Query         537021.9.peg.577_1
Match_columns 44
No_of_seqs    1 out of 3
Neff          1.0 
Searched_HMMs 39220
Date          Tue May 24 21:45:46 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i peg_577.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam06155 DUF971 Protein of un  51.3     3.7 9.4E-05   21.9  -0.3   24    3-27     62-86  (88)
  2 TIGR01008 rpsC_E_A ribosomal p  30.4      17 0.00044   18.9   0.4   18   27-44    120-137 (204)
  3 KOG3877 consensus               28.9      21 0.00054   18.5   0.6   24    7-31    369-392 (393)
  4 TIGR01937 nqrB NADH:ubiquinone  27.8      14 0.00035   19.3  -0.4   13   18-30    380-392 (508)
  5 pfam06489 Orthopox_A49R Orthop   9.3 1.1E+02  0.0029   15.3   0.5   13   14-26     16-28  (112)
  6 PRK04439 S-adenosylmethionine    7.9 1.1E+02  0.0029   15.3   0.0   18   26-43    298-315 (400)
  7 pfam01941 AdoMet_Synthase S-ad   7.4 1.3E+02  0.0032   15.1   0.1   18   26-43    297-314 (396)
  8 pfam02281 Transposase_Tn5 Tran   7.2      91  0.0023   15.7  -0.7   13   19-31     73-85  (109)
  9 pfam07105 DUF1367 Protein of u   5.1 1.5E+02  0.0038   14.8  -0.6   16   25-40    124-150 (196)
 10 pfam10994 DUF2817 Protein of u   4.8 1.8E+02  0.0047   14.3  -0.3   17    9-25    206-222 (341)

No 1  
>pfam06155 DUF971 Protein of unknown function (DUF971). This family consists of several short bacterial proteins and one sequence from Oryza sativa. The function of this family is unknown.
Probab=51.35  E-value=3.7  Score=21.91  Aligned_cols=24  Identities=42%  Similarity=0.721  Sum_probs=17.7

Q ss_pred             HHHHCCCCCCEEHHHHH-HHHHCCEE
Q ss_conf             01202265510034564-20100011
Q 537021.9.peg.5    3 EVIGSYGYNTKIVSDLH-TGIASWHT   27 (44)
Q Consensus         3 evigsygyntkivsdlh-tgiaswht   27 (44)
                      |.+|.|+++-.- ||-| |||-+|--
T Consensus        62 ~~VG~YAl~i~f-sDGH~tGIy~~~~   86 (88)
T pfam06155        62 EPVGNYAVRIVF-SDGHDSGIYSWDY   86 (88)
T ss_pred             EECCCCEEEEEE-CCCCCCCCCCHHH
T ss_conf             871885068787-7998773326799


No 2  
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703   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 S3 is one of the proteins from the small ribosomal subunit. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=30.39  E-value=17  Score=18.91  Aligned_cols=18  Identities=50%  Similarity=0.750  Sum_probs=15.7

Q ss_pred             EEECCCCCCCEEEEEEEC
Q ss_conf             110376447534311329
Q 537021.9.peg.5   27 TIEAGAEKEPISISGKIT   44 (44)
Q Consensus        27 tieagaekepisisgkit   44 (44)
                      -.+|||.---|.||||+|
T Consensus       120 iM~aGAkGvEv~iSGKL~  137 (204)
T TIGR01008       120 IMEAGAKGVEVTISGKLT  137 (204)
T ss_pred             HHHCCCCEEEEEEECCHH
T ss_conf             982569527999827417


No 3  
>KOG3877 consensus
Probab=28.85  E-value=21  Score=18.54  Aligned_cols=24  Identities=38%  Similarity=0.634  Sum_probs=18.7

Q ss_pred             CCCCCCEEHHHHHHHHHCCEEEECC
Q ss_conf             2265510034564201000111037
Q 537021.9.peg.5    7 SYGYNTKIVSDLHTGIASWHTIEAG   31 (44)
Q Consensus         7 sygyntkivsdlhtgiaswhtieag   31 (44)
                      ++|||++ +.|-..+...|||+..+
T Consensus       369 ~pGYna~-~GD~~~~lk~~~~~~~~  392 (393)
T KOG3877         369 GPGYNAK-NGDHQAGLKAWHTGHHL  392 (393)
T ss_pred             CCCCCCC-CCHHHHHHHHHHHCCCC
T ss_conf             8975555-54067766656404668


No 4  
>TIGR01937 nqrB NADH:ubiquinone oxidoreductase, Na(+)-translocating, B subunit; InterPro: IPR010966   This entry represents the NqrB subunit of the six-protein (NqrA to NqrF), membrane-associated Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria . The Nqr complex catalyses the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of sodium ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. Both the NqrB and NqrC subunits contain a FMN cofactor that is covalently attached by a phosphate group to a threonine residue .; GO: 0010181 FMN binding, 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0006118 electron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=27.77  E-value=14  Score=19.35  Aligned_cols=13  Identities=46%  Similarity=0.917  Sum_probs=10.1

Q ss_pred             HHHHHHCCEEEEC
Q ss_conf             6420100011103
Q 537021.9.peg.5   18 LHTGIASWHTIEA   30 (44)
Q Consensus        18 lhtgiaswhtiea   30 (44)
                      +-||||||.++-+
T Consensus       380 ~~t~IASWri~a~  392 (508)
T TIGR01937       380 ILTGIASWRIMAG  392 (508)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9985888999999


No 5  
>pfam06489 Orthopox_A49R Orthopoxvirus A49R protein. This family consists of several Orthopoxvirus A49R proteins. The function of this family is unknown.
Probab=9.28  E-value=1.1e+02  Score=15.27  Aligned_cols=13  Identities=54%  Similarity=0.654  Sum_probs=10.6

