Query 024580
Match_columns 265
No_of_seqs 166 out of 924
Neff 3.6
Searched_HMMs 46136
Date Fri Mar 29 05:45:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024580.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024580hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00165 S18 ribosomal protei 99.9 2.3E-28 4.9E-33 185.5 6.8 66 165-230 4-69 (70)
2 PRK00391 rpsR 30S ribosomal pr 99.9 7.6E-28 1.6E-32 186.3 7.5 67 164-230 12-78 (79)
3 PRK13401 30S ribosomal protein 99.9 9E-28 2E-32 187.3 7.6 68 164-231 11-78 (82)
4 COG0238 RpsR Ribosomal protein 99.9 4.2E-26 9.2E-31 175.3 5.9 64 163-226 12-75 (75)
5 PRK13400 30S ribosomal protein 99.9 2.6E-25 5.5E-30 188.5 7.6 68 164-231 20-87 (147)
6 CHL00077 rps18 ribosomal prote 99.9 2.3E-25 5E-30 175.2 6.4 66 164-231 15-80 (86)
7 PF01084 Ribosomal_S18: Riboso 99.9 3.9E-22 8.4E-27 144.5 5.5 51 176-226 4-54 (54)
8 KOG3162 Mitochondrial/chloropl 99.8 8.9E-19 1.9E-23 150.9 5.6 72 167-240 67-139 (159)
9 KOG4021 Mitochondrial ribosoma 99.1 4E-11 8.7E-16 107.7 4.4 65 167-231 109-174 (239)
10 cd00630 RNAP_largest_subunit_C 21.2 27 0.0006 30.4 -0.4 29 178-206 80-108 (158)
No 1
>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=99.95 E-value=2.3e-28 Score=185.50 Aligned_cols=66 Identities=36% Similarity=0.633 Sum_probs=62.6
Q ss_pred CCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCccc
Q 024580 165 RVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTT 230 (265)
Q Consensus 165 r~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~ 230 (265)
|++.|++|..++..|||||+++|++|||+.|+|+||++||+|+|+||+|++|||+||.||||||+.
T Consensus 4 r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRriTgl~~k~Qr~l~~aIKrAR~~~LlP~~~ 69 (70)
T TIGR00165 4 RKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRRLARAIKRARYLALLPYVK 69 (70)
T ss_pred CCCCCCccCCCCCcCCccCHHHHHHhcCCCCeEcCCccCCcCHHHHHHHHHHHHHHHHHhcCCccC
Confidence 456799998888899999999999999999999999999999999999999999999999999985
No 2
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=99.95 E-value=7.6e-28 Score=186.34 Aligned_cols=67 Identities=37% Similarity=0.620 Sum_probs=64.0
Q ss_pred CCCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCccc
Q 024580 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTT 230 (265)
Q Consensus 164 rr~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~ 230 (265)
++++.|++|..++..|||||+++|++|||++|+|+||++||+|+|+||+|++|||+||.||||||+.
T Consensus 12 ~r~k~c~~c~~~~~~iDYKnv~lL~~Fis~~GkIlprriTG~~~k~Qr~l~~aIkrAR~~~LlPf~~ 78 (79)
T PRK00391 12 RRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLATAIKRARFLALLPYVD 78 (79)
T ss_pred CCCCCCcccCCCCCcCCccCHHHHHHhcCCCceEcCcccCCcCHHHHHHHHHHHHHHHHhhCCCccC
Confidence 5567899999998889999999999999999999999999999999999999999999999999985
No 3
>PRK13401 30S ribosomal protein S18; Provisional
Probab=99.94 E-value=9e-28 Score=187.28 Aligned_cols=68 Identities=28% Similarity=0.553 Sum_probs=64.9
Q ss_pred CCCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCcccc
Q 024580 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTTM 231 (265)
Q Consensus 164 rr~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~~ 231 (265)
++++.|++|..++++|||||+++|++|||++|||+||++||||+|+||+|++||||||.||||||+..
