Query 032859
Match_columns 132
No_of_seqs 131 out of 208
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 06:49:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032859.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032859hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08561 Ribosomal_L37: Mitoch 100.0 8.2E-33 1.8E-37 194.8 5.1 82 49-130 2-84 (85)
2 KOG3435 Mitochondrial/chloropl 100.0 6.4E-32 1.4E-36 203.0 6.1 113 19-131 13-127 (127)
3 KOG3435 Mitochondrial/chloropl 92.9 0.031 6.7E-07 42.7 0.1 28 62-89 78-105 (127)
4 COG0758 Smf Predicted Rossmann 63.5 3.2 7E-05 36.2 0.9 24 71-94 77-100 (350)
5 PRK01202 glycine cleavage syst 33.3 25 0.00054 26.0 1.3 50 57-114 74-125 (127)
6 PF14475 Mso1_Sec1_bdg: Sec1-b 30.6 17 0.00037 22.8 0.1 15 63-84 27-41 (41)
7 TIGR00527 gcvH glycine cleavag 29.0 29 0.00064 25.7 1.1 51 57-115 73-125 (127)
8 PRK13380 glycine cleavage syst 29.0 41 0.00089 25.6 1.9 52 57-115 81-133 (144)
9 PHA02616 VP2/VP3; Provisional 24.9 39 0.00084 28.3 1.2 18 80-97 20-41 (259)
10 PF10940 DUF2618: Protein of u 24.8 39 0.00084 21.1 0.9 14 2-15 5-18 (40)
11 PF04614 Pex19: Pex19 protein 23.7 44 0.00094 27.5 1.3 15 103-117 161-175 (248)
No 1
>PF08561 Ribosomal_L37: Mitochondrial ribosomal protein L37; InterPro: IPR013870 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 [, ]. This entry includes yeast MRPL37 a mitochondrial ribosomal protein [].
Probab=99.97 E-value=8.2e-33 Score=194.81 Aligned_cols=82 Identities=46% Similarity=0.793 Sum_probs=74.7
Q ss_pred cccccccccccc-ccceecccCCCCccCCCCCCchhhhhccCCccchHHHhhcCCCCCCHHHHHHHHhHHHHHHHHhccc
Q 032859 49 SILSKEVKSTTV-VGANILKEGSDPKVLPDSEYPDWLWHLLEKRPALSELKMKNIETLPYEDLKRFLKLDNRAKIKENNS 127 (132)
Q Consensus 49 ~~v~~~~~~~~~-~g~Ni~K~g~dp~~~~D~eYP~WLw~lld~~~~l~~l~~~~~e~l~~~~~kR~lkl~nR~kIK~nN~ 127 (132)
+++.|+|+++|+ +|+||+|+|+||+|+||+|||+|||+|+|+.+...++...+.+..++++.+||+|++||++||+|||
T Consensus 2 ~~~~ss~~~gt~l~GlNi~K~g~DP~al~D~EYP~WLW~lld~~~~~~~~~~~~~~~~~~~~~~r~~r~~rr~~IK~~N~ 81 (85)
T PF08561_consen 2 PVETSSCPAGTVLKGLNILKDGKDPVALPDSEYPEWLWTLLDPKPKKSELKDPDEEGATRKERRRYLRKERRQKIKENNF 81 (85)
T ss_pred CcCCCcccccceeeeeeeecCCCCCccCCcchhhHHHHHhcCCccccccccccchhhhhHHHHHHHHHHHHHHHHHHHhH
Confidence 356688887665 7999999999999999999999999999999988888777778889999999999999999999999
Q ss_pred ccc
Q 032859 128 VKA 130 (132)
Q Consensus 128 lka 130 (132)
|++
T Consensus 82 l~~ 84 (85)
T PF08561_consen 82 LKK 84 (85)
T ss_pred hhc
Confidence 986
No 2
>KOG3435 consensus Mitochondrial/chloroplast ribosomal protein L54/L37 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=6.4e-32 Score=202.98 Aligned_cols=113 Identities=58% Similarity=0.833 Sum_probs=103.7
