Query 039147
Match_columns 71
No_of_seqs 102 out of 226
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 06:45:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039147hhsearch_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 2.8E-29 6E-34 187.1 2.0 67 1-68 1-76 (261)
2 PTZ00118 40S ribosomal protein 99.9 4.8E-29 1E-33 185.9 1.9 67 1-68 1-76 (262)
3 PRK04313 30S ribosomal protein 99.9 2.9E-26 6.2E-31 168.9 1.5 63 5-68 1-72 (237)
4 PTZ00223 40S ribosomal protein 99.9 1.1E-25 2.3E-30 168.8 1.6 63 5-68 2-73 (273)
5 COG1471 RPS4A Ribosomal protei 99.9 1.5E-24 3.2E-29 160.9 3.0 65 2-67 1-74 (241)
6 KOG0378 40S ribosomal protein 99.9 6.6E-24 1.4E-28 158.9 2.0 66 1-67 1-75 (263)
7 PF08071 RS4NT: RS4NT (NUC023) 99.7 3.2E-17 7E-22 92.9 1.6 33 3-36 1-38 (38)
8 COG3012 Uncharacterized protei 16.5 69 0.0015 23.0 0.8 17 55-71 109-125 (151)
9 PF12005 DUF3499: Protein of u 13.6 91 0.002 21.6 0.8 18 6-23 45-67 (123)
10 PF03242 LEA_3: Late embryogen 13.4 99 0.0022 20.1 0.9 14 17-31 59-72 (93)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=99.95 E-value=2.8e-29 Score=187.13 Aligned_cols=67 Identities=39% Similarity=0.512 Sum_probs=64.6
Q ss_pred CCccchhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCce
Q 039147 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANENY 68 (71)
Q Consensus 1 Ma~g~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~~ 68 (71)
||||+++|||||+||+ |++|+|||+|| ||||+++|||||++||||+|+||+|. +|++|+.+++||.-
T Consensus 1 m~~g~kkHlKRl~AP~~W~l~kk~g~~a~rps-pGPH~~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkv 76 (261)
T PLN00036 1 MARGLKKHLKRLNAPKHWMLDKLGGAFAPKPS-SGPHKKRECLPLLLILRNRLKYALTYREVQAILMQRHVKVDGKV 76 (261)
T ss_pred CCCCcccccccccCccccccccccCeeccCCC-CCCCccccccccHHHHHhHhhhhccHHHHHHHHhCCeEEECCEE
Confidence 9999999999999999 99999999999 99999999999999999999999995 69999999999864
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=99.95 E-value=4.8e-29 Score=185.92 Aligned_cols=67 Identities=31% Similarity=0.481 Sum_probs=64.5
Q ss_pred CCccchhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCce
Q 039147 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANENY 68 (71)
Q Consensus 1 Ma~g~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~~ 68 (71)
||||+++|||||+||+ |++|+|||+|| ||||+++|||||++||||+|+||+|. +|++|+.+++||.-
T Consensus 1 m~~g~kkHlKRl~AP~~W~i~kk~~~~a~rps-pGPHk~~eslPL~i~LRd~LkyA~t~rEak~Il~~~~V~VDGkv 76 (262)
T PTZ00118 1 MGKGIKKHMKRINAPSHWMLDKLGGQYAPKTS-PGPHKLRECLPLVILLRNRLKYALTYDEVKLIVIQKIVKVDGKV 76 (262)
T ss_pred CCCCcccccccccCccccccccccceeccCCC-CCCCccccccccHHHHHhhhhhhccHHHHHHHHHCCcEEECCEE
Confidence 9999999999999999 99999999999 99999999999999999999999995 69999999999864
No 3
>PRK04313 30S ribosomal protein S4e; Validated
Probab=99.92 E-value=2.9e-26 Score=168.94 Aligned_cols=63 Identities=19% Similarity=0.171 Sum_probs=59.9
Q ss_pred chhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCce
Q 039147 5 LKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANENY 68 (71)
Q Consensus 5 ~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~~ 68 (71)
|++|||||+||+ ||+++|||+|| ||||+++|||||+++|||+|+||+|. +|++|..+++||.-
T Consensus 1 ~~kHlKRl~AP~~W~i~kk~~~~a~kps-pGPH~~~~siPL~iiLRd~L~yA~t~rEak~Il~~~~V~VDGkv 72 (237)
T PRK04313 1 MMRHLKRLAAPKSWPIPRKEYKWTVKPS-PGPHSIEESIPLLVVLRDVLGYADTAREAKKIINEGKVLVDGRV 72 (237)
T ss_pred CCccccceeCCcccccccccceeccCCC-CCCCCcccccccHHHHHhHhhhhccHHHHHHHHhCCcEEECCEE
Confidence 579999999999 99999999999 99999999999999999999999996 69999999999864
No 4
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=99.91 E-value=1.1e-25 Score=168.82 Aligned_cols=63 Identities=29% Similarity=0.363 Sum_probs=59.5
Q ss_pred chhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCce
Q 039147 5 LKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANENY 68 (71)
Q Consensus 5 ~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~~ 68 (71)
.++|||||+||+ |++|+|||+|| ||||+++|||||++||||+|+||+|. +|++|..+++||.-
T Consensus 2 ~kkHlKRl~AP~~W~i~kk~~~~a~rps-pGPH~~~esiPL~iiLRd~LkyA~t~rEak~Il~~~~V~VDGkv 73 (273)
T PTZ00223 2 AKKHLKRLYAPKDWMLSKLTGVFAPRPR-AGPHKLRECLPLLIIIRNRLKYALNAREAQMILRQGLVCVDGKP 73 (273)
T ss_pred ccchhhhhcCccccccccccceeccCCC-CCCCccccccccHHHHHHHhhhhccHHHHHHHHhCCeEEECCEE
Confidence 368999999999 99999999999 99999999999999999999999995 69999999999864
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.5e-24 Score=160.89 Aligned_cols=65 Identities=23% Similarity=0.278 Sum_probs=60.3
Q ss_pred CccchhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCc
Q 039147 2 ARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANEN 67 (71)
Q Consensus 2 a~g~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~ 67 (71)
|||+++|||||+||+ ||+++|||+|+ ||||++++|+||++++||+|+||+|. +|-++.-+++||.
