Query 031723
Match_columns 154
No_of_seqs 125 out of 327
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 04:28:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031723.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031723hhsearch_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 4.7E-42 1E-46 278.5 4.9 105 45-151 1-108 (212)
2 COG5196 ERD2 ER lumen protein 100.0 2.5E-35 5.4E-40 236.8 5.9 105 45-151 1-109 (214)
3 PF00810 ER_lumen_recept: ER l 99.9 4.4E-26 9.6E-31 177.9 4.2 79 72-152 1-84 (147)
4 KOG3211 Predicted endoplasmic 89.8 0.78 1.7E-05 38.7 5.4 63 64-126 50-112 (230)
5 PF04193 PQ-loop: PQ loop repe 86.8 0.85 1.8E-05 29.5 3.0 30 64-93 21-50 (61)
6 smart00679 CTNS Repeated motif 85.9 0.52 1.1E-05 26.9 1.5 22 64-85 7-28 (32)
7 PF02109 DAD: DAD family; Int 56.2 60 0.0013 24.6 6.5 69 11-79 12-90 (112)
8 TIGR00951 2A43 Lysosomal Cysti 52.3 10 0.00023 31.2 2.0 27 64-90 23-49 (220)
9 PF06363 Picorna_P3A: Picornav 43.5 37 0.00079 25.3 3.5 51 6-71 45-95 (100)
10 PF04612 T2SM: Type II secreti 41.7 8.6 0.00019 29.1 0.0 35 8-42 1-35 (160)
11 COG4095 Uncharacterized conser 39.6 1.4E+02 0.0031 21.9 6.1 40 51-90 11-50 (89)
12 PTZ00154 40S ribosomal protein 32.6 34 0.00074 26.8 2.0 27 50-83 50-76 (134)
13 PF14007 YtpI: YtpI-like prote 29.6 1.1E+02 0.0023 22.3 4.1 58 2-67 20-78 (89)
14 PF02790 COX2_TM: Cytochrome C 28.6 74 0.0016 21.3 3.0 39 113-151 38-77 (84)
15 PF00833 Ribosomal_S17e: Ribos 23.7 58 0.0012 25.1 1.9 27 50-83 50-76 (121)
16 PF05186 Dpy-30: Dpy-30 motif; 23.7 46 0.001 20.7 1.1 18 3-20 25-42 (42)
17 PF10192 GpcrRhopsn4: Rhodopsi 23.2 1.4E+02 0.003 24.7 4.2 11 138-148 218-228 (257)
18 TIGR02611 conserved hypothetic 23.2 69 0.0015 24.7 2.2 33 8-40 78-110 (121)
19 KOG1623 Multitransmembrane pro 23.2 90 0.0019 26.7 3.1 33 45-77 2-41 (243)
20 KOG0187 40S ribosomal protein 20.7 50 0.0011 25.8 1.0 27 50-83 50-76 (134)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=4.7e-42 Score=278.46 Aligned_cols=105 Identities=43% Similarity=0.717 Sum_probs=100.7
Q ss_pred CchHHhHhhhHHHHHHHHHHHHhhccccccccccchhHHHHHHhhhhhcceee---ecchhHHHHHHHHHHHHHHHHHHh
Q 031723 45 HDNLFVAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFV---MEYDIHTLLDLATLATTLWVIYMI 121 (154)
Q Consensus 45 ~n~fr~lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~LyalVf~tRl~~~f~---s~Yn~~t~mki~~i~~s~~iiyli 121 (154)
||+||++||++|++||++|++||+|+|||+|||+|||+|||+||++||+|+|. |.|| |+||++++++|.++||||
T Consensus 1 mn~fr~~gd~~H~~~i~vLi~Ki~ktrsCaGiSlKSQ~L~Alvf~~Ryldlf~~~~s~yn--t~mki~fl~~t~~ivymi 78 (212)
T KOG3106|consen 1 MNNFRFAGDLSHLAAIIVLILKIWKTKSCAGISLKSQELFALVFATRYLDLFTFYESLYN--TIMKIAFLASTLWIVYMI 78 (212)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHhcCccccccchHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999988874 5665 999999999999999999