Q ss_pred hchhhhhhhhhcccccccCCCC-CCCCCCcccccccccccc-ccccceecccCCCCccCCCCCCchhhhhccCCccchHH
Q 032859 19 VGKVGQRTFAAGASKAKKGGKG-AASDAPKASILSKEVKST-TVVGANILKEGSDPKVLPDSEYPDWLWHLLEKRPALSE 96 (132)
Q Consensus 19 ~~~~~~R~yA~~~~k~kkg~Kg-~~~~a~k~~~v~~~~~~~-~~~g~Ni~K~g~dp~~~~D~eYP~WLw~lld~~~~l~~ 96 (132)
...+++|+||..+++.++.|+| +..+.++.+++.++|+.+ |+||.||+|+|.||+||||+|||+|||+++|.+|.+.|
T Consensus 13 ~~~~~~rt~a~~a~kask~g~~~~~~~~~kvs~~~~~~ks~~tv~~~n~~k~g~d~kiLPdseyPdwLw~l~~~~pv~~e 92 (127)
T KOG3435|consen 13 QFSVYARTLAARASKASKSGKGGGSYDKPKVSVETDAIKSDATVCGANYLKDGHDPKILPDSEYPDWLWKLLDKDPVLLE 92 (127)
T ss_pred HHHHHHhcccchhhhhhhccccCCccccCcccccccccccchhhHHHHHhhcCCCCccCCCCcCcchhHhhCCCCcccHH
Confidence 3567889999877899999988 777888888888899976 99999999999999999999999999999999999998
Q ss_pred HhhcCCCCCCHHHHHHHHhHHHHHHHHhccccccc
Q 032859 97 LKMKNIETLPYEDLKRFLKLDNRAKIKENNSVKAK 131 (132)
Q Consensus 97 l~~~~~e~l~~~~~kR~lkl~nR~kIK~nN~lkak 131 (132)
..+.+.++..+++++|++++.+|.+||+||||++|
T Consensus 93 ~~e~~~~~~~~~~~kr~~kla~r~rikqnn~l~kk 127 (127)
T KOG3435|consen 93 DLEKPEETWLYDDLKRFRKLATRSRIKQNNFLKKK 127 (127)
T ss_pred hccCcccchhhHhHHHHHHHHHHHHHHhcchhhcC
Confidence 88888899999999999999999999999999986
No 3
>KOG3435 consensus Mitochondrial/chloroplast ribosomal protein L54/L37 [Translation, ribosomal structure and biogenesis]
Probab=92.90 E-value=0.031 Score=42.71 Aligned_cols=28 Identities=25% Similarity=0.247 Sum_probs=23.0
Q ss_pred cceecccCCCCccCCCCCCchhhhhccC
Q 032859 62 GANILKEGSDPKVLPDSEYPDWLWHLLE 89 (132)
Q Consensus 62 g~Ni~K~g~dp~~~~D~eYP~WLw~lld 89 (132)
+.-+.-.+.||++++|.|||+|+|.+.|
T Consensus 78 dwLw~l~~~~pv~~e~~e~~~~~~~~~~ 105 (127)
T KOG3435|consen 78 DWLWKLLDKDPVLLEDLEKPEETWLYDD 105 (127)
T ss_pred chhHhhCCCCcccHHhccCcccchhhHh
Confidence 3444447899999999999999999873
No 4
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=63.51 E-value=3.2 Score=36.19 Aligned_cols=24 Identities=29% Similarity=0.482 Sum_probs=19.8
Q ss_pred CCccCCCCCCchhhhhccCCccch
Q 032859 71 DPKVLPDSEYPDWLWHLLEKRPAL 94 (132)
Q Consensus 71 dp~~~~D~eYP~WLw~lld~~~~l 94 (132)
-.....|++||+||.++.+|++.|
T Consensus 77 ~~i~~~d~~YP~~Lk~i~~pP~vL 100 (350)
T COG0758 77 KIITLGDEDYPKLLKEINDPPPVL 100 (350)
T ss_pred eEeccCCccchHHHHhccCCCeEE
Confidence 345778999999999999998643
No 5
>PRK01202 glycine cleavage system protein H; Provisional
Probab=33.27 E-value=25 Score=26.04 Aligned_cols=50 Identities=24% Similarity=0.475 Sum_probs=32.8
Q ss_pred ccccccceecccCCCCccCCCCCCch-hhhhccCCcc-chHHHhhcCCCCCCHHHHHHHH
Q 032859 57 STTVVGANILKEGSDPKVLPDSEYPD-WLWHLLEKRP-ALSELKMKNIETLPYEDLKRFL 114 (132)
