-------------------------------------------------------------------------------- Domain name : PF01299.9_Lamp Domain size : 338 Domain Description : Lysosome-associated membrane glycoprotein (Lamp) Domain gathering score : -87.0000 Domain trusted cutoff : -86.0000 Domain architecture : non-TM/SP [1 327], TM [328 369] -------------------------------------------------------------------------------- Example 1 gi|63652501|ref|XP_487300.2| PREDICTED: hypothetical protein [Mus musculus] 321 (length) 50 280 .. (wrt seq) 1 338 [] (wrt HMM) No.of residues in non-TM/SP region : 202 [62%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- ATP-synt_S1 Vacuolar ATP synthase subunit S1 (ATP6S1) -124.6 4.4e-07 1 Lamp Lysosome-associated membrane glycoprotein -71.3 0.00014 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ATP-synt_S1 1/1 2 284 .. 1 485 [] -124.6 4.4e-07 Lamp 1/1 50 280 .. 1 338 [] -71.3 0.00014 Alignments of top-scoring domains: ATP-synt_S1: domain 1 of 1, from 2 to 284: score -124.6, E = 4.4e-07 *->LFsalaissiasaateqqVPllLWSSdreiggeqaeklaghitseeq +++s+ +a k +g+ gi|6365250 2 V---FSVSLDQI---------------------LARKNVGS------ 18 LvsYLnpALslGPrNVLlFLQdklSieDFtAyGGvfGNKQDSaFpNlesa Q+S gi|6365250 19 ---------------------------------------QES-------- 21 leaSsSqLVlsAvdWyAssvvyiilqeeLgssplhvDqLISkIDnTLgel +s ++ v g+ gi|6365250 22 -----------------------------SSKEVVVRN---------GQK 33 kLNdsvpaLlvvRLpYvAtdeLmsakEvLegnDevIGqVLsllksedVPY + + p R+p I q + +s gi|6365250 34 NSGEVKPVQNFTRIP--------------------IAQTFNYNLS----- 58 TavytalrPsrvieclfvqRCRleGfsLGRqLLlTvvvqpkkePLplsYn + + + + + p+ + gi|6365250 59 ---------------------------------NKPWSTFSHHN-PVQFS 74 daaeePcILlWAanLsvsyLRddedaeYdLtsgtfGksvslkltGslcnd + + PcIL+W + +v + ++ dLt G+ + ++ s c + gi|6365250 75 RDG-IPCILFWTKRITVKF-KNQTWL--DLTDEALGQNTTVDTGNSNCSE 120 ttarLFnvlnYkaFemlkgdsldliFvlsgrffpVSARnwfvmdnVeleg a L +l + + +d +F+l+ + + wf++++Ve++ gi|6365250 121 ESATL--SLKFG--DDEDPKDIDIRFTLTN-YNKLASQSWFSLHRVEIIF 165 dgnYKsAkfnasqsinaPaeYSfkcqsVsSWSLvCGqkqaLLvPrnakdd + + A+fna i+a ++YS++cq VsS aLL + + d gi|6365250 166 NNS-VQATFNATG-IYALSTYSYRCQRVSSLR----RNDALLLLSSSDDV 209 avkwglvledFQIQlFNVtgkPEKWleaeqFsyQAsDCAGFFSpGIWMGL ++ w +++ dFQIQ+F+ g +qF+ A DC FSp I GL gi|6365250 210 TSLWEVTFIDFQIQGFSIKG--------AQFAQ-ARDCSSSFSPAILIGL 250 itaLlliliLtYGLhMimSLkTMDRFDDPKGpaIvvpq<-* +L l+l+L Y LhM+ L+ DR I+ p gi|6365250 251 AMSLILLLVLAYALHMLIYLRYLDRH----YEFITSPD 284 Lamp: domain 1 of 1, from 50 to 280: score -71.3, E = 0.00014 *->YsvteltfsynlsDttlFPnatskgvkTvtsstdaikaptnttyrCv + tf ynls + P +t +++++v s d+i+ + gi|6365250 50 AQ----TFNYNLSNK---PWSTFSHHNPVQFSRDGIPCIL------- 