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!