--------------------------------------------------------------------------------
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  