Q ss_pred hcccccccccCCCccchhhhhhhhhhhhhh
Q 031723 122 RFNLRSSYMEDKDNFAIYYVVSFLPFMPIF 151 (154)
Q Consensus 122 ~~k~k~TYd~~~DtF~~~yLivP~~~la~~ 151 (154)
++|+|+|||+|+|||+++|+++||+++|.+
T Consensus 79 ~~k~~~tYd~~~DtFri~~llvp~~vlsl~ 108 (212)
T KOG3106|consen 79 RFKLRATYDKEKDTFRIEYLLVPSAVLSLL 108 (212)
T ss_pred HHHHHHHHhcccCceeEEEEehhheeeeee
Confidence 999999999999999999999999999875
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.5e-35 Score=236.81 Aligned_cols=105 Identities=27% Similarity=0.527 Sum_probs=101.1
Q ss_pred CchHHhHhhhHHHHHHHHHHHHhhccccccccccchhHHHHHHhhhhhccee----eecchhHHHHHHHHHHHHHHHHHH
Q 031723 45 HDNLFVAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSF----VMEYDIHTLLDLATLATTLWVIYM 120 (154)
Q Consensus 45 ~n~fr~lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~LyalVf~tRl~~~f----~s~Yn~~t~mki~~i~~s~~iiyl 120 (154)
+|.||++||++|++|+.+|++||.++|+|+|+|+|||.||++||++||+|.+ .|+|| .+||++||+++.|++++
T Consensus 1 m~~Fr~lGD~~Hlasi~vLih~ik~tr~csGlSlKtq~Ly~lVfitRYldLf~f~~~slYn--~lMki~FI~s~~yI~~l 78 (214)
T COG5196 1 MDTFRFLGDFLHLASIAVLIHKIKRTRSCSGLSLKTQFLYSLVFITRYLDLFDFYARSLYN--SLMKILFIGSQVYILFL 78 (214)
T ss_pred CcHHHHHhHHHHHHHHHHHHHHhhhcceecceehHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999999999999999999999999999998865 58998 99999999999999999
Q ss_pred hhcccccccccCCCccchhhhhhhhhhhhhh
Q 031723 121 IRFNLRSSYMEDKDNFAIYYVVSFLPFMPIF 151 (154)
Q Consensus 121 i~~k~k~TYd~~~DtF~~~yLivP~~~la~~ 151 (154)
|++++++|||+..|||+++++++||++++++
T Consensus 79 m~~~~r~tYdk~lDtF~i~~ll~gsav~slf 109 (214)
T COG5196 79 MRFKYRSTYDKKLDTFNILTLLVGSAVFSLF 109 (214)
T ss_pred HHhcccchHHHhhhhhhhhhhhhhhhhheee
Confidence 9999999999999999999999999999876
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=99.92 E-value=4.4e-26 Score=177.86 Aligned_cols=79 Identities=30% Similarity=0.582 Sum_probs=73.9
Q ss_pred cccccccchhHHHHHHhhhhhcce--ee---ecchhHHHHHHHHHHHHHHHHHHhhcccccccccCCCccchhhhhhhhh
Q 031723 72 TCAGLSLKSQELTAIFLAVRLYCS--FV---MEYDIHTLLDLATLATTLWVIYMIRFNLRSSYMEDKDNFAIYYVVSFLP 146 (154)
Q Consensus 72 ScsGISlKTQ~LyalVf~tRl~~~--f~---s~Yn~~t~mki~~i~~s~~iiyli~~k~k~TYd~~~DtF~~~yLivP~~ 146 (154)
||+|+|+|||+||++||++||+|. +. +.|| ++||++++++|++++|+|+.|||+|||+|+|+|+++++++||+
T Consensus 1 S~~GlSlktq~ly~~vf~~Ryldl~~f~~~~s~y~--~~~k~~~i~~s~~iiyli~~~~~~Ty~~~~D~f~~~~li~p~~ 78 (147)
T PF00810_consen 1 SCSGLSLKTQILYAIVFLTRYLDLFWFESYLSLYN--TIMKVFFIVSSLYIIYLIFFKYKSTYDKEIDTFRLEYLIVPCF 78 (147)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHH--HHHHHHHHHHHHHHHHhhheeehhhhhccccchhhhHHHHHHH
Confidence 899999999999999999999887 43 5666 9999999999999999999999999999999999999999999
Q ss_pred hhhhhh
Q 031723 147 FMPIFL 152 (154)
Q Consensus 147 ~la~~l 152 (154)
++|.+.
T Consensus 79 vLa~i~ 84 (147)
T PF00810_consen 79 VLALIF 84 (147)
T ss_pred HHHHHH
Confidence 998763
No 4
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=89.85 E-value=0.78 Score=38.68 Aligned_cols=63 Identities=22% Similarity=0.277 Sum_probs=49.8
Q ss_pred HHHhhccccccccccchhHHHHHHhhhhhcceeeecchhHHHHHHHHHHHHHHHHHHhhcccc
Q 031723 64 IYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFVMEYDIHTLLDLATLATTLWVIYMIRFNLR 126 (154)
Q Consensus 64 l~Ki~~tkScsGISlKTQ~LyalVf~tRl~~~f~s~Yn~~t~mki~~i~~s~~iiyli~~k~k 126 (154)
+.||...||+.|+|.-+|+|=.+-++.-+--++.+=|+.-+.+|..++..+..++-++-+.|+
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgytvtl~Y~~~~g~pFss~gE~~fLl~Q~vili~~if~f~ 112 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYTVTLSYSYTSGYPFSSYGEYPFLLLQAVILILCIFHFS 112 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHHheeeehhhcCCCchhHHHHHHHHHHHHHHHHHHHHhc
Confidence 689999999999999999998887775432233444444578899999999988888888777
No 5
>PF04193 PQ-loop: PQ loop repeat
Probab=86.78 E-value=0.85 Score=29.52 Aligned_cols=30 Identities=33% Similarity=0.168 Sum_probs=26.5
Q ss_pred HHHhhccccccccccchhHHHHHHhhhhhc
Q 031723 64 IYKLMKEKTCAGLSLKSQELTAIFLAVRLY 93 (154)
Q Consensus 64 l~Ki~~tkScsGISlKTQ~LyalVf~tRl~ 93 (154)
++|.+|+||+.|+|.-+..+..+-.+++..
T Consensus 21 i~~~~k~ks~~glS~~~~~l~~~g~~~~~~ 50 (61)
T PF04193_consen 21 IIKNYKRKSTGGLSLWFLLLWLIGSILWVL 50 (61)
T ss_pred HHHHHHccccccccHHHHHHHHHHHHHHHH
Confidence 699999999999999999998888877753
No 6
>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=85.87 E-value=0.52 Score=26.92 Aligned_cols=22 Identities=32% Similarity=0.249 Sum_probs=18.1
Q ss_pred HHHhhccccccccccchhHHHH
Q 031723 64 IYKLMKEKTCAGLSLKSQELTA 85 (154)
Q Consensus 64 l~Ki~~tkScsGISlKTQ~Lya 85 (154)
++|++++||+.|+|.-...+-.