82 ssttvpmtnVtvtfsDvtlqAylqngtfSktetrCeaDktpTpsPttaPt gi|6365250 - -------------------------------------------------- - tapapstVaTpvPsPtttPvPssPavGnYsVtngNgtyCLLAsMGLQLNi + +V+++N+t L gi|6365250 83 ----------FWTKRI-------------TVKFKNQT---------WLDL 100 tyekk.dnktvtrlfNInPnkTtasGsCgsqtatLeLlWGsfengtvLtf t+e +++n+t + t + +C+ ++atL+L G +e ++++ gi|6365250 101 TDEALgQNTT----------VDTGNSNCSEESATLSLKFGDDEDPKDIDI 140 tFtlnnss.....skfyLseVslsltlldesfpdasenptFsasNssLsa Ftl+n ++ ++s f L+ V + + + + tF+a + gi|6365250 141 RFTLTNYNklasqSWFSLHRVEIIFNN------SVQA--TFNA-----TG 177 lqapvGsSYkCnkeQslqvseafqeell..........alntfnLqVQAF a SY+C + sl+ ++a+ ll+++++ ++ ++ + q Q F gi|6365250 178 IYALSTYSYRCQRVSSLRRNDALL--LLsssddvtslwEVTFIDFQIQGF 225 nvtgnkkFstaeECslDdnsmLiPIaVGaALaGLvliVLIAY....lIGR ++g + F+ a +Cs+ s+ I +G+A + +l+V +AY + lI + gi|6365250 226 SIKGAQ-FAQARDCSS---SFSPAILIGLAMSLILLLV-LAYalhmLIYL 270 rRsharGYQti<-* r + +Y+ i gi|6365250 271 RYLDR-HYEFI 280 Example 2 gi|82952178|ref|XP_916963.1| PREDICTED: hypothetical protein [Mus musculus] 321 (length) 50 280 .. (wrt seq) 1 338 [] (wrt HMM) No.of residues in non-TM/SP region : 202 [62%(over non-TM/SP length)] Scores for sequence family classification: Model Description Score E-value N -------- ----------- ----- ------- --- ATP-synt_S1 Vacuolar ATP synthase subunit S1 (ATP6S1) -124.5 4.4e-07 1 Lamp Lysosome-associated membrane glycoprotein -71.3 0.00014 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ATP-synt_S1 1/1 2 284 .. 1 485 [] -124.5 4.4e-07 Lamp 1/1 50 280 .. 1 338 [] -71.3 0.00014 Alignments of top-scoring domains: ATP-synt_S1: domain 1 of 1, from 2 to 284: score -124.5, E = 4.4e-07 *->LFsalaissiasaateqqVPllLWSSdreiggeqaeklaghitseeq +++s+ +a k +g+ gi|8295217 2 V---FSVSLDQI---------------------LARKNVGS------ 18 LvsYLnpALslGPrNVLlFLQdklSieDFtAyGGvfGNKQDSaFpNlesa Q+S gi|8295217 19 ---------------------------------------QES-------- 21 leaSsSqLVlsAvdWyAssvvyiilqeeLgssplhvDqLISkIDnTLgel +s ++ v g+ gi|8295217 22 -----------------------------SSKEVVVRN---------GQK 33 kLNdsvpaLlvvRLpYvAtdeLmsakEvLegnDevIGqVLsllksedVPY + + p R+p I q + +s gi|8295217 34 NSGEVKPVQNFTRIP--------------------IAQTFNYNLS----- 58 TavytalrPsrvieclfvqRCRleGfsLGRqLLlTvvvqpkkePLplsYn + + + + + p+ + gi|8295217 59 ---------------------------------NKPWSTFSHHN-PVQFS 74 daaeePcILlWAanLsvsyLRddedaeYdLtsgtfGksvslkltGslcnd + + PcIL+W + +v + ++ dLt G+ + ++ s c + gi|8295217 75 RDG-IPCILFWTKRITVKF-KNQTWL--DLTDEALGQNTTVDTGNSNCSE 120 ttarLFnvlnYkaFemlkgdsldliFvlsgrffpVSARnwfvmdnVeleg a L +l + + +d +F+l+ + + wf++++Ve++ gi|8295217 121 ESATL--SLKFG--DDEDPKDIDIRFTLTN-YNKLASQSWFSLHRVEIIF 165 