Q Consensus 57 ~~~~~g~Ni~K~g~dp~~~~D~eYP~-WLw~lld~~~-~l~~l~~~~~e~l~~~~~kR~l 114 (132)
+|+++-+|--- ..||.++.++.|-+ ||+.+....+ .+++| ++.+++..++
T Consensus 74 sG~Vv~vN~~l-~~~p~~ln~~p~~~gWl~~v~~~~~~~~~~L-------~~~~~Y~~~~ 125 (127)
T PRK01202 74 SGEVVEVNEAL-EDSPELVNEDPYGEGWLFKIKPSDESELDDL-------LDAEAYEALI 125 (127)
T ss_pred CeEEEEEhHHh-hhCcHhhcCCCCCCceEEEEEeCCHHHHHhC-------CCHHHHHHHh
Confidence 56776665322 47899999999986 9999964432 22333 5666666654
No 6
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=30.63 E-value=17 Score=22.81 Aligned_cols=15 Identities=27% Similarity=0.722 Sum_probs=10.5
Q ss_pred ceecccCCCCccCCCCCCchhh
Q 032859 63 ANILKEGSDPKVLPDSEYPDWL 84 (132)
Q Consensus 63 ~Ni~K~g~dp~~~~D~eYP~WL 84 (132)
.++|.+. ---||+||
T Consensus 27 ~~yY~~k-------~~~~P~WL 41 (41)
T PF14475_consen 27 RKYYTEK-------GRPFPGWL 41 (41)
T ss_pred HHHHHHc-------CCCCCCcC
Confidence 4677765 34589998
No 7
>TIGR00527 gcvH glycine cleavage system H protein. The genome of Aquifex aeolicus contains one protein scoring above the trusted cutoff and clustering with other bacterial H proteins, and four more proteins clustering together and scoring below the trusted cutoff; it seems doubtful that all of these homologs are authentic H protein. The Chlamydial homolog of H protein is nearly as divergent as the Aquifex outgroup, is not accompanied by P and T proteins, is not included in the seed alignment, and consequently also scores below the trusted cutoff.
Probab=29.02 E-value=29 Score=25.72 Aligned_cols=51 Identities=25% Similarity=0.366 Sum_probs=33.9
Q ss_pred ccccccceecccCCCCccCCCCCCch-hhhhccCCcc-chHHHhhcCCCCCCHHHHHHHHh
Q 032859 57 STTVVGANILKEGSDPKVLPDSEYPD-WLWHLLEKRP-ALSELKMKNIETLPYEDLKRFLK 115 (132)
Q Consensus 57 ~~~~~g~Ni~K~g~dp~~~~D~eYP~-WLw~lld~~~-~l~~l~~~~~e~l~~~~~kR~lk 115 (132)
+|+++.+|- .=..||.++-++.|-+ ||..+....+ .++.| ++.++++.++.
T Consensus 73 sG~Vv~vN~-~l~~~P~lln~~py~~gWl~~i~~~~~~~~~~L-------l~~~~Y~~~~~ 125 (127)
T TIGR00527 73 SGTVVEVND-ALEDSPELVNEDPYGGGWLIKVKLSDESELEGL-------MDAEQYEATLE 125 (127)
T ss_pred cEEEEEehH-hhhhChHHHhCCCccCcEEEEEecCCHHHHHhc-------CCHHHHHHHhh
Confidence 678866662 2256799999999965 9999964432 12222 67777877764
No 8
>PRK13380 glycine cleavage system protein H; Provisional
Probab=29.00 E-value=41 Score=25.64 Aligned_cols=52 Identities=27% Similarity=0.510 Sum_probs=34.2
Q ss_pred ccccccceecccCCCCccCCCCCCch-hhhhccCCccchHHHhhcCCCCCCHHHHHHHHh
Q 032859 57 STTVVGANILKEGSDPKVLPDSEYPD-WLWHLLEKRPALSELKMKNIETLPYEDLKRFLK 115 (132)
Q Consensus 57 ~~~~~g~Ni~K~g~dp~~~~D~eYP~-WLw~lld~~~~l~~l~~~~~e~l~~~~~kR~lk 115 (132)
+|+++.+|.- =..||.++-.+-|-+ ||..+-...+ .+++ . -++.+++..++.