T Consensus 11 ~r~k~c~~~~~~~~~iDYKnv~lL~~Fis~~GkIlpRR~TGl~~k~QR~l~~AIKrAR~laLlPf~~~ 78 (82)
T PRK13401 11 TKAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQVATAIKNAREMALLPYPGR 78 (82)
T ss_pred CCCCCCCcccCCCCcCCccCHHHHHHhcCCCccCcCcccCCcCHHHHHHHHHHHHHHHHHhcCccccC
Confidence 45678999999999999999999999999999999999999999999999999999999999999975
No 4
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=4.2e-26 Score=175.33 Aligned_cols=64 Identities=41% Similarity=0.638 Sum_probs=61.2
Q ss_pred CCCCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcC
Q 024580 163 TRRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLM 226 (265)
Q Consensus 163 ~rr~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLL 226 (265)
+++++.|+||..++++|||||+++|++||||.|||+||++||+|+|+||+|++||||||.||||
T Consensus 12 ~rrrk~c~~~~~~~~~iDYKd~~~L~rfise~GKI~prRiTG~sak~QR~la~AIKRAR~laLl 75 (75)
T COG0238 12 FRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQRRLARAIKRARYLALL 75 (75)
T ss_pred cccccccccccccCCccCccCHHHHHHHhcccCcccccccccccHHHHHHHHHHHHHHHHHhcC
Confidence 3567899999998999999999999999999999999999999999999999999999999997
No 5
>PRK13400 30S ribosomal protein S18; Provisional
Probab=99.92 E-value=2.6e-25 Score=188.52 Aligned_cols=68 Identities=28% Similarity=0.448 Sum_probs=64.3
Q ss_pred CCCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCcccc
Q 024580 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTTM 231 (265)
Q Consensus 164 rr~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~~ 231 (265)
+|++.|++|..++..|||||+++|++|||++|||+|||+||+|+||||+|++||||||.||||||+..
T Consensus 20 ~RrK~C~~c~~~~~~IDYKNv~lL~~FISe~GKIlPRRiTGlcaK~QRkLakAIKRAR~laLLPfv~~ 87 (147)
T PRK13400 20 PKRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRALANAIKRARFIALMPFVSE 87 (147)
T ss_pred CCCCCCCccCCCCCccCCcCHHHHHHhcCcCccCcCcccCCcCHHHHHHHHHHHHHHHHHhccccccc
Confidence 45678999988888899999999999999999999999999999999999999999999999999975
No 6
>CHL00077 rps18 ribosomal protein S18
Probab=99.92 E-value=2.3e-25 Score=175.15 Aligned_cols=66 Identities=30% Similarity=0.541 Sum_probs=61.7
Q ss_pred CCCccCcccccCCCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCcccc
Q 024580 164 RRVEFEVTTKKVLEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTTM 231 (265)
Q Consensus 164 rr~k~c~~~~~~i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~~ 231 (265)
.|++.|++|... .|||||++||++|||++|+|+||++||+|+|+||+|++|||+||.||||||++.
T Consensus 15 ~rrk~~~~~~~~--~iDYKnv~lL~~Fis~~GkIlpRriTGl~~K~QR~l~~aIKrAR~~gLlP~~~~ 80 (86)
T CHL00077 15 FRRRLPPIQSGD--RIDYKNMSLLSRFISEQGKILSRRVTRLTLKQQRLITKAIKQARILSLLPFLNN 80 (86)
T ss_pred cccCCCCCCCCC--cCCccCHHHHHHhcCCCCeEcCcccCCcCHHHHHHHHHHHHHHHHHhcCCcccc
Confidence 457789998763 699999999999999999999999999999999999999999999999999985
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=99.86 E-value=3.9e-22 Score=144.48 Aligned_cols=51 Identities=47% Similarity=0.795 Sum_probs=49.3
