Query         gi|254780475|ref|YP_003064888.1| 50S ribosomal protein L33 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 55
No_of_seqs    108 out of 436
Neff          4.1 
Searched_HMMs 39220
Date          Sun May 29 16:58:09 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780475.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01023 rpmG_bact ribosomal   99.9 1.9E-26 4.7E-31  158.9   4.9   55    1-55      1-67  (67)
  2 PRK00595 rpmG 50S ribosomal pr  99.9 1.5E-24 3.9E-29  148.9   6.1   53    1-53      1-53  (53)
  3 CHL00104 rpl33 ribosomal prote  99.8 4.7E-22 1.2E-26  135.8   4.3   53    1-53      1-65  (66)
  4 pfam00471 Ribosomal_L33 Riboso  99.8   4E-21   1E-25  131.0   5.2   48    6-53      1-48  (48)
  5 COG0267 RpmG Ribosomal protein  99.8 7.4E-21 1.9E-25  129.6   5.4   48    6-53      3-50  (50)
  6 PRK00504 rpmG 50S ribosomal pr  99.8 1.2E-19 3.1E-24  123.2   4.1   49    5-53      2-50  (50)
  7 KOG3505 consensus               99.5 1.8E-15 4.5E-20  101.5   0.4   53    1-55      1-55  (55)
  8 PRK05767 rpl44e 50S ribosomal   91.7   0.064 1.6E-06   30.6   0.9   21   35-55      6-26  (91)
  9 COG1631 RPL42A Ribosomal prote  90.4    0.15 3.7E-06   28.7   1.7   20   35-54      6-25  (94)
 10 PTZ00157 60S ribosomal protein  63.5     2.7 6.8E-05   22.1   0.7   19   35-53      7-26  (85)
 11 PRK02244 DNA-directed RNA poly  37.5      18 0.00045   17.8   1.4   20   33-52     11-34  (44)
 12 TIGR02181 GRX_bact glutaredoxi  35.5      14 0.00036   18.4   0.6   18   37-54      6-32  (82)
 13 pfam00935 Ribosomal_L44 Riboso  31.6      35 0.00089   16.3   2.1   15    4-18     47-61  (77)
 14 KOG3084 consensus               25.9      20 0.00051   17.6   0.1   21   34-54    147-167 (345)
 15 pfam08772 NOB1_Zn_bind Nin one  22.1      37 0.00095   16.1   0.9   31    9-51      8-38  (73)

No 1  
>TIGR01023 rpmG_bact ribosomal protein L33; InterPro: IPR001705   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 L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities , , , groups:  Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33.    L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.93  E-value=1.9e-26  Score=158.87  Aligned_cols=55  Identities=51%  Similarity=0.645  Sum_probs=52.3

Q ss_pred             CCC-CCE--EEEEEEECCCCC---------CEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEEC
Q ss_conf             987-762--699999517788---------7598354889983336994131744634466886509
Q gi|254780475|r    1 MAK-AAT--IKIKLISSAGTG---------SFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus         1 MaK-~~r--~~I~L~st~~tg---------~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~KiK   55 (55)
                      ||+ +.+  ++|.|+||+|+|         +||+|+||+||.||||||+||||+||+||||+|+|||
T Consensus         1 Ma~K~~~~r~~i~L~ct~c~~nPdkrs~Gv~~YtT~KN~Rn~~eKLeL~Kycp~~RkHvlhkE~KiK   67 (67)
T TIGR01023         1 MAKKGARARELIRLVCTACTGNPDKRSNGVRNYTTTKNRRNKPEKLELRKYCPVVRKHVLHKEAKIK   67 (67)
T ss_pred             CCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEEEEECCCCCCHHHHEECCCCCCCCCEEEEEEEECC
T ss_conf             9610687623788640688888774648633000101888884571012588814853201541049


No 2  
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=99.90  E-value=1.5e-24  Score=148.85  Aligned_cols=53  Identities=55%  Similarity=0.772  Sum_probs=51.9

Q ss_pred             CCCCCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             98776269999951778875983548899833369941317446344668865
Q gi|254780475|r    1 MAKAATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         1 MaK~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |||+.|++|+|+|+||+|+||+|+||++|+||||||+||||+|++||+|+|+|
T Consensus         1 ~~k~~R~~I~L~ct~~~~~~Y~T~KNkrn~perlelkKycp~~rkHtlhkE~K   53 (53)
T PRK00595          1 AAKGMRVKIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKHVLHKETK   53 (53)
T ss_pred             CCCCCEEEEEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCCEEEEEECC
T ss_conf             98776028999980788778887265788952068982287774047277349


