Query 028473
Match_columns 208
No_of_seqs 162 out of 912
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 12:02:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028473hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 CHL00103 rpl35 ribosomal prote 99.9 6.2E-24 1.4E-28 153.9 5.2 61 144-204 1-61 (65)
2 PRK00172 rpmI 50S ribosomal pr 99.9 1.6E-23 3.4E-28 151.1 5.2 61 144-204 1-61 (65)
3 COG0291 RpmI Ribosomal protein 99.9 1.7E-23 3.8E-28 152.7 4.4 61 144-204 1-61 (65)
4 TIGR00001 rpmI_bact ribosomal 99.9 4.6E-23 9.9E-28 148.1 5.1 60 145-204 1-60 (63)
5 PF01632 Ribosomal_L35p: Ribos 99.9 2.1E-22 4.5E-27 143.0 2.4 60 145-204 1-60 (61)
6 KOG4316 Uncharacterized conser 87.6 0.18 3.9E-06 43.3 0.2 61 144-204 77-137 (172)
7 KOG0932 Guanine nucleotide exc 32.7 47 0.001 34.3 3.5 22 27-48 596-617 (774)
8 PF14538 Raptor_N: Raptor N-te 31.2 52 0.0011 27.2 3.0 47 31-81 71-118 (154)
9 COG1360 MotB Flagellar motor p 25.8 59 0.0013 28.3 2.5 61 16-77 123-187 (244)
10 PRK15058 cytochrome b562; Prov 18.8 63 0.0014 26.8 1.2 33 24-56 35-67 (128)
No 1
>CHL00103 rpl35 ribosomal protein L35
Probab=99.89 E-value=6.2e-24 Score=153.94 Aligned_cols=61 Identities=28% Similarity=0.331 Sum_probs=59.8
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
|||||||+||+|||+|||+|||+|.+||++|++++||.+++|+|+++.+|+++|+++|++|
T Consensus 1 MpKmKT~k~a~KRFKvT~sGKvkr~~a~k~H~l~kKs~krkR~L~~~~~v~~~d~~~ik~~ 61 (65)
T CHL00103 1 MPKLKTRKAAAKRYKKTGNGKFLRRKAFKSHLLQKKSSKQKRKLSQTVCVSKGDSKSIKLM 61 (65)
T ss_pred CCccccchhhhheeEecCCCCEEeccCCccccccCCCHHHHHhcCCCeeECHHHHHHHHHh
Confidence 6999999999999999999999999999999999999999999999999999999999886
No 2
>PRK00172 rpmI 50S ribosomal protein L35; Reviewed
Probab=99.89 E-value=1.6e-23 Score=151.08 Aligned_cols=61 Identities=43% Similarity=0.546 Sum_probs=59.6
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
|||||||+||+|||++||+|||+|++||++|++++||.+++|+|+++.+|+++|+++|++|
T Consensus 1 MpKmKT~k~akKRFk~T~~GKi~r~~a~k~H~~~~Ks~k~kR~lr~~~~v~~~~~k~ik~~ 61 (65)
T PRK00172 1 MPKMKTKSGAAKRFKVTGSGKVKRKHAGKRHILTKKSTKRKRQLRGTTVVSKADAKRVKRM 61 (65)
T ss_pred CCCcccchhhhheeEEcCCCCEEeccCCCccccccCCHHHHHhcCCCeeECHHHHHHHHHh
Confidence 6999999999999999999999999999999999999999999999999999999999974
No 3
>COG0291 RpmI Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=1.7e-23 Score=152.66 Aligned_cols=61 Identities=41% Similarity=0.532 Sum_probs=59.6
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
||||||++||+|||++||+|||+|++||++|++++|+.+++|+||+..+|+++|.++|++|
T Consensus 1 MPKmKT~k~aaKRFK~T~~Gkikr~~A~k~H~l~kKs~k~kR~Lr~~~~v~~~d~k~v~~~ 61 (65)