Q ss_pred CCccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcC
Q 024580 176 LEDADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLM 226 (265)
Q Consensus 176 i~~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLL 226 (265)
...+||||+.+|++||+++|+|+||++||||+|+||+|++|||+||.||||
T Consensus 4 ~~~idykn~~lL~~Fi~~~GkIl~rr~Tgl~~k~Qr~l~~aIkrAR~~gLl 54 (54)
T PF01084_consen 4 NEYIDYKNVELLSQFISPTGKILPRRITGLCAKQQRKLAKAIKRARQLGLL 54 (54)
T ss_dssp SSSSSSSSHHHHGCGBTTSSSBSTHHHHTSTHHHHHHHHHHHHHHHHTTSS
T ss_pred CCcCCcCCHHHHHHHcCcccceehhhhccccHHHHHHHHHHHHHHHHhhCC
Confidence 457999999999999999999999999999999999999999999999997
No 8
>KOG3162 consensus Mitochondrial/chloroplast ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.75 E-value=8.9e-19 Score=150.93 Aligned_cols=72 Identities=39% Similarity=0.572 Sum_probs=60.0
Q ss_pred ccCcccccCCC-ccCCCCHHHHHHhcCcCCccccccccCCCHHHHHHHHHHHHHHHHcCcCCccccCCcccccCc
Q 024580 167 EFEVTTKKVLE-DADFRNVKFLTQFITEAGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTTMGTKSFAFGK 240 (265)
Q Consensus 167 k~c~~~~~~i~-~iDYKNv~LLsqFIs~~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~~~~~~~v~~~ 240 (265)
+.|+.|..+|+ .++||||.||+|||++.|.|+||++||||+|+||+|++||++||.+||||++. +.++-..+
T Consensus 67 ~~c~~c~~~Vd~~~~yknv~iLsqFv~~~G~il~RkiTGLc~k~Qrki~~aI~~A~~~GlmP~~~--~~~~~~~~ 139 (159)
T KOG3162|consen 67 PQCILCTKGVDIKLSYKNVLLLSQFVSEDGGILPRKITGLCAKNQRKIERAIKRARAAGLMPVTN--TGPIWSRD 139 (159)
T ss_pred ccCcccccCCCcccccCccchhhhhcccccceecchhhhhhHHHHHHHHHHHHHHHHhccccccc--cCcccccc
Confidence 34666666553 34699999999999999999999999999999999999999999999999655 45555543
No 9
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=99.13 E-value=4e-11 Score=107.72 Aligned_cols=65 Identities=20% Similarity=0.320 Sum_probs=61.5
Q ss_pred ccCcccccCCCccCCCCHHHHHHhcCc-CCccccccccCCCHHHHHHHHHHHHHHHHcCcCCcccc
Q 024580 167 EFEVTTKKVLEDADFRNVKFLTQFITE-AGIIIKRSMSGISAKAQRKVAREIKTARAFGLMPFTTM 231 (265)
Q Consensus 167 k~c~~~~~~i~~iDYKNv~LLsqFIs~-~GkIlpRriTGLcaK~QRkLakAIKRAR~mGLLPfv~~ 231 (265)
..||+|.+....+||+|+.||.|||++ +|+|+.-..||||.|++.+|..||.+||..|+|-|.+.
T Consensus 109 npCPICRDeyL~~DyRN~~LlEQF~~~htg~~i~y~ktGlC~kqh~rL~~a~qkArdhG~lty~Vp 174 (239)
T KOG4021|consen 109 NPCPICRDEYLYFDYRNPGLLEQFLADHTGQPIDYLKTGLCRKQHTRLRAALQKARDHGTLTYGVP 174 (239)
T ss_pred CCCCccccceEEEeccCHHHHHHHhccCCCCchhhhhcchHHHHHHHHHHHHHHhhhcCeEEecCC
Confidence 369999999888999999999999999 99999999999999999999999999999999998764
No 10
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=21.23 E-value=27 Score=30.41 Aligned_cols=29 Identities=21% Similarity=0.357 Sum_probs=26.9
Q ss_pred ccCCCCHHHHHHhcCcCCccccccccCCC
Q 024580 178 DADFRNVKFLTQFITEAGIIIKRSMSGIS 206 (265)
Q Consensus 178 ~iDYKNv~LLsqFIs~~GkIlpRriTGLc 206 (265)
.||+|.+.||..+||-.|.+.+=...|+.
T Consensus 80 ~V~~rHl~LIAD~MT~~G~~~ginr~g~~ 108 (158)
T cd00630 80 SVDRRHIELIADVMTYSGGLRGVTRSGFR 108 (158)
T ss_pred eecHHHHHHHHHHHhcCCccccccccccc
Confidence 58999999999999999999999888884
Done!