Query 030255
Match_columns 180
No_of_seqs 14 out of 16
Neff 1.6
Searched_HMMs 46136
Date Fri Mar 29 10:57:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030255.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030255hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01632 Ribosomal_L35p: Ribos 98.2 6.4E-07 1.4E-11 61.4 1.6 35 145-179 1-35 (61)
2 PRK00172 rpmI 50S ribosomal pr 98.2 8.3E-07 1.8E-11 61.9 1.9 34 146-179 3-36 (65)
3 TIGR00001 rpmI_bact ribosomal 97.9 6.5E-06 1.4E-10 57.3 1.9 34 146-179 2-35 (63)
4 CHL00103 rpl35 ribosomal prote 96.4 0.0018 3.8E-08 45.8 1.9 34 145-178 2-35 (65)
5 COG0291 RpmI Ribosomal protein 95.8 0.0042 9E-08 44.6 1.2 32 146-177 3-34 (65)
6 KOG0932 Guanine nucleotide exc 43.6 22 0.00047 35.5 3.0 22 27-48 596-617 (774)
7 PF14538 Raptor_N: Raptor N-te 41.8 19 0.00041 28.4 1.9 44 31-77 71-114 (154)
8 COG3359 Predicted exonuclease 20.1 61 0.0013 29.2 1.5 19 16-35 155-173 (278)
9 KOG0431 Auxilin-like protein a 19.4 25 0.00054 32.2 -1.0 20 156-175 354-373 (453)
10 cd08796 Death_IRAK-M Death dom 19.3 74 0.0016 23.7 1.6 22 27-49 2-23 (89)
No 1
>PF01632 Ribosomal_L35p: Ribosomal protein L35; InterPro: IPR021137 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 [, ]. L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit []. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes []. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2QBE_3 2QBG_3 3SGF_7 2QOV_3 3J0Y_6 3I22_3 3E1D_W 1VS6_3 2VHN_3 1VS8_3 ....
Probab=98.19 E-value=6.4e-07 Score=61.35 Aligned_cols=35 Identities=37% Similarity=0.522 Sum_probs=28.2
Q ss_pred eeccccccccccceecCCcceeeeccccccccccC
Q 030255 145 IKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 145 ~KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
.|||..++.+.||+.+++|.|.||+.|++|+..-|
T Consensus 1 pKmKT~k~a~KRFk~t~sGkikr~~agk~H~~~~K 35 (61)
T PF01632_consen 1 PKMKTHKSAAKRFKVTGSGKIKRKRAGKRHLLTKK 35 (61)
T ss_dssp ---S-HHHHHTTEEEESSSEEEEE-SSSSSSSSSS
T ss_pred CCccchhhhHhheeEcCCCeEEeccCCcccccccC
Confidence 38999999999999999999999999999998654
No 2
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed
Probab=98.17 E-value=8.3e-07 Score=61.94 Aligned_cols=34 Identities=44% Similarity=0.624 Sum_probs=32.1
Q ss_pred eccccccccccceecCCcceeeeccccccccccC
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
|||..++.+.||+.+++|+|.||++|++|++..|
T Consensus 3 KmKT~k~akKRFk~T~~GKi~r~~a~k~H~~~~K 36 (65)
T PRK00172 3 KMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKK 36 (65)
T ss_pred CcccchhhhheeEEcCCCCEEeccCCCccccccC
Confidence 8999999999999999999999999999988654
No 3
>TIGR00001 rpmI_bact ribosomal protein L35. This ribosomal protein is found in bacteria and organelles only. It is not closely related to any eukaryotic or archaeal ribosomal protein.
Probab=97.88 E-value=6.5e-06 Score=57.31 Aligned_cols=34 Identities=35% Similarity=0.546 Sum_probs=31.9
Q ss_pred eccccccccccceecCCcceeeeccccccccccC
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLK 179 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~K 179 (180)
|||.-++.+.||+.+++|+|.||++|++|+...|
T Consensus 2 KmKT~~~akKRFK~T~tGKvkr~~a~k~H~l~~K 35 (63)
T TIGR00001 2 KMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKK 35 (63)
T ss_pred CcccchhhhhheEEcCCCCEEecccCcccccccC
Confidence 8999999999999999999999999999997654
No 4
>CHL00103 rpl35 ribosomal protein L35
Probab=96.45 E-value=0.0018 Score=45.79 Aligned_cols=34 Identities=21% Similarity=0.276 Sum_probs=31.2
Q ss_pred eeccccccccccceecCCcceeeecccccccccc
Q 030255 145 IKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHL 178 (180)
Q Consensus 145 ~KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh~ 178 (180)
-|||.-++-+.||+.+.+|+|.|.++|++|..--
T Consensus 2 pKmKT~k~a~KRFKvT~sGKvkr~~a~k~H~l~k 35 (65)
T CHL00103 2 PKLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQK 35 (65)
T ss_pred CccccchhhhheeEecCCCCEEeccCCccccccC
Confidence 3899999999999999999999999999998653
No 5
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=95.79 E-value=0.0042 Score=44.63 Aligned_cols=32 Identities=38% Similarity=0.615 Sum_probs=29.7
Q ss_pred eccccccccccceecCCcceeeeccccccccc
Q 030255 146 KMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAH 177 (180)
Q Consensus 146 KiK~ySSyK~RFR~m~dG~irRwr~GKrHnAh 177 (180)
|||--++-+.||+.+.+|+|.|+++|++|-..
