Query gi|254780481|ref|YP_003064894.1| 50S ribosomal protein L34 [Candidatus Liberibacter asiaticus str. psy62] Match_columns 44 No_of_seqs 108 out of 336 Neff 3.0 Searched_HMMs 39220 Date Sun May 29 18:19:00 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i 254780481.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PRK00399 rpmH 50S ribosomal pr 99.9 9.7E-26 2.5E-30 138.8 3.2 44 1-44 1-44 (44) 2 COG0230 RpmH Ribosomal protein 99.9 1.1E-24 2.9E-29 133.9 2.8 44 1-44 1-44 (44) 3 pfam00468 Ribosomal_L34 Riboso 99.9 3.2E-24 8.3E-29 131.8 3.2 44 1-44 1-44 (44) 4 TIGR01030 rpmH_bact ribosomal 99.8 2.4E-21 6.1E-26 118.6 2.4 44 1-44 1-44 (44) 5 KOG4612 consensus 99.7 1.5E-18 3.8E-23 105.7 2.1 42 3-44 64-105 (105) 6 CHL00115 rpl34 ribosomal prote 99.5 2.9E-15 7.3E-20 90.6 2.1 43 2-44 3-45 (46) 7 cd04934 ACT_AK-Hom3_1 CT domai 10.9 90 0.0023 14.8 0.5 12 12-23 11-22 (73) 8 TIGR01505 tartro_sem_red 2-hyd 10.3 1E+02 0.0027 14.5 0.6 17 1-26 222-238 (291) 9 KOG4076 consensus 6.8 2.4E+02 0.0061 12.8 1.2 26 17-42 38-63 (121) 10 cd04912 ACT_AKiii-LysC-EC-like 5.1 2.3E+02 0.0059 12.9 0.4 7 16-22 15-21 (75) No 1 >PRK00399 rpmH 50S ribosomal protein L34; Reviewed Probab=99.91 E-value=9.7e-26 Score=138.77 Aligned_cols=44 Identities=64% Similarity=0.984 Sum_probs=43.5 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 98876787841012332355415977799999999700265229 Q gi|254780481|r 1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) ||||||||+++|+++|||++||+|++||+||++|++|||+.||| T Consensus 1 mKRTyQPs~~kRkr~hGFr~Rm~T~~GRkVl~rRR~KGR~~Lsa 44 (44) T PRK00399 1 MKRTYQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLTA 44 (44) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCHHCCC T ss_conf 98767872335311121888834520099999999816221279 No 2 >COG0230 RpmH Ribosomal protein L34 [Translation, ribosomal structure and biogenesis] Probab=99.90 E-value=1.1e-24 Score=133.86 Aligned_cols=44 Identities=64% Similarity=0.972 Sum_probs=43.3 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 98876787841012332355415977799999999700265229 Q gi|254780481|r 1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) ||||||||+++|+++|||++||+|++||+||++|++|||+.||+ T Consensus 1 mkrTyQPs~~kRkr~hGFraRM~Tk~GR~vl~~RR~KGR~~Ls~ 44 (44) T COG0230 1 MKRTYQPSKRKRKRTHGFRARMATKNGRKVLARRRAKGRKRLSV 44 (44) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC T ss_conf 97666874003300042788844532089999999748711579 No 3 >pfam00468 Ribosomal_L34 Ribosomal protein L34. Probab=99.89 E-value=3.2e-24 Score=131.75 Aligned_cols=44 Identities=64% Similarity=0.998 Sum_probs=43.2 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 98876787841012332355415977799999999700265229 Q gi|254780481|r 1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) ||+|||||+++|+++|||++||+|++||+||++|++|||+.||+ T Consensus 1 ~krT~qps~~kRkr~hGFr~Rm~T~~GRkvl~rRr~KGR~~Ls~ 44 (44) T pfam00468 1 MKRTYQPSNRKRKRTHGFRARMATKNGRKVLKRRRAKGRKRLTV 44 (44) T ss_pred CCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHCCCCCCCC T ss_conf 98767873001001123888815641499999999848810459 No 4 >TIGR01030 rpmH_bact ribosomal protein L34; InterPro: IPR000271 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 L34 is one of the proteins from the large subunit of the prokaryotic ribosome. It is a small basic protein of 44 to 51 amino-acid residues . L34 belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups: Eubacterial L34, Red algal chloroplast L34, Cyanelle L34.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome. Probab=99.82 E-value=2.4e-21 Score=118.57 Aligned_cols=44 Identities=61% Similarity=1.022 Sum_probs=43.1 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 98876787841012332355415977799999999700265229 Q gi|254780481|r 1 MKRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 1 mKrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) ||||||||++++++.|||++||.|.+||+||..||+|||..