Query 028101
Match_columns 214
No_of_seqs 48 out of 50
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 06:15:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0238 RpsR Ribosomal protein 99.8 7.7E-22 1.7E-26 147.9 2.2 50 163-212 12-61 (75)
2 PRK13401 30S ribosomal protein 99.8 8.2E-20 1.8E-24 138.6 2.8 50 163-212 10-59 (82)
3 TIGR00165 S18 ribosomal protei 99.8 7.5E-20 1.6E-24 134.7 2.4 49 164-212 3-51 (70)
4 PRK00391 rpsR 30S ribosomal pr 99.8 2.4E-19 5.2E-24 134.6 2.8 49 164-212 12-60 (79)
5 PRK13400 30S ribosomal protein 99.7 5.2E-19 1.1E-23 146.2 2.9 49 164-212 20-68 (147)
6 CHL00077 rps18 ribosomal prote 99.6 4.3E-17 9.3E-22 124.8 2.3 47 164-212 15-61 (86)
7 PF01084 Ribosomal_S18: Riboso 99.5 8.4E-15 1.8E-19 102.9 1.3 37 176-212 4-40 (54)
8 KOG3162 Mitochondrial/chloropl 99.2 1.3E-11 2.8E-16 103.2 2.8 76 100-212 37-113 (159)
9 KOG4021 Mitochondrial ribosoma 94.9 0.012 2.5E-07 52.6 1.3 43 168-210 110-153 (239)
10 PF06072 Herpes_US9: Alphaherp 20.3 67 0.0015 23.9 1.5 15 41-55 4-18 (60)
No 1
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.83 E-value=7.7e-22 Score=147.92 Aligned_cols=50 Identities=26% Similarity=0.397 Sum_probs=48.0
Q ss_pred CCCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 163 TRRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 163 ~~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
.+|+|+|+||+++++.||||||++|++||||.|||+|||+||+||||||.
T Consensus 12 ~rrrk~c~~~~~~~~~iDYKd~~~L~rfise~GKI~prRiTG~sak~QR~ 61 (75)
T COG0238 12 FRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQRR 61 (75)
T ss_pred cccccccccccccCCccCccCHHHHHHHhcccCcccccccccccHHHHHH
Confidence 37889999999999999999999999999999999999999999999984
No 2
>PRK13401 30S ribosomal protein S18; Provisional
Probab=99.77 E-value=8.2e-20 Score=138.56 Aligned_cols=50 Identities=18% Similarity=0.324 Sum_probs=47.7
Q ss_pred CCCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 163 TRRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 163 ~~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
.+|+|+|+||...++.||||||++|++||||+|||+|||+||+|+||||.
T Consensus 10 ~~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRR~TGl~~k~QR~ 59 (82)
T PRK13401 10 PTKAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQ 59 (82)
T ss_pred CCCCCCCCcccCCCCcCCccCHHHHHHhcCCCccCcCcccCCcCHHHHHH
Confidence 37889999999999999999999999999999999999999999999984
No 3
>TIGR00165 S18 ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically.
Probab=99.77 E-value=7.5e-20 Score=134.70 Aligned_cols=49 Identities=22% Similarity=0.392 Sum_probs=46.6
Q ss_pred CCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 164 ~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
+|+++|++|.+.++.+|||||++|++||||.|||+|||+||+|+||||.
T Consensus 3 ~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRriTgl~~k~Qr~ 51 (70)
T TIGR00165 3 RRKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRR 51 (70)
T ss_pred CCCCCCCccCCCCCcCCccCHHHHHHhcCCCCeEcCCccCCcCHHHHHH
Confidence 4678999999999999999999999999999999999999999999984
No 4
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=99.76 E-value=2.4e-19 Score=134.57 Aligned_cols=49 Identities=24% Similarity=0.377 Sum_probs=47.1
Q ss_pred CCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 164 ~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
+|++.|+||...++.||||||++|++|||+.|||+|||+||+|+||||.
T Consensus 12 ~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~~GkIlprriTG~~~k~Qr~ 60 (79)
T PRK00391 12 RRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQ 60 (79)
T ss_pred CCCCCCcccCCCCCcCCccCHHHHHHhcCCCceEcCcccCCcCHHHHHH
Confidence 6789999999999999999999999999999999999999999999984
No 5
>PRK13400 30S ribosomal protein S18; Provisional
Probab=99.74 E-value=5.2e-19 Score=146.18 Aligned_cols=49 Identities=12% Similarity=0.174 Sum_probs=47.1
Q ss_pred CCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 164 ~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
+|+|+|+||.+.+..||||||++|++||||+|||+|||+||+|+||||.
T Consensus 20 ~RrK~C~~c~~~~~~IDYKNv~lL~~FISe~GKIlPRRiTGlcaK~QRk 68 (147)
T PRK13400 20 PKRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRA 68 (147)
T ss_pred CCCCCCCccCCCCCccCCcCHHHHHHhcCcCccCcCcccCCcCHHHHHH
Confidence 6789999999999999999999999999999999999999999999984
No 6
>CHL00077 rps18 ribosomal protein S18
Probab=99.65 E-value=4.3e-17 Score=124.77 Aligned_cols=47 Identities=23% Similarity=0.367 Sum_probs=44.0
Q ss_pred CCcceeeehhhhhhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 164 ~R~K~c~ft~evlekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
.|+++|++|... .||||||++|++|||++|+|+|||+||+|||+||.
