gemmi-protools 1.1.0__py3-none-any.whl

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Files changed (20) hide show
  1. gemmi_protools/__init__.py +5 -0
  2. gemmi_protools/data/CD1/CD21029_review.fasta +141 -0
  3. gemmi_protools/data/MHC/MHC_combined.hmm +1092 -0
  4. gemmi_protools/data/MHC/MHC_combined.hmm.h3f +0 -0
  5. gemmi_protools/data/MHC/MHC_combined.hmm.h3i +0 -0
  6. gemmi_protools/data/MHC/MHC_combined.hmm.h3m +0 -0
  7. gemmi_protools/data/MHC/MHC_combined.hmm.h3p +0 -0
  8. gemmi_protools/io/__init__.py +3 -0
  9. gemmi_protools/io/convert.py +93 -0
  10. gemmi_protools/io/reader.py +911 -0
  11. gemmi_protools/tools/__init__.py +3 -0
  12. gemmi_protools/tools/align.py +336 -0
  13. gemmi_protools/tools/dockq.py +128 -0
  14. gemmi_protools/tools/mesh.py +197 -0
  15. gemmi_protools/tools/pdb_annot.py +862 -0
  16. gemmi_protools-1.1.0.dist-info/METADATA +46 -0
  17. gemmi_protools-1.1.0.dist-info/RECORD +20 -0
  18. gemmi_protools-1.1.0.dist-info/WHEEL +5 -0
  19. gemmi_protools-1.1.0.dist-info/licenses/LICENSE +21 -0
  20. gemmi_protools-1.1.0.dist-info/top_level.txt +1 -0
gemmi_protools/__init__.py ADDED
@@ -0,0 +1,5 @@
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+ """
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+ @Author: Luo Jiejian
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+ """
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+ from gemmi_protools.io.convert import gemmi2bio, bio2gemmi
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+ from gemmi_protools.io.reader import StructureParser, is_cif, is_pdb
gemmi_protools/data/CD1/CD21029_review.fasta ADDED
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+ >O62848|reviewed|Antigen-presenting glycoprotein CD1d|taxID:9940
2
+ MGCLLFLVLLEFQKIWGSFEAPQTSFPFRFLQISSFANHSWTRTDGLMWLGELQPYTWRNESSTIRFLKHWSQGTFSDQQ
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+ WEQLQHTFQVYRSSFTRDIREFVKMLPGDYPFEIQISGGCELLPRNISESFLRAALQEKDVLSFQGMSWVSAPDAPPWSQ
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+ VVCKVLNEDQGTKETVHWLLHDICPELVKGLMQTGKSELEKQVKPEAWLSSGPSPGPDRLLLGCHVSGFYPKPVWVMWMR
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+ GEQEEPGTQQGDVMPNADSTWYLRVTLEVAAGEAAGLSCRVKHSSLGDQDIILYWDGKRVSRGLIVVLVILVFVLLFVGG
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+ LVFWFRKHRRYQDIS
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+ >P06126|reviewed|T-cell surface glycoprotein CD1a|taxID:9606
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+ MLFLLLPLLAVLPGDGNADGLKEPLSFHVTWIASFYNHSWKQNLVSGWLSDLQTHTWDSNSSTIVFLCPWSRGNFSNEEW
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+ KELETLFRIRTIRSFEGIRRYAHELQFEYPFEIQVTGGCELHSGKVSGSFLQLAYQGSDFVSFQNNSWLPYPVAGNMAKH
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+ FCKVLNQNQHENDITHNLLSDTCPRFILGLLDAGKAHLQRQVKPEAWLSHGPSPGPGHLQLVCHVSGFYPKPVWVMWMRG
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+ EQEQQGTQRGDILPSADGTWYLRATLEVAAGEAADLSCRVKHSSLEGQDIVLYWEHHSSVGFIILAVIVPLLLLIGLALW
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+ FRKRCFC
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+ >P11609|reviewed|Antigen-presenting glycoprotein CD1d1|taxID:10090
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+ MRYLPWLLLWAFLQVWGQSEAQQKNYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQ
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+ WEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSW
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+ LDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSADGHRQLVCHVSGFYPKPVWVMW
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+ MRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWDARQAPVGLIVFIVLIMLVVVGA
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+ VVYYIWRRRSAYQDIR
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+ >P11610|reviewed|Antigen-presenting glycoprotein CD1d2|taxID:10090
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+ MRYLPCLLLWAFLQVWGQSEVQQKNYTFRCLQTSSFANISWSRTDSLILLGDLQTHRWSNDSATISFTKPWSQGKLSNQQ
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+ WEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSTGCEMYPGNASESFFHVAFQGKYAVRFRGTSWQRVLGAPSW
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+ LDLPIKVLNADQGTSATVQTLLNDTWPQFARGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHLQLVCHVSGFYPKPVWVMW
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+ MRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYWDARQAPVGLIVFIVLIMLVVVGA
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+ VVYYIWRRRSAYQDIR
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+ >P15812|reviewed|T-cell surface glycoprotein CD1e, membrane-associated|taxID:9606
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+ MLLLFLLFEGLCCPGENTAAPQALQSYHLAAEEQLSFRMLQTSSFANHSWAHSEGSGWLGDLQTHGWDTVLGTIRFLKPW
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+ SHGNFSKQELKNLQSLFQLYFHSFIQIVQASAGQFQLEYPFEIQILAGCRMNAPQIFLNMAYQGSDFLSFQGISWEPSPG
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+ AGIRAQNICKVLNRYLDIKEILQSLLGHTCPRFLAGLMEAGESELKRKVKPEAWLSCGPSPGPGRLQLVCHVSGFYPKPV
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+ WVMWMRGEQEQRGTQRGDVLPNADETWYLRATLDVAAGEAAGLSCRVKHSSLGGHDLIIHWGGYSIFLILICLTVIVTLV
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+ ILVVVDSRLKKQSSNKNILSPHTPSPVFLMGANTQDTKNSRHQFCLAQVSWIKNRVLKKWKTRLNQLW
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+ >P15813|reviewed|Antigen-presenting glycoprotein CD1d|taxID:9606
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+ MGCLLFLLLWALLQAWGSAEVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQ
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+ WETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVN
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+ LAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMR
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+ GEQEQQGTQPGDILPNADETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWGGSYTSMGLIALAVLACLLFLLIVG
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+ FTSRFKRQTSYQGVL
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+ >P23043|reviewed|Antigen-presenting glycoprotein CD1d|taxID:9988
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+ LQRSFPFHGLQISSFVNSSQTRTDCLAWLGELQTHSWSNDSDTIHFLKPWSQGTFNFQQWEQVQNELWVYRLSVTRDIHD
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+ FVKLLKLTYPIELQVFAGCEMHPGNTSESFFHVAYQGMHVLSFRGTLWETAPGTPPFVKLVVKELNLDHGTREMIQELLN
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+ NTCPQFVSGLIEAGRSELEKQVKPEAWLSSGPSPGPGRLLLVCRVSGFYPKPVQVMWMRGDQEQPHTRQGDFLPNADGTW
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+ YLRVTLDVAAGDAAGLSCRVKHSSLGGQDIYPVLG
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+ >P29016|reviewed|T-cell surface glycoprotein CD1b|taxID:9606
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+ MLLLPFQLLAVLFPGGNSEHAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDKE
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+ VAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGLDFLSVKNASCVPSPEGGSRAQ
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+ KFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKADLQRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMR
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+ GEQEQQGTQLGDILPNANWTWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRNPTSIGSIVLAIIVPSLLLLLCLA
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+ LWYMRRRSYQNIP
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+ >P29017|reviewed|T-cell surface glycoprotein CD1c|taxID:9606
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+ MLFLQFLLLALLLPGGDNADASQEHVSFHVIQIFSFVNQSWARGQGSGWLDELQTHGWDSESGTIIFLHNWSKGNFSNEE
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+ LSDLELLFRFYLFGLTREIQDHASQDYSKYPFEVQVKAGCELHSGKSPEGFFQVAFNGLDLLSFQNTTWVPSPGCGSLAQ
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+ SVCHLLNHQYEGVTETVYNLIRSTCPRFLLGLLDAGKMYVHRQVRPEAWLSSRPSLGSGQLLLVCHASGFYPKPVWVTWM
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+ RNEQEQLGTKHGDILPNADGTWYLQVILEVASEEPAGLSCRVRHSSLGGQDIILYWGHHFSMNWIALVVIVPLVILIVLV
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+ LWFKKHCSYQDIL
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+ >P80943|reviewed|T-cell surface glycoprotein CD1b-3|taxID:9940
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+ GLQEFQFEYPFVIQGIAGCELHSGKAIQSFLRAGFEGLDFVSIENHSCVPEPEGGSEAQWFCVFITQYQGILAIIDRLLS
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+ KTCPRYLLGVLDAGKAELHRQVKPEAWLSSGPTPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEQPGTQQGNIILNADWTW
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+ YLRVTLDVAAGEAAGLSCRVKHSSLGDQDIILYWGHPMYIGLIFVAIIVPSLILLICLALWFWRRWSYQTVL
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+ >Q28565|reviewed|T-cell surface glycoprotein CD1b-1|taxID:9940
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+ MLLLPLLLLAVIVPGGDNEDVFQGPTSFHVIQISTFANSTWAQNQGSGWLDNLQLYGWDSDPGTTIFLKPWSKGNFSDEE
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+ VTELEELFRVYLIGFTLEVQDHVSEFQLEYPFVIQDIAGCELHPGKAVESFLKGAFGGLDFVSIKNDSCAPVPEGGSMAQ
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+ RFYELIIQYHAICDTIAKLLLETCPRYFLSVLDAGKAELQRQVKPEAWLSSGPTPGPGRLLLVCHVSGFYPKPVWVMWMR
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+ GEQEEPGTQQGDIMPNANWTWHLRATLDVAAGEAAGLSCRVKHSSLGDQDIVLYWGHPTSTGLIFVAIIVSSLILLICLA
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+ LWFWRRWSYLTIL
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+ >Q29422|reviewed|T-cell surface glycoprotein CD1b-2|taxID:9940
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+ MLLLPLLLLGVILPGGDNEDVFQGPTSFHLKQISTFVNSTWAQNLGSGWLDDLQIHGWESDSGTAIFLKPWSKGNFSDEE
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+ ITELVDLFRVYLIGFIREVQDRVNEFQLEYPFVIQVIEGCELHSGEAIESSLRGALGGLDVLRIQNHSCMPAPDSGNRGQ
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+ KLCALLSQYQGTSDIIERLVSETCPRYLLGVLDAGKAELQRQVKPEAWLSSGPTPGPGRLLLVCHVSGFYPKPVQVIWMR
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+ GKQEQPGTQQGDIMPNADWTWYLRVTLNVAAGEAAGLSCRVKHSSLGDQDIILYWGHPTSIGLILVAIIVPSLILSICLA
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+ LWFWRRWSYQNIL
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+ >Q4ACW4|reviewed|Antigen-presenting glycoprotein CD1d|taxID:9598
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+ MGCLLFLLLWALLQAWGSAEVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQ
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+ WETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILSFQGTSWEPTQEAPLWVN
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+ LAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELEKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMR
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+ GEQEQQDTQPGDILPNADETWYLRATLDVAAGEAAGLSCRVKHSSLEGQDIILYWGGSYTSVGLIVLAVLACLLFLLIVG
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+ FTSRFKRQTSYQGVL
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+ >Q5YB65|reviewed|T-cell surface glycoprotein CD1b|taxID:37293
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+ MLLLPFQLLAVLFPGGNSEHAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDKE
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+ VAELEEIFRVYILGFAREVQDFAGDFQMKYPFEIQGIAGCGLHSGGAIVSFLRGALGGLDFLSVKNASCVPSPEGGSRAQ
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+ KVCALIMQYQGIMEIVRLLLYKTCPRYLLGVLNAGKADLQGKMKPEAWLSSGPSPGPGRLLLVCHVSGFCPKPVWVMWMP
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+ GEQEQQGTQLGDILPNANWTWYLRATLDVAAGEAAGLSCRVKHSSLEGQDIILYWSNPTSIGSIVLAIIVPSLLLLLCLA
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+ LWYMRRRSYQNIP
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+ >Q63493|reviewed|Antigen-presenting glycoprotein CD1d|taxID:10116
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+ MLYLPCLLLWAFPQFWGQSEVQQNYTFGCLQISSFANRSWSRTDSVVWLGDLQTHRWSNDSDTISFTKPWSQGKFSNQQW
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+ EKLQHMFQVYRTSFTRDIKEIVKMMSPKEDYPIEVQLSAGCEMYPGNASESFLHVAFQGEYVVRFHGTSWQKVPEAPSWL
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+ DLPIKMLNADEGTRETVQILLNDTCPQFVRGLLEAGKPDLEKQEKPVAWLSRGPNPAHGHLQLVCHVSGFHPKPVWVMWM
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+ RGDQEQGGTHRGDILPNADETWYLQATLDVEAGDEAGLACRVKHSSLEGQDIILYWGGRQVSPVLIFLIVGVLVLVVCAV
87
+ AYYIIRKRRRSYQDIM
88
+ >Q9QZY5|reviewed|T-cell surface glycoprotein CD1e, membrane-associated|taxID:10141
89
+ MLLLILLFFKGLVCHEKSIVGPQPLGWHHPAEAEEPLIFRLLHIASFKNHSWSHSQASAWIGDLQTHGWNSTMGTIQFLK
90
+ PWSQGDFSKEELKNFEALFRLYFHDFPREVHAFAHQFQFEYPFELQISGGCKNVGKTSENFLNGAYQGSDLLSFQRSSWE
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+ PSPGAGSRAQKVCEVLSYYKDITEIVQSLLSSVCPRFLSGLIAAGKSELERQVKPEVWLSRGPSPGRGRLQLVCHVSGFH
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+ PKPVWVMWMKGQQEQKGTKTGDIPNADETWYLQATLDVAEREATGLSCRVKHSSLGGHDIIIHWGGYSILLILMYVAVIV
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+ TLVTLIVMGSWHRKQSSNRNVLSSYISNPTFPLENDTQCPRSSALQLHSAQESWIKNRILKWKRSLNQFW
94
+ >Q9QZY6|reviewed|T-cell surface glycoprotein CD1c3|taxID:10141
95
+ MLFLQFLFLDVVLGGSITKNVVQENISFYLMQISSYANQSWVQNCGSGWLGELQTHGWDSESGTIIFLHTWSRGNFSNEE
96
+ LEDIPLLFHVYFSGLSLEVQDRVSQLQIKYPFDIQARAGCELHSGEPPKGFLYGALNGLNFLSYQNKSWVPSPEGGNRAQ
97
+ KVCDLLNTYEGIKETAYHLIRDTCPRFLLGLLDAGKMDLQRQVRPEVWLSSSPNLKPGRLLLACHVSGFYPKPIWVMWMR
98
+ GAQEQLETKQGDILPHADGTWYLRVTLDVAAKEAAGLSCRVRHSSLRDQDIILYWGHGLSVILITFAVIVPLVLLIILVL
99
+ LCKKCCTYQGIP
100
+ >Q9QZY7|reviewed|T-cell surface glycoprotein CD1c2|taxID:10141
101
+ MLFLQFLFVDVVLGGSITENVVQENISLYLMQISSYANQSWTQNLGSAWLDQLQTHSWDSESGTIIFLHAWSRGNFSNEE
102
+ VTDMQLLLRVHFAELTLDVHQQASQLQFKYPFDIQVRLGCELHSRETTKSFLHVAFNGLNFLSFQHKSCVPSPEGETRAQ
103
+ KACDILNTYEATKEIAYYVMNDICPRLLLSLLEAGKMDLQRQVRPEVWLSSSPNLEPGRLLLACHVSGFYPKPIWVMWMR
104
+ GAQEQLETKQGDILPHADGTWYLRVTLNVVAEEAAGLSCRVRHSSLRDQDIILYWGHGLSVILIALAVIVPLVLLIVLVL
105
+ LCKKRCTYQGIP
106
+ >Q9QZY8|reviewed|T-cell surface glycoprotein CD1c1|taxID:10141
107
+ MLFLHFLFLDVVLGGSITENVVQENISFYVMQISSYANKSWVQNHGSGWLDELQTHGWDSESDKIIFLHTWSRGNFSNEE
108
+ LEDLQLLFHAYFSGLALRIQHQPSQLEVKYPFEVQARAGCELHSGEHTKGFIHAAVNGLNFLSYQNKSLVPSPEGGTRAQ
109
+ KFCDLFNTYEGIRETVYYLIRDTCPRFLLGLLDAGKMDLQRQVRPEVWLSSSPNLEPGRLLLACHVSGFYPKPIWVMWMR
110
+ GAQEQLETKQGDILPHADGTWYLRVTLDVAAREAAGLSCRVRHSSLRDQDIILYWGHGLSVILITFAVIVPLVLLIVLML
111
+ LYKKRCTYQGIQ
112
+ >Q9QZY9|reviewed|T-cell surface glycoprotein CD1b4|taxID:10141
113
+ MLLLALAFFFPAGDTQNVLPGKISFYGIQISTFFNHTVVENRGSGWLGDMEISSWDSEKETIIFRKPWSKGNFSNDEILE
114
+ VEEIFQVYFFGFVREAQKHMSDFQVEYPFEIQVISGCEVNSHRSFDYFMRVAVKGLDLLSIKNHSCWPAPEGVSRAQEIW
115
+ TLILQYKRICDTVEILLTKTCPRYLMSVIEAGKSDLQKQVKPDAWLSQGPSPGPGLLQLVCHVSGFYPKPVWVMWMRGDK
116
+ ELPETQKRDVLPNADETWYLRVTLDVAAEEAAGLSCRVKHSSLEGQDIILYWGHSISIGWIILAVLVPCLIVLVLFILWF
117
+ YRRWSYEDIF
118
+ >Q9QZZ0|reviewed|T-cell surface glycoprotein CD1b3|taxID:10141
119
+ MLLLELVFFAVLFPVGDTQDAFQEPISFHITQITSFVNSSWVKYQLSGWLGDLQIHGMDSDSGTAIFLKPWSKGNFSNEE
120
+ MSEVVELFRVYIVAFIRETKAHVNALQMEYPFEIQGIAGCELHSGGAIVSFLQGAFGGLDFVSFKNSSCVPAPEGGSRAQ
121
+ TVCKLLAPYHDIFYTVEKLLYETCPQYLLGVLQAGKADLHRQVKPKAWLSSGSTHEPGHLQLVCHVSGFYPKPVWVMWMR
122
+ GEQELPETQRGDILPNADGTWYLRVTLDVVTEEATGLSCRVKHSSLGGQDIVLYWGHSNPIGWVILAIVSCLIFFLCFAL
123
+ WYFRRLRCEGIF
124
+ >Q9QZZ1|reviewed|T-cell surface glycoprotein CD1b2|taxID:10141
125
+ MLLLVLALLAVLFPAGDTQDAFPEPISYYVTQSSSFFNSTWAQNQASGWLGDIQIDGWNSDSGTIIFRