Query 033206
Match_columns 125
No_of_seqs 111 out of 336
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 11:07:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033206.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033206hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3106 ER lumen protein retai 100.0 4E-55 8.7E-60 341.9 7.7 124 1-125 1-212 (212)
2 COG5196 ERD2 ER lumen protein 100.0 2.6E-47 5.7E-52 295.1 8.4 125 1-125 1-214 (214)
3 PF00810 ER_lumen_recept: ER l 99.8 1E-20 2.2E-25 142.3 3.5 33 28-60 1-35 (147)
4 PF04193 PQ-loop: PQ loop repe 90.9 0.51 1.1E-05 29.4 4.1 36 16-51 17-52 (61)
5 smart00679 CTNS Repeated motif 88.8 0.3 6.6E-06 26.9 1.6 22 20-41 7-28 (32)
6 TIGR00951 2A43 Lysosomal Cysti 71.5 3.3 7.2E-05 32.8 2.4 31 16-46 19-49 (220)
7 PTZ00154 40S ribosomal protein 70.6 2.8 6.1E-05 31.6 1.6 27 5-38 49-75 (134)
8 PF00833 Ribosomal_S17e: Ribos 55.1 7.9 0.00017 28.7 1.6 27 5-38 49-75 (121)
9 KOG3211 Predicted endoplasmic 53.6 10 0.00022 30.9 2.1 26 20-45 50-75 (230)
10 KOG0187 40S ribosomal protein 46.9 15 0.00032 27.6 1.9 27 5-38 49-75 (134)
11 COG4095 Uncharacterized conser 44.2 52 0.0011 23.2 4.2 39 7-45 11-49 (89)
12 PF03083 MtN3_slv: Sugar efflu 35.6 56 0.0012 21.4 3.3 36 4-39 3-41 (87)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4e-55 Score=341.92 Aligned_cols=124 Identities=56% Similarity=0.974 Sum_probs=121.9
Q ss_pred CchhhhhhhhHHHHHHHHHHHHHHhhhhccccccchhHHHHHHHHhhhhhcccchHHHHH--------------------
Q 033206 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCSGVSLKTQELYALVFTTRYLDIFTDFVSIRL-------------------- 60 (125)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ly~~vf~~Ryldl~~~~~s~Yn-------------------- 60 (125)
||.||++||++|++|+++|+.||+|+|||+|+|+|||+|||+||++||+|+|+.+.|.||
T Consensus 1 mn~fr~~gd~~H~~~i~vLi~Ki~ktrsCaGiSlKSQ~L~Alvf~~Ryldlf~~~~s~ynt~mki~fl~~t~~ivymi~~ 80 (212)
T KOG3106|consen 1 MNNFRFAGDLSHLAAIIVLILKIWKTKSCAGISLKSQELFALVFATRYLDLFTFYESLYNTIMKIAFLASTLWIVYMIRF 80 (212)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 899999999999999999999999999999999999999999999999999998999998
Q ss_pred ----------------------------------------HHHHHHH----------------------------HHHhh
Q 033206 61 ----------------------------------------MFSVIVE----------------------------IAYRG 72 (125)
Q Consensus 61 ----------------------------------------tFSiyLE----------------------------G~yR~ 72 (125)
|||+||| |+||+
T Consensus 81 k~~~tYd~~~DtFri~~llvp~~vlsl~i~~~~t~~eilWtFsiyLEsVaILPQL~~lq~tg~~E~~TahYvfaLG~yR~ 160 (212)
T KOG3106|consen 81 KLRATYDKEKDTFRIEYLLVPSAVLSLLINHSFTILEILWTFSIYLESVAILPQLFMLQKTGEAETITAHYLFALGLYRA 160 (212)
T ss_pred HHHHHHhcccCceeEEEEehhheeeeeeecCCccHHHHHHHHHHHHHHHHHhHHHHHHHhcCCccchHHHHHHHHHHHHH
Confidence 9999999 99999
Q ss_pred hhhhcceeEeeeCCcccchHHhHHHHHHHHHHhhhhheeeeecccCccccCCC
Q 033206 73 LYILNWVYRYFTEPHYVHWIPWISGLVQTLLYADFFYYYFDSWKNNKNLQLPA 125 (125)
Q Consensus 73 ly~~~Wi~ry~~~~~~~~~~~i~~givQt~ly~DFfy~Y~~~v~~G~~~~lp~ 125 (125)
+|++|||+|+.+|+.+ |+++++||+|||++||||||+|+++|++|||++||+
T Consensus 161 ly~~~WI~r~~~e~~~-~~iai~agiVQT~ly~DFfy~Y~~~v~~g~~~~LP~ 212 (212)
T KOG3106|consen 161 LYIANWIYRYVTEDFW-DPIAIVAGIVQTVLYADFFYLYVTKVLQGKKLKLPA 212 (212)
T ss_pred HHHHHHHHHHHhhccc-cchHHHHHHHHHHHHHhHHHHHHHHHHcCCcCCCCC
Confidence 9999999999999987 999999999999999999999999999999999996