dgnYKsAkfnasqsinaPaeYSfkcqsVsSWSLvCGqkqaLLvPrnakdd + + A+fna i+a ++YS++cq VsS aLL + + d gi|8295217 166 NNS-VQATFNATG-IYALSTYSYRCQRVSSLR----RNDALLLLSSSDDV 209 avkwglvledFQIQlFNVtgkPEKWleaeqFsyQAsDCAGFFSpGIWMGL ++ w +++ dFQIQ+F+ g +qF+ A DC FSp I GL gi|8295217 210 TNLWEVTFIDFQIQGFSIKG--------AQFAQ-ARDCSSSFSPAILIGL 250 itaLlliliLtYGLhMimSLkTMDRFDDPKGpaIvvpq<-* +L l+l+L Y LhM+ L+ DR I+ p gi|8295217 251 AMSLILLLVLAYALHMLIYLRYLDRH----YEFITSPD 284 Lamp: domain 1 of 1, from 50 to 280: score -71.3, E = 0.00014 *->YsvteltfsynlsDttlFPnatskgvkTvtsstdaikaptnttyrCv + tf ynls + P +t +++++v s d+i+ + gi|8295217 50 AQ----TFNYNLSNK---PWSTFSHHNPVQFSRDGIPCIL------- 82 ssttvpmtnVtvtfsDvtlqAylqngtfSktetrCeaDktpTpsPttaPt gi|8295217 - -------------------------------------------------- - tapapstVaTpvPsPtttPvPssPavGnYsVtngNgtyCLLAsMGLQLNi + +V+++N+t L gi|8295217 83 ----------FWTKRI-------------TVKFKNQT---------WLDL 100 tyekk.dnktvtrlfNInPnkTtasGsCgsqtatLeLlWGsfengtvLtf t+e +++n+t + t + +C+ ++atL+L G +e ++++ gi|8295217 101 TDEALgQNTT----------VDTGNSNCSEESATLSLKFGDDEDPKDIDI 140 tFtlnnss.....skfyLseVslsltlldesfpdasenptFsasNssLsa Ftl+n ++ ++s f L+ V + + + + tF+a + gi|8295217 141 RFTLTNYNklasqSWFSLHRVEIIFNN------SVQA--TFNA-----TG 177 lqapvGsSYkCnkeQslqvseafqeell..........alntfnLqVQAF a SY+C + sl+ ++a+ ll+++++ ++ ++ + q Q F gi|8295217 178 IYALSTYSYRCQRVSSLRRNDALL--LLsssddvtnlwEVTFIDFQIQGF 225 nvtgnkkFstaeECslDdnsmLiPIaVGaALaGLvliVLIAY....lIGR ++g + F+ a +Cs+ s+ I +G+A + +l+V +AY + lI + gi|8295217 226 SIKGAQ-FAQARDCSS---SFSPAILIGLAMSLILLLV-LAYalhmLIYL 270 rRsharGYQti<-* r + +Y+ i gi|8295217 271 RYLDR-HYEFI 280 Revised version of example 1 and 2 gi|225007585|ref|NP_001139351.1|predicted gene, EG435376 [Mus musculus] 336 (length) Scores for sequence family classification (score includes all domains): Model Description Score E-value N -------- ----------- ----- ------- --- ATP-synt_S1 Vacuolar ATP synthase subunit S1 (ATP6S1) -106.2 6.5e-08 1 Lamp Lysosome-associated membrane glycoprotein -71.3 0.00014 1 DUF2463 Protein of unknown function (DUF2463) -156.1 5.5 1 DUF1753 Golgi protein of unknown function (DUF175 -137.4 8.1 1 TLP-20 Nucleopolyhedrovirus telokin-like protein -81.9 9.5 1 Parsed for domains: Model Domain seq-f seq-t hmm-f hmm-t score E-value -------- ------- ----- ----- ----- ----- ----- ------- ATP-synt_S1 1/1 6 299 .. 1 485 [] -106.2 6.5e-08 TLP-20 1/1 26 177 .. 1 229 [] -81.9 9.5 Lamp 1/1 65 295 .. 1 338 [] -71.3 0.00014 DUF2463 1/1 137 285 .. 1 214 [] -156.1 5.5 DUF1753 1/1 157 314 .. 