Query 028301
Match_columns 211
No_of_seqs 112 out of 360
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 09:23:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028301.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028301hhsearch_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 1.5E-63 3.3E-68 421.4 10.7 162 45-209 1-169 (212)
2 COG5196 ERD2 ER lumen protein 100.0 2.6E-53 5.6E-58 354.7 12.2 161 46-209 2-170 (214)
3 PF00810 ER_lumen_recept: ER l 100.0 7.1E-50 1.5E-54 327.1 11.3 137 72-209 1-146 (147)
4 TIGR00951 2A43 Lysosomal Cysti 95.6 0.28 6.1E-06 42.7 12.1 141 58-200 17-181 (220)
5 KOG3211 Predicted endoplasmic 95.2 0.24 5.3E-06 43.6 10.3 120 64-189 50-169 (230)
6 PF04193 PQ-loop: PQ loop repe 89.3 0.54 1.2E-05 32.1 3.5 40 54-93 11-50 (61)
7 smart00679 CTNS Repeated motif 82.3 0.97 2.1E-05 27.1 1.7 22 64-85 7-28 (32)
8 PF04193 PQ-loop: PQ loop repe 78.9 9.6 0.00021 25.8 6.0 39 162-200 2-44 (61)
9 COG4095 Uncharacterized conser 44.0 87 0.0019 24.1 5.8 42 169-210 12-55 (89)
10 PF02790 COX2_TM: Cytochrome C 40.3 33 0.00072 24.4 2.9 44 112-155 37-81 (84)
11 PF02109 DAD: DAD family; Int 31.9 1.9E+02 0.0042 23.0 6.2 58 11-68 12-73 (112)
12 PF01306 LacY_symp: LacY proto 29.6 1.2E+02 0.0026 29.1 5.5 49 160-211 259-308 (412)
13 PF05297 Herpes_LMP1: Herpesvi 26.2 22 0.00048 33.2 0.0 38 35-72 37-76 (381)
14 PTZ00154 40S ribosomal protein 26.0 51 0.0011 27.1 2.1 27 49-82 49-75 (134)
15 PF06363 Picorna_P3A: Picornav 23.6 1.1E+02 0.0023 24.0 3.3 29 42-70 66-94 (100)
16 TIGR00951 2A43 Lysosomal Cysti 20.6 5.6E+02 0.012 22.1 9.0 34 64-97 158-191 (220)
No 1
>KOG3106 consensus ER lumen protein retaining receptor [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=1.5e-63 Score=421.45 Aligned_cols=162 Identities=42% Similarity=0.681 Sum_probs=155.4
Q ss_pred CcHHHHHhhHHHHHHHHHHHHHhhccccccccccchhHHHHHHHHhhhcceee-eechHHHHHHHHHHHHHHHHHHHhhc
Q 028301 45 HDNLFVAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFV-MEYDIHTLLDLATLATTLWVIYMIRF 123 (211)
Q Consensus 45 ~n~f~llgdl~Hl~s~~iLl~KI~~~KS~~GiSlKTQ~Ly~iVf~~Rl~~~f~-~~y~~~t~~k~~~i~~s~~iiylm~~ 123 (211)
+|.||++||++|++|+++|++||+|+|||+|||+|||+|||+||++||+|.|. .++++||+||+++++++.+++|+|++
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 58999999999999999999999999999999999999999999999999987 56778899999999999999999999