T Consensus 7 i~~~~~~ks~~glS~~~~~l~~ 28 (32)
T smart00679 7 IIKNYRRKSTEGLSILFVLLWL 28 (32)
T ss_pred HHHHHHcCCcCcCCHHHHHHHH
Confidence 5799999999999987766543
No 7
>PF02109 DAD: DAD family; InterPro: IPR003038 Members of this family are thought to be integral membrane proteins. Some members of this family have been shown to cause apoptosis if mutated [], these proteins are known as DAD for defender against death. The family also includes the epsilon subunit of the oligosaccharyltransferase that is involved in N-linked glycosylation [].; GO: 0016021 integral to membrane
Probab=56.21 E-value=60 Score=24.65 Aligned_cols=69 Identities=17% Similarity=0.279 Sum_probs=46.9
Q ss_pred HHHHHHhCCCceee---hHHHHHHHHHHHHHHHHHhcCchHH-hHhhhHHHHHHHHHH--HHhhccccc----cccccc
Q 031723 11 VSTWVRRQPPKVKA---FLAVVSGMAALVLLRFIVHDHDNLF-VAAEAVHSIGISVLI--YKLMKEKTC----AGLSLK 79 (154)
Q Consensus 11 ~~~~l~~~~~~vk~---~~g~~~~~~~~~~l~~~~~d~n~fr-~lgDl~Hl~si~iLl--~Ki~~tkSc----sGISlK 79 (154)
...+.++.|+|+|+ ++.+++.+-++-++|-..-+.-+|. ++|-+.-..|-.+|. .+++-+.+. .|+|.+
T Consensus 12 ~~~Y~~~Tp~rlkliD~fl~f~~~~gilQfvYc~lvgtFPFNaFLsGf~s~VG~fVL~vsLR~Q~~p~n~~~f~~is~e 90 (112)
T PF02109_consen 12 WQSYLKKTPQRLKLIDAFLAFLVLTGILQFVYCILVGTFPFNAFLSGFISCVGQFVLTVSLRIQLNPENKSEFPGISPE 90 (112)
T ss_pred HHHHHHhCCchhhhHHHHHHHHHHHHHHHHhHheeecCCchHHHHHHHHHHHHHHHHHHHHHHhcccccccccCCCChh
Confidence 44788999999998 5666666667777887777666665 677777777777775 455555323 356654
No 8
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=52.30 E-value=10 Score=31.21 Aligned_cols=27 Identities=26% Similarity=0.294 Sum_probs=21.5
Q ss_pred HHHhhccccccccccchhHHHHHHhhh
Q 031723 64 IYKLMKEKTCAGLSLKSQELTAIFLAV 90 (154)
Q Consensus 64 l~Ki~~tkScsGISlKTQ~LyalVf~t 90 (154)
++|++|+||++|+|+-.-.+-.+-+++
T Consensus 23 i~~n~k~ks~~GlS~~~~~l~~~g~~~ 49 (220)
T TIGR00951 23 IIKNWRRKSAEGLSFDFVMLNLVGFTA 49 (220)
T ss_pred HHHHHhccccCCcCHHHHHHHHHHHHH
Confidence 689999999999999997755444433
No 9
>PF06363 Picorna_P3A: Picornaviridae P3A protein; InterPro: IPR009419 The viral polyprotein of parechoviruses contains: coat protein VP0 (P1AB); coat protein VP3 (P1C); coat protein VP1 (P1D); picornain 2A (3.4.22.29 from EC, core protein P2A); core protein P2B; core protein P2C; core protein P3A; genome-linked protein VPg (P3B); picornain 3C (3.4.22.28 from EC, MEROPS peptidase subfamily 3CF: parechovirus picornain 3C (P3C))[]. This entry consists of the parechovirus P3A protein. P3A has been identified as a genome-linked protein (VPg), which is involved in replication [].; GO: 0019012 virion
Probab=43.45 E-value=37 Score=25.33 Aligned_cols=51 Identities=22% Similarity=0.421 Sum_probs=31.3
Q ss_pred ChHHHHHHHHHhCCCceeehHHHHHHHHHHHHHHHHHhcCchHHhHhhhHHHHHHHHHHHHhhccc
Q 031723 6 RPIHAVSTWVRRQPPKVKAFLAVVSGMAALVLLRFIVHDHDNLFVAAEAVHSIGISVLIYKLMKEK 71 (154)
Q Consensus 6 ~~~~~~~~~l~~~~~~vk~~~g~~~~~~~~~~l~~~~~d~n~fr~lgDl~Hl~si~iLl~Ki~~tk 71 (154)
...+++..|++.+..+ | +-|+..+-.-|-+.+-++..+||+.|.+++.|..
T Consensus 45 ~a~~kv~~W~~~k~k~---~------------~~FV~RNk~W~T~~S~~tS~isIL~LV~~~~KKe 95 (100)
T PF06363_consen 45 TACDKVKSWVKNKMKS---M------------LSFVERNKAWFTVVSAVTSFISILLLVTKIFKKE 95 (100)
T ss_pred HHHHHHHHHHHHHHHH---H------------HHHHHHcchHhhHHHHHHHHHHHHHHHHHHHhhh
Confidence 3445566777665432 2 2244444444555566677889999998887653
No 10
>PF04612 T2SM: Type II secretion system (T2SS), protein M; InterPro: IPR007690 General secretion pathway (GSP) protein M is a membrane protein involved in the export of proteins in bacteria. It consists of a short cytosolic N-terminal domain, a transmembrane domain, and a C-terminal periplasmic domain. The precise function of this protein is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers [],; GO: 0006858 extracellular transport; PDB: 1UV7_A.
Probab=41.69 E-value=8.6 Score=29.09 Aligned_cols=35 Identities=20% Similarity=0.485 Sum_probs=0.0
Q ss_pred HHHHHHHHHhCCCceeehHHHHHHHHHHHHHHHHH
Q 031723 8 IHAVSTWVRRQPPKVKAFLAVVSGMAALVLLRFIV 42 (154)
Q Consensus 8 ~~~~~~~l~~~~~~vk~~~g~~~~~~~~~~l~~~~ 42 (154)
++++..|....+++.|..+.+.+++++++++|+++
T Consensus 1 m~~l~~~w~~ls~REr~ll~~~~~~l~~~l~~~~~ 35 (160)
T PF04612_consen 1 MQQLKQWWQSLSPRERRLLLVLGVVLLLALLYLLL 35 (160)
T ss_dssp -----------------------------------
T ss_pred ChHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999888888877888755
No 11
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=39.62 E-value=1.4e+02 Score=21.89 Aligned_cols=40 Identities=23% Similarity=0.233 Sum_probs=29.1
Q ss_pred HhhhHHHHHHHHHHHHhhccccccccccchhHHHHHHhhh
Q 031723 51 AAEAVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAV 90 (154)
Q Consensus 51 lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~LyalVf~t 90 (154)
.|...-.++++-=..|+.|+|+.+++|+-+-....+-++.
T Consensus 11 ia~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~ia~~l 50 (89)
T COG4095 11 IAGILTTFAFLPQLIKIIKTKNTASISLPMFIILNIALFL 50 (89)
T ss_pred HHHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHH
Confidence 4455556677777899999999999998776655554443
No 12
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=32.59 E-value=34 Score=26.84 Aligned_cols=27 Identities=33% Similarity=0.380 Sum_probs=19.4
Q ss_pred hHhhhHHHHHHHHHHHHhhccccccccccchhHH
Q 031723 50 VAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQEL 83 (154)
Q Consensus 50 ~lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~L 83 (154)
++|=..|+ .|-.......|||+|.||=
T Consensus 50 IAGYIThl-------mkri~~gpvrgis~klqee 76 (134)
T PTZ00154 50 IAGFVTHL-------MKRIQKGPVRGISLKLQEE 76 (134)
T ss_pred HHHHHHHH-------HhhhccCCccccceehhHH
Confidence 55555554 4555667899999999983
No 13
>PF14007 YtpI: YtpI-like protein
Probab=29.62 E-value=1.1e+02 Score=22.31 Aligned_cols=58 Identities=12% Similarity=0.209 Sum_probs=35.8
Q ss_pred CCCCChHHHHHHHHHhCCCceeehHHHHHHHHHHHHHHHHHhcCchHH-hHhhhHHHHHHHHHHHHh
Q 031723 2 RAPKRPIHAVSTWVRRQPPKVKAFLAVVSGMAALVLLRFIVHDHDNLF-VAAEAVHSIGISVLIYKL 67 (154)
Q Consensus 2 ~~~~~~~~~~~~~l~~~~~~vk~~~g~~~~~~~~~~l~~~~~d~n~fr-~lgDl~Hl~si~iLl~Ki 67 (154)
+|.++|.|+ +|.+ .|-.+++|.++..+++-=+ +. +++..+ +.|-..-+++..-+..-+
T Consensus 20 ~Rs~~p~~k--~~~~---aka~ialG~fl~~fgiNQ~--~~-~~st~~~iV~~ifl~lG~~n~~~G~ 78 (89)
T PF14007_consen 20 FRSKDPMEK--KWYS---AKANIALGIFLILFGINQM--FL-FGSTVRLIVGAIFLVLGLFNLFAGI 78 (89)
T ss_pred hhcCCHHHH--HHHH---HHHHHHHHHHHHHHHHHHH--HH-cccHHHHHHHHHHHHHhHHHHHHHH
Confidence 456778776 4443 4567899999999974433 22 555554 566666666665555433
No 14