1 294 [] -137.4 8.1 Alignments of top-scoring domains: ATP-synt_S1: domain 1 of 1, from 6 to 299: score -106.2, E = 6.5e-08 *->LFsalaissiasaateqqVPllLWSSdreiggeqaeklaghitseeq L +++s+++ + gi|2250075 6 L---FSFSLLFL--CM------------------------------- 16 LvsYLnpALslGPrNVLlFLQdklSieDFtAyGGvfGNKQDSaFpNlesa +F gi|2250075 17 ------------------------------------------VF------ 18 leaSsSqLVlsAvdWyAssvvyiilqeeLgssplhvDqLISkIDnTLgel ++s +Dq gi|2250075 19 -----------------------------SVS---LDQ------------ 24 kLNdsvpaLlvvRLpYvAtdeLmsakEvLegnDe.vIGqVLsllksedVP +a + v ++ s+kEv n +++ G+V gi|2250075 25 -----ILARKNV------GSQESSSKEVVVRNGQkNSGEV---------- 53 YTavytalrPsrvieclfvqRCRleGfsLGRqLLlTvvvqpkkePLplsY +P + + ++ + L + + + + + p+ + gi|2250075 54 --------KPVQNFTRIPI----AQT--FNYNLSNKPWSTFSHHN-PVQF 88 ndaaeePcILlWAanLsvsyLRddedaeYdLtsgtfGksvslkltGslcn + + PcIL+W + +v + ++ dLt G+ + ++ s c gi|2250075 89 SRDG-IPCILFWTKRITVKF-KNQTWL--DLTDEALGQNTTVDTGNSNCS 134 dttarLFnvlnYkaFemlkgdsldliFvlsgrffpVSARnwfvmdnVele + a L +l + + +d +F+l+ + + wf++++Ve++ gi|2250075 135 EESATL--SLKFG--DDEDPKDIDIRFTLTN-YNKLASQSWFSLHRVEII 179 gdgnYKsAkfnasqsinaPaeYSfkcqsVsSWSLvCGqkqaLLvPrnakd + + A+fna i+a ++YS++cq VsS aLL + + d gi|2250075 180 FNNS-VQATFNATG-IYALSTYSYRCQRVSSLR----RNDALLLLSSSDD 223 davkwglvledFQIQlFNVtgkPEKWleaeqFsyQAsDCAGFFSpGIWMG ++ w +++ dFQIQ+F+ g +qF+ A DC FSp I G gi|2250075 224 VTSLWEVTFIDFQIQGFSIKG--------AQFAQ-ARDCSSSFSPAILIG 264 LitaLlliliLtYGLhMimSLkTMDRFDDPKGpaIvvpq<-* L +L l+l+L Y LhM+ L+ DR I+ p gi|2250075 265 LAMSLILLLVLAYALHMLIYLRYLDRH----YEFITSPD 299 TLP-20: domain 1 of 1, from 26 to 177: score -81.9, E = 9.5 CS XXXXXX----EEEEEEE-SS-..TTE..EEEEE-S-EEE---S-EEE *->MAtnnngTvDIaVyvtlldeddeknvItLsFiVqdEYhLKKlgVGAY A +n+g + +++ kn +V+ + + gi|2250075 26 LARKNVGSQESSSKEVVVRNGQ-KNS----GEVKPVQNFTR------ 61 CS EEEE---.....GGGGGGGTSEEEEEESSSEEEEEEEESS-SS--EEEEE avnVldsekisrqlLnaLhnkaystvaCGdYvvlyNlvengeygInvILF + ++ + + L nk+ st++ ++N v+ ++ gI ILF gi|2250075 62 -IPIAQT---FNYNL---SNKPWSTFS------HHNPVQFSRDGIPCILF 98 CS ESS-EEE-TT-EEEEE................EEE-XXXXXXXXXXXXXX nkkpikLKKgsciFkIsYvdDdddkthvvssnkkvtndkkltdavvehss +k+i+ K Fk +d+ +e + gi|2250075 99 WTKRITVK-----FKN----------------------QTWLDLTDEALG 121 CS X.....................XXXXXXXXXXXXXXXXX..XXXXXXXXX ndadsqqaksaiapeSDesdsgsatVededddDDddadaDYaatiesega + + s+ + +sat + +dD d+ d gi|2250075 122 QNTTVDTGNSN-------CSEESATLSLKFGDDEDPKDI----------- 153 CS XXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXX agaggggdsaeissdeepappKkQKLDeseQd<-* + + +++ ++ + ++ + ++ gi|2250075 154 -----DIRFTLTNYNKLASQ---SWFSLHRVE 177 Lamp: domain 1 of 1, from 65 to 295: score -71.3, E = 0.00014 *->YsvteltfsynlsDttlFPnatskgvkTvtsstdaikaptnttyrCv + tf ynls + P +t +++++v s d+i+ + gi|2250075 65 AQ----TFNYNLSNK---PWSTFSHHNPVQFSRDGIPCIL------- 