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.6e-47 Score=295.08 Aligned_cols=125 Identities=47% Similarity=0.724 Sum_probs=119.6
Q ss_pred CchhhhhhhhHHHHHHHHHHHHHHhhhhccccccchhHHHHHHHHhhhhhcc-cchHHHHH-------------------
Q 033206 1 MNIFRLAGDMTHLASVLVLLLKIHTIKSCSGVSLKTQELYALVFTTRYLDIF-TDFVSIRL------------------- 60 (125)
Q Consensus 1 mn~fr~~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ly~~vf~~Ryldl~-~~~~s~Yn------------------- 60 (125)
||.||++||++|++|+.+|++||.++|||+|+|+|||.||++||++||+|++ ++++|+||
T Consensus 1 m~~Fr~lGD~~Hlasi~vLih~ik~tr~csGlSlKtq~Ly~lVfitRYldLf~f~~~slYn~lMki~FI~s~~yI~~lm~ 80 (214)
T COG5196 1 MDTFRFLGDFLHLASIAVLIHKIKRTRSCSGLSLKTQFLYSLVFITRYLDLFDFYARSLYNSLMKILFIGSQVYILFLMR 80 (214)
T ss_pred CcHHHHHhHHHHHHHHHHHHHHhhhcceecceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 8999999999999999999999999999999999999999999999999999 57788888
Q ss_pred -----------------------------------------HHHHHHH----------------------------HHHh
Q 033206 61 -----------------------------------------MFSVIVE----------------------------IAYR 71 (125)
Q Consensus 61 -----------------------------------------tFSiyLE----------------------------G~yR 71 (125)
|||+||| |+||
T Consensus 81 ~~~r~tYdk~lDtF~i~~ll~gsav~slff~~~~tisnvlwtfS~wLESVAILPQL~mLq~~GeteslT~hYvfamgLYR 160 (214)
T COG5196 81 FKYRSTYDKKLDTFNILTLLVGSAVFSLFFTRGGTISNVLWTFSLWLESVAILPQLVMLQEAGETESLTSHYVFAMGLYR 160 (214)
T ss_pred hcccchHHHhhhhhhhhhhhhhhhhheeeecCCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeHHHHHHHHHHHH
Confidence 9999999 9999
Q ss_pred hhhhhcceeEeeeCCcccchHHhHHHHHHHHHHhhhhheeeeecccCccccCCC
Q 033206 72 GLYILNWVYRYFTEPHYVHWIPWISGLVQTLLYADFFYYYFDSWKNNKNLQLPA 125 (125)
Q Consensus 72 ~ly~~~Wi~ry~~~~~~~~~~~i~~givQt~ly~DFfy~Y~~~v~~G~~~~lp~ 125 (125)
++|++|||+|+..+.+-.+-+++.||++||+||.|||+.|++.|.+||+++||+
T Consensus 161 alYip~wI~r~~~~~kk~~~iai~aGivQTlLY~DFf~iYyr~V~rGk~f~LP~ 214 (214)
T COG5196 161 ALYIPYWILRKVYDIKKTGNIAIAAGIVQTLLYLDFFAIYYRYVFRGKSFSLPS 214 (214)
T ss_pred HhhhhHHHHHhhhcccccccchhHHHHHHHHHHHHhHHhhhhhhhcccccCCCC
Confidence 999999999998885445999999999999999999999999999999999996
No 3
>PF00810 ER_lumen_recept: ER lumen protein retaining receptor; InterPro: IPR000133 Proteins resident in the lumen of the endoplasmic reticulum (ER) contain a C-terminal tetrapeptide, commonly known as Lys-Asp-Glu-Leu (KDEL) in mammals and His-Asp-Glu-Leu (HDEL) in yeast (Saccharomyces cerevisiae) that acts as a signal for their retrieval from subsequent compartments of the secretory pathway. The receptor for this signal is a ~26 kDa Golgi membrane protein, initially identified as the ERD2 gene product in S. cerevisiae. The receptor molecule, known variously as the ER lumen protein retaining receptor or the 'KDEL receptor', is believed to cycle between the cis side of the Golgi apparatus and the ER. It has also been characterised in a number of other species, including plants, Plasmodium, Drosophila and mammals. In mammals, 2 highly related forms of the receptor are known. The KDEL receptor is a highly hydrophobic protein of 220 residues; its sequence exhibits 7 hydrophobic regions, all of which have been suggested to traverse the membrane []. More recently, however, it has been suggested that only 6 of these regions are transmembrane (TM), resulting in both N- and C-termini on the cytoplasmic side of the membrane.; GO: 0046923 ER retention sequence binding, 0006621 protein retention in ER lumen, 0016021 integral to membrane
Probab=99.81 E-value=1e-20 Score=142.25 Aligned_cols=33 Identities=64% Similarity=1.042 Sum_probs=29.6
Q ss_pred hccccccchhHHHHHHHHhhhhhc--ccchHHHHH
Q 033206 28 SCSGVSLKTQELYALVFTTRYLDI--FTDFVSIRL 60 (125)
Q Consensus 28 S~~GiSlktQ~ly~~vf~~Ryldl--~~~~~s~Yn 60 (125)
||+|+|+|||+||++|+++||+|+ ++.+.+.||
T Consensus 1 S~~GlSlktq~ly~~vf~~Ryldl~~f~~~~s~y~ 35 (147)
T PF00810_consen 1 SCSGLSLKTQILYAIVFLTRYLDLFWFESYLSLYN 35 (147)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Confidence 899999999999999999999999 666666666
No 4
>PF04193 PQ-loop: PQ loop repeat
Probab=90.92 E-value=0.51 Score=29.41 Aligned_cols=36 Identities=25% Similarity=0.099 Sum_probs=29.1
Q ss_pred HHHHHHHHHhhhhccccccchhHHHHHHHHhhhhhc
Q 033206 16 VLVLLLKIHTIKSCSGVSLKTQELYALVFTTRYLDI 51 (125)
Q Consensus 16 ~~iLl~ki~~~kS~~GiSlktQ~ly~~vf~~Ryldl 51 (125)
.+==+.|.+|+||+.|+|..+..+..+..+++-+..
T Consensus 17 ~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~~~~ 52 (61)
T PF04193_consen 17 FLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWVLYS 52 (61)
T ss_pred HHhHHHHHHHccccccccHHHHHHHHHHHHHHHHHH
Confidence 333368899999999999999999998888775543
No 5
>smart00679 CTNS Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. Function unknown, but likely to be associated with the glycosylation machinery.
Probab=88.79 E-value=0.3 Score=26.86 Aligned_cols=22 Identities=27% Similarity=0.274 Sum_probs=18.0
Q ss_pred HHHHHhhhhccccccchhHHHH
Q 033206 20 LLKIHTIKSCSGVSLKTQELYA 41 (125)
Q Consensus 20 l~ki~~~kS~~GiSlktQ~ly~ 41 (125)
+.|++|+||+.|+|.-...+-.
T Consensus 7 i~~~~~~ks~~glS~~~~~l~~ 28 (32)
T smart00679 7 IIKNYRRKSTEGLSILFVLLWL 28 (32)
T ss_pred HHHHHHcCCcCcCCHHHHHHHH
Confidence 5789999999999987766544
No 6
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=71.54 E-value=3.3 Score=32.80 Aligned_cols=31 Identities=26% Similarity=0.247 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhhhccccccchhHHHHHHHHh
Q 033206 16 VLVLLLKIHTIKSCSGVSLKTQELYALVFTT 46 (125)
Q Consensus 16 ~~iLl~ki~~~kS~~GiSlktQ~ly~~vf~~ 46 (125)
.+==+.|.+|+||++|+|+..-.+-.+.+++
T Consensus 19 ~~PQi~~n~k~ks~~GlS~~~~~l~~~g~~~ 49 (220)
T TIGR00951 19 FYPQIIKNWRRKSAEGLSFDFVMLNLVGFTA 49 (220)
T ss_pred HhhHHHHHHhccccCCcCHHHHHHHHHHHHH
Confidence 3334678999999999999988765554433
No 7
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=70.57 E-value=2.8 Score=31.60 Aligned_cols=27 Identities=44% Similarity=0.576 Sum_probs=20.4
Q ss_pred hhhhhhHHHHHHHHHHHHHHhhhhccccccchhH
Q 033206 5 RLAGDMTHLASVLVLLLKIHTIKSCSGVSLKTQE 38 (125)
Q Consensus 5 r~~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ 38 (125)
|++|...|+ .|-.....+.|||+|.|+
T Consensus 49 rIAGYIThl-------mkri~~gpvrgis~klqe 75 (134)
T PTZ00154 49 KIAGFVTHL-------MKRIQKGPVRGISLKLQE 75 (134)
T ss_pred HHHHHHHHH-------HhhhccCCccccceehhH
Confidence 677777775 344456789999999997
No 8
>PF00833 Ribosomal_S17e: Ribosomal S17; InterPro: IPR001210 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 archaebacterial ribosomal proteins can be grouped in this family of ribosomal proteins, S17e. They include, vertebrate, Drosophila and Neurospora crassa (crp-3) S17's as well as yeast S17a (RP51A) and S17b (RP51B) and archaebacterial S17e [, , ].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1RQ6_A 2XZM_V 2XZN_V 3IZ6_Q 3IZB_Q 3O30_K 3O2Z_K 3U5G_R 3U5C_R.
Probab=55.12 E-value=7.9 Score=28.70 Aligned_cols=27 Identities=41% Similarity=0.578 Sum_probs=19.5
Q ss_pred hhhhhhHHHHHHHHHHHHHHhhhhccccccchhH
Q 033206 5 RLAGDMTHLASVLVLLLKIHTIKSCSGVSLKTQE 38 (125)
Q Consensus 5 r~~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ 38 (125)
|++|...|+ .|-.+.....|+|+|.|+
T Consensus 49 kIAGYvThl-------mKriq~g~vrgis~klqE 75 (121)
T PF00833_consen 49 KIAGYVTHL-------MKRIQRGPVRGISIKLQE 75 (121)
T ss_dssp HHHHHHHHH-------HHHHTSSSSTTCSSCCCC
T ss_pred HHHHHHHHH-------HHHHHhccccccchhhhH
Confidence 567777765 344456678899999996
No 9
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=53.64 E-value=10 Score=30.87 Aligned_cols=26 Identities=31% Similarity=0.423 Sum_probs=22.8
Q ss_pred HHHHHhhhhccccccchhHHHHHHHH
Q 033206 20 LLKIHTIKSCSGVSLKTQELYALVFT 45 (125)
Q Consensus 20 l~ki~~~kS~~GiSlktQ~ly~~vf~ 45 (125)
+.||...||+.|+|.-+|+|=.+.++
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgyt 75 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYT 75 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHH
Confidence 57899999999999999998777664
No 10
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=46.88 E-value=15 Score=27.65 Aligned_cols=27 Identities=41% Similarity=0.656 Sum_probs=19.6
Q ss_pred hhhhhhHHHHHHHHHHHHHHhhhhccccccchhH
Q 033206 5 RLAGDMTHLASVLVLLLKIHTIKSCSGVSLKTQE 38 (125)
Q Consensus 5 r~~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ 38 (125)
+++|...|+ ..+|.+. .+.|||+|.|+
T Consensus 49 kIAGyvtHL------mkrIqkG-pvRGISiKLQE 75 (134)
T KOG0187|consen 49 KIAGYVTHL------MKRIQKG-PVRGISIKLQE 75 (134)
T ss_pred HHHHHHHHH------HHHHHcC-CccceeEeecH
Confidence 467777775 3455554 78999999997
No 11
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=44.22 E-value=52 Score=23.23 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=29.6
Q ss_pred hhhhHHHHHHHHHHHHHHhhhhccccccchhHHHHHHHH
Q 033206 7 AGDMTHLASVLVLLLKIHTIKSCSGVSLKTQELYALVFT 45 (125)
Q Consensus 7 ~gd~~hl~s~~iLl~ki~~~kS~~GiSlktQ~ly~~vf~ 45 (125)
.|-..-.++++-=+.|+.|+|+.+++|+-.-....+..+
T Consensus 11 ia~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~ia~~ 49 (89)
T COG4095 11 IAGILTTFAFLPQLIKIIKTKNTASISLPMFIILNIALF 49 (89)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHH
Confidence 455666778888889999999999999877665555443
No 12
>PF03083 MtN3_slv: Sugar efflux transporter for intercellular exchange; InterPro: IPR004316 This family includes proteins such as Drosophila saliva [], MtN3 involved in root nodule development [] and proteins involved in activation and expression of recombination activation genes (RAGs) []. Although the molecular function of these proteins is unknown, they are almost certainly transmembrane proteins. This signature maps to transmembrane helices which are found in two copies in most members of the family.; GO: 0016021 integral to membrane
Probab=35.63 E-value=56 Score=21.41 Aligned_cols=36 Identities=14% Similarity=0.155 Sum_probs=24.9
Q ss_pred hhhhhhhHHHHHH---HHHHHHHHhhhhccccccchhHH
Q 033206 4 FRLAGDMTHLASV---LVLLLKIHTIKSCSGVSLKTQEL 39 (125)
Q Consensus 4 fr~~gd~~hl~s~---~iLl~ki~~~kS~~GiSlktQ~l 39 (125)
+..+|....++.. +--+.++.|+||.+++|.-....
T Consensus 3 lg~~~~~~~i~~~~spl~~i~~v~k~ks~~~~~~~~~~~ 41 (87)
T PF03083_consen 3 LGILASVSSIIMFLSPLPQIRQVIKTKSTGSVSFPPFLA 41 (87)
T ss_pred eeHHHHHHHHHHHHHHHHHHHHHHhCCCCCccceehhHH
Confidence 3455555555444 36678999999999999875443
Done!