>PF02790 COX2_TM: Cytochrome C oxidase subunit II, transmembrane domain This family corresponds to chains b and o.; InterPro: IPR011759 Cytochrome c oxidase (1.9.3.1 from EC) [, ] is an oligomeric enzymatic complex which is a component of the respiratory chain and is involved in the transfer of electrons from cytochrome c to oxygen. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. The enzyme complex consists of 3-4 subunits (prokaryotes) to up to 13 polypeptides (mammals). Subunit 2 (CO II) transfers the electrons from cytochrome c to the catalytic subunit 1. It contains two adjacent transmembrane regions in its N terminus and the major part of the protein is exposed to the periplasmic or to the mitochondrial intermembrane space, respectively. CO II provides the substrate-binding site and contains a copper centre called Cu(A) (see IPR001505 from INTERPRO), probably the primary acceptor in cytochrome c oxidase. An exception is the corresponding subunit of the cbb3-type oxidase which lacks the copper A redox-centre. Several bacterial CO II have a C-terminal extension that contains a covalently bound haem c. The N-terminal domain of cytochrome C oxidase contains two transmembrane alpha-helices. ; GO: 0004129 cytochrome-c oxidase activity, 0005507 copper ion binding, 0009055 electron carrier activity, 0022900 electron transport chain, 0016021 integral to membrane; PDB: 3VRJ_C 2EIN_B 3AG3_B 2DYR_O 3AG1_B 2EIK_O 3ASN_B 1OCR_B 2EIJ_B 1OCC_O ....
Probab=28.61 E-value=74 Score=21.30 Aligned_cols=39 Identities=8% Similarity=0.304 Sum_probs=18.4
Q ss_pred HHHHHHHHhhc-ccccccccCCCccchhhhhhhhhhhhhh
Q 031723 113 TTLWVIYMIRF-NLRSSYMEDKDNFAIYYVVSFLPFMPIF 151 (154)
Q Consensus 113 ~s~~iiyli~~-k~k~TYd~~~DtF~~~yLivP~~~la~~ 151 (154)
.....+|.+.. +....+..+..+.-.-.-++|++++..+
T Consensus 38 V~~~l~~~~~~~~~~~~~~~~~~~lE~~WTiiP~iiLl~l 77 (84)
T PF02790_consen 38 VFYFLIYFLFNSKFPNKFFNHNNKLEIIWTIIPAIILLFL 77 (84)
T ss_dssp HHHHHHHHHHHSSSS--S---SHHHHHHHHHHHHHHHHHH
T ss_pred EeeecccccccccccccccccchhhhhhhhHHHHHHHHHH
Confidence 33444454444 3333333333344445788998877443
No 15
>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=23.73 E-value=58 Score=25.13 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=19.2
Q ss_pred hHhhhHHHHHHHHHHHHhhccccccccccchhHH
Q 031723 50 VAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQEL 83 (154)
Q Consensus 50 ~lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~L 83 (154)
++|=..|+ .|-.......|+|+|.|+=
T Consensus 50 IAGYvThl-------mKriq~g~vrgis~klqEe 76 (121)
T PF00833_consen 50 IAGYVTHL-------MKRIQRGPVRGISIKLQEE 76 (121)
T ss_dssp HHHHHHHH-------HHHHTSSSSTTCSSCCCCH
T ss_pred HHHHHHHH-------HHHHHhccccccchhhhHH
Confidence 55555554 4555677889999999973
No 16
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=23.68 E-value=46 Score=20.74 Aligned_cols=18 Identities=22% Similarity=0.643 Sum_probs=12.7
Q ss_pred CCCChHHHHHHHHHhCCC
Q 031723 3 APKRPIHAVSTWVRRQPP 20 (154)
Q Consensus 3 ~~~~~~~~~~~~l~~~~~ 20 (154)
|..||++-+..||-++++
T Consensus 25 rP~DPi~~La~~Ll~~~p 42 (42)
T PF05186_consen 25 RPEDPIEFLAEYLLKHNP 42 (42)
T ss_dssp --SSHHHHHHHHHHHHG-
T ss_pred CCCChHHHHHHHHHHhCc
Confidence 568899988888887754
No 17
>PF10192 GpcrRhopsn4: Rhodopsin-like GPCR transmembrane domain; InterPro: IPR019336 G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (http://www.gpcr.org/7tm/). This region of 270 amino acids is the seven transmembrane alpha-helical domains included within five GPCRRHODOPSN4 motifs of a G-protein-coupled-receptor (GPCR) protein, conserved from nematodes to humans [].