No 3  
>CHL00104 rpl33 ribosomal protein L33
Probab=99.85  E-value=4.7e-22  Score=135.84  Aligned_cols=53  Identities=28%  Similarity=0.334  Sum_probs=49.6

Q ss_pred             CCC--CCEEEEEEEECCCCCCE----------EEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             987--76269999951778875----------983548899833369941317446344668865
Q gi|254780475|r    1 MAK--AATIKIKLISSAGTGSF----------YVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         1 MaK--~~r~~I~L~st~~tg~~----------Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |||  +.|+.|.|+|++|...+          |+|+||++|+|+||||+||||+|++|++|+|+|
T Consensus         1 MAK~K~~Ri~ItLeCt~c~~~~~~k~~~g~sRYtT~KNRrNtp~RLELkKfcp~c~kHTiHkEiK   65 (66)
T CHL00104          1 MAKGKDVRITVILECTSCVRNGVNKESTGISRYITQKNRHNTPNRLELKKFCPYCYKHTIHGEIK   65 (66)
T ss_pred             CCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCEECCCCCCCCCCEEEECCCCCCCCEEEEHHHC
T ss_conf             98777864899998204200587656777430061366789810322100085534300230213


No 4  
>pfam00471 Ribosomal_L33 Ribosomal protein L33.
Probab=99.83  E-value=4e-21  Score=131.01  Aligned_cols=48  Identities=38%  Similarity=0.486  Sum_probs=46.7

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             269999951778875983548899833369941317446344668865
Q gi|254780475|r    6 TIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         6 r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |++|.|+|++|+++||+|+||++++||||||+||||+|++||+|+|+|
T Consensus         1 r~~i~L~ct~c~~~nY~t~KNk~~~~erLelkKycp~c~kHtlhkE~K   48 (48)
T pfam00471         1 RVKITLECTECGGRNYTTTKNKRNTPERLELKKYCPKCRKHTLHKETK   48 (48)
T ss_pred             CCEEEEEEECCCCEEEEECCCCCCCCCEEEEECCCCCCCCEEEEEECC
T ss_conf             958999983788753776267688954178970284426546575339


No 5  
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=99.82  E-value=7.4e-21  Score=129.59  Aligned_cols=48  Identities=44%  Similarity=0.549  Sum_probs=47.1

Q ss_pred             EEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             269999951778875983548899833369941317446344668865
Q gi|254780475|r    6 TIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         6 r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      |+.|+|+|+||+|+||+|++|+++.|+||||+||||+||+||+|+|+|
T Consensus         3 r~ki~L~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~khtlhkE~K   50 (50)
T COG0267           3 RVKIKLACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKHTLHKETK   50 (50)
T ss_pred             CCEEEEEEECCCCEEEEEEECCCCCCCEEEEEECCCCCCCEEEEEECC
T ss_conf             516999974468712898652678953177970185456377773049


No 6  
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=99.78  E-value=1.2e-19  Score=123.24  Aligned_cols=49  Identities=31%  Similarity=0.372  Sum_probs=47.5

Q ss_pred             CEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEE
Q ss_conf             6269999951778875983548899833369941317446344668865
Q gi|254780475|r    5 ATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGK   53 (55)
Q Consensus         5 ~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~K   53 (55)
                      .|+.|.|+|++|..+||+|+||++++|+||||+||||+|++||+|+|+|
T Consensus         2 mr~~i~L~Ct~C~~rNY~T~Knk~~~~~RLelkKyC~~c~kHTlHkE~K   50 (50)
T PRK00504          2 MRKKITLACTECKSRNYTTKKNKKNTPERLELKKFCPHCNKHTLHKETK   50 (50)
T ss_pred             CCCEEEEEECCCCCCCCEECCCCCCCCCEEEEECCCCCCCCEECCCCCC
T ss_conf             7615899805567754142466677865157853286668830340459


No 7  
>KOG3505 consensus
Probab=99.51  E-value=1.8e-15  Score=101.46  Aligned_cols=53  Identities=47%  Similarity=0.825  Sum_probs=48.4