Q ss_pred cccccccccccccchhhhHHHHHHHHHHhCCCCCcchhhHHHHHHHHHHhhhhhhhHHHHhhhcCC--cchhHHHHHHHH
Q 028301 124 NLRSSYMEDKDNFAIYYVVVPCAVLALLIHPSTSHNILNRIFWAFCVYLEAVSVLPQLRVMQNTKV--PFSRLLNHSQPI 201 (211)
Q Consensus 124 k~k~TYd~~~Dtf~~~~liip~~vLAli~hp~~~~~~~~eilWtFSiyLEsVAILPQL~mlqk~g~--~~Tshyv~al~~ 201 (211)
|+|+|||+|+|||+++|+++||+++|+++||+. .+.|++||||+|||||||||||+|+||+|| ++|+||++|+|+
T Consensus 81 k~~~tYd~~~DtFri~~llvp~~vlsl~i~~~~---t~~eilWtFsiyLEsVaILPQL~~lq~tg~~E~~TahYvfaLG~ 157 (212)
T KOG3106|consen 81 KLRATYDKEKDTFRIEYLLVPSAVLSLLINHSF---TILEILWTFSIYLESVAILPQLFMLQKTGEAETITAHYLFALGL 157 (212)
T ss_pred HHHHHHhcccCceeEEEEehhheeeeeeecCCc---cHHHHHHHHHHHHHHHHHhHHHHHHHhcCCccchHHHHHHHHHH
Confidence 999999999999999999999999999999984 499999999999999999999999999998 999999999995
Q ss_pred ----HHHHHHHh
Q 028301 202 ----MYLRLVLR 209 (211)
Q Consensus 202 ----~~~~~~~~ 209 (211)
|..||++|
T Consensus 158 yR~ly~~~WI~r 169 (212)
T KOG3106|consen 158 YRALYIANWIYR 169 (212)
T ss_pred HHHHHHHHHHHH
Confidence 55799987
No 2
>COG5196 ERD2 ER lumen protein retaining receptor [Intracellular trafficking and secretion]
Probab=100.00 E-value=2.6e-53 Score=354.75 Aligned_cols=161 Identities=26% Similarity=0.513 Sum_probs=149.7
Q ss_pred cHHHHHhhHHHHHHHHHHHHHhhccccccccccchhHHHHHHHHhhhcceeeeec--hHHHHHHHHHHHHHHHHHHHhhc
Q 028301 46 DNLFVAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFVMEY--DIHTLLDLATLATTLWVIYMIRF 123 (211)
Q Consensus 46 n~f~llgdl~Hl~s~~iLl~KI~~~KS~~GiSlKTQ~Ly~iVf~~Rl~~~f~~~y--~~~t~~k~~~i~~s~~iiylm~~ 123 (211)
|+||++||++|++|+.+|+.||.++|+|+|+|+|||.||++||++||+|.|...+ -+|.+||+++|+++.|++++|+.
T Consensus 2 ~~Fr~lGD~~Hlasi~vLih~ik~tr~csGlSlKtq~Ly~lVfitRYldLf~f~~~slYn~lMki~FI~s~~yI~~lm~~ 81 (214)
T COG5196 2 DTFRFLGDFLHLASIAVLIHKIKRTRSCSGLSLKTQFLYSLVFITRYLDLFDFYARSLYNSLMKILFIGSQVYILFLMRF 81 (214)
T ss_pred cHHHHHhHHHHHHHHHHHHHHhhhcceecceehHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 7899999999999999999999999999999999999999999999998863221 24599999999999999999999
Q ss_pred cccccccccccccchhhhHHHHHHHHHHhCCCCCcchhhHHHHHHHHHHhhhhhhhHHHHhhhcCC--cchhHHHHHHHH
Q 028301 124 NLRSSYMEDKDNFAIYYVVVPCAVLALLIHPSTSHNILNRIFWAFCVYLEAVSVLPQLRVMQNTKV--PFSRLLNHSQPI 201 (211)
Q Consensus 124 k~k~TYd~~~Dtf~~~~liip~~vLAli~hp~~~~~~~~eilWtFSiyLEsVAILPQL~mlqk~g~--~~Tshyv~al~~ 201 (211)
