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!