Query         gi|254780437|ref|YP_003064850.1| 30S ribosomal protein S21 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 95
No_of_seqs    109 out of 269
Neff          3.9 
Searched_HMMs 39220
Date          Sun May 29 18:22:05 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780437.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12441 30S ribosomal protein  99.8 2.5E-19 6.5E-24  129.0   6.6   61   19-79      1-62  (62)
  2 TIGR00030 S21p ribosomal prote  99.7 3.8E-18 9.6E-23  122.4   5.2   56   20-75      1-57  (58)
  3 PRK00270 rpsU 30S ribosomal pr  99.7 4.7E-17 1.2E-21  116.3   7.8   63   19-81      1-64  (66)
  4 COG0828 RpsU Ribosomal protein  99.7 1.7E-16 4.4E-21  113.1   7.6   64   19-82      1-65  (67)
  5 pfam01165 Ribosomal_S21 Riboso  99.5 8.1E-15 2.1E-19  103.8   6.1   55   20-74      1-56  (57)
  6 cd04917 ACT_AKiii-LysC-EC_2 AC  26.6      58  0.0015   15.1   3.1   29   12-40     34-62  (64)
  7 PRK08178 acetolactate synthase  26.2      44  0.0011   15.8   1.9   53    6-64     38-91  (96)
  8 TIGR03595 Obg_CgtA_exten Obg f  26.2      59  0.0015   15.0   3.2   26   27-52     27-52  (69)
  9 TIGR02177 PorB_KorB 2-oxoacid:  25.1      31 0.00078   16.6   0.9   19   11-29     92-110 (302)
 10 TIGR00263 trpB tryptophan synt  23.3      53  0.0014   15.3   1.9   28   19-49    344-371 (412)
 11 PRK00286 xseA exodeoxyribonucl  22.8      34 0.00087   16.4   0.8   28   26-53    103-130 (443)

No 1  
>PRK12441 30S ribosomal protein S21; Reviewed
Probab=99.78  E-value=2.5e-19  Score=128.97  Aligned_cols=61  Identities=54%  Similarity=0.757  Sum_probs=58.3

Q ss_pred             EEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0688872795-899999999999643449998743512695589999999998889999999
Q gi|254780437|r   19 AVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRK   79 (95)
Q Consensus        19 ~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK   79 (95)
                      +++|.|+||| +|+|||+||++|+++|||.||+.++||||||++++|++++|++|.+|.+++
T Consensus         1 m~qV~v~dNe~~e~ALRrfKr~~~r~Gv~~e~k~r~~yEkPse~rkRkka~AvrR~rk~~rk   62 (62)
T PRK12441          1 MTQVLVRENEPVEVALRRFKRKIQKEGLFAEMRERRAYEKPSEKRKRKKAAAVRRLRKRARK   62 (62)
T ss_pred             CCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             97247268964999999999999981009999988730283899999999999999987349


No 2  
>TIGR00030 S21p ribosomal protein S21; InterPro: IPR001911   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 , .   Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryote ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins. The small ribosomal subunit protein S21 contains 55-70 amino acid residues, and has only been found in eubacteria to date, though it has been reported that plant chloroplasts and mammalian mitochondria contain ribosomal subunit protein S21. Experimental evidence has revealed that S21 is well exposed on the surface of the Escherichia coli ribosome , and is one of the 'split proteins': these are a discrete group that are selectively removed from 30S subunits under low salt conditions and are required for the formation of activated 30S reconstitution intermediate (RI*) particles.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.73  E-value=3.8e-18  Score=122.41  Aligned_cols=56  Identities=46%  Similarity=0.713  Sum_probs=53.9

Q ss_pred             EEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             688872795-89999999999964344999874351269558999999999888999
Q gi|254780437|r   20 VYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRK   75 (95)
Q Consensus        20 i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K   75 (95)
                      ++|.|++|| ||.|||.||+++++||||.+++.++||||||++|+++.++|++|..|
T Consensus         1 ~~V~V~eges~d~ALr~FKr~~~ke~i~~~~k~r~~YekPs~~R~~k~~~a~kr~~k   57 (58)
T TIGR00030         1 PTVKVKEGESIDSALRRFKRKVEKEGILRELKKREYYEKPSERRRRKEKAAAKRIRK   57 (58)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             902511588788999998576159999999875304888137899999999875314


No 3  
>PRK00270 rpsU 30S ribosomal protein S21; Reviewed
Probab=99.70  E-value=4.7e-17  Score=116.27  Aligned_cols=63  Identities=46%  Similarity=0.699  Sum_probs=58.5

Q ss_pred             EEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0688872795-89999999999964344999874351269558999999999888999999999
Q gi|254780437|r   19 AVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIA   81 (95)
Q Consensus        19 ~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~~   81 (95)
                      ++.|.|++|| +|.|||+||++|+++||+.|++.++||||||++++++..+|.++.+|..++..
T Consensus         1 M~~V~v~e~E~~e~ALrrFKr~~~k~Gi~~e~r~r~~yEkPs~krkrK~~aa~kr~~k~~~~~~   64 (66)
T PRK00270          1 MPKVKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLRREN   64 (66)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9821508998599999999999998544999998884148199999999999999999998870


No 4  
>COG0828 RpsU Ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=99.67  E-value=1.7e-16  Score=113.12  Aligned_cols=64  Identities=48%  Similarity=0.674  Sum_probs=59.6

Q ss_pred             EEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0688872795-899999999999643449998743512695589999999998889999999998
Q gi|254780437|r   19 AVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQ   82 (95)
Q Consensus        19 ~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~K~~rK~~~   82 (95)
                      +++|.|++|| +|.|||.||++++++|||.|++.++|||+||++++++.++|.+|..|..++...
T Consensus         1 M~~v~V~ene~~d~ALrrFKr~~~k~gil~e~k~r~~yEkPs~krkrK~a~a~kr~~k~~~k~~~   65 (67)
T COG0828           1 MPQVKVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRKEQQ   65 (67)
T ss_pred             CCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             98027369973999999999999998699999999832370199999999999999999998751


No 5  
>pfam01165 Ribosomal_S21 Ribosomal protein S21.
Probab=99.55  E-value=8.1e-15  Score=103.77  Aligned_cols=55  Identities=53%  Similarity=0.795  Sum_probs=51.5

Q ss_pred             EEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             688872795-8999999999996434499987435126955899999999988899
Q gi|254780437|r   20 VYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSR   74 (95)
Q Consensus        20 i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrRkk~ea~kR~~   74 (95)
                      +.|.|.+|| +|.||+.|+++|+++||++|++.++||||||++++++..++.+|..
T Consensus         1 v~V~v~~~e~~e~Alrrfkr~~~~~gi~~e~r~rr~yekPs~krkrk~~~a~rr~~   56 (57)
T pfam01165         1 VEVKVKENENIESALRRFKRKVEKNGILRELRRRRFYEKPSEKRKRKRREARRRRR   56 (57)
T ss_pred             CEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHC
T ss_conf             94352799979999999999999847199999999732849999999999998634


No 6  
>cd04917 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second 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). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.56  E-value=58  Score=15.09  Aligned_cols=29  Identities=14%  Similarity=0.368  Sum_probs=23.7

Q ss_pred             CCCCCCCEEEEEEECCCHHHHHHHHHHHH
Q ss_conf             04543310688872795899999999999
Q gi|254780437|r   12 SEGREISAVYVLVRDNNVEQALRVLKKKM   40 (95)
Q Consensus        12 ~~~k~~~~i~V~V~~nnvE~AlR~lKrkv   40 (95)
                      ++|-.-..+.+.|.+.+.++|++.|...+
T Consensus        34 sqGaSe~Nis~lV~~~d~~~al~~Lh~~f   62 (64)
T cd04917          34 CYGASNHNLCFLVKEEDKDEVVQRLHSRL   62 (64)
T ss_pred             EECCCCCEEEEEEEHHHHHHHHHHHHHHH
T ss_conf             60687444999996678999999999986


No 7  
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=26.25  E-value=44  Score=15.76  Aligned_cols=53  Identities=21%  Similarity=0.292  Sum_probs=33.3

Q ss_pred             HHHHHHCCCCCCCEEEEEEECCC-HHHHHHHHHHHHHHCCHHHHHHHHHHCCCHHHHHHH
Q ss_conf             56654204543310688872795-899999999999643449998743512695589999
Q gi|254780437|r    6 AFRGIFSEGREISAVYVLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVR   64 (95)
Q Consensus         6 ~~~~~~~~~k~~~~i~V~V~~nn-vE~AlR~lKrkv~~eGi~~elR~R~~YEKPsekRrR   64 (95)
                      ++...-++...++-|++.|.+++ +|+.++-|.|.+.      -++-.++-+.||.-|-.
T Consensus        38 SL~v~~te~~~~SRiTivv~~d~~leQi~kQL~KLid------Vi~V~~l~~~~sV~REL   91 (96)
T PRK08178         38 GILCLPIQDSDKSRIWLLVNDDQRLEQMISQIDKLED------VLKVRRNQSDPTMFNKI   91 (96)
T ss_pred             EEEEEECCCCCCEEEEEEECCCCCHHHHHHHHHHCCC------EEEEEECCCCCHHHHHH
T ss_conf             0788513899810899998898448999999861507------69999889984199999


