Query 035442
Match_columns 54
No_of_seqs 106 out of 218
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 03:00:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035442.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035442hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00036 40S ribosomal protein 99.9 7.5E-28 1.6E-32 169.5 0.5 53 1-54 1-58 (261)
2 PTZ00118 40S ribosomal protein 99.9 9.8E-28 2.1E-32 169.0 0.5 53 1-54 1-58 (262)
3 PRK04313 30S ribosomal protein 99.9 9.3E-25 2E-29 152.1 0.1 49 5-54 1-54 (237)
4 COG1471 RPS4A Ribosomal protei 99.9 5.8E-24 1.3E-28 149.1 2.2 51 2-53 1-56 (241)
5 PTZ00223 40S ribosomal protein 99.9 3.9E-24 8.5E-29 151.6 0.2 49 5-54 2-55 (273)
6 KOG0378 40S ribosomal protein 99.8 3.9E-22 8.4E-27 141.3 2.3 53 1-54 1-58 (263)
7 PF08071 RS4NT: RS4NT (NUC023) 99.7 4.3E-18 9.4E-23 91.6 1.6 33 3-36 1-38 (38)
8 PF08528 Whi5: Whi5 like; Int 19.0 19 0.00041 17.6 -1.1 9 44-52 2-10 (25)
9 PF12005 DUF3499: Protein of u 15.3 84 0.0018 20.5 0.9 18 6-23 45-67 (123)
10 KOG0008 Transcription initiati 15.0 28 0.00061 30.9 -1.7 19 28-50 682-700 (1563)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=99.93 E-value=7.5e-28 Score=169.54 Aligned_cols=53 Identities=47% Similarity=0.612 Sum_probs=51.9
Q ss_pred CcchhhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCcccC
Q 035442 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRWY 54 (54)
Q Consensus 1 m~~g~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~ 54 (54)
||||+++|||||+||+ |++++|||+|| ||||+++|||||+|||||+|+||+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~l~kk~g~~a~rps-pGPH~~~eslPL~i~LRd~LkyA~t~ 58 (261)
T PLN00036 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPS-SGPHKKRECLPLLLILRNRLKYALTY 58 (261)
T ss_pred CCCCcccccccccCccccccccccCeeccCCC-CCCCccccccccHHHHHhHhhhhccH
Confidence 9999999999999999 99999999999 99999999999999999999999985
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=99.93 E-value=9.8e-28 Score=169.02 Aligned_cols=53 Identities=38% Similarity=0.553 Sum_probs=51.9
Q ss_pred CcchhhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCcccC
Q 035442 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRWY 54 (54)
Q Consensus 1 m~~g~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~ 54 (54)
||||+++|||||+||+ |++++|||+|| ||||+++|||||+|||||+|+||+|+
T Consensus 1 m~~g~kkHlKRl~AP~~W~i~kk~~~~a~rps-pGPHk~~eslPL~i~LRd~LkyA~t~ 58 (262)
T PTZ00118 1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTS-PGPHKLRECLPLVILLRNRLKYALTY 58 (262)
T ss_pred CCCCcccccccccCccccccccccceeccCCC-CCCCccccccccHHHHHhhhhhhccH
Confidence 9999999999999999 99999999999 99999999999999999999999985
No 3
>PRK04313 30S ribosomal protein S4e; Validated
Probab=99.89 E-value=9.3e-25 Score=152.09 Aligned_cols=49 Identities=24% Similarity=0.260 Sum_probs=47.1
Q ss_pred hhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCcccC
Q 035442 5 LKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRWY 54 (54)
Q Consensus 5 ~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~ 54 (54)
|++|||||+||+ |++++||++|| ||||+++|||||+|||||+|+||+|+
T Consensus 1 ~~kHlKRl~AP~~W~i~kk~~~~a~kps-pGPH~~~~siPL~iiLRd~L~yA~t~ 54 (237)
T PRK04313 1 MMRHLKRLAAPKSWPIPRKEYKWTVKPS-PGPHSIEESIPLLVVLRDVLGYADTA 54 (237)
T ss_pred CCccccceeCCcccccccccceeccCCC-CCCCCcccccccHHHHHhHhhhhccH
Confidence 579999999999 99999999999 99999999999999999999999984
No 4
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=5.8e-24 Score=149.15 Aligned_cols=51 Identities=31% Similarity=0.407 Sum_probs=49.5
Q ss_pred cchhhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCccc
Q 035442 2 ARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRW 53 (54)
Q Consensus 2 ~~g~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~ 53 (54)
|||+++|||||+||+ ||+++|+++|+ ||||++++|+||++++||+|+||++
T Consensus 1 a~g~~~HlKRl~aP~~w~i~rK~~kw~~~P~-pGPH~~~~slPL~~iiRd~LkyAd~ 56 (241)
T COG1471 1 ARGPKRHLKRLAAPKSWPIPRKTGKWAVRPS-PGPHKAEESLPLLVIIRDYLKYADN 56 (241)
T ss_pred CCchhhhhhhccCCceEEeccccceEeccCC-CCCCcccccccEEeeehhHHHhccc