97 ssttvpmtnVtvtfsDvtlqAylqngtfSktetrCeaDktpTpsPttaPt gi|2250075 - -------------------------------------------------- - tapapstVaTpvPsPtttPvPssPavGnYsVtngNgtyCLLAsMGLQLNi + +V+++N+t L gi|2250075 98 ----------FWTKRI-------------TVKFKNQT---------WLDL 115 tyekk.dnktvtrlfNInPnkTtasGsCgsqtatLeLlWGsfengtvLtf t+e +++n+t + t + +C+ ++atL+L G +e ++++ gi|2250075 116 TDEALgQNTT----------VDTGNSNCSEESATLSLKFGDDEDPKDIDI 155 tFtlnnss.....skfyLseVslsltlldesfpdasenptFsasNssLsa Ftl+n ++ ++s f L+ V + + + + tF+a + gi|2250075 156 RFTLTNYNklasqSWFSLHRVEIIFNN------SVQA--TFNA-----TG 192 lqapvGsSYkCnkeQslqvseafqeell..........alntfnLqVQAF a SY+C + sl+ ++a+ ll+++++ ++ ++ + q Q F gi|2250075 193 IYALSTYSYRCQRVSSLRRNDALL--LLsssddvtslwEVTFIDFQIQGF 240 nvtgnkkFstaeECslDdnsmLiPIaVGaALaGLvliVLIAY....lIGR ++g + F+ a +Cs+ s+ I +G+A + +l+V +AY + lI + gi|2250075 241 SIKGAQ-FAQARDCSS---SFSPAILIGLAMSLILLLV-LAYalhmLIYL 285 rRsharGYQti<-* r + +Y+ i gi|2250075 286 RYLDR-HYEFI 295 DUF2463: domain 1 of 1, from 137 to 285: score -156.1, E = 5.5 *->FPalmYfIfdKDrFeesPfLRFItlLLPFSYSAvQYllLLhtNWkss +a + f D+ +++ RF + Y L +W s gi|2250075 137 -SATLSLKFGDDEDPKDIDIRFTLT---------NYNKLASQSWFSL 173 hKpEgiLhkiLYylLNlLLlaFaiISILSIIaFti.........dkWenn h+ E ++N + a+ + I a+ + + + ++ ++ + n gi|2250075 174 HRVE--------IIFNNS--VQATFNATGIYALSTysyrcqrvsSLRR-N 212 dDllfySiiLPSFfvPpTYLLSTSCdLvpgqIgFTDTGinilIDlLILLc d+ll LLS+S d ++ T +ID I + gi|2250075 213 DALL---------------LLSSSDDVTSLW---EVT----FIDFQIQGF 240 pivslvlvlvleeseCCYypYfaiiSsILILiRlLkEkylPSkkSSlPtA +i + + + + SS++ + gi|2250075 241 SIKGAQF----AQAR--DC-------------------------SSSFSP 259 pWRVaiFvlILiLaifvYafiaygsi<-* + + + L +++Ya+ + + + gi|2250075 260 AILIGLAMSLILLLVLAYALHMLIYL 285 DUF1753: domain 1 of 1, from 157 to 314: score -137.4, E = 8.1 *->mrlssrflriprPkRnitsFLGFmsLkiGaELIllfaifNKvsGLYG +l ++++++ sL +E+I gi|2250075 157 FTLTNY-NKLASQS--------WFSLHR-VEII-------------- 179 lLaLFtGypLsflQvlmYLySvltLasflwgLphIrNRkqSplqaLllaw F ++ +Q ++++ + +L +++ ++ S++ + +l++ gi|2250075 180 ----FNNS----VQATFNATGIYALSTYSYRCQRVS----SLRRNDALLL 217 lYalDtllnalYTllFaltWFltipQntqdgdttgPaSqkdddladlals l + D + ++l+ + F +d + +g gi|2250075 218 LSSSDDV-TSLWEVTF------------IDFQIQG--------------- 239 reeisrpteegqvsadsasPGqrkqlesavwqrEsafSmallvffwllRf + g++ a + + ++s ++ +++m+l++ gi|2250075 240 ------FSIKGAQFAQARD-----CSSSFSPAILIGLAMSLIL------- 271 YFaLVvlSYArkllrhntyvalPLsARGKAkalahptkgrstsiasiage L+vl+YA ++l y+++ ++ + ++ s++ gi|2250075 272 ---LLVLAYALHMLIYLRYLDRH--------YEFITSPDHFPSLR----- 305 adidrEPFsegapdGeGwqGKykrymvsvgRgYWlggdkEDegeewa<-* ++ + ee++ gi|2250075 306 --------------------ALDTG------------------EEKE 314