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!