||+ T Consensus 1 ~kRT~qp~~~~r~r~~GF~aRM~T~~GR~vl~~RR~KgR~~L~v 44 (44) T TIGR01030 1 MKRTYQPSNLKRKRTHGFRARMATKNGRKVLKRRRAKGRKKLTV 44 (44) T ss_pred CCCCCCCCCCCCCCCCCHHHHHCCHHHHHHHHHHHHCCCCCCCC T ss_conf 97554876543223232011021331068998753034222479 No 5 >KOG4612 consensus Probab=99.72 E-value=1.5e-18 Score=105.72 Aligned_cols=42 Identities=50% Similarity=0.829 Sum_probs=40.3 Q ss_pred CCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 876787841012332355415977799999999700265229 Q gi|254780481|r 3 RTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 3 rTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) -+|||||+||||+|||++|.+|++|++||.+|+.||||+||- T Consensus 64 NeYQPSn~KRKrkhGfl~R~~s~~G~~vl~rR~lKGR~~LSH 105 (105) T KOG4612 64 NEYQPSNLKRKRKHGFLARAKSKQGSKVLKRRKLKGRWFLSH 105 (105) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCC T ss_conf 755850555431101566514610369999998646201259 No 6 >CHL00115 rpl34 ribosomal protein L34; Reviewed Probab=99.52 E-value=2.9e-15 Score=90.62 Aligned_cols=43 Identities=49% Similarity=0.733 Sum_probs=41.5 Q ss_pred CCCCCCCCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 8876787841012332355415977799999999700265229 Q gi|254780481|r 2 KRTYNPSNIVRKRRCGFLARMSTRSGIRILNRRRSKGRKRLSA 44 (44) Q Consensus 2 KrTyQPs~~kRkr~HGF~~Rm~T~~GRkvL~rRr~KGR~~Lsa 44 (44) |||+|+++++..+++||++||+|+.||+||+.||.|||+.|+. T Consensus 3 KrTl~gt~~kk~r~SGFraRm~t~~GRkil~~RRrKGRkkl~~ 45 (46) T CHL00115 3 KRTLSGTKRKKIRKSGFRARMATPQGRKILNARRRKGRKKLAV 45 (46) T ss_pred CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCC T ss_conf 4224821557787531565227854058999998645400155 No 7 >cd04934 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydro Probab=10.88 E-value=90 Score=14.77 Aligned_cols=12 Identities=42% Similarity=0.653 Sum_probs=8.3 Q ss_pred CHHHHHHHHHHC Q ss_conf 012332355415 Q gi|254780481|r 12 RKRRCGFLARMS 23 (44) Q Consensus 12 Rkr~HGF~~Rm~ 23 (44) .--.|||+++.= T Consensus 11 m~~ahGFLa~vF 22 (73) T cd04934 11 KSLSHGFLARIF 22 (73) T ss_pred HHHHHHHHHHHH T ss_conf 133517899999 No 8 >TIGR01505 tartro_sem_red 2-hydroxy-3-oxopropionate reductase; InterPro: IPR006398 These sequences represent 2-hydroxy-3-oxopropionate reductase (1.1.1.60 from EC), also called tartronate semialdehyde reductase. It follows glyoxylate carboligase and precedes glycerate kinase in D-glycerate pathway of glyoxylate degradation. The eventual product, 3-phosphoglycerate, is an intermediate of glycolysis and is readily metabolized. Tartronic semialdehyde, the substrate of this enzyme, may also come from other pathways, such as D-glucarate catabolism , .; GO: 0008679 2-hydroxy-3-oxopropionate reductase activity, 0046487 glyoxylate metabolic process. Probab=10.31 E-value=1e+02 Score=14.48 Aligned_cols=17 Identities=24% Similarity=0.737 Sum_probs=9.0 Q ss_pred CCCCCCCCCCCCHHHHHHHHHHCCHH Q ss_conf 98876787841012332355415977 Q gi|254780481|r 1 MKRTYNPSNIVRKRRCGFLARMSTRS 26 (44) Q Consensus 1 mKrTyQPs~~kRkr~HGF~~Rm~T~~ 26 (44) |+|+|.| ||+--+..|. T Consensus 222 ~~R~FkP---------GFrIdLH~KD 238 (291) T TIGR01505 222 LDRDFKP---------GFRIDLHQKD 238 (291) T ss_pred CCCCCCC---------CCEEHHHHHH T ss_conf 2578879---------8530531655 No 9 >KOG4076 consensus Probab=6.75 E-value=2.4e+02 Score=12.82 Aligned_cols=26 Identities=27% Similarity=0.372 Sum_probs=20.7 Q ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHH Q ss_conf 23554159777999999997002652 Q gi|254780481|r 17 GFLARMSTRSGIRILNRRRSKGRKRL 42 (44) Q Consensus 17 GF~~Rm~T~~GRkvL~rRr~KGR~~L 42 (44) =|.+-+.-++|-..|..|..|||++. T Consensus 38 ky~~~GklP~~sd~l~krlQkgrKyF 63 (121) T KOG4076 38 KYPSYGKLPGGSDFLRKRLQKGRKYF 63 (121) T ss_pred HHHHHCCCCCCCHHHHHHHHHCCCCC T ss_conf 88873778761289999998404133 No 10 >cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD Probab=5.09 E-value=2.3e+02 Score=12.88 Aligned_cols=7 Identities=57% Similarity=1.094 Sum_probs=0.0 Q ss_pred HHHHHHH Q ss_conf 3235541 Q gi|254780481|r 16 CGFLARM 22 (44) Q Consensus 16 HGF~~Rm 22 (44) |||++++ T Consensus 15 ~GFLa~v 21 (75) T cd04912 15 HGFLAKV 21 (75) T ss_pred CCHHHHH T ss_conf 3289999 Done!