Query         537021.9.peg.42_1
Match_columns 44
No_of_seqs    106 out of 118
Neff          2.6 
Searched_HMMs 39220
Date          Mon May 23 06:54:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_42.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK00831 rpmJ 50S ribosomal pr  99.9 2.5E-23 6.5E-28  138.2   4.2   41    4-44      1-41  (41)
  2 pfam00444 Ribosomal_L36 Riboso  99.8 3.5E-19 8.9E-24  117.4   3.7   38    4-44      1-38  (38)
  3 COG0257 RpmJ Ribosomal protein  99.7 4.7E-19 1.2E-23  116.8   2.2   38    4-44      1-38  (38)
  4 KOG4122 consensus               99.7 8.7E-19 2.2E-23  115.4   3.5   38    4-44      1-38  (38)
  5 PRK00465 rpmJ 50S ribosomal pr  99.7 1.4E-17 3.6E-22  109.3   4.0   37    4-44      1-37  (37)
  6 TIGR01022 rpmJ_bact ribosomal   98.7 1.1E-08 2.9E-13   64.7   2.9   37    4-44      1-37  (37)
  7 CHL00029 rpl36 ribosomal prote  97.5   1E-05 2.6E-10   49.8  -1.7   26    4-32      1-26  (26)
  8 TIGR00059 L17 ribosomal protei  17.9      41   0.001   16.7   0.3   12   33-44     89-100 (125)
  9 pfam10984 DUF2794 Protein of u  16.8      70  0.0018   15.5   1.3   17   27-44     47-63  (85)
 10 pfam11267 DUF3067 Protein of u  16.1   1E+02  0.0026   14.6   2.0   13   19-31     17-29  (99)

No 1  
>PRK00831 rpmJ 50S ribosomal protein L36; Validated
Probab=99.88  E-value=2.5e-23  Score=138.21  Aligned_cols=41  Identities=61%  Similarity=0.929  Sum_probs=40.7

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||+||||+||.||+||++|||+||+|||||+|||||||||
T Consensus         1 MKV~sSlKs~k~r~~~c~vVrRrGr~yVInK~nPr~KaRQG   41 (41)
T PRK00831          1 MKVRNSLKSLKNRHRDCQIVRRKGRVYVINKKNPRFKARQG   41 (41)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEECCEEEEEECCCCCHHHCCC
T ss_conf             94688899998637786599862539999679942342069


No 2  
>pfam00444 Ribosomal_L36 Ribosomal protein L36.
Probab=99.76  E-value=3.5e-19  Score=117.43  Aligned_cols=38  Identities=47%  Similarity=0.730  Sum_probs=35.7

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||++|||.   +|+||++|||+|++||||++||+||||||
T Consensus         1 MKVr~SvKk---~c~~C~~vrR~gr~~Vick~nprhKqRQg   38 (38)
T pfam00444         1 MKVRSSVKK---RCKDCKIVRRKGRVYVICKTNPRHKQRQG   38 (38)
T ss_pred             CCHHHHHHH---HCCCCEEEEECCEEEEEECCCCCHHHCCC
T ss_conf             950256672---08887599965789999389973231069


No 3  
>COG0257 RpmJ Ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=99.74  E-value=4.7e-19  Score=116.80  Aligned_cols=38  Identities=47%  Similarity=0.712  Sum_probs=35.6

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||++|+|+   +|+||++|||+|++||||++||+||||||
T Consensus         1 MKV~~SvK~---~c~~CkivrRkGrv~VIck~~prhKqrQg   38 (38)
T COG0257           1 MKVRASVKK---RCRDCKIVRRKGRVYVICKKNPKHKQRQG   38 (38)
T ss_pred             CCCCCCCCC---CCCCCEEEEECCEEEEEECCCCCHHHHCC
T ss_conf             931134544---36776589755879999169963332169


No 4  
>KOG4122 consensus
Probab=99.74  E-value=8.7e-19  Score=115.44  Aligned_cols=38  Identities=34%  Similarity=0.531  Sum_probs=35.7

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||++|||+.|   +|||+|+|+||+||||++|||||||||
T Consensus         1 fKvk~svkk~C---~~Cy~VrRrgR~yViC~~~prHKqrqg   38 (38)
T KOG4122           1 FKVKASVKKRC---KDCYLVRRRGRVYVICKTHPRHKQRQG   38 (38)
T ss_pred             CCHHHHHHHHH---HHCEEEEECCCEEEECCCCCCHHHHCC
T ss_conf             95157899864---112689872619999279941343069


No 5  
>PRK00465 rpmJ 50S ribosomal protein L36; Reviewed
Probab=99.69  E-value=1.4e-17  Score=109.33  Aligned_cols=37  Identities=43%  Similarity=0.691  Sum_probs=35.5

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||++|+|++|+   +|++|||+|++|||| +||+||||||
T Consensus         1 MKVr~SVKk~C~---~CkvirR~g~v~ViC-~npkHKQRQG   37 (37)
T PRK00465          1 MKVRASVKKICE---KCKVIKRKGVVRVIC-ANPKHKQRQG   37 (37)
T ss_pred             CCCHHHHHHHHH---CCEEEEECCEEEEEE-CCCCCHHCCC
T ss_conf             950367898741---177998478799996-8986200079