Q ss_pred             CCC--CCEEEEEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEEEEEC
Q ss_conf             987--7626999995177887598354889983336994131744634466886509
Q gi|254780475|r    1 MAK--AATIKIKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus         1 MaK--~~r~~I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E~KiK   55 (55)
                      |||  +++.+|+|+|+|||||+|.+++++  ..++|++.+|||++++||||.|.|++
T Consensus         1 ~~K~k~kn~lirlvStAgtGf~~~~s~~k--~~~klt~~kYDPvVkr~VLF~E~Kmk   55 (55)
T KOG3505           1 MAKRKKKNMLIRLVSTAGTGFFYVKSRKK--LAEKLTFRKYDPVVKRHVLFTEQKMK   55 (55)
T ss_pred             CCCCHHHHHHHHHHHHCCCCEEEEEECCC--CCCCCEEEECCCHHEEEEEEEHHCCC
T ss_conf             96311132689888753662699973444--03002245417002015666511069


No 8  
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=91.75  E-value=0.064  Score=30.59  Aligned_cols=21  Identities=24%  Similarity=0.420  Sum_probs=16.4

Q ss_pred             EEEECCCCCCCEEEEEEEEEC
Q ss_conf             994131744634466886509
Q gi|254780475|r   35 VKNKYDPVIRKHVEFKEGKIK   55 (55)
Q Consensus        35 el~Ky~p~~~kHvl~~E~KiK   55 (55)
                      +++-|||.|++|++|.-+..|
T Consensus         6 ~~~tYCp~CkkHt~H~V~~yK   26 (91)
T PRK05767          6 KIRTYCPYCKTHTEHEVERVK   26 (91)
T ss_pred             HHHHHCCCCCCCCCEEEEEEC
T ss_conf             432228142576524899962


No 9  
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=90.39  E-value=0.15  Score=28.71  Aligned_cols=20  Identities=25%  Similarity=0.448  Sum_probs=15.9

Q ss_pred             EEEECCCCCCCEEEEEEEEE
Q ss_conf             99413174463446688650
Q gi|254780475|r   35 VKNKYDPVIRKHVEFKEGKI   54 (55)
Q Consensus        35 el~Ky~p~~~kHvl~~E~Ki   54 (55)
                      ..+-|||.|++|++|.-...
T Consensus         6 ~~~tyCp~CkkhT~H~V~~~   25 (94)
T COG1631           6 KRRTYCPYCKKHTIHKVERV   25 (94)
T ss_pred             CEEECCCCCCCCEEEEEEEH
T ss_conf             10010846345503566532


No 10 
>PTZ00157 60S ribosomal protein L44; Provisional
Probab=63.54  E-value=2.7  Score=22.11  Aligned_cols=19  Identities=21%  Similarity=0.275  Sum_probs=13.9

Q ss_pred             EEEECCC-CCCCEEEEEEEE
Q ss_conf             9941317-446344668865
Q gi|254780475|r   35 VKNKYDP-VIRKHVEFKEGK   53 (55)
Q Consensus        35 el~Ky~p-~~~kHvl~~E~K   53 (55)
                      +.+-||| .|++|+.|+-+-
T Consensus         7 ~~~tyC~~kC~kHt~HkVtq   26 (85)
T PTZ00157          7 KRKTYCRDKCNKHTSHKVSQ   26 (85)
T ss_pred             HHHHHCCCCCCCCCCCEEEE
T ss_conf             12100643137877646876


No 11 
>PRK02244 DNA-directed RNA polymerase subunit P; Provisional
Probab=37.48  E-value=18  Score=17.84  Aligned_cols=20  Identities=25%  Similarity=0.376  Sum_probs=15.4

Q ss_pred             EEEEEEC----CCCCCCEEEEEEE
Q ss_conf             3699413----1744634466886
Q gi|254780475|r   33 KMVKNKY----DPVIRKHVEFKEG   52 (55)
Q Consensus        33 klel~Ky----~p~~~kHvl~~E~   52 (55)
                      +.|+-.|    ||.|...+|++|-
T Consensus        11 ~Veid~y~gvRCpyCGHRiL~KER   34 (44)
T PRK02244         11 KVEIDEYGGVRCPYCGHRILLKER   34 (44)
T ss_pred             EEEEECCCCCCCCCCCCEEEEEEC
T ss_conf             577631266717865638887316