No 8  
>TIGR03595 Obg_CgtA_exten Obg family GTPase CgtA, C-terminal extension. CgtA (see model TIGR02729) is a broadly conserved member of the obg family of GTPases associated with ribosome maturation. This model represents a unique C-terminal domain found in some but not all sequences of CgtA. This region is preceded, and may be followed, by a region of low-complexity sequence.
Probab=26.21  E-value=59  Score=15.05  Aligned_cols=26  Identities=27%  Similarity=0.371  Sum_probs=22.3

Q ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             95899999999999643449998743
Q gi|254780437|r   27 NNVEQALRVLKKKMQGEGVLRELKMR   52 (95)
Q Consensus        27 nnvE~AlR~lKrkv~~eGi~~elR~R   52 (95)
                      =+-+.|+..|.+.+.+-||.+.|++.
T Consensus        27 ~~~~ea~~rf~~~Lk~~Gv~~~L~~~   52 (69)
T TIGR03595        27 FNNDENLRRFARKLKKLGVEDALRKA   52 (69)
T ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHC
T ss_conf             99999999999999988978999986


No 9  
>TIGR02177 PorB_KorB 2-oxoacid:acceptor oxidoreductase, beta subunit, pyruvate/2-ketoisovalerate family; InterPro: IPR011896    A number of anaerobic and microaerophilic species lack pyruvate dehydrogenase and have instead a four subunit, oxygen-sensitive pyruvate oxidoreductase, with either ferredoxins or flavodoxins used as the acceptor. Several related four-subunit enzymes may exist in the same species. This entry describes the beta subunits, representing mostly pyruvate and 2-ketoisovalerate specific enzymes..
Probab=25.08  E-value=31  Score=16.62  Aligned_cols=19  Identities=42%  Similarity=0.597  Sum_probs=16.0

Q ss_pred             HCCCCCCCEEEEEEECCCH
Q ss_conf             2045433106888727958
Q gi|254780437|r   11 FSEGREISAVYVLVRDNNV   29 (95)
Q Consensus        11 ~~~~k~~~~i~V~V~~nnv   29 (95)
                      -+.|+.+.+|+|.|.||.|
T Consensus        92 va~gRRN~dIt~l~~DN~V  110 (302)
T TIGR02177        92 VAAGRRNVDITVLVHDNQV  110 (302)
T ss_pred             HHHHCCCCCCEEEEECCEE
T ss_conf             7541147882488424705


No 10 
>TIGR00263 trpB tryptophan synthase, beta subunit; InterPro: IPR006654   Tryptophan synthase catalyzes the last step in the biosynthesis of tryptophan , :  L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H_2O  It has two functional domains, each found in bacteria and plants on a separate subunit: alpha chain (IPR002028 from INTERPRO) is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and beta chain is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together on a single multifunctional protein .   The beta chain of the enzyme, represented here, requires pyridoxal-phosphate as a cofactor. The pyridoxal-phosphate group is attached to a lysine residue. The region around this lysine residue also contains two histidine residues which are part of the pyridoxal-phosphate binding site.; GO: 0004834 tryptophan synthase activity, 0006568 tryptophan metabolic process.
Probab=23.28  E-value=53  Score=15.28  Aligned_cols=28  Identities=32%  Similarity=0.534  Sum_probs=20.7

Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCCHHHHH
Q ss_conf             0688872795899999999999643449998
Q gi|254780437|r   19 AVYVLVRDNNVEQALRVLKKKMQGEGVLREL   49 (95)
Q Consensus        19 ~i~V~V~~nnvE~AlR~lKrkv~~eGi~~el   49 (95)
                      .-++.|-|   +.||+-|+..+..|||+.=|
T Consensus       344 a~Y~~iTD---~EAl~AF~~l~~~EGIIPAL  371 (412)
T TIGR00263       344 AEYEAITD---DEALEAFKLLSRNEGIIPAL  371 (412)
T ss_pred             EEEEECCH---HHHHHHHHHHHHHCCCCCCH
T ss_conf             56630688---99999999987716873423


No 11 
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=22.76  E-value=34  Score=16.35  Aligned_cols=28  Identities=25%  Similarity=0.377  Sum_probs=23.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             7958999999999996434499987435
Q gi|254780437|r   26 DNNVEQALRVLKKKMQGEGVLRELKMRG   53 (95)
Q Consensus        26 ~nnvE~AlR~lKrkv~~eGi~~elR~R~   53 (95)
                      .|++..++..+|+++..||+|..-+.+.
T Consensus       103 ~G~L~~~~e~lk~kL~~eGlFd~~~Kk~  130 (443)
T PRK00286        103 IGALAQAFEQLKEKLAAEGLFDPERKKP  130 (443)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             2189999999999997777968777899


Done!