T Consensus 15 ~rrk~~~~~~~~--~iDYKnv~lL~~Fis~~GkIlpRriTGl~~K~QR~ 61 (86)
T CHL00077 15 FRRRLPPIQSGD--RIDYKNMSLLSRFISEQGKILSRRVTRLTLKQQRL 61 (86)
T ss_pred cccCCCCCCCCC--cCCccCHHHHHHhcCCCCeEcCcccCCcCHHHHHH
Confidence 577999999984 79999999999999999999999999999999984
No 7
>PF01084 Ribosomal_S18: Ribosomal protein S18; InterPro: IPR001648 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 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 eukaryotic 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 S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli [], and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein []. S18 belongs to a family of ribosomal proteins [] that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2UXD_R 3I8G_U 3UZ7_U 1N33_R 2XSY_R 3V24_R 3OGY_R 2XUY_R 2XFZ_R 3UXT_R ....
Probab=99.48 E-value=8.4e-15 Score=102.86 Aligned_cols=37 Identities=32% Similarity=0.511 Sum_probs=35.1
Q ss_pred hhcccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 176 LEDADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 176 lekiDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
.+.+|||||++|++|||+.|+|+|||+||+|+|+||.
T Consensus 4 ~~~idykn~~lL~~Fi~~~GkIl~rr~Tgl~~k~Qr~ 40 (54)
T PF01084_consen 4 NEYIDYKNVELLSQFISPTGKILPRRITGLCAKQQRK 40 (54)
T ss_dssp SSSSSSSSHHHHGCGBTTSSSBSTHHHHTSTHHHHHH
T ss_pred CCcCCcCCHHHHHHHcCcccceehhhhccccHHHHHH
Confidence 3689999999999999999999999999999999984
No 8
>KOG3162 consensus Mitochondrial/chloroplast ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.16 E-value=1.3e-11 Score=103.19 Aligned_cols=76 Identities=18% Similarity=0.252 Sum_probs=62.8
Q ss_pred cccccccccchhhHHHHHHhhhcccCCCccCCCCcccCCCCCCCCCCccCCCCCCCCCccccCCCCcceeeehhhhhh-c
Q 028101 100 GESVNTTLSDGMQGKLREAARHFEYDSEEVDKDDYAFRPDVSFKTGMTYEPKDLDLTKPGVRKTRRVEFEVTTKKVLE-D 178 (214)
Q Consensus 100 ~e~~~dtl~DGmd~kL~~aA~~f~~~~~e~d~~dy~~rpd~~f~~G~ty~~~Dldltkp~~~k~~R~K~c~ft~evle-k 178 (214)
.+.. +-..+|+.++.+++..++.+++.+. .+.|..|...++ +
T Consensus 37 ~~tq-~~~~~~~~~s~~e~~~~~~n~~~~~------------------------------------~~~c~~c~~~Vd~~ 79 (159)
T KOG3162|consen 37 NETQ-ENSKGGVSSSSKELPIASNNPEKKS------------------------------------EPQCILCTKGVDIK 79 (159)
T ss_pred eecc-cCCccccccchhhhhhhcCCCcccC------------------------------------cccCcccccCCCcc
Confidence 3466 5788999999999999999887722 366776655543 4
Q ss_pred ccccCHHHHHhhcccccceeecccchhhhhhhhh
Q 028101 179 ADFRNVKFLTQFITEAGIIIKRSMVMLLKFLEKT 212 (214)
Q Consensus 179 iDYKnV~fL~~FITE~GKIiPRR~TG~sAK~Qr~ 212 (214)
.+||||.+|++||+|.|.|+||++||+|+|.||.
T Consensus 80 ~~yknv~iLsqFv~~~G~il~RkiTGLc~k~Qrk 113 (159)
T KOG3162|consen 80 LSYKNVLLLSQFVSEDGGILPRKITGLCAKNQRK 113 (159)
T ss_pred cccCccchhhhhcccccceecchhhhhhHHHHHH
Confidence 5699999999999999999999999999999984
No 9
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=94.92 E-value=0.012 Score=52.62 Aligned_cols=43 Identities=21% Similarity=0.156 Sum_probs=38.1
Q ss_pred eeeehhhhhhcccccCHHHHHhhccc-ccceeecccchhhhhhh
Q 028101 168 FEVTTKKVLEDADFRNVKFLTQFITE-AGIIIKRSMVMLLKFLE 210 (214)
Q Consensus 168 ~c~ft~evlekiDYKnV~fL~~FITE-~GKIiPRR~TG~sAK~Q 210 (214)
-|+.|-+.--++||+|+++|.+||.+ +|-||-=-.||+|.|+.
T Consensus 110 pCPICRDeyL~~DyRN~~LlEQF~~~htg~~i~y~ktGlC~kqh 153 (239)
T KOG4021|consen 110 PCPICRDEYLYFDYRNPGLLEQFLADHTGQPIDYLKTGLCRKQH 153 (239)
T ss_pred CCCccccceEEEeccCHHHHHHHhccCCCCchhhhhcchHHHHH
Confidence 49999888889999999999999987 57788888999999864
No 10
>PF06072 Herpes_US9: Alphaherpesvirus tegument protein US9; InterPro: IPR009278 This family consists of several US9 and related proteins from the Alphaherpesviruses. The function of the US9 protein is unknown although in Bovine herpesvirus 5 Us9 is essential for the anterograde spread of the virus from the olfactory mucosa to the bulb [].; GO: 0019033 viral tegument
Probab=20.29 E-value=67 Score=23.95 Aligned_cols=15 Identities=53% Similarity=0.815 Sum_probs=12.2
Q ss_pred CCCCCCChhHHHHhh
Q 028101 41 SQGNNEPADEFERRI 55 (214)
Q Consensus 41 ~qs~nEs~d~fe~r~ 55 (214)
..|.||+|.+|=.||
T Consensus 4 SESDnETA~~FL~Rv 18 (60)
T PF06072_consen 4 SESDNETATEFLRRV 18 (60)
T ss_pred CccccccHHHHHHHH
Confidence 357789999998887
Done!