No 12 
>TIGR02181 GRX_bact glutaredoxin 3; InterPro: IPR011900   Glutaredoxins , , , also known as thioltransferases (disulphide reductases, are small proteins of approximately one hundred amino-acid residues which utilise glutathione and NADPH as cofactors. Oxidized glutathione is regenerated by glutathione reductase. Together these components compose the glutathione system .    Glutaredoxin functions as an electron carrier in the glutathione-dependent synthesis of deoxyribonucleotides by the enzyme ribonucleotide reductase. Like thioredoxin, which functions in a similar way, glutaredoxin possesses an active centre disulphide bond . It exists in either a reduced or an oxidized form where the two cysteine residues are linked in an intramolecular disulphide bond.   Glutaredoxin has been sequenced in a variety of species. On the basis of extensive sequence similarity, it has been proposed  that Vaccinia virus protein O2L is most probably a glutaredoxin. Finally, it must be noted that Bacteriophage T4 thioredoxin seems also to be evolutionary related. In position 5 of the pattern T4 thioredoxin has Val instead of Pro.    This family of glutaredoxins includes the E. coli protein GrxC (Grx3) which appears to have a secondary role in reducing ribonucleotide reductase (in the absence of GrxA) possibly indicating a role in the reduction of other protein disulphides .; GO: 0006118 electron transport, 0045454 cell redox homeostasis.
Probab=35.49  E-value=14  Score=18.35  Aligned_cols=18  Identities=33%  Similarity=0.503  Sum_probs=12.6

Q ss_pred             EECCCCC--------CCEE-EEEEEEE
Q ss_conf             4131744--------6344-6688650
Q gi|254780475|r   37 NKYDPVI--------RKHV-EFKEGKI   54 (55)
Q Consensus        37 ~Ky~p~~--------~kHv-l~~E~Ki   54 (55)
                      +.|||.|        .|=| -|.|.+|
T Consensus         6 ~~~CPYC~rAK~LL~~kGv~~~~Ei~v   32 (82)
T TIGR02181         6 KPYCPYCSRAKALLESKGVGTFTEIRV   32 (82)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCEEEEC
T ss_conf             599880268899998569886303445


No 13 
>pfam00935 Ribosomal_L44 Ribosomal protein L44.
Probab=31.59  E-value=35  Score=16.28  Aligned_cols=15  Identities=13%  Similarity=0.186  Sum_probs=11.1

Q ss_pred             CCEEEEEEEECCCCC
Q ss_conf             762699999517788
Q gi|254780475|r    4 AATIKIKLISSAGTG   18 (55)
Q Consensus         4 ~~r~~I~L~st~~tg   18 (55)
                      .+++.++|.|++|.-
T Consensus        47 TKKi~Lrl~C~~C~~   61 (77)
T pfam00935        47 TKKIVLRLRCTECKK   61 (77)
T ss_pred             CEEEEEEEEECCCCH
T ss_conf             004899999632683


No 14 
>KOG3084 consensus
Probab=25.91  E-value=20  Score=17.55  Aligned_cols=21  Identities=19%  Similarity=0.156  Sum_probs=14.8

Q ss_pred             EEEEECCCCCCCEEEEEEEEE
Q ss_conf             699413174463446688650
Q gi|254780475|r   34 MVKNKYDPVIRKHVEFKEGKI   54 (55)
Q Consensus        34 lel~Ky~p~~~kHvl~~E~Ki   54 (55)
                      +..-||||.|..-+.++|..-
T Consensus       147 ~skykFCp~CG~~tkp~e~g~  167 (345)
T KOG3084         147 VSKYKFCPGCGSPTKPEEAGT  167 (345)
T ss_pred             HHHHCCCCCCCCCCCCCCCCC
T ss_conf             987310756689864356885


No 15 
>pfam08772 NOB1_Zn_bind Nin one binding (NOB1) Zn-ribbon like. This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1.
Probab=22.14  E-value=37  Score=16.12  Aligned_cols=31  Identities=13%  Similarity=0.111  Sum_probs=19.6

Q ss_pred             EEEEECCCCCCEEEEECCCCCCCCEEEEEECCCCCCCEEEEEE
Q ss_conf             9999517788759835488998333699413174463446688
Q gi|254780475|r    9 IKLISSAGTGSFYVTKKNSRTMSGKMVKNKYDPVIRKHVEFKE   51 (55)
Q Consensus         9 I~L~st~~tg~~Y~T~knk~~~~~klel~Ky~p~~~kHvl~~E   51 (55)
                      -.|.|.||    |.++++        .-+.|||.|.-.+|-+-
T Consensus         8 ~~lrC~aC----f~~t~~--------~~k~FCpkCGn~TL~rv   38 (73)
T pfam08772         8 WILRCHAC----FKTTPD--------MTKQFCPKCGNATLRRV   38 (73)
T ss_pred             HEEEEEEC----CCCCCC--------CCCCCCCCCCCCCEEEE
T ss_conf             10354232----348489--------76612753699901699


Done!