Query psy1718
Match_columns 142
No_of_seqs 101 out of 188
Neff 2.3
Searched_HMMs 46136
Date Fri Aug 16 23:54:23 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1718.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1718hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00196 60S ribosomal protein 100.0 6.9E-33 1.5E-37 204.1 4.3 61 1-61 22-82 (98)
2 PF01158 Ribosomal_L36e: Ribos 100.0 2.5E-32 5.4E-37 200.5 1.7 61 1-61 22-82 (98)
3 KOG3452|consensus 100.0 3.1E-30 6.8E-35 191.9 3.8 61 1-61 24-84 (102)
4 COG5051 RPL36A Ribosomal prote 99.9 2.7E-22 5.9E-27 148.4 3.1 62 1-62 24-85 (97)
5 PF13058 DUF3920: Protein of u 36.4 26 0.00057 27.7 1.9 29 25-60 97-125 (126)
6 smart00407 IGc1 Immunoglobulin 31.0 38 0.00082 21.9 1.7 17 103-119 9-25 (75)
7 COG0057 GapA Glyceraldehyde-3- 25.6 30 0.00066 30.8 0.7 35 76-110 281-317 (335)
8 KOG2659|consensus 23.7 65 0.0014 27.3 2.3 45 12-56 82-132 (228)
9 cd05896 Ig1_IL1RAPL-1_like Fir 23.5 96 0.0021 23.1 2.9 21 98-118 18-49 (104)
10 cd00096 Ig Immunoglobulin doma 21.9 86 0.0019 16.5 1.9 21 99-119 2-22 (74)
11 PF12169 DNA_pol3_gamma3: DNA 21.8 1.2E+02 0.0026 21.5 3.1 34 19-52 4-39 (143)
12 KOG0396|consensus 21.3 77 0.0017 29.0 2.4 25 32-56 196-220 (389)
No 1
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=99.97 E-value=6.9e-33 Score=204.08 Aligned_cols=61 Identities=48% Similarity=0.834 Sum_probs=59.4
Q ss_pred CCcCcccCCCCcchHHHHHHhhhhccccchhHhHHHHhhccchhhHHHHHHhhhhceeecc
Q psy1718 1 MRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLYVLRS 61 (142)
Q Consensus 1 ~R~SrrKG~lTKrtKfVRdiIREV~GFAPYERRaMELLKVSKDKRALKFaKKRLGTHiRr~ 61 (142)
+|||+++|.+|||++||||||+|||||||||+|+|||||+|+||+||||+|||||||+||-
T Consensus 22 ~r~s~rkg~~tkr~~fVr~vIrEV~GfaPYErr~mELLkv~kdKrAlKfaKkRlGth~RaK 82 (98)
T PTZ00196 22 PSPSKRKGLLSKRKRLVKDVIREVCGFSPYERRMIELLKVGKDKRALKYAKKRLGTHKRAK 82 (98)
T ss_pred CCcccccCCCCchhHHHHHHHHHHhcccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999984
No 2
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=99.97 E-value=2.5e-32 Score=200.54 Aligned_cols=61 Identities=69% Similarity=0.985 Sum_probs=56.8
Q ss_pred CCcCcccCCCCcchHHHHHHhhhhccccchhHhHHHHhhccchhhHHHHHHhhhhceeecc
Q psy1718 1 MRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLYVLRS 61 (142)
Q Consensus 1 ~R~SrrKG~lTKrtKfVRdiIREV~GFAPYERRaMELLKVSKDKRALKFaKKRLGTHiRr~ 61 (142)
+|||+++|.+|||++||||||+|||||||||+|+||||++|+||+||||+|||||||+||-
T Consensus 22 ~r~s~~kg~~tk~~kfvr~vIrEv~GfaPYEkr~mELlkv~kdKrAlKf~KKRlGth~RAK 82 (98)
T PF01158_consen 22 PRPSRRKGRLTKRTKFVRDVIREVCGFAPYEKRAMELLKVSKDKRALKFAKKRLGTHIRAK 82 (98)
T ss_dssp --STTS-SHHCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHHHH
T ss_pred CCcccccCccchhHHHHHHHHHHhcCCChHHHHHHHHHhcchhHHHHHHHHHHhhhhHHHH
Confidence 5899999999999999999999999999999999999999999999999999999999973
No 3
>KOG3452|consensus
Probab=99.96 E-value=3.1e-30 Score=191.91 Aligned_cols=61 Identities=64% Similarity=0.868 Sum_probs=59.6
