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_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 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_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_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