score=16.28 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=15.0 Q ss_pred HHHHHCCCEEECHHHHHHHHHHH Q ss_conf 11101363343311013444445 Q 537021.9.peg.3 16 LLPMMDCNVFLDPIWIKNIFVPL 38 (42) Q Consensus 16 llpmmdcnvfldpiwiknifvpl 38 (42) +.|.++.|. |++|||.|-|- T Consensus 278 i~P~~~~~I---Pi~IkNt~~P~ 297 (304) T cd04248 278 AKGLRQAGI---PLRVKNTFEPD 297 (304) T ss_pred HHHHHHCCC---CEEEECCCCCC T ss_conf 999998699---88980689989 No 6 >pfam10845 DUF2576 Protein of unknown function (DUF2576). The function of this viral family of proteins is unknown. Probab=10.25 E-value=64 Score=16.21 Aligned_cols=10 Identities=50% Similarity=0.906 Sum_probs=7.7 Q ss_pred HHCCCEEECH Q ss_conf 0136334331 Q 537021.9.peg.3 19 MMDCNVFLDP 28 (42) Q Consensus 19 mmdcnvfldp 28 (42) -.|||-||+. T Consensus 37 gFDCNrfL~s 46 (48) T pfam10845 37 GFDCNRFLRS 46 (48) T ss_pred CCCHHHHHCC T ss_conf 7646665016 No 7 >KOG3257 consensus Probab=9.57 E-value=1.5e+02 Score=14.44 Aligned_cols=14 Identities=57% Similarity=0.928 Sum_probs=11.6 Q ss_pred EEEEECCCHHHHHH Q ss_conf 07998497443111 Q 537021.9.peg.3 5 SFIIITPPATVLLP 18 (42) Q Consensus 5 sfiiitppatvllp 18 (42) .|+|-|||++.||- T Consensus 81 tf~iktPpts~lL~ 94 (168) T KOG3257 81 TFIIKTPPTSWLLK 94 (168) T ss_pred EEEECCCCHHHHHH T ss_conf 89964897489999 No 8 >TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY; InterPro: IPR014154 This entry represents pleiotropic repressors in Bacillus subtilis, CodY, and other Firmicutes (low-GC Gram-positive bacteria) that respond to intracellular levels of GTP and branched chain amino acids. All have a C-terminal helix-turn-helix DNA-binding region.. Probab=9.42 E-value=1.4e+02 Score=14.60 Aligned_cols=14 Identities=36% Similarity=0.888 Sum_probs=11.0 Q ss_pred HHHHHHHHCCCEEE Q ss_conf 44311101363343 Q 537021.9.peg.3 13 ATVLLPMMDCNVFL 26 (42) Q Consensus 13 atvllpmmdcnvfl 26 (42) |.+|--.||||+|+ T Consensus 30 a~~L~Dvi~~N~yv 43 (255) T TIGR02787 30 AELLADVIDCNAYV 43 (255) T ss_pred HHHHHHHHHCCEEE T ss_conf 99987784588568 No 9 >TIGR01605 PYST-D Plasmodium yoelii subtelomeric family PYST-D; InterPro: IPR006492 The proteins in this set represent a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. These genes are generally very short (ca. 50 residues). There are no obvious homologs to these genes in any other organism. . Probab=8.92 E-value=1.2e+02 Score=14.90 Aligned_cols=16 Identities=38% Similarity=0.636 Sum_probs=9.5 Q ss_pred CEEECHHHHHHHHHHH Q ss_conf 3343311013444445 Q 537021.9.peg.3 23 NVFLDPIWIKNIFVPL 38 (42) Q Consensus 23 nvfldpiwiknifvpl 38 (42) -||+|||.=-.+=+-| T Consensus 5 ~vf~ePIFGLGlSi~L 20 (55) T TIGR01605 5 IVFLEPIFGLGLSITL 20 (55) T ss_pred EEEECCCCCCHHHHHH T ss_conf 8874583300488999 No 10 >cd04244 AAK_AK-LysC-like AAK_AK-LysC-like: Amino Acid Kinase Superfamily (AAK), AK-LysC-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive AK isoenzyme found in higher plants. The lysine-sensitive AK isoenzyme is a monofunctional protein. It is involved in the overall regulation of the aspartate pathway and can be synergistically inhibited by S-adenosylmethionine. Also included in this CD is an uncharacterized LysC-like AK found in Euryarchaeota and some bacteria. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Probab=8.14 E-value=83 Score=15.66 Aligned_cols=19 Identities=37% Similarity=0.782 Sum_probs=0.0 Q ss_pred HHHHHCCCEEECHHHHHHHHHH Q ss_conf 1110136334331101344444 Q 537021.9.peg.3 16 LLPMMDCNVFLDPIWIKNIFVP 37 (42) Q Consensus 16 llpmmdcnvfldpiwiknifvp 37 (42) +.|.|..|+ ||+|||.|-| T Consensus 272 i~p~~~~~I---Pi~Iknt~~p 290 (298) T cd04244 272 VEPAMEKGI---PVRVKNTFNP 290 (298) T ss_pred HHHHHHCCC---CEEEECCCCC T ss_conf 999998799---6899389998 Done!