Q ss_pred CCcCcccCCCCcchHHHHHHhhhhccccchhHhHHHHhhccchhhHHHHHHhhhhceeecc
Q psy1718 1 MRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLYVLRS 61 (142)
Q Consensus 1 ~R~SrrKG~lTKrtKfVRdiIREV~GFAPYERRaMELLKVSKDKRALKFaKKRLGTHiRr~ 61 (142)
||+|+++|.+|||++||++||+|||||||||+|+||||++|+||+|+||+|||||||+||-
T Consensus 24 pr~s~~kg~~sk~tkfvr~lirEv~G~aPyErr~meLlkvskdkrA~K~lKkRlGth~RAk 84 (102)
T KOG3452|consen 24 PRQSRRKGETSKRTKFVRDLIREVAGFAPYERRAMELLKVSKDKRALKLLKKRLGTHKRAK 84 (102)
T ss_pred CCcCccccchhhhHHHHHHHHHHHhCCChHHHHHHHHHHHcccHHHHHHHHHHhhHHHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999985
No 4
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.7e-22 Score=148.37 Aligned_cols=62 Identities=47% Similarity=0.727 Sum_probs=60.2
Q ss_pred CCcCcccCCCCcchHHHHHHhhhhccccchhHhHHHHhhccchhhHHHHHHhhhhceeecce
Q psy1718 1 MRPSRLKGIQTKNTKFTRDLVREVCGHAPYEKRAMELLKVSKDKRALKFLKRRVSLYVLRSA 62 (142)
Q Consensus 1 ~R~SrrKG~lTKrtKfVRdiIREV~GFAPYERRaMELLKVSKDKRALKFaKKRLGTHiRr~~ 62 (142)
.|||+++|.++++++||+++++|++||+|||+++||||+.|.||+|.|.+|||||+|+||.+
T Consensus 24 ~rps~kkgq~s~Rt~fvrsivrEiaGlsPyErr~i~Lirns~~krArKlakKRLGs~kRAka 85 (97)
T COG5051 24 ERPSRKKGQLSKRTEFVRSIVREIAGLSPYERRVIELIRNSQDKRARKLAKKRLGSLKRAKA 85 (97)
T ss_pred CCcchhhhccccHHHHHHHHHHHHccCCHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHHHH
Confidence 48999999999999999999999999999999999999999999999999999999999975
No 5
>PF13058 DUF3920: Protein of unknown function (DUF3920)
Probab=36.40 E-value=26 Score=27.66 Aligned_cols=29 Identities=41% Similarity=0.684 Sum_probs=24.8
Q ss_pred ccccchhHhHHHHhhccchhhHHHHHHhhhhceeec
Q psy1718 25 CGHAPYEKRAMELLKVSKDKRALKFLKRRVSLYVLR 60 (142)
Q Consensus 25 ~GFAPYERRaMELLKVSKDKRALKFaKKRLGTHiRr 60 (142)
.|-.|||.|.||- | |.+|+-..|...+|+
T Consensus 97 vg~e~yEeR~ie~-----D--Ar~FAe~kl~ey~~r 125 (126)
T PF13058_consen 97 VGKEPYEERWIEK-----D--ARAFAERKLDEYKRR 125 (126)
T ss_pred eccchHHHHHHHH-----H--HHHHHHHHHHHHhcC
Confidence 7999999999984 5 999999998877765
No 6
>smart00407 IGc1 Immunoglobulin C-Type.
Probab=30.99 E-value=38 Score=21.87 Aligned_cols=17 Identities=29% Similarity=0.704 Sum_probs=13.1
Q ss_pred ccccccceeEeeeeccC
Q psy1718 103 ESFYHNSIMLTWYKLST 119 (142)
Q Consensus 103 ~~~~~~~~~~~~~~~~~ 119 (142)
..||-..|.++|||-..
T Consensus 9 ~gf~P~~i~v~W~k~g~ 25 (75)
T smart00407 9 SGFYPPDITVTWLRNGQ 25 (75)
T ss_pred EeEeCCCCEEEEEECCE
Confidence 35787889999999543
No 7
>COG0057 GapA Glyceraldehyde-3-phosphate dehydrogenase/erythrose-4-phosphate dehydrogenase [Carbohydrate transport and metabolism]
Probab=25.56 E-value=30 Score=30.75 Aligned_cols=35 Identities=31% Similarity=0.369 Sum_probs=29.6
Q ss_pred hhhhhhhcccccceeeccccCce--eeeeccccccce
Q psy1718 76 ATRDIIRDRESSHFQLSQKIPTT--FVKCESFYHNSI 110 (142)
Q Consensus 76 ~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~ 110 (142)
..+|++-+.+||-|.-+|.+-.. |||.-++|||-.
