Query 537021.9.peg.563_1
Match_columns 37
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Tue May 24 20:16:14 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_563.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4147 consensus 20.0 30 0.00077 18.0 0.1 10 18-27 106-115 (127)
2 KOG4154 consensus 11.4 93 0.0024 15.8 0.7 16 21-36 63-78 (178)
3 TIGR00512 aIF-2BI_fam translat 11.2 80 0.002 16.1 0.3 22 9-31 233-255 (306)
4 PRK01678 rpmE2 50S ribosomal p 10.9 1.2E+02 0.0031 15.2 1.1 18 1-18 44-61 (86)
5 KOG0978 consensus 10.0 47 0.0012 17.2 -1.2 12 23-35 648-659 (698)
6 COG1095 RPB7 DNA-directed RNA 9.4 1.2E+02 0.003 15.3 0.6 19 6-24 90-108 (183)
7 TIGR01802 CM_pl-yst chorismate 8.6 1.1E+02 0.0027 15.5 0.1 15 7-21 71-86 (273)
8 TIGR00105 L31 ribosomal protei 8.2 1.9E+02 0.0048 14.3 1.3 18 2-19 35-52 (77)
9 KOG4704 consensus 8.0 1.5E+02 0.0038 14.8 0.7 21 9-29 241-265 (431)
10 pfam01197 Ribosomal_L31 Riboso 7.5 2.3E+02 0.0058 14.0 1.5 17 2-18 34-50 (69)
No 1
>KOG4147 consensus
Probab=20.04 E-value=30 Score=18.04 Aligned_cols=10 Identities=60% Similarity=1.208 Sum_probs=8.2
Q ss_pred HHHHHHHHCC
Q ss_conf 0344431112
Q 537021.9.peg.5 18 APISFFCKEA 27 (37)
Q Consensus 18 apisffckea 27 (37)
..|||||+|+
T Consensus 106 TEis~F~~ed 115 (127)
T KOG4147 106 TEISFFCEED 115 (127)
T ss_pred HHHHHHHHHH
T ss_conf 1344643999
No 2
>KOG4154 consensus
Probab=11.38 E-value=93 Score=15.77 Aligned_cols=16 Identities=38% Similarity=0.820 Sum_probs=13.4
Q ss_pred HHHHHCCCCCCEEEEE
Q ss_conf 4431112233114641
Q 537021.9.peg.5 21 SFFCKEARWKDAVLCF 36 (37)
Q Consensus 21 sffckearwkdavlcf 36 (37)
--|||+++-|..-+|+
T Consensus 63 ~kfck~~k~ke~r~cy 78 (178)
T KOG4154 63 IKFCKAAKGKEHRFCY 78 (178)
T ss_pred HHHHHHHCCCCCEEEE
T ss_conf 9999986187530453
No 3
>TIGR00512 aIF-2BI_fam translation initiation factor, putative, aIF-2BI family; InterPro: IPR005251 This family contains proteins designated as translation initiation factor 2B subunit 1 (alpha) and 5-methylthioribose-1-phosphate isomerase (MTNA, 5.3.1.23 from EC, ). The delineation of this family is based in part on a discussion and neighbour-joining phylogenetic study , , of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. The archaeal proteins are related to the common ancestor of eIF-2B alpha, beta, and delta rather then specifically to any one of them, and that designation of particular archaeal members as corresponding to eIF-2B alpha or eIF-2B delta is imprecise. It has been suggested that designating the archaeal proteins as translation initiation factors remains unproven. 5-methylthioribose-1-phosphate isomerase (MTNA) participates in the methionine salvage pathway catalysing the isomerisation of 5-methylthioribose-1-phosphate to 5-methylthio ribulose-1-phosphate . The methionine salvage pathway leads to the synthesis of methionine from methylthioadenosine, the end product of the spermidine and spermine anabolism in many species..
Probab=11.20 E-value=80 Score=16.09 Aligned_cols=22 Identities=45% Similarity=0.763 Sum_probs=15.0
Q ss_pred HHCCEEEEEHHHHHHHHCCCC-CC
Q ss_conf 017323240034443111223-31
Q 537021.9.peg.5 9 DEFPFFVGVAPISFFCKEARW-KD 31 (37)
Q Consensus 9 defpffvgvapisffckearw-kd 31 (37)
-.-||||- ||.|-|=-+..- +|
T Consensus 233 h~IPFyVA-APlSTFD~~~~~G~D 255 (306)
T TIGR00512 233 HNIPFYVA-APLSTFDTEVSAGKD 255 (306)
T ss_pred CCCCCEEE-CCCCCCCHHCCCCCC
T ss_conf 69883340-876300021068982
No 4
>PRK01678 rpmE2 50S ribosomal protein L31 type B; Reviewed
Probab=10.87 E-value=1.2e+02 Score=15.24 Aligned_cols=18 Identities=39% Similarity=0.737 Sum_probs=13.8
Q ss_pred CEEEEECHHHCCEEEEEH
Q ss_conf 889961020173232400
Q 537021.9.peg.5 1 LVFVDISCDEFPFFVGVA 18 (37)
Q Consensus 1 lvfvdiscdefpffvgva 18 (37)
++-+||+-.--|||.|-.
T Consensus 44 ~~~vdi~S~~HPFyTG~q 61 (86)
T PRK01678 44 LVKVEVSSASHPFYTGKQ 61 (86)
T ss_pred EEEEEECCCCCCCEECCE
T ss_conf 698610688885481876
No 5
>KOG0978 consensus
Probab=9.96 E-value=47 Score=17.16 Aligned_cols=12 Identities=58% Similarity=1.329 Sum_probs=9.1
Q ss_pred HHHCCCCCCEEEE
Q ss_conf 3111223311464
Q 537021.9.peg.5 23 FCKEARWKDAVLC 35 (37)
Q Consensus 23 fckearwkdavlc 35 (37)
-|+ .||||+|+-
T Consensus 648 ~Cn-~R~Kd~vI~ 659 (698)
T KOG0978 648 VCN-TRWKDAVIT 659 (698)
T ss_pred CCC-CCHHHHHHH
T ss_conf 766-755668998
No 6
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=9.38 E-value=1.2e+02 Score=15.30 Aligned_cols=19 Identities=26% Similarity=0.488 Sum_probs=15.7
Q ss_pred ECHHHCCEEEEEHHHHHHH
Q ss_conf 1020173232400344431
Q 537021.9.peg.5 6 ISCDEFPFFVGVAPISFFC 24 (37)
Q Consensus 6 iscdefpffvgvapisffc 24 (37)
.+|++|-+||++.|..-|-
T Consensus 90 v~~~~~G~fV~igp~dglv 108 (183)
T COG1095 90 VEVVEFGAFVRIGPLDGLV 108 (183)
T ss_pred EEEEECCEEEEECCCCCCC
T ss_conf 9996144699963622211
No 7
>TIGR01802 CM_pl-yst chorismate mutase; InterPro: IPR008238 Chorismate mutase (CM; 5.4.99.5 from EC) catalyses the reaction at the branch point of the biosynthetic pathway leading to the three aromatic amino acids, phenylalanine, tryptophan and tyrosine (chorismic acid is the last common intermediate, and CM leads to the L-phenylalanine/L-tyrosine branch). It is part of the shikimate pathway, which is present only in bacteria, fungi and plants. Members of this family, which are restricted to plants and fungi, contain a chorismate mutase domain of the AroQ class (eukaryotic type) and have an all-helical structure. The monomer consists of a catalytic and a regulatory domain covalently linked by a loop, which functions as a molecular hinge. They are monofunctional, allosteric enzymes and are subject to allosteric inhibition by tyrosine and activation by tryptophan. The three types of CM are AroQ class, prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, eukaryotic type; and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved . For additional information please see , , , , , , , .; GO: 0004106 chorismate mutase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=8.57 E-value=1.1e+02 Score=15.53 Aligned_cols=15 Identities=47% Similarity=0.786 Sum_probs=9.4
Q ss_pred CHHHCCEEE-EEHHHH
Q ss_conf 020173232-400344
Q 537021.9.peg.5 7 SCDEFPFFV-GVAPIS 21 (37)
Q Consensus 7 scdefpffv-gvapis 21 (37)
|=||+|||- .--|-+
T Consensus 71 SPDE~PFfPlD~Lp~P 86 (273)
T TIGR01802 71 SPDEYPFFPLDKLPKP 86 (273)
T ss_pred CCCCCCCCCCCCCCCC
T ss_conf 6788888871114543
No 8
>TIGR00105 L31 ribosomal protein L31; InterPro: IPR002150 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 L31 is one of the proteins from the large ribosomal subunit. L31 is a protein of 66 to 97 amino-acid residues which has only been found so far in bacteria and in some plant and algal chloroplasts.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=8.19 E-value=1.9e+02 Score=14.33 Aligned_cols=18 Identities=28% Similarity=0.615 Sum_probs=14.4
Q ss_pred EEEEECHHHCCEEEEEHH
Q ss_conf 899610201732324003
Q 537021.9.peg.5 2 VFVDISCDEFPFFVGVAP 19 (37)
Q Consensus 2 vfvdiscdefpffvgvap 19 (37)
+-|||+-.--|||.|-.-
T Consensus 35 ~~~dics~CHPFYtG~~~ 52 (77)
T TIGR00105 35 INIDICSKCHPFYTGKQK 52 (77)
T ss_pred EEEEECCCCCCCEECCEE
T ss_conf 468864898894204403
No 9
>KOG4704 consensus
Probab=7.96 E-value=1.5e+02 Score=14.79 Aligned_cols=21 Identities=48% Similarity=0.653 Sum_probs=13.9
Q ss_pred HHCCEE-EEEHHHHHH---HHCCCC
Q ss_conf 017323-240034443---111223
Q 537021.9.peg.5 9 DEFPFF-VGVAPISFF---CKEARW 29 (37)
Q Consensus 9 defpff-vgvapisff---ckearw 29 (37)
|+-||| ||+|-|||. -+|..|
T Consensus 241 d~kPff~V~~adi~~les~~~e~gy 265 (431)
T KOG4704 241 DLKPFFSVGLADISTLESNDLEEGY 265 (431)
T ss_pred CCCCEEEEECCCCCCHHHCCCCCCE
T ss_conf 6775279872446204430334636
No 10
>pfam01197 Ribosomal_L31 Ribosomal protein L31.
Probab=7.54 E-value=2.3e+02 Score=13.95 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=13.7
Q ss_pred EEEEECHHHCCEEEEEH
Q ss_conf 89961020173232400
Q 537021.9.peg.5 2 VFVDISCDEFPFFVGVA 18 (37)
Q Consensus 2 vfvdiscdefpffvgva 18 (37)
+.+||+-.--|||.|-.
T Consensus 34 i~vdi~s~cHPfyTG~~ 50 (69)
T pfam01197 34 IKIDVCSACHPFYTGKQ 50 (69)
T ss_pred EEEEECCCCCCEECCCE
T ss_conf 99986489888481987
Done!