Probab=23.20 E-value=1.4e+02 Score=24.71 Aligned_cols=11 Identities=0% Similarity=0.265 Sum_probs=7.0
Q ss_pred hhhhhhhhhhh
Q 031723 138 IYYVVSFLPFM 148 (154)
Q Consensus 138 ~~yLivP~~~l 148 (154)
.+++..|..++
T Consensus 218 lWFl~~Pv~~~ 228 (257)
T PF10192_consen 218 LWFLSLPVIVI 228 (257)
T ss_pred HHHHHHHHHHH
Confidence 45677777644
No 18
>TIGR02611 conserved hypothetical protein TIGR02611. Members of this family are Actinobacterial putative proteins of about 150 amino acids in length with three apparent transmembrane helix and an unusual motif with consensus sequence PGPGW.
Probab=23.17 E-value=69 Score=24.73 Aligned_cols=33 Identities=15% Similarity=0.126 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCceeehHHHHHHHHHHHHHHH
Q 031723 8 IHAVSTWVRRQPPKVKAFLAVVSGMAALVLLRF 40 (154)
Q Consensus 8 ~~~~~~~l~~~~~~vk~~~g~~~~~~~~~~l~~ 40 (154)
..+...|+.+|+..+|..++..++++++..++.
T Consensus 78 ~~~~~~W~~~q~~~~r~~~~~~~~~~v~~vl~~ 110 (121)
T TIGR02611 78 YDEFFAWYADQHVRVRNLLLGSLIVVIWAVLAG 110 (121)
T ss_pred HHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHH
Confidence 455779999999999988877777776655554
No 19
>KOG1623 consensus Multitransmembrane protein [General function prediction only]
Probab=23.17 E-value=90 Score=26.65 Aligned_cols=33 Identities=21% Similarity=0.332 Sum_probs=0.0
Q ss_pred CchHH-hHhhhHHHHHHHHHH------HHhhccccccccc
Q 031723 45 HDNLF-VAAEAVHSIGISVLI------YKLMKEKTCAGLS 77 (154)
Q Consensus 45 ~n~fr-~lgDl~Hl~si~iLl------~Ki~~tkScsGIS 77 (154)
+|..+ ++|++.+..+++.-+ ++|+|+||.+|.|
T Consensus 2 ~~~~~~l~~i~~~~is~~~fl~pv~tf~~I~KkkS~e~~s 41 (243)
T KOG1623|consen 2 GNVLLFLFGILGNIISFGVFLSPVPTFRRIRKKKSVEGFS 41 (243)
T ss_pred cchHHHHHHHHHHHHhHHHhhcCchhHHHhhcccCcCCCC
No 20
>KOG0187 consensus 40S ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=20.73 E-value=50 Score=25.82 Aligned_cols=27 Identities=30% Similarity=0.410 Sum_probs=19.7
Q ss_pred hHhhhHHHHHHHHHHHHhhccccccccccchhHH
Q 031723 50 VAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQEL 83 (154)
Q Consensus 50 ~lgDl~Hl~si~iLl~Ki~~tkScsGISlKTQ~L 83 (154)
++|=..|| .-+|.+. ...|||.|.||-
T Consensus 50 IAGyvtHL------mkrIqkG-pvRGISiKLQEE 76 (134)
T KOG0187|consen 50 IAGYVTHL------MKRIQKG-PVRGISIKLQEE 76 (134)
T ss_pred HHHHHHHH------HHHHHcC-CccceeEeecHH
Confidence 66777775 3455555 789999999984
Done!