T Consensus 1 a~g~~~HlKRl~aP~~w~i~rK~~kw~~~P~-pGPH~~~~slPL~~iiRd~LkyAd~~REa~~Ii~~g~v~VDG~ 74 (241)
T COG1471 1 ARGPKRHLKRLAAPKSWPIPRKTGKWAVRPS-PGPHKAEESLPLLVIIRDYLKYADNAREARKILSEGKVLVDGK 74 (241)
T ss_pred CCchhhhhhhccCCceEEeccccceEeccCC-CCCCcccccccEEeeehhHHHhccchHHHHHHHhcCcEEECCE
Confidence 679999999999999 99999999999 99999999999999999999999995 5777888888873
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=6.6e-24 Score=158.87 Aligned_cols=66 Identities=36% Similarity=0.447 Sum_probs=63.9
Q ss_pred CCccchhccccccCCC-----ccccccccCCCCCCCCCCCcccceeeeecccccCcccc----hhhheeeeeecCc
Q 039147 1 MARYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSECMPFICGPKNRLIPGRWN----PCCMSQILKANEN 67 (71)
Q Consensus 1 Ma~g~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~slPL~i~lRd~Lk~A~~~----~ic~q~~ik~~~~ 67 (71)
|++|+++||||++||+ |++|+|||+|| +|||+++||+||++|+|++|+||+|+ +|+||+.||+|+.
T Consensus 1 m~~g~k~hlKr~~ap~~wmldk~~G~fa~~ps-~gphk~reclpl~~~~~~~Lkya~~~~e~~~I~~qr~i~v~gk 75 (263)
T KOG0378|consen 1 MARGPKKHLKRLAAPKHWMLDKLGGVFAPMPS-SGPHKLRECLPLIVFLRNRLKYALNGKEVKKILMQREIKVDGK 75 (263)
T ss_pred CCcchhhhhhhhcccHhheecccCcEEecCCC-CCCcccccceeEEEEeehhhhhhhcccHHHHHHHHhhhhccce
Confidence 8999999999999999 99999999999 99999999999999999999999997 5999999999984
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=99.65 E-value=3.2e-17 Score=92.91 Aligned_cols=33 Identities=45% Similarity=0.595 Sum_probs=19.0
Q ss_pred ccchhccccccCCC-----ccccccccCCCCCCCCCCCc
Q 039147 3 RYLKKHQKRLNARG-----TCSGTFAPKPLIPQTNSGSE 36 (71)
Q Consensus 3 ~g~~kHlKRl~AP~-----kk~~~fa~kps~pGPH~~~~ 36 (71)
+|+++||||++||+ |++++|||+|| ||||+++|
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
>COG3012 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=16.46 E-value=69 Score=22.99 Aligned_cols=17 Identities=18% Similarity=0.327 Sum_probs=14.2
Q ss_pred hhhheeeeeecCceeeC
Q 039147 55 PCCMSQILKANENYCFL 71 (71)
Q Consensus 55 ~ic~q~~ik~~~~~~~~ 71 (71)
.++.++|+|+||+.-|+
T Consensus 109 ~~ErSrFvk~ngrWyyi 125 (151)
T COG3012 109 HHERSRFVKINGRWYYI 125 (151)
T ss_pred hhhhhhheEECCEEEEE
Confidence 47889999999998764
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=13.62 E-value=91 Score=21.58 Aligned_cols=18 Identities=39% Similarity=0.595 Sum_probs=14.7
Q ss_pred hhccccccCCC-----ccccccc
Q 039147 6 KKHQKRLNARG-----TCSGTFA 23 (71)
Q Consensus 6 ~kHlKRl~AP~-----kk~~~fa 23 (71)
..|-.||+||+ +..+.|+
T Consensus 45 ~~Ha~rlTaP~GWevvR~~~~~~ 67 (123)
T PF12005_consen 45 AEHAERLTAPRGWEVVRLEGPFA 67 (123)
T ss_pred HHHHhcccCCCCcEEEeccCCCC
Confidence 46899999999 7777774
No 10
>PF03242 LEA_3: Late embryogenesis abundant protein; InterPro: IPR004926 Late-embryogenesis abundant (LEA) genes encode a diverse group of proteins that accumulate to high levels during the maturation phase of seed development []. This group includes LEA-5 [], whose expression is induced by salt, drought and heat stress [], and related proteins. ; GO: 0006950 response to stress
Probab=13.37 E-value=99 Score=20.09 Aligned_cols=14 Identities=14% Similarity=0.399 Sum_probs=10.8
Q ss_pred ccccccccCCCCCCC
Q 039147 17 TCSGTFAPKPLIPQT 31 (71)
Q Consensus 17 kk~~~fa~kps~pGP 31 (71)
+++..|+|.|. +|=
T Consensus 59 ~~~~~W~pDPv-TGy 72 (93)
T PF03242_consen 59 KEKSSWMPDPV-TGY 72 (93)
T ss_pred ccccccccCCC-Ccc
Confidence 45567999999 884
Done!