T COG0291 1 MPKMKTKKGAAKRFKITGTGKIKRKHAGKRHILTKKSTKRKRHLRKTAVVSKADLKRVKRL 61 (65)
T ss_pred CCccchhhhhHhheeecCCCcEEecccccccccccCCHHHHHhccCCceeCHHHHHHHHHh
Confidence 7999999999999999999999999999999999999999999999999999999999875
No 4
>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=99.88 E-value=4.6e-23 Score=148.06 Aligned_cols=60 Identities=38% Similarity=0.491 Sum_probs=58.9
Q ss_pred cCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 145 IKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 145 pKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
||||||+||+|||++||+|||+|++||++|++++|+.+++|+|+++++|+++|+++|++|
T Consensus 1 pKmKT~~~akKRFK~T~tGKvkr~~a~k~H~l~~Ks~k~kR~L~~~~~v~~~~~~~ik~~ 60 (63)
T TIGR00001 1 PKMKTHKAAAKRFKITGSGKIKRKKAGKRHLLTKKSSKRKRNLRKKAIVSAGDLKRVKLL 60 (63)
T ss_pred CCcccchhhhhheEEcCCCCEEecccCcccccccCCHHHHHhcCCCeeECHHHHHHHHHh
Confidence 799999999999999999999999999999999999999999999999999999999986
No 5
>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=99.85 E-value=2.1e-22 Score=142.99 Aligned_cols=60 Identities=45% Similarity=0.565 Sum_probs=54.3
Q ss_pred cCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 145 IKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 145 pKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
||||||+|++|||++||||+|+|++||++|++++||.+++|+|++..+|+++|++.|++|
T Consensus 1 pKmKT~k~a~KRFk~t~sGkikr~~agk~H~~~~Ks~krkr~Lr~~~~v~~~~~k~ikkl 60 (61)
T PF01632_consen 1 PKMKTHKSAAKRFKVTGSGKIKRKRAGKRHLLTKKSSKRKRRLRKTTLVHKADVKRIKKL 60 (61)
T ss_dssp ---S-HHHHHTTEEEESSSEEEEE-SSSSSSSSSSSCHCTTTTSCEEESSSHHHHHHTTT
T ss_pred CCccchhhhHhheeEcCCCeEEeccCCcccccccCCHHHHHHcCCCEEECHHHHHHHHHh
Confidence 799999999999999999999999999999999999999999999999999999999986
No 6
>KOG4316 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.56 E-value=0.18 Score=43.28 Aligned_cols=61 Identities=21% Similarity=0.265 Sum_probs=56.8
Q ss_pred ccCcccCcccccceEeccCccEEeecCCcccccCCCChHHHhhcCCCeeeChhcHHHHHhc
Q 028473 144 KIKMKSYSSYKSRFRTMNDGQVRRWHEGKRHNAHLKSKKSKRRLRQPALVPLAYAKVMKKL 204 (208)
Q Consensus 144 mpKMKThKgAkKRFKVTgSGKIKRkrAGKrHlLtKKSsKRKRrLRK~~~VskaD~KrIKkm 204 (208)
+.|.||-+++-+||+-...|--.|.++|+.-++-+|+.-.+++|.....-++++-+.+.+|
T Consensus 77 kGkrktvkaVldRFkRL~~G~WIr~h~Gr~Kkl~kK~~a~~krl~~~vfcnktQs~lLDKm 137 (172)
T KOG4316|consen 77 KGKRKTVKAVLDRFKRLHCGLWIRAHPGRHKKLYKKDEAWQKRLLYYVFCNKTQSELLDKM 137 (172)
T ss_pred hcccccHHHHHHHHHhcccCeeeeecCchhhhhhhcCHHHHHHHHHhheechHHHHHHHHH
Confidence 5788999999999999999999999999999999999999999999999999988888776
No 7