T Consensus 81 sG~Vv~vN~~-l~~~P~lln~dpy~~gWl~~v~~~d~--~~~~--~--Ll~~~~y~~~~~ 133 (144)
T PRK13380 81 TGEVVEVNEA-LEDSPELVNEDPYGEGWFFRFKPANP--EELK--Q--LLDGDAADRLLK 133 (144)
T ss_pred CEEEEEEHHh-hhhChHHhcCCCCCCCeEEEEEECCH--HHHH--h--cCCHHHHHHHHH
Confidence 6788777743 246899998899965 9999954332 2221 1 166777777765
No 9
>PHA02616 VP2/VP3; Provisional
Probab=24.88 E-value=39 Score=28.33 Aligned_cols=18 Identities=44% Similarity=1.075 Sum_probs=13.6
Q ss_pred Cchhhhhc----cCCccchHHH
Q 032859 80 YPDWLWHL----LEKRPALSEL 97 (132)
Q Consensus 80 YP~WLw~l----ld~~~~l~~l 97 (132)
-|||||++ |-+-|++.+.
T Consensus 20 vPDWlfn~vas~LpElPslqdv 41 (259)
T PHA02616 20 VPDWLFNLVASYLPELPSLQDV 41 (259)
T ss_pred ccHHHHHHHHHhcccCCCHHHH
Confidence 49999999 6666776654
No 10
>PF10940 DUF2618: Protein of unknown function (DUF2618); InterPro: IPR021237 This bacterial family of proteins has no known function. The sequences within the family are highly conserved.
Probab=24.81 E-value=39 Score=21.11 Aligned_cols=14 Identities=29% Similarity=0.401 Sum_probs=12.3
Q ss_pred chhhHHHhhhhhhh
Q 032859 2 AMNQITSLRSFIMV 15 (132)
Q Consensus 2 ~~~~~r~~r~~~~~ 15 (132)
+|..||.+|+++..
T Consensus 5 lMaHIRRtrHiMmp 18 (40)
T PF10940_consen 5 LMAHIRRTRHIMMP 18 (40)
T ss_pred HHHHHHhhhhhhch
Confidence 58999999999874
No 11
>PF04614 Pex19: Pex19 protein family; InterPro: IPR006708 Peroxisome(s) form an intracellular compartment, bounded by a typical lipid bilayer membrane. Peroxisome functions are often specialised by organism and cell type; two widely distributed and well-conserved functions are H2O2-based respiration and fatty acid beta-oxidation. Other functions include ether lipid (plasmalogen) synthesis and cholesterol synthesis in animals, the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. PEX genes encode the machinery ("peroxins") required to assemble the peroxisome. Membrane assembly and maintenance requires three of these (peroxins 3, 16, and 19) and may occur without the import of the matrix (lumen) enzymes. Matrix protein import follows a branched pathway of soluble recycling receptors, with one branch for each class of peroxisome targeting sequence (two are well characterised), and a common trunk for all. At least one of these receptors, Pex5p, enters and exits peroxisomes as it functions. Proliferation of the organelle is regulated by Pex11p. Peroxisome biogenesis is remarkably conserved among eukaryotes. A group of fatal, inherited neuropathologies are recognised as peroxisome biogenesis diseases. ; GO: 0005777 peroxisome; PDB: 2WL8_B 2W85_B.
Probab=23.73 E-value=44 Score=27.51 Aligned_cols=15 Identities=33% Similarity=0.397 Sum_probs=9.3
Q ss_pred CCCCHHHHHHHHhHH
Q 032859 103 ETLPYEDLKRFLKLD 117 (132)
Q Consensus 103 e~l~~~~~kR~lkl~ 117 (132)
..++.+++.||.+..
T Consensus 161 ~~l~~ed~~rY~~Q~ 175 (248)
T PF04614_consen 161 SKLSAEDYERYEKQY 175 (248)
T ss_dssp CCS-HHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHHH
Confidence 356777777776553
Done!