Confidence 579999999999999 99999999999 9999999999999999999999987
No 5
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=99.88 E-value=3.9e-24 Score=151.55 Aligned_cols=49 Identities=37% Similarity=0.450 Sum_probs=47.2
Q ss_pred hhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCcccC
Q 035442 5 LKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRWY 54 (54)
Q Consensus 5 ~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~ 54 (54)
.++|||||+||+ |++++|||+|| ||||+++|||||+|||||+|+||+|+
T Consensus 2 ~kkHlKRl~AP~~W~i~kk~~~~a~rps-pGPH~~~esiPL~iiLRd~LkyA~t~ 55 (273)
T PTZ00223 2 AKKHLKRLYAPKDWMLSKLTGVFAPRPR-AGPHKLRECLPLLIIIRNRLKYALNA 55 (273)
T ss_pred ccchhhhhcCccccccccccceeccCCC-CCCCccccccccHHHHHHHhhhhccH
Confidence 479999999999 99999999999 99999999999999999999999985
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=3.9e-22 Score=141.26 Aligned_cols=53 Identities=42% Similarity=0.432 Sum_probs=52.1
Q ss_pred CcchhhhhhccccCCC-----ccccccccCCCCCCCCCCCCccceeeeecccccCcccC
Q 035442 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSEFMPFICGPKNRLKPGRWY 54 (54)
Q Consensus 1 m~~g~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~ 54 (54)
|++|+++||||++||+ |++|+|||+|| +|||+++||+||++|+||+|+||+||
T Consensus 1 m~~g~k~hlKr~~ap~~wmldk~~G~fa~~ps-~gphk~reclpl~~~~~~~Lkya~~~ 58 (263)
T KOG0378|consen 1 MARGPKKHLKRLAAPKHWMLDKLGGVFAPMPS-SGPHKLRECLPLIVFLRNRLKYALNG 58 (263)
T ss_pred CCcchhhhhhhhcccHhheecccCcEEecCCC-CCCcccccceeEEEEeehhhhhhhcc
Confidence 8999999999999999 99999999999 99999999999999999999999986
No 7
>PF08071 RS4NT: RS4NT (NUC023) domain; InterPro: IPR013843 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the N-terminal region of these proteins.; PDB: 2XZM_W 2XZN_W 3U5G_E 3U5C_E.
Probab=99.70 E-value=4.3e-18 Score=91.61 Aligned_cols=33 Identities=45% Similarity=0.595 Sum_probs=19.0
Q ss_pred chhhhhhccccCCC-----ccccccccCCCCCCCCCCCC
Q 035442 3 RYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSE 36 (54)
Q Consensus 3 ~g~~kHlKRl~AP~-----k~~~~~a~kps~pGPH~~~~ 36 (54)
+|+++||||++||+ |++++||++|| ||||+++|
T Consensus 1 ~G~kkHlKRl~AP~~W~i~kk~~~~a~rps-pGPH~~~e 38 (38)
T PF08071_consen 1 RGPKKHLKRLAAPKSWMIDKKTGKFAPRPS-PGPHKLRE 38 (38)
T ss_dssp -S-----BCCCS-GGGT--SSSSSB------SSSS-CCC
T ss_pred CCcccccccccCCcccccccccCccccCCC-CCCccCCC
Confidence 58999999999998 99999999999 99999986
No 8
>PF08528 Whi5: Whi5 like; InterPro: IPR013734 This is a short conserved sequence found in the Nrm1/Whi5 transcription factors. Nrm1 is a negative regulatory component of the MBF complex involved in cell-cycle-dependent transcription []. Whi5 is a transcriptional repressor that negatively regulates G1-specific, SBF- and MBF-dependent transcription [, ].
Probab=18.98 E-value=19 Score=17.56 Aligned_cols=9 Identities=22% Similarity=0.283 Sum_probs=6.8
Q ss_pred ecccccCcc
Q 035442 44 PKNRLKPGR 52 (54)
Q Consensus 44 lRd~Lk~A~ 52 (54)
||.||.||.
T Consensus 2 Lr~RL~lA~ 10 (25)
T PF08528_consen 2 LRTRLQLAM 10 (25)
T ss_pred HHHHHhHhH
Confidence 577888874
No 9
>PF12005 DUF3499: Protein of unknown function (DUF3499); InterPro: IPR021888 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 125 to 163 amino acids in length.
Probab=15.27 E-value=84 Score=20.53 Aligned_cols=18 Identities=39% Similarity=0.595 Sum_probs=14.5
Q ss_pred hhhhccccCCC-----ccccccc
Q 035442 6 KKHQKRLNARG-----TCSGTFA 23 (54)
Q Consensus 6 ~kHlKRl~AP~-----k~~~~~a 23 (54)
..|-.||+||+ +..+.|+
T Consensus 45 ~~Ha~rlTaP~GWevvR~~~~~~ 67 (123)
T PF12005_consen 45 AEHAERLTAPRGWEVVRLEGPFA 67 (123)
T ss_pred HHHHhcccCCCCcEEEeccCCCC
Confidence 46899999999 7777674
No 10
>KOG0008 consensus Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=14.95 E-value=28 Score=30.85 Aligned_cols=19 Identities=37% Similarity=0.436 Sum_probs=15.1
Q ss_pred CCCCCCCCCccceeeeecccccC
Q 035442 28 IPQTNSGSEFMPFICGPKNRLKP 50 (54)
Q Consensus 28 ~pGPH~~~~slPL~i~lRd~Lk~ 50 (54)
+||||+.+ +-.++||+|+.
T Consensus 682 VpgPnSKk----~tt~~~nrLkv 700 (1563)
T KOG0008|consen 682 VPGPNSKK----LTTFLRNRLKV 700 (1563)
T ss_pred cCCCcchh----HHHHHHHHHHH
Confidence 59999987 56788888874
Done!