Q ss_pred             EHHHHHHHHHCCE
Q ss_conf             0345642010001
Q 537021.9.peg.5   14 IVSDLHTGIASWH   26 (44)
Q Consensus        14 ivsdlhtgiaswh   26 (44)
                      .|||.||..||-.
T Consensus        16 yvsdmhtelasis   28 (112)
T pfam06489        16 YVSDMHTELASIS   28 (112)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8888888999899


No 6  
>PRK04439 S-adenosylmethionine synthetase; Provisional
Probab=7.88  E-value=1.1e+02  Score=15.27  Aligned_cols=18  Identities=44%  Similarity=0.687  Sum_probs=15.8

Q ss_pred             EEEECCCCCCCEEEEEEE
Q ss_conf             111037644753431132
Q 537021.9.peg.5   26 HTIEAGAEKEPISISGKI   43 (44)
Q Consensus        26 htieagaekepisisgki   43 (44)
                      .+.||-|-|.|++--|||
T Consensus       298 msmEAaAGKNPv~HVGKI  315 (400)
T PRK04439        298 MSMEAAAGKNPVNHVGKI  315 (400)
T ss_pred             CCCCCCCCCCCCCCCHHH
T ss_conf             655223789972300389


No 7  
>pfam01941 AdoMet_Synthase S-adenosylmethionine synthetase (AdoMet synthetase). This family consists of several archaebacterial S-adenosylmethionine synthetase C(AdoMet synthetase or MAT) (EC 2.5.1.6). S-Adenosylmethionine (AdoMet) occupies a central role in the metabolism of all cells. The biological roles of AdoMet include acting as the primary methyl group donor, as a precursor to the polyamines, and as a progenitor of a 5'-deoxyadenosyl radical. S-Adenosylmethionine synthetase catalyses the only known route of AdoMet biosynthesis. The synthetic process occurs in a unique reaction in which the complete triphosphate chain is displaced from ATP and a sulfonium ion formed. MATs from various organisms contain ~400-amino acid polypeptide chains.
Probab=7.39  E-value=1.3e+02  Score=15.07  Aligned_cols=18  Identities=44%  Similarity=0.687  Sum_probs=15.7

Q ss_pred             EEEECCCCCCCEEEEEEE
Q ss_conf             111037644753431132
Q 537021.9.peg.5   26 HTIEAGAEKEPISISGKI   43 (44)
Q Consensus        26 htieagaekepisisgki   43 (44)
                      .+.||-|-|.|++--|||
T Consensus       297 msmEAaAGKNPv~HVGKI  314 (396)
T pfam01941       297 MSMEAAAGKNPVNHVGKI  314 (396)
T ss_pred             CCCCCCCCCCCCCCCHHH
T ss_conf             654223689972410388


No 8  
>pfam02281 Transposase_Tn5 Transposase Tn5 dimerization domain. Transposons are mobile DNA sequences capable of replication and insertion into the chromosome. Typically transposons code for the transposase enzyme, which catalyses insertion, found between terminal inverted repeats. Tn5 has a unique method of self- regulation in which a truncated version of the transposase enzyme acts as an inhibitor. The catalytic domain of the Tn5 transposon is found in pfam01609. This domain mediates dimerization in the known structure.
Probab=7.19  E-value=91  Score=15.71  Aligned_cols=13  Identities=54%  Similarity=0.943  Sum_probs=9.4

Q ss_pred             HHHHHCCEEEECC
Q ss_conf             4201000111037
Q 537021.9.peg.5   19 HTGIASWHTIEAG   31 (44)
Q Consensus        19 htgiaswhtieag   31 (44)
                      .||+|||.++=.|
T Consensus        73 rTG~asw~~lWeG   85 (109)
T pfam02281        73 RTGIASWGALWEG   85 (109)
T ss_pred             CCCCCCHHHHHHH
T ss_conf             6672319999988


No 9  
>pfam07105 DUF1367 Protein of unknown function (DUF1367). This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=5.06  E-value=1.5e+02  Score=14.76  Aligned_cols=16  Identities=69%  Similarity=1.041  Sum_probs=0.0

Q ss_pred             CEEEECC-----------CCCCCEEEE
Q ss_conf             0111037-----------644753431
Q 537021.9.peg.5   25 WHTIEAG-----------AEKEPISIS   40 (44)
Q Consensus        25 whtieag-----------aekepisis   40 (44)
                      |-||+||           .-|||-|||
T Consensus       124 wvti~AGfYd~~~~pdG~~rke~kSIS  150 (196)
T pfam07105       124 WVTVEAGHYDVIQLPDGSLRKEPRSIS  150 (196)
T ss_pred             HHHHHCCCCEEEECCCCCEEEEEEECC
T ss_conf             999972441457779997564231021


No 10 
>pfam10994 DUF2817 Protein of unknown function (DUF2817). This family of proteins has no known function.
Probab=4.82  E-value=1.8e+02  Score=14.33  Aligned_cols=17  Identities=35%  Similarity=0.585  Sum_probs=0.0

Q ss_pred             CCCCEEHHHHHHHHHCC
Q ss_conf             65510034564201000
Q 537021.9.peg.5    9 GYNTKIVSDLHTGIASW   25 (44)
Q Consensus         9 gyntkivsdlhtgiasw   25 (44)
                      ++..-+.-|+|||+..|
T Consensus       206 ~~~~v~~ID~HTGlGp~  222 (341)
T pfam10994       206 GAERVAWIDLHTGLGPY  222 (341)
T ss_pred             CCCEEEEEEECCCCCCC
T ss_conf             57679999967788989


Done!