Query 041965
Match_columns 166
No_of_seqs 111 out of 501
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 12:32:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041965.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041965hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2667 COPII vesicle protein 100.0 1.9E-48 4.1E-53 338.9 16.6 143 23-165 234-378 (379)
2 PF07970 COPIIcoated_ERV: Endo 100.0 1.7E-45 3.7E-50 301.8 12.4 123 24-146 97-222 (222)
3 PF10399 UCR_Fe-S_N: Ubiquitin 51.5 4.1 8.8E-05 25.1 -0.4 31 118-148 8-38 (41)
4 COG3765 WzzB Chain length dete 44.2 19 0.0004 32.0 2.4 39 104-144 297-335 (347)
5 PF10661 EssA: WXG100 protein 32.0 22 0.00048 27.5 0.9 13 130-142 128-140 (145)
6 PRK13718 conjugal transfer pro 31.8 60 0.0013 22.9 2.9 52 102-163 26-77 (84)
7 PF05365 UCR_UQCRX_QCR9: Ubiqu 29.6 53 0.0012 21.4 2.3 29 129-157 14-42 (55)
8 KOG4085 Uncharacterized conser 28.5 36 0.00079 26.9 1.6 20 123-142 26-45 (175)
9 PF07413 Herpes_UL37_2: Betahe 27.6 61 0.0013 27.9 2.9 40 115-154 228-270 (276)
10 PF11888 DUF3408: Protein of u 23.7 82 0.0018 23.7 2.7 32 122-153 87-119 (136)
11 KOG2014 SMT3/SUMO-activating c 23.0 26 0.00056 30.8 -0.2 11 130-140 286-296 (331)
12 PF01034 Syndecan: Syndecan do 21.8 31 0.00068 23.3 0.1 8 132-139 12-19 (64)
13 PF00673 Ribosomal_L5_C: ribos 21.4 1E+02 0.0022 21.9 2.7 23 112-134 1-23 (95)
14 PF00858 ASC: Amiloride-sensit 20.8 2.8E+02 0.006 23.7 5.8 37 100-136 386-422 (439)
15 KOG0910 Thioredoxin-like prote 20.3 88 0.0019 24.5 2.3 21 60-80 108-128 (150)
No 1
>KOG2667 consensus COPII vesicle protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.9e-48 Score=338.87 Aligned_cols=143 Identities=45% Similarity=0.809 Sum_probs=135.2
Q ss_pred CcCcccEEeeEeeeCCCCCCCCCCCCCceeeecCCceeEEEEEEEEEEEEEecCCceeeeeeeEEEEEEEeecC-CC-CC
Q 041965 23 KNVNVSHVIHDLSFGPKYPGIHNPLDGTVRMLHDTSGTFKYYIKIVPTEYRYISKDVLPTNQFSVTEYFSTFNE-FD-RT 100 (166)
Q Consensus 23 ~~~N~SH~I~~lsFG~~~p~~~~PLdg~~~i~~~~~~~~~YflkvVPT~y~~~~~~~~~t~qYSvt~~~~~~~~-~~-~~ 100 (166)
+++||||+|||||||+++|+..|||||+..++.++..+|+||+|||||.|++..+.++.|||||||++.+.... .+ .+
T Consensus 234 ~~~n~SH~InhLSFG~~~p~~~nPLdG~~~~~~~~~~~~~Yf~KvVPT~y~~~~~~~~~T~QysVt~~~~~~~~~~~~~~ 313 (379)
T KOG2667|consen 234 DNLNFSHRINHLSFGEYIPGIVNPLDGTNFIANEHLTTFQYFLKVVPTVYKYKSGRVIDTNQYSVTEYEYVLHSHRAKSG 313 (379)
T ss_pred ccCCceEEEeeeccCCCCcccccCCCCccccccCCccceeeEEEEcceEEEeecCceecceeeeeeeeEEeccccccccC
Confidence 57999999999999999999999999998888888999999999999999988999999999999999888862 33 38
Q ss_pred cceEEEEEeccceEEEEEeeeccHHHHHHHHhhhhcceeehhhhhHHHHHHHHHHHcCCcccCCC
Q 041965 101 WPAVYFLYDLSPITVTIKEERRSFLHLITRLCAVLGGTFALTGMLDRWMYRLLEALTKPSARSVL 165 (166)
Q Consensus 101 ~PgI~F~Yd~SPi~V~~~~~r~s~~~flt~lcAIiGGvftv~giiD~~~~~~~~~~~k~~~~~~~ 165 (166)
+|||||+||+|||+|+++|+|+||++|||||||||||+|||+||||++++++.+.+++|++.+++
T Consensus 314 ~PGifF~YelSPl~V~v~E~r~sf~~Flt~lCAIiGGvftvagiid~~~~~~~~~i~~k~~~gk~ 378 (379)
T KOG2667|consen 314 IPGIFFKYELSPLMVKVTEERQSFSHFLTRLCAIIGGVFTVAGILDSLLYHILELIKGKIALGKY 378 (379)
T ss_pred CCeEEEEEecCceEEEEEeccccHHHHHHHHHHHhcceeehHHHHHHHHHHHHHHHhcchhhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999988876
No 2
>PF07970 COPIIcoated_ERV: Endoplasmic reticulum vesicle transporter ; InterPro: IPR012936 This domain occurs in many hypothetical proteins, and also two partially characterised proteins. One of these proteins, PTX1 Q96RQ1 from SWISSPROT, is a homeodomain-containing transcription factor involved in regulating all pituitary hormone genes []. This protein is down regulated in prostate carcinoma []. The other protein, ERGIC-32 Q969X5 from SWISSPROT, is involved in protein transport from the ER to the Golgi [].
Probab=100.00 E-value=1.7e-45 Score=301.81 Aligned_cols=123 Identities=45% Similarity=0.836 Sum_probs=115.5
Q ss_pred cCcccEEeeEeeeCCCCCCCCCCCCCceee--ecCCceeEEEEEEEEEEEEEecCCceeeeeeeEEEEEEEeecCCC-CC
Q 041965 24 NVNVSHVIHDLSFGPKYPGIHNPLDGTVRM--LHDTSGTFKYYIKIVPTEYRYISKDVLPTNQFSVTEYFSTFNEFD-RT 100 (166)
Q Consensus 24 ~~N~SH~I~~lsFG~~~p~~~~PLdg~~~i--~~~~~~~~~YflkvVPT~y~~~~~~~~~t~qYSvt~~~~~~~~~~-~~ 100 (166)
.+|+||+|||||||+++|+..|||||+.++ .++...+++||||||||.|...++..++|||||+|++.+.+.... .+
T Consensus 97 ~~N~SH~I~~lsFG~~~~~~~~PLdg~~~~~~~~~~~~~~~YflkvVPT~y~~~~~~~~~t~qYsvt~~~~~~~~~~~~~ 176 (222)
T PF07970_consen 97 KFNFSHTINHLSFGEEIPGIVNPLDGTQKIVQTDNGNYMYQYFLKVVPTTYEDLDGFSIETYQYSVTEHSRPLNGGSSGG 176 (222)
T ss_pred CCCCCeEEEEEEeccccccccccccCccccccCCCCceeEEEEEEEeeeeeEeccccccccccccceeeeeeccCCCCCC
Confidence 799999999999999999999999999884 466789999999999999999887767999999999999987654 78
Q ss_pred cceEEEEEeccceEEEEEeeeccHHHHHHHHhhhhcceeehhhhhH
Q 041965 101 WPAVYFLYDLSPITVTIKEERRSFLHLITRLCAVLGGTFALTGMLD 146 (166)
Q Consensus 101 ~PgI~F~Yd~SPi~V~~~~~r~s~~~flt~lcAIiGGvftv~giiD 146 (166)
+|||||+||||||+|+++++|+||+||||+||||||||||++||||
T Consensus 177 ~PGI~F~Yd~SPi~v~~~~~r~s~~~flt~lcaIiGGvftv~gliD 222 (222)
T PF07970_consen 177 LPGIFFKYDFSPIMVVITEDRKSFLHFLTRLCAIIGGVFTVAGLID 222 (222)
T ss_pred CceEEEEEeceeEEEEEEEecCCHHHHHHHHHHHhchHheEEEecC
Confidence 9999999999999999999999999999999999999999999998
No 3
>PF10399 UCR_Fe-S_N: Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal; InterPro: IPR019470 This entry represents the TAT-signal region found in the iron-sulphur subunit of Ubiquinol-cytochrome C reductase (also known as the cytochrome bc1 complex). This enzymex is an oligomeric membrane protein complex that is a component of respiratory and photosynthetic electron transfer chains. It couples the transfer of electrons from ubiquinol to cytochrome c with the generation of a protein gradient across the membrane []. This entry is associated with IPR017941 from INTERPRO, IPR004192 from INTERPRO and IPR015248 from INTERPRO. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0055114 oxidation-reduction process; PDB: 1ZRT_R 2QJY_R 2FYN_L 2QJK_O 2QJP_I 2YIU_F.
Probab=51.47 E-value=4.1 Score=25.09 Aligned_cols=31 Identities=23% Similarity=0.326 Sum_probs=23.7
Q ss_pred EeeeccHHHHHHHHhhhhcceeehhhhhHHH
Q 041965 118 KEERRSFLHLITRLCAVLGGTFALTGMLDRW 148 (166)
Q Consensus 118 ~~~r~s~~~flt~lcAIiGGvftv~giiD~~ 148 (166)
..+|+.|+...+...|.+|++.++.-+++++
T Consensus 8 ~~~RRdFL~~at~~~gavG~~~~a~Pfv~s~ 38 (41)
T PF10399_consen 8 DPTRRDFLTIATSAVGAVGAAAAAWPFVSSM 38 (41)
T ss_dssp --HHHHHHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567888888889999999888887777664
No 4
>COG3765 WzzB Chain length determinant protein [Cell envelope biogenesis, outer membrane]
Probab=44.25 E-value=19 Score=31.99 Aligned_cols=39 Identities=18% Similarity=0.230 Sum_probs=29.2
Q ss_pred EEEEEeccceEEEEEeeeccHHHHHHHHhhhhcceeehhhh
Q 041965 104 VYFLYDLSPITVTIKEERRSFLHLITRLCAVLGGTFALTGM 144 (166)
Q Consensus 104 I~F~Yd~SPi~V~~~~~r~s~~~flt~lcAIiGGvftv~gi 144 (166)
--|+|+-+|..=+.+. .|=--+++-+.|+|||++.+...
T Consensus 297 ~~yRYl~~P~~Pvkrd--~PrrA~ilil~~LiGgm~g~g~v 335 (347)
T COG3765 297 STYRYLQKPTLPVKRD--SPRRAIILILGALIGGMLGAGVV 335 (347)
T ss_pred eEEEecCCCCCCCcCC--CcchHHHHHHHHHHHHHHHHHHH
Confidence 3578888886544322 46678999999999999988763
No 5
>PF10661 EssA: WXG100 protein secretion system (Wss), protein EssA; InterPro: IPR018920 The Wss (WXG100 protein secretion system) in Staphylococcus aureus seems to be encoded by a locus of eight ORFs, called ess (eSAT-6 secretion system) []. This locus encodes, amongst several other proteins, EssA, a protein predicted to possess one transmembrane domain. Due to its predicted membrane location and its absolute requirement for WXG100 protein secretion, it has been speculated that EssA could form a secretion apparatus in conjunction with YukC and YukAB. Proteins homologous to EssA, YukC, EsaA and YukD were absent from mycobacteria []. Members of this family are associated with type VII secretion of WXG100 family targets in the Firmicutes, but not in the Actinobacteria. This highly divergent protein family consists largely of a central region of highly polar low-complexity sequence containing occasional LF motifs in weak repeats about 17 residues in length, flanked by hydrophobic N- and C-terminal regions.
Probab=31.95 E-value=22 Score=27.51 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=7.0
Q ss_pred HHhhhhcceeehh
Q 041965 130 RLCAVLGGTFALT 142 (166)
Q Consensus 130 ~lcAIiGGvftv~ 142 (166)
.||+|+||+|+++
T Consensus 128 ~ll~i~~giy~~~ 140 (145)
T PF10661_consen 128 ILLAICGGIYVVL 140 (145)
T ss_pred HHHHHHHHHHHHH
Confidence 4455556665544
No 6
>PRK13718 conjugal transfer protein TrbE; Provisional
Probab=31.76 E-value=60 Score=22.92 Aligned_cols=52 Identities=21% Similarity=0.371 Sum_probs=27.6
Q ss_pred ceEEEEEeccceEEEEEeeeccHHHHHHHHhhhhcceeehhhhhHHHHHHHHHHHcCCcccC
Q 041965 102 PAVYFLYDLSPITVTIKEERRSFLHLITRLCAVLGGTFALTGMLDRWMYRLLEALTKPSARS 163 (166)
Q Consensus 102 PgI~F~Yd~SPi~V~~~~~r~s~~~flt~lcAIiGGvftv~giiD~~~~~~~~~~~k~~~~~ 163 (166)
|.|++++| +|+-+.....+..-++=+|+ |+++.+ --+++.+...+.++.+|+
T Consensus 26 PviywSWD----tVK~TTa~d~l~a~~iI~~~--gv~~~~----ly~ffs~Ltkl~~~d~~k 77 (84)
T PRK13718 26 PVIYWSWD----TVKETTADDMLAAVFVILYS--GVLLFI----LYFFFSALTKLQKHDERK 77 (84)
T ss_pred ceEEEEeh----hccccchhHHHHHHHHHHHH--hHHHHH----HHHHHHHHHHHHhccccc
Confidence 99999999 34444444444443333332 333333 345555555555555543
No 7
>PF05365 UCR_UQCRX_QCR9: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like; InterPro: IPR008027 The UQCRX/QCR9 protein is the 9/10 subunit of complex III, and is a protein of about 7 kDa. Deletion of QCR9 results in the inability of Saccharomyces cerevisiae to grow on a fermentable carbon source []. The protein is part of the mitchondrial respiratory chain. ; GO: 0008121 ubiquinol-cytochrome-c reductase activity, 0006122 mitochondrial electron transport, ubiquinol to cytochrome c, 0005740 mitochondrial envelope; PDB: 3CX5_T 2IBZ_I 1KYO_I 3CXH_T 1EZV_I 1P84_I 1KB9_I 3H1L_W 3L71_W 3L73_W ....
Probab=29.65 E-value=53 Score=21.35 Aligned_cols=29 Identities=14% Similarity=0.354 Sum_probs=20.4
Q ss_pred HHHhhhhcceeehhhhhHHHHHHHHHHHc
Q 041965 129 TRLCAVLGGTFALTGMLDRWMYRLLEALT 157 (166)
Q Consensus 129 t~lcAIiGGvftv~giiD~~~~~~~~~~~ 157 (166)
+=+.+|++|.|+.-..+|......-+.++
T Consensus 14 ~y~~~i~~gaf~fe~~fd~~~d~~w~~~N 42 (55)
T PF05365_consen 14 TYVLTIFAGAFFFERAFDSATDKIWDSIN 42 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHhcc
Confidence 34678888998888777777765555544
No 8
>KOG4085 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.55 E-value=36 Score=26.85 Aligned_cols=20 Identities=20% Similarity=0.330 Sum_probs=16.7
Q ss_pred cHHHHHHHHhhhhcceeehh
Q 041965 123 SFLHLITRLCAVLGGTFALT 142 (166)
Q Consensus 123 s~~~flt~lcAIiGGvftv~ 142 (166)
=|+.|+.++.||+|+++.+.
T Consensus 26 Ww~r~l~rl~gilgaf~~~~ 45 (175)
T KOG4085|consen 26 WWYRWLCRLSGILGAFSCAI 45 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 35899999999999988653
No 9
>PF07413 Herpes_UL37_2: Betaherpesvirus immediate-early glycoprotein UL37; InterPro: IPR010880 This family consists of several Betaherpesvirus immediate-early glycoprotein UL37 sequences. The human cytomegalovirus (HCMV) UL37 immediate-early regulatory protein is a type I integral membrane N-glycoprotein which traffics through the ER and the Golgi network [].
Probab=27.59 E-value=61 Score=27.90 Aligned_cols=40 Identities=15% Similarity=0.200 Sum_probs=28.0
Q ss_pred EEEEeeeccHHHH---HHHHhhhhcceeehhhhhHHHHHHHHH
Q 041965 115 VTIKEERRSFLHL---ITRLCAVLGGTFALTGMLDRWMYRLLE 154 (166)
Q Consensus 115 V~~~~~r~s~~~f---lt~lcAIiGGvftv~giiD~~~~~~~~ 154 (166)
..+..+.+.+.+. ++++|+++||.|++.+++=-++-...+
T Consensus 228 ~~~~~~~~~l~~~~~~~~g~~~v~~G~~~lL~LFc~l~~~~Rr 270 (276)
T PF07413_consen 228 FILRVDYRALGHWLAALIGMFFVASGAFMLLSLFCCLSIWRRR 270 (276)
T ss_pred EEEecCCcchhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 3444555566655 889999999999999877655544333
No 10
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=23.73 E-value=82 Score=23.75 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=26.7
Q ss_pred ccHHHHHHHHhhhhc-ceeehhhhhHHHHHHHH
Q 041965 122 RSFLHLITRLCAVLG-GTFALTGMLDRWMYRLL 153 (166)
Q Consensus 122 ~s~~~flt~lcAIiG-Gvftv~giiD~~~~~~~ 153 (166)
..+..=|.++..+|| +=.+++|+||.++.+=+
T Consensus 87 ~e~h~~l~~Iv~~ig~~~~si~~yidNIL~~Hl 119 (136)
T PF11888_consen 87 RETHERLSRIVRVIGERKMSISGYIDNILRHHL 119 (136)
T ss_pred HHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHH
Confidence 467788999999999 66999999999986533
No 11
>KOG2014 consensus SMT3/SUMO-activating complex, AOS1/RAD31 component [Posttranslational modification, protein turnover, chaperones]
Probab=23.01 E-value=26 Score=30.79 Aligned_cols=11 Identities=55% Similarity=1.120 Sum_probs=9.0
Q ss_pred HHhhhhcceee
Q 041965 130 RLCAVLGGTFA 140 (166)
Q Consensus 130 ~lcAIiGGvft 140 (166)
=+|||||||.+
T Consensus 286 Pv~AvVGGiva 296 (331)
T KOG2014|consen 286 PVCAVVGGILA 296 (331)
T ss_pred chhhhhhhHhH
Confidence 47999999873
No 12
>PF01034 Syndecan: Syndecan domain; InterPro: IPR001050 The syndecans are transmembrane proteoglycans which are involved in the organisation of cytoskeleton and/or actin microfilaments, and have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions [, ]. Structurally, these proteins consist of four separate domains: A signal sequence; An extracellular domain (ectodomain) of variable length whose sequence is not evolutionary conserved in the various forms of syndecans. The ectodomain contains the sites of attachment of the heparan sulphate glycosaminoglycan side chains; A transmembrane region; A highly conserved cytoplasmic domain of about 30 to 35 residues, which could interact with cytoskeletal proteins. The proteins known to belong to this family are: Syndecan 1. Syndecan 2 or fibroglycan. Syndecan 3 or neuroglycan or N-syndecan. Syndecan 4 or amphiglycan or ryudocan. Drosophila syndecan. Caenorhabditis elegans probable syndecan (F57C7.3). Syndecan-4, a transmembrane heparan sulphate proteoglycan, is a coreceptor with integrins in cell adhesion. It has been suggested to form a ternary signalling complex with protein kinase Calpha and phosphatidylinositol 4,5-bisphosphate (PIP2). Structural studies have demonstrated that the cytoplasmic domain undergoes a conformational transition and forms a symmetric dimer in the presence of phospholipid activator PIP2, and whose overall structure in solution exhibits a twisted clamp shape having a cavity in the centre of dimeric interface. In addition, it has been observed that the syndecan-4 variable domain interacts, strongly, not only with fatty acyl groups but also the anionic head group of PIP2. These findings indicate that PIP2 promotes oligomerisation of the syndecan-4 cytoplasmic domain for transmembrane signalling and cell-matrix adhesion [, ].; GO: 0008092 cytoskeletal protein binding, 0016020 membrane; PDB: 1EJQ_B 1EJP_B 1YBO_C 1OBY_Q.
Probab=21.85 E-value=31 Score=23.30 Aligned_cols=8 Identities=38% Similarity=0.634 Sum_probs=0.0
Q ss_pred hhhhccee
Q 041965 132 CAVLGGTF 139 (166)
Q Consensus 132 cAIiGGvf 139 (166)
.|+|+|+.
T Consensus 12 aavIaG~V 19 (64)
T PF01034_consen 12 AAVIAGGV 19 (64)
T ss_dssp --------
T ss_pred HHHHHHHH
Confidence 45555543
No 13
>PF00673 Ribosomal_L5_C: ribosomal L5P family C-terminus; InterPro: IPR002132 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 [, ]. Ribosomal protein L5, ~180 amino acids in length, is one of the proteins from the large ribosomal subunit. In Escherichia coli, L5 is known to be involved in binding 5S RNA to the large ribosomal subunit. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , , ], groups: Eubacterial L5. Algal chloroplast L5. Cyanelle L5. Archaebacterial L5. Mammalian L11. Tetrahymena thermophila L21. Dictyostelium discoideum (Slime mold) L5 Saccharomyces cerevisiae (Baker's yeast) L16 (39A). Plant mitochondrial L5. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1IQ4_B 2ZJR_D 2ZJP_D 3PIO_D 3CF5_D 2ZJQ_D 3DLL_D 3PIP_D 2WDL_G 3UZN_G ....
Probab=21.42 E-value=1e+02 Score=21.90 Aligned_cols=23 Identities=13% Similarity=0.426 Sum_probs=21.3
Q ss_pred ceEEEEEeeeccHHHHHHHHhhh
Q 041965 112 PITVTIKEERRSFLHLITRLCAV 134 (166)
Q Consensus 112 Pi~V~~~~~r~s~~~flt~lcAI 134 (166)
||.+++|-+.+..+.||-+++.+
T Consensus 1 PiG~kvTLRg~~m~~FL~kli~~ 23 (95)
T PF00673_consen 1 PIGCKVTLRGKKMYEFLDKLITI 23 (95)
T ss_dssp EEEEEEEEEHHHHHHHHHHHHHT
T ss_pred CeEEEEEEccHHHHHHHHHHHHH
Confidence 88999999999999999999877
No 14
>PF00858 ASC: Amiloride-sensitive sodium channel; InterPro: IPR001873 The apical membrane of many tight epithelia contains sodium channels that are primarily characterised by their high affinity to the diuretic blocker amiloride [, , , ]. These channels mediate the first step of active sodium reabsorption essential for the maintenance of body salt and water homeostasis []. In vertebrates, the channels control reabsorption of sodium in kidney, colon, lung and sweat glands; they also play a role in taste perception. Members of the epithelial Na+ channel (ENaC) family fall into four subfamilies, termed alpha, beta, gamma and delta []. The proteins exhibit the same apparent topology, each with two transmembrane (TM) spanning segments, separated by a large extracellular loop. In most ENaC proteins studied to date, the extracellular domains are highly conserved and contain numerous cysteine residues, with flanking C-terminal amphipathic TM regions, postulated to contribute to the formation of the hydrophilic pores of the oligomeric channel protein complexes. It is thought that the well-conserved extracellular domains serve as receptors to control the activities of the channels. Vertebrate ENaC proteins are similar to degenerins of Caenorhabditis elegans []: deg-1, del-1, mec-4, mec-10 and unc-8. These proteins can be mutated to cause neuronal degradation, and are also thought to form sodium channels. Structurally, the proteins that belong to this family consist of about 510 to 920 amino acid residues. They are made of an intracellular N terminus region followed by a transmembrane domain, a large extracellular loop, a second transmembrane segment and a C-terminal intracellular tail [].; GO: 0005272 sodium channel activity, 0006814 sodium ion transport, 0016020 membrane; PDB: 2QTS_B 3S3W_C 3IJ4_A 3S3X_A 3HGC_A 2K2B_A.
Probab=20.85 E-value=2.8e+02 Score=23.71 Aligned_cols=37 Identities=11% Similarity=0.265 Sum_probs=29.4
Q ss_pred CcceEEEEEeccceEEEEEeeeccHHHHHHHHhhhhc
Q 041965 100 TWPAVYFLYDLSPITVTIKEERRSFLHLITRLCAVLG 136 (166)
Q Consensus 100 ~~PgI~F~Yd~SPi~V~~~~~r~s~~~flt~lcAIiG 136 (166)
..--+.+.|+=-|.....++..-++.+||.++.|++|
T Consensus 386 ~~~~l~i~~~~~~~~~~~~~~~~~~~~ll~~iGG~~g 422 (439)
T PF00858_consen 386 NLAVLNIYFKELPYERYRRSPAYTWSDLLSDIGGILG 422 (439)
T ss_dssp HEEEEEEEEEEEEEEEEEEEESS-HHHHHHHHHHHHH
T ss_pred chhhHHhhhccceEEEEEEecccchhhHHHHhhhHHH
Confidence 4567788888888888888888999999998877776
No 15
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=20.30 E-value=88 Score=24.52 Aligned_cols=21 Identities=24% Similarity=0.331 Sum_probs=17.7
Q ss_pred eEEEEEEEEEEEEEecCCcee
Q 041965 60 TFKYYIKIVPTEYRYISKDVL 80 (166)
Q Consensus 60 ~~~YflkvVPT~y~~~~~~~~ 80 (166)
.-+|.++.|||.....+|...
T Consensus 108 a~~Y~I~avPtvlvfknGe~~ 128 (150)
T KOG0910|consen 108 AEDYEISAVPTVLVFKNGEKV 128 (150)
T ss_pred HhhcceeeeeEEEEEECCEEe
Confidence 457999999999998888654
Done!