>KOG0932 consensus Guanine nucleotide exchange factor EFA6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.71 E-value=47 Score=34.29 Aligned_cols=22 Identities=36% Similarity=0.548 Sum_probs=20.0
Q ss_pred ccccCchHHHHHHHHHHhhhhh
Q 028473 27 ALFDAPSAVEMQRLCNKLRTLT 48 (208)
Q Consensus 27 ~~~~~~~~~~m~~~~~klr~~~ 48 (208)
-||.||+..|||-.|+++-..|
T Consensus 596 ~LFQaps~eEmqsWi~rIN~vA 617 (774)
T KOG0932|consen 596 FLFQAPSQEEMQSWIERINLVA 617 (774)
T ss_pred EEEeCCCHHHHHHHHHHHHHHH
Confidence 5899999999999999998775
No 8
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=31.17 E-value=52 Score=27.24 Aligned_cols=47 Identities=26% Similarity=0.547 Sum_probs=32.7
Q ss_pred CchHHHHHHHHHHhhhhhhccccccccc-cCCCCCCCCCCCCCCCcccccCC
Q 028473 31 APSAVEMQRLCNKLRTLTLSSSRRLLFQ-SHAPIHRPFHSAPSSKWRLSPLF 81 (208)
Q Consensus 31 ~~~~~~m~~~~~klr~~~~~s~r~~~~~-~~~~~~~~~h~~~~~~~~~~~~~ 81 (208)
.|+..|+.++|.+||.-+.. .|-|.|| ||.- ++|.-. ...|=+...+
T Consensus 71 dpt~e~~~~~~~~~R~~a~~-~RvLFHYnGhGv-P~Pt~~--GeIw~f~~~~ 118 (154)
T PF14538_consen 71 DPTVEDLKRLCQSLRRNAKD-ERVLFHYNGHGV-PRPTEN--GEIWVFNKNY 118 (154)
T ss_pred CCCHHHHHHHHHHHHhhCCC-ceEEEEECCCCC-CCCCCC--CeEEEEcCCC
Confidence 58999999999999998887 5666554 6644 555433 3477554433
No 9
>COG1360 MotB Flagellar motor protein [Cell motility and secretion]
Probab=25.82 E-value=59 Score=28.27 Aligned_cols=61 Identities=20% Similarity=0.311 Sum_probs=47.5
Q ss_pred ccccceeccccccccCchHHHHHHHHHHhhhhhh----ccccccccccCCCCCCCCCCCCCCCccc
Q 028473 16 ETNQRVSFNNKALFDAPSAVEMQRLCNKLRTLTL----SSSRRLLFQSHAPIHRPFHSAPSSKWRL 77 (208)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~m~~~~~klr~~~~----~s~r~~~~~~~~~~~~~~h~~~~~~~~~ 77 (208)
+..-+|++.+..+|+.-+|+.+..+-+.|.-++. ....++.-.|| ..-+|+|..--++|.|
T Consensus 123 ~~gl~i~i~~~~~F~~gsa~~~~~~~~~l~~ia~~l~~~~~~~I~I~GH-TDn~p~~~~~~sNWeL 187 (244)
T COG1360 123 EEGLVISISDSLMFASGSAVVQPEFRDLLLKIAKLLADIPNGNIRIEGH-TDNVPIKGSFYSNWEL 187 (244)
T ss_pred CCccEEEeeccccccccccccCHHHHHHHHHHHHHHhhcCCCeEEEEeC-CCCCCcCCCCCchHHH
Confidence 4566889999999999999988777777777652 22237777899 5589999987778987
No 10
>PRK15058 cytochrome b562; Provisional
Probab=18.80 E-value=63 Score=26.75 Aligned_cols=33 Identities=21% Similarity=0.254 Sum_probs=28.3
Q ss_pred cccccccCchHHHHHHHHHHhhhhhhccccccc
Q 028473 24 NNKALFDAPSAVEMQRLCNKLRTLTLSSSRRLL 56 (208)
Q Consensus 24 ~~~~~~~~~~~~~m~~~~~klr~~~~~s~r~~~ 56 (208)
|.+++-.|.++.||+.-+++||.+++++-+..+
T Consensus 35 ~~k~~~~A~~a~~~k~al~~mr~aa~~Ak~~~P 67 (128)
T PRK15058 35 NLKVVEKTDNAAEVKDALTKMRAAALDAQKATP 67 (128)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHhccCC
Confidence 556777899999999999999999999987643
Done!