T Consensus 3 KmKT~k~aaKRFK~T~~Gkikr~~A~k~H~l~ 34 (65)
T COG0291 3 KMKTKKGAAKRFKITGTGKIKRKHAGKRHILT 34 (65)
T ss_pred ccchhhhhHhheeecCCCcEEecccccccccc
Confidence 78889999999999999999999999999654
No 6
>KOG0932 consensus Guanine nucleotide exchange factor EFA6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=43.58 E-value=22 Score=35.50 Aligned_cols=22 Identities=36% Similarity=0.548 Sum_probs=20.2
Q ss_pred ccccCchHHHHHHHHHhhhhcc
Q 030255 27 ALFDAPSAVEMQRLCNKLRTLT 48 (180)
Q Consensus 27 ~~~~~~~~~~MqrlctKLRs~a 48 (180)
-||.||+..|||-.|+++-..|
T Consensus 596 ~LFQaps~eEmqsWi~rIN~vA 617 (774)
T KOG0932|consen 596 FLFQAPSQEEMQSWIERINLVA 617 (774)
T ss_pred EEEeCCCHHHHHHHHHHHHHHH
Confidence 5899999999999999998775
No 7
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=41.83 E-value=19 Score=28.42 Aligned_cols=44 Identities=25% Similarity=0.541 Sum_probs=31.2
Q ss_pred CchHHHHHHHHHhhhhcccccccchhcccCCCCCCCCccCCCCCccc
Q 030255 31 APSAVEMQRLCNKLRTLTLSSSRRLLFQSHAPIHRPFHSAPSSKWRL 77 (180)
Q Consensus 31 ~~~~~~MqrlctKLRs~a~~SsRrllh~sh~p~~~pl~~A~s~kw~~ 77 (180)
.|+..|+.++|.+||.-|.. .|-|+|-.----++| .++...|-+
T Consensus 71 dpt~e~~~~~~~~~R~~a~~-~RvLFHYnGhGvP~P--t~~GeIw~f 114 (154)
T PF14538_consen 71 DPTVEDLKRLCQSLRRNAKD-ERVLFHYNGHGVPRP--TENGEIWVF 114 (154)
T ss_pred CCCHHHHHHHHHHHHhhCCC-ceEEEEECCCCCCCC--CCCCeEEEE
Confidence 58999999999999998877 778888443233454 234456755
No 8
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=20.11 E-value=61 Score=29.18 Aligned_cols=19 Identities=53% Similarity=0.644 Sum_probs=14.9
Q ss_pred ccccceeccccccccCchHH
Q 030255 16 ETNQRVSFNNKALFDAPSAV 35 (180)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~ 35 (180)
.-|--||||+|| ||.|-..
T Consensus 155 ~~~~lvsfNGka-FD~Pfik 173 (278)
T COG3359 155 DFNMLVSFNGKA-FDIPFIK 173 (278)
T ss_pred CcceEEEecCcc-cCcHHHH
Confidence 346779999987 8999654
No 9
>KOG0431 consensus Auxilin-like protein and related proteins containing DnaJ domain [General function prediction only]
Probab=19.44 E-value=25 Score=32.22 Aligned_cols=20 Identities=45% Similarity=0.797 Sum_probs=15.6
Q ss_pred cceecCCcceeeeccccccc
Q 030255 156 RFRTMNDGQVRRWHEGKRHN 175 (180)
Q Consensus 156 RFR~m~dG~irRwr~GKrHn 175 (180)
|-..+-|=+|+||-+||.-|
T Consensus 354 r~~e~~d~~I~~W~~GKE~N 373 (453)
T KOG0431|consen 354 RLMEPLDEEIRRWSEGKEGN 373 (453)
T ss_pred hhcchHHHHHHHhccccccc
Confidence 44455678999999999866
No 10
>cd08796 Death_IRAK-M Death domain of Interleukin 1 Receptor Associated Kinase-M. Death Domain (DD) of Interleukin-1 Receptor-Associated Kinase M (IRAK-M). IRAKs are essential components of innate immunity and inflammation in mammals and other vertebrates. They are involved in signal transduction pathways involving IL-1 and IL-18 receptors, Toll-like receptors(TLRs), nuclear factor-kappaB (NF-kB), and mitogen-activated protein kinases (MAPKs). IRAKs contain an N-terminal DD domain and a C-terminal kinase domain. IRAK-M, also called IRAK-3, is an inactive kinase present only in macrophages in an inducible manner. It is a negative regulator of TLR signaling and it contributes to the attenuation of NF-kB activation. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitme
Probab=19.29 E-value=74 Score=23.69 Aligned_cols=22 Identities=32% Similarity=0.451 Sum_probs=17.5
Q ss_pred ccccCchHHHHHHHHHhhhhccc
Q 030255 27 ALFDAPSAVEMQRLCNKLRTLTL 49 (180)
Q Consensus 27 ~~~~~~~~~~MqrlctKLRs~a~ 49 (180)
.|||-|.. +||+||.-|-++..
T Consensus 2 ~ly~lP~~-v~~~lc~~LDs~~~ 23 (89)
T cd08796 2 LLFDLPPV-LLGSLCALLDSGVG 23 (89)
T ss_pred chhhCCHH-HHHHHHHHhcCCCc
Confidence 57898865 69999999887653
Done!