++++||||..|||+++++++||+++|+++|.+ +.+.+++||||+|||||||||||+|+||.|| ++|+||++|.|+
T Consensus 82 ~~r~tYdk~lDtF~i~~ll~gsav~slff~~~---~tisnvlwtfS~wLESVAILPQL~mLq~~GeteslT~hYvfamgL 158 (214)
T COG5196 82 KYRSTYDKKLDTFNILTLLVGSAVFSLFFTRG---GTISNVLWTFSLWLESVAILPQLVMLQEAGETESLTSHYVFAMGL 158 (214)
T ss_pred cccchHHHhhhhhhhhhhhhhhhhheeeecCC---ccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcceeHHHHHHHHHH
Confidence 99999999999999999999999999999876 6699999999999999999999999999999 999999999996
Q ss_pred HH----HHHHHh
Q 028301 202 MY----LRLVLR 209 (211)
Q Consensus 202 ~~----~~~~~~ 209 (211)
|| -+|.+|
T Consensus 159 YRalYip~wI~r 170 (214)
T COG5196 159 YRALYIPYWILR 170 (214)
T ss_pred HHHhhhhHHHHH
Confidence 54 577776
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=100.00 E-value=7.1e-50 Score=327.12 Aligned_cols=137 Identities=34% Similarity=0.631 Sum_probs=127.3
Q ss_pred cccccccchhHHHHHHHHhhhcce--eeee-chHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhhhHHHHHHH
Q 028301 72 TCAGLSLKSQELTAIFLAVRLYCS--FVME-YDIHTLLDLATLATTLWVIYMIRFNLRSSYMEDKDNFAIYYVVVPCAVL 148 (211)
Q Consensus 72 S~~GiSlKTQ~Ly~iVf~~Rl~~~--f~~~-y~~~t~~k~~~i~~s~~iiylm~~k~k~TYd~~~Dtf~~~~liip~~vL 148 (211)
||+|+|+|||+||++|+++||+|+ +... ..+|++||++++++|++++|+|+.|||+|||+++|+|+..++++||++|
T Consensus 1 S~~GlSlktq~ly~~vf~~Ryldl~~f~~~~s~y~~~~k~~~i~~s~~iiyli~~~~~~Ty~~~~D~f~~~~li~p~~vL 80 (147)
T PF00810_consen 1 SCSGLSLKTQILYAIVFLTRYLDLFWFESYLSLYNTIMKVFFIVSSLYIIYLIFFKYKSTYDKEIDTFRLEYLIVPCFVL 80 (147)
T ss_pred CcchhhHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhhheeehhhhhccccchhhhHHHHHHHHH
Confidence 799999999999999999999998 4321 1246999999999999999999999999999999999999999999999
Q ss_pred HHHhCCCCCcchhhHHHHHHHHHHhhhhhhhHHHHhhhcCC--cchhHHHHHHHHH----HHHHHHh
Q 028301 149 ALLIHPSTSHNILNRIFWAFCVYLEAVSVLPQLRVMQNTKV--PFSRLLNHSQPIM----YLRLVLR 209 (211)
Q Consensus 149 Ali~hp~~~~~~~~eilWtFSiyLEsVAILPQL~mlqk~g~--~~Tshyv~al~~~----~~~~~~~ 209 (211)
|+++|| .+++++.|++||||+|||||||+|||+|+||+|| ++||||+++||++ .+||++|
T Consensus 81 a~i~~p-~~~~~~~ei~wtfSi~LEsvAIlPQL~m~~k~~~ve~ltshYv~~Lg~yR~ly~~~Wi~r 146 (147)
T PF00810_consen 81 ALIFHP-LNSFFFLEILWTFSIYLESVAILPQLFMLQKTGEVENLTSHYVFALGLYRALYLLNWIYR 146 (147)