No 6  
>TIGR01022 rpmJ_bact ribosomal protein L36; InterPro: IPR000473   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 L36 is the smallest protein from the large subunit of the prokaryotic ribosome. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities  can be grouped into: bacterial L36; algal and plant chloroplast L36; Cyanelle L36. L36 is a small basic and cysteine-rich protein of 37 amino-acid residues. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=98.67  E-value=1.1e-08  Score=64.67  Aligned_cols=37  Identities=43%  Similarity=0.728  Sum_probs=35.0

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEEECCCCCHHHCCC
Q ss_conf             97458899885016787099988889999877975232079
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVick~nPrhK~RQG   44 (44)
                      |||++|+|.+|+   +|++++|.+.++|||. +|+|+|+||
T Consensus         1 mkv~~svk~~C~---~Ck~i~r~~~~~v~C~-~~~h~q~~~   37 (37)
T TIGR01022         1 MKVRASVKKICE---KCKIIKRKGVVRVICK-NPKHKQRQG   37 (37)
T ss_pred             CCCCHHHHHHHH---CCCEEECCCEEEEEEC-CCCCCCCCC
T ss_conf             942135665553---2624302556888753-742222369


No 7  
>CHL00029 rpl36 ribosomal protein L36
Probab=97.47  E-value=1e-05  Score=49.81  Aligned_cols=26  Identities=27%  Similarity=0.507  Sum_probs=24.6

Q ss_pred             EEEHHHHHHHHHCCCCCEEEEECCEEEEE
Q ss_conf             97458899885016787099988889999
Q 537021.9.peg.4    4 VKVRNSLRVLKLRHRGNKVVRRKNVIRIV   32 (44)
Q Consensus         4 MKvr~Slk~lk~r~~~c~~VrRkGrvyVi   32 (44)
                      |||++|++++|+   +|+++||+|+++||
T Consensus         1 mKvRaSvrkIC~---~crlirr~~~l~vi   26 (26)
T CHL00029          1 MKIRASVRKICE---KCRLIRRRGRIIVI   26 (26)
T ss_pred             CCHHHHHHHHHH---HHHHHHHCCCEEEC
T ss_conf             943789999999---97999974857769


No 8  
>TIGR00059 L17 ribosomal protein L17; InterPro: IPR000456   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 L17 is one of the proteins from the large ribosomal subunit. Bacterial L17 is a protein of 120 to 130 amino-acid residues while yeast YmL8 is twice as large (238 residues). The N-terminal half of YmL8 is colinear with the sequence of L17 from Escherichia coli.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=17.90  E-value=41  Score=16.66  Aligned_cols=12  Identities=33%  Similarity=0.891  Sum_probs=9.3

Q ss_pred             ECCCCCHHHCCC
Q ss_conf             877975232079
Q 537021.9.peg.4   33 NKLNPRFKVRQG   44 (44)
Q Consensus        33 ck~nPrhK~RQG   44 (44)
                      .+--|||.+|+|
T Consensus        89 ~~iaPry~~R~G  100 (125)
T TIGR00059        89 SEIAPRYAQRNG  100 (125)
T ss_pred             HHHCCCCCCCCC
T ss_conf             530553234877


No 9  
>pfam10984 DUF2794 Protein of unknown function (DUF2794). This is a bacterial family of proteins with unknown function.
Probab=16.78  E-value=70  Score=15.46  Aligned_cols=17  Identities=24%  Similarity=0.456  Sum_probs=13.1

Q ss_pred             CEEEEEECCCCCHHHCCC
Q ss_conf             889999877975232079
Q 537021.9.peg.4   27 NVIRIVNKLNPRFKVRQG   44 (44)
Q Consensus        27 GrvyVick~nPrhK~RQG   44 (44)
                      .-+|-|.| ||+.+.+||
T Consensus        47 ~Pl~~I~K-~~k~~~~~~   63 (85)
T pfam10984        47 RPLYRIEK-RPALARKQG   63 (85)
T ss_pred             CCCEEEEE-CCCCCCCCC
T ss_conf             84189996-788877786


No 10 
>pfam11267 DUF3067 Protein of unknown function (DUF3067). This family of proteins has no known function.
Probab=16.07  E-value=1e+02  Score=14.65  Aligned_cols=13  Identities=23%  Similarity=0.378  Sum_probs=0.0

Q ss_pred             CCEEEEECCEEEE
Q ss_conf             8709998888999
Q 537021.9.peg.4   19 GNKVVRRKNVIRI   31 (44)
Q Consensus        19 ~c~~VrRkGrvyV   31 (44)
                      |-++++++|++|.
T Consensus        17 Dvql~~~~~~iyl   29 (99)
T pfam11267        17 DVQLRRRRGRIYL   29 (99)
T ss_pred             EEEEEEECCEEEE
T ss_conf             5689898799887


Done!