T Consensus 281 Vs~D~~~~~~ssI~d~~~t~~~~~~~vk~~~wydNE~ 317 (335)
T COG0057 281 VSSDFNGDPHSSIFDASATIVLGGNLVKLVAWYDNEW 317 (335)
T ss_pred cccccCCCcceeEEEccceEeccCcEEEEEEEEeccc
Confidence 45788899999999999887655 999999999953
No 8
>KOG2659|consensus
Probab=23.66 E-value=65 Score=27.29 Aligned_cols=45 Identities=18% Similarity=0.285 Sum_probs=33.3
Q ss_pred cchHHHHHHhhhhccccc------hhHhHHHHhhccchhhHHHHHHhhhhc
Q psy1718 12 KNTKFTRDLVREVCGHAP------YEKRAMELLKVSKDKRALKFLKRRVSL 56 (142)
Q Consensus 12 KrtKfVRdiIREV~GFAP------YERRaMELLKVSKDKRALKFaKKRLGT 56 (142)
.-..++.++-.|+..-.. -..+.+||++.++-..|++|++-+|--
T Consensus 82 ~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~ 132 (228)
T KOG2659|consen 82 EAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAP 132 (228)
T ss_pred HHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccc
Confidence 334455666666665554 356999999999999999999987643
No 9
>cd05896 Ig1_IL1RAPL-1_like First immunoglobulin (Ig)-like domain of X-linked interleukin-1 receptor accessory protein-like 1 (IL1RAPL-1). Ig1_ IL1RAPL-1_like: domain similar to the first immunoglobulin (Ig)-like domain of X-linked interleukin-1 receptor accessory protein-like 1 (IL1RAPL-1). IL-1 alpha and IL-1 beta are cytokines which participates in the regulation of inflammation, immune responses, and hematopoiesis. These cytokines bind to the IL-1 receptor type 1 (IL1R1), which is activated on additional association with an accessory protein, IL1RAP. IL-1 also binds a second receptor designated type II (IL1R2). Mature IL1R1 consists of three Ig-like domains, a transmembrane domain, and a large cytoplasmic domain. Mature IL1R2 is organized similarly except that it has a short cytoplasmic domain. The latter does not initiate signal transduction. A naturally occurring cytokine IL-1RA (IL-1 receptor antagonist) is widely expressed and binds to IL-1 receptors, inhibiting the binding of
Probab=23.52 E-value=96 Score=23.07 Aligned_cols=21 Identities=43% Similarity=0.961 Sum_probs=15.3
Q ss_pred eeeeecccc----------ccc-eeEeeeecc
Q psy1718 98 TFVKCESFY----------HNS-IMLTWYKLS 118 (142)
Q Consensus 98 ~~~~~~~~~----------~~~-~~~~~~~~~ 118 (142)
--++|-.|| +.+ +.++|||-+
T Consensus 18 v~l~C~~~~~~~~~~~~~~~~~~~~v~WyK~~ 49 (104)
T cd05896 18 VRIKCALFYGYIRTNYSMAQSAGLSLMWYKSS 49 (104)
T ss_pred EEEECCCccccccccccccccCCceEEEEECC
Confidence 357999998 333 379999964
No 10
>cd00096 Ig Immunoglobulin domain. Ig: immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as, T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as, butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=21.87 E-value=86 Score=16.50 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=16.7
Q ss_pred eeeeccccccceeEeeeeccC
Q psy1718 99 FVKCESFYHNSIMLTWYKLST 119 (142)
Q Consensus 99 ~~~~~~~~~~~~~~~~~~~~~ 119 (142)
.+.|.....+...+.||+...
T Consensus 2 ~l~C~~~~~~~~~~~W~~~~~ 22 (74)
T cd00096 2 TLTCLASGPPPPTITWLKNGK 22 (74)
T ss_pred EEEEEecCCCCCcEEEEECCE
Confidence 467888888888999998754
No 11
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=21.85 E-value=1.2e+02 Score=21.46 Aligned_cols=34 Identities=24% Similarity=0.356 Sum_probs=24.5
Q ss_pred HHhhhhccccchhH--hHHHHhhccchhhHHHHHHh
Q psy1718 19 DLVREVCGHAPYEK--RAMELLKVSKDKRALKFLKR 52 (142)
Q Consensus 19 diIREV~GFAPYER--RaMELLKVSKDKRALKFaKK 52 (142)
+-|+++.|..+.|. .+++.|-.++-+.|++.+.+
T Consensus 4 e~V~~~lG~v~~~~i~~l~~ai~~~d~~~~l~~~~~ 39 (143)
T PF12169_consen 4 EDVREILGLVDEEQIFELLDAILEGDAAEALELLNE 39 (143)
T ss_dssp HHHHHHHTHTSTHHHHHHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 56899999999986 45555556777777777665
No 12
>KOG0396|consensus
Probab=21.28 E-value=77 Score=29.04 Aligned_cols=25 Identities=28% Similarity=0.491 Sum_probs=21.8
Q ss_pred HhHHHHhhccchhhHHHHHHhhhhc
Q psy1718 32 KRAMELLKVSKDKRALKFLKRRVSL 56 (142)
Q Consensus 32 RRaMELLKVSKDKRALKFaKKRLGT 56 (142)
++.+||+++.+-.+|..|+||-+++
T Consensus 196 QefIELi~~~~~~~Ai~~akk~f~~ 220 (389)
T KOG0396|consen 196 QEFIELIKVDNYDKAIAFAKKHFAP 220 (389)
T ss_pred HHHHHHHHhccHHHHHHHHHHHHhh
Confidence 3678999999999999999998765
Done!