T ss_pred HHHHhc-cccchHHHHHHHHHHHHHHHHHhHHHHHHHHhcCeeehHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999 7789999999999999999999999999999998 9999999999955 5789887
No 4
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=95.60 E-value=0.28 Score=42.66 Aligned_cols=141 Identities=16% Similarity=0.167 Sum_probs=69.2
Q ss_pred HHHHHHHHHhhccccccccccchhHHHHHHHHhh-------hcce-eeeech---HHHHHHHHHHHH-----HHHHHHHh
Q 028301 58 IGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVR-------LYCS-FVMEYD---IHTLLDLATLAT-----TLWVIYMI 121 (211)
Q Consensus 58 ~s~~iLl~KI~~~KS~~GiSlKTQ~Ly~iVf~~R-------l~~~-f~~~y~---~~t~~k~~~i~~-----s~~iiylm 121 (211)
.+.+==+.|++|+||++|+|+..-.+-.+.+++- +++. ...+|. +....|-++++. ++.+.+.+
T Consensus 17 ~~~~PQi~~n~k~ks~~GlS~~~~~l~~~g~~~~~~yn~~~~~~~~~~~~~~~~~~~v~~edl~~ai~~~il~~l~~~q~ 96 (220)
T TIGR00951 17 ISFYPQIIKNWRRKSAEGLSFDFVMLNLVGFTAYVIFNFLQLYCWSITNEFPLSSPGVTQNDVFFTLHAILICFIVLHQC 96 (220)
T ss_pred HHHhhHHHHHHhccccCCcCHHHHHHHHHHHHHHHHHHHHHhcchhhhhccccccCCCcHHHHHHHHHHHHHHHHHHHHH
Confidence 3444446999999999999999988655555443 2211 111121 111112222222 22222222
Q ss_pred hccccccccccccccc--h--hhhHHHHHHHHHHhCCCCCcchhhHHHHHHHHHHhhhhhhhHHHHhhhcCC----cchh
Q 028301 122 RFNLRSSYMEDKDNFA--I--YYVVVPCAVLALLIHPSTSHNILNRIFWAFCVYLEAVSVLPQLRVMQNTKV----PFSR 193 (211)
Q Consensus 122 ~~k~k~TYd~~~Dtf~--~--~~liip~~vLAli~hp~~~~~~~~eilWtFSiyLEsVAILPQL~mlqk~g~----~~Ts 193 (211)
. ++.....+...+.. . .++.+.+..+..+..+. ..-.+.+.++...+-+-.++-+||..+-.|.|- ++-+
T Consensus 97 ~-~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~-~~l~~l~~l~~iki~is~ikyiPQi~~Ny~~ksT~glSi~~ 174 (220)
T TIGR00951 97 G-DYERGWQRVSNPWILRILVALLACFATLLVALLSPI-TPLAFVTMLSYIKVAVTLVKYFPQAATNYHNKSTGQLSIIT 174 (220)
T ss_pred h-hccccccccchhHHHHHHHHHHHHHHHHHHHHHhcC-ChHHHHHHHHHHHHHHHHHHHhHHHHHHHhcCCCCcCCHHH
Confidence 1 22111111111111 1 12222233333333322 223466777777888888899999999988653 5555
Q ss_pred HHHHHHH
Q 028301 194 LLNHSQP 200 (211)
Q Consensus 194 hyv~al~ 200 (211)
-+.-..|
T Consensus 175 i~Ld~~G 181 (220)
T TIGR00951 175 VFLDFTG 181 (220)
T ss_pred HHHHHHH
Confidence 4444444
No 5
>KOG3211 consensus Predicted endoplasmic reticulum membrane protein Lec35/MPDU1 involved in monosaccharide-P-dolichol utilization [General function prediction only]
Probab=95.24 E-value=0.24 Score=43.58 Aligned_cols=120 Identities=18% Similarity=0.213 Sum_probs=73.1
Q ss_pred HHHhhccccccccccchhHHHHHHHHhhhcceeeeechHHHHHHHHHHHHHHHHHHHhhccccccccccccccchhhhHH
Q 028301 64 IYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFVMEYDIHTLLDLATLATTLWVIYMIRFNLRSSYMEDKDNFAIYYVVV 143 (211)
Q Consensus 64 l~KI~~~KS~~GiSlKTQ~Ly~iVf~~Rl~~~f~~~y~~~t~~k~~~i~~s~~iiylm~~k~k~TYd~~~Dtf~~~~lii 143 (211)
+.||...||+.|+|.-+|+|=.+-+..-+--...+.|+.-+.+|..++..+.+++-++-+.|+-.- -..|.+--.+.++
T Consensus 50 I~kI~aakSa~GLSv~s~~LElvgytvtl~Y~~~~g~pFss~gE~~fLl~Q~vili~~if~f~~~~-~~~v~~l~~~~~v 128 (230)
T KOG3211|consen 50 IMKIRAAKSARGLSVVSLLLELVGYTVTLSYSYTSGYPFSSYGEYPFLLLQAVILILCIFHFSGQT-VTVVQFLGYIALV 128 (230)
T ss_pred HHHHHhhcccccccHHHHHHHHHHHHheeeehhhcCCCchhHHHHHHHHHHHHHHHHHHHHhccce-eehhhHHHHHHHH
Confidence 489999999999999999988777766432223334445578999999999998888888877111 1123333333333
Q ss_pred HHHHHHHHhCCCCCcchhhHHHHHHHHHHhhhhhhhHHHHhhhcCC
Q 028301 144 PCAVLALLIHPSTSHNILNRIFWAFCVYLEAVSVLPQLRVMQNTKV 189 (211)
Q Consensus 144 p~~vLAli~hp~~~~~~~~eilWtFSiyLEsVAILPQL~mlqk~g~ 189 (211)
+....+ +..+ .++.+..=+-.+-.-.++=+||..-..|++.
T Consensus 129 ~~~~~s----k~~p-~~~~~L~~~~~l~i~v~sr~~Qi~~n~~~~~ 169 (230)
T KOG3211|consen 129 VSVLAS----KALP-LWIITLAQNLCLPIVVVSRLLQIQCNYHNRS 169 (230)
T ss_pred HHHHHH----hhhh-HHHHHHHHhcCchhhhHHHHHHHHHHhcccc
Confidence 322222 2111 2233444344444445777788877776543
No 6
>PF04193 PQ-loop: PQ loop repeat
Probab=89.28 E-value=0.54 Score=32.10 Aligned_cols=40 Identities=28% Similarity=0.120 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHhhccccccccccchhHHHHHHHHhhhc
Q 028301 54 AVHSIGISVLIYKLMKEKTCAGLSLKSQELTAIFLAVRLY 93 (211)
Q Consensus 54 l~Hl~s~~iLl~KI~~~KS~~GiSlKTQ~Ly~iVf~~Rl~ 93 (211)
..-+++.+==++|.+|+||+.|+|.-+..+..+..+++..
T Consensus 11 ~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g~~~~~~ 50 (61)
T PF04193_consen 11 VLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIGSILWVL 50 (61)
T ss_pred HHHHHHHHhHHHHHHHccccccccHHHHHHHHHHHHHHHH
Confidence 3334444445699999999999999999988887777743
No 7
>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=82.35 E-value=0.97 Score=27.07 Aligned_cols=22 Identities=32% Similarity=0.249 Sum_probs=18.1
Q ss_pred HHHhhccccccccccchhHHHH
Q 028301 64 IYKLMKEKTCAGLSLKSQELTA 85 (211)
Q Consensus 64 l~KI~~~KS~~GiSlKTQ~Ly~ 85 (211)
++|++++||+.|+|.-...+-.
T Consensus 7 i~~~~~~ks~~glS~~~~~l~~ 28 (32)
T smart00679 7 IIKNYRRKSTEGLSILFVLLWL 28 (32)
T ss_pred HHHHHHcCCcCcCCHHHHHHHH
Confidence 5799999999999987766543
No 8
>PF04193 PQ-loop: PQ loop repeat
Probab=78.90 E-value=9.6 Score=25.77 Aligned_cols=39 Identities=23% Similarity=0.140 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHhhhhhhhHHHHhhhcCC----cchhHHHHHHH
Q 028301 162 NRIFWAFCVYLEAVSVLPQLRVMQNTKV----PFSRLLNHSQP 200 (211)
Q Consensus 162 ~eilWtFSiyLEsVAILPQL~mlqk~g~----~~Tshyv~al~ 200 (211)
.+++...+.-+++++-+||+....|++. +++...+...|
T Consensus 2 ~~~~g~i~~~~~~~~~lPQi~~~~k~ks~~glS~~~~~l~~~g 44 (61)
T PF04193_consen 2 SNILGIISIVLWIISFLPQIIKNYKRKSTGGLSLWFLLLWLIG 44 (61)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHccccccccHHHHHHHHHH
Confidence 4678889999999999999999999874 67666665555
No 9
>COG4095 Uncharacterized conserved protein [Function unknown]
Probab=44.02 E-value=87 Score=24.10 Aligned_cols=42 Identities=24% Similarity=0.204 Sum_probs=30.7
Q ss_pred HHHHhhhhhhhHHHHhhhcCC--cchhHHHHHHHHHHHHHHHhc
Q 028301 169 CVYLEAVSVLPQLRVMQNTKV--PFSRLLNHSQPIMYLRLVLRG 210 (211)
Q Consensus 169 SiyLEsVAILPQL~mlqk~g~--~~Tshyv~al~~~~~~~~~~~ 210 (211)
+--+-.+|.+||+.-.-|+++ +++--..-.+.+.+.-|+.-|
T Consensus 12 a~ilttf~flPQ~iki~ktK~t~~Isl~~fii~~ia~~lwliyg 55 (89)
T COG4095 12 AGILTTFAFLPQLIKIIKTKNTASISLPMFIILNIALFLWLIYG 55 (89)
T ss_pred HHHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHH
Confidence 334557899999999999886 666666666777777776554
No 10
>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=40.25 E-value=33 Score=24.38 Aligned_cols=44 Identities=18% Similarity=0.525 Sum_probs=21.4
Q ss_pred HHHHHHHHHhhc-cccccccccccccchhhhHHHHHHHHHHhCCC
Q 028301 112 ATTLWVIYMIRF-NLRSSYMEDKDNFAIYYVVVPCAVLALLIHPS 155 (211)
Q Consensus 112 ~~s~~iiylm~~-k~k~TYd~~~Dtf~~~~liip~~vLAli~hp~ 155 (211)
......+|.+.. +..+.+..+.++.-....++|++++..+.-|+
T Consensus 37 ~V~~~l~~~~~~~~~~~~~~~~~~~lE~~WTiiP~iiLl~l~~pS 81 (84)
T PF02790_consen 37 FVFYFLIYFLFNSKFPNKFFNHNNKLEIIWTIIPAIILLFLAFPS 81 (84)
T ss_dssp HHHHHHHHHHHHSSSS--S---SHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eEeeecccccccccccccccccchhhhhhhhHHHHHHHHHHHhhh
Confidence 333444444444 33333333333444457888988887776543
No 11
>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=31.93 E-value=1.9e+02 Score=23.01 Aligned_cols=58 Identities=19% Similarity=0.272 Sum_probs=39.0
Q ss_pred HHHHHhhCCCceee---HHHHHHHHHHHHHHHHHHhcCcHHHH-HhhHHHHHHHHHHHHHhh
Q 028301 11 VSTWVRRQPPKVKA---FLAVVSGMAALVLLRFIVHDHDNLFV-AAEAVHSIGISVLIYKLM 68 (211)
Q Consensus 11 ~~~~l~~~~~~v~~---~~~~~~~~~~~~~~~~~~~d~n~f~l-lgdl~Hl~s~~iLl~KI~ 68 (211)
...+.++.|+|+|+ ++.+.+.+-++-++|-..-+.-.|.- +|-+.-+.|-.+|...++
T Consensus 12 ~~~Y~~~Tp~rlkliD~fl~f~~~~gilQfvYc~lvgtFPFNaFLsGf~s~VG~fVL~vsLR 73 (112)
T PF02109_consen 12 WQSYLKKTPQRLKLIDAFLAFLVLTGILQFVYCILVGTFPFNAFLSGFISCVGQFVLTVSLR 73 (112)
T ss_pred HHHHHHhCCchhhhHHHHHHHHHHHHHHHHhHheeecCCchHHHHHHHHHHHHHHHHHHHHH
Confidence 44778999999997 56666666677777776664444432 667777777776664443
No 12
>PF01306 LacY_symp: LacY proton/sugar symporter; InterPro: IPR022814 In bacteria there are a number of families of transport proteins, including symporters and antiporters, that mediate the intake of a variety of sugars with the concomitant uptake of hydrogen ions (proton symporters) []. The lacY family of Escherichia coli and Klebsiella pneumoniae are proton/beta-galactoside symporters, which, like most sugar transporters, are integral membrane proteins with 12 predicted transmembrane (TM) regions. Also similar to the lacY family are the rafinose (rafB) and sucrose (cscB) permeases from E. coli []. This entry also includes bacterial phenylproprionate permease.; PDB: 1PV7_B 1PV6_A 2Y5Y_B 2CFQ_A 2V8N_B 2CFP_A.
Probab=29.64 E-value=1.2e+02 Score=29.07 Aligned_cols=49 Identities=22% Similarity=0.399 Sum_probs=38.0
Q ss_pred hhhHHHHHHHHHHhhhhhhhHHHHhhhcCC-cchhHHHHHHHHHHHHHHHhcC
Q 028301 160 ILNRIFWAFCVYLEAVSVLPQLRVMQNTKV-PFSRLLNHSQPIMYLRLVLRGF 211 (211)
Q Consensus 160 ~~~eilWtFSiyLEsVAILPQL~mlqk~g~-~~Tshyv~al~~~~~~~~~~~~ 211 (211)
...-.+|+..+.+|+.-+.+-=.+++|.|- +. .+.|-.+|-+||+.-|+
T Consensus 259 ~~~G~l~s~~v~~E~~~m~~~p~li~rig~k~~---Lllag~i~~iRi~~~~~ 308 (412)
T PF01306_consen 259 QMYGYLWSVQVFLEALMMFFSPWLINRIGAKNL---LLLAGVIMAIRIIGSGF 308 (412)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHH---HHHHHHHHHHHHHHHHT
T ss_pred hHHhHHHHHHHHHHHHHHHHHHHHHHhcChHhH---HHHHHHHHHHHHHHHhh
Confidence 456788999999999999999999999885 32 35566688889887553
No 13
>PF05297 Herpes_LMP1: Herpesvirus latent membrane protein 1 (LMP1); InterPro: IPR007961 This family consists of several latent membrane protein 1 or LMP1s mostly from Epstein-Barr virus (strain GD1) (HHV-4) (Human herpesvirus 4). LMP1 of HHV-4 is a 62-65 kDa plasma membrane protein possessing six membrane spanning regions, a short cytoplasmic N terminus and a long cytoplasmic carboxy tail of 200 amino acids. HHV-4 virus latent membrane protein 1 (LMP1) is essential for HHV-4 mediated transformation and has been associated with several cases of malignancies. HHV-4-like viruses in Macaca fascicularis (Cynomolgus monkeys) have been associated with high lymphoma rates in immunosuppressed monkeys [].; GO: 0019087 transformation of host cell by virus, 0016021 integral to membrane; PDB: 1CZY_E 1ZMS_B.
Probab=26.24 E-value=22 Score=33.18 Aligned_cols=38 Identities=21% Similarity=0.186 Sum_probs=0.0
Q ss_pred HHHHHHHHhcCcHHHH--HhhHHHHHHHHHHHHHhhcccc
Q 028301 35 LVLLRFIVHDHDNLFV--AAEAVHSIGISVLIYKLMKEKT 72 (211)
Q Consensus 35 ~~~~~~~~~d~n~f~l--lgdl~Hl~s~~iLl~KI~~~KS 72 (211)
++-+|.+|||+.-.-. +.++.-+.-++|++.-+.|+|-
T Consensus 37 l~w~~iimsd~t~~a~~vl~sfAvvliiIIiIImlF~RrL 76 (381)
T PF05297_consen 37 LVWFFIIMSDLTQGALTVLYSFAVVLIIIIIIIMLFKRRL 76 (381)
T ss_dssp ----------------------------------------
T ss_pred HHHHHHHHhccccchHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3345568888875543 6666666666666776777664
No 14
>PTZ00154 40S ribosomal protein S17; Provisional
Probab=26.05 E-value=51 Score=27.13 Aligned_cols=27 Identities=33% Similarity=0.374 Sum_probs=20.7
Q ss_pred HHHhhHHHHHHHHHHHHHhhccccccccccchhH
Q 028301 49 FVAAEAVHSIGISVLIYKLMKEKTCAGLSLKSQE 82 (211)
Q Consensus 49 ~llgdl~Hl~s~~iLl~KI~~~KS~~GiSlKTQ~ 82 (211)
+++|...|+ .|-.+...+.|||+|.|+
T Consensus 49 rIAGYIThl-------mkri~~gpvrgis~klqe 75 (134)
T PTZ00154 49 KIAGFVTHL-------MKRIQKGPVRGISLKLQE 75 (134)
T ss_pred HHHHHHHHH-------HhhhccCCccccceehhH
Confidence 557777775 455666789999999997
No 15
>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=23.63 E-value=1.1e+02 Score=23.96 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=19.1
Q ss_pred HhcCcHHHHHhhHHHHHHHHHHHHHhhcc
Q 028301 42 VHDHDNLFVAAEAVHSIGISVLIYKLMKE 70 (211)
Q Consensus 42 ~~d~n~f~llgdl~Hl~s~~iLl~KI~~~ 70 (211)
+.+-.-+-+.+-++..+||+.|.+|+.|.
T Consensus 66 ~RNk~W~T~~S~~tS~isIL~LV~~~~KK 94 (100)
T PF06363_consen 66 ERNKAWFTVVSAVTSFISILLLVTKIFKK 94 (100)
T ss_pred HHcchHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 33444444455566778899999888765
No 16
>TIGR00951 2A43 Lysosomal Cystine Transporter.
Probab=20.55 E-value=5.6e+02 Score=22.13 Aligned_cols=34 Identities=21% Similarity=0.096 Sum_probs=30.1
Q ss_pred HHHhhccccccccccchhHHHHHHHHhhhcceee
Q 028301 64 IYKLMKEKTCAGLSLKSQELTAIFLAVRLYCSFV 97 (211)
Q Consensus 64 l~KI~~~KS~~GiSlKTQ~Ly~iVf~~Rl~~~f~ 97 (211)
++..+++||..|+|..|..|-....+.|.++...
T Consensus 158 i~~Ny~~ksT~glSi~~i~Ld~~G~lqri~ts~~ 191 (220)
T TIGR00951 158 AATNYHNKSTGQLSIITVFLDFTGLLQRIFQSVN 191 (220)
T ss_pred HHHHHhcCCCCcCCHHHHHHHHHHHHHHHHHHHH
Confidence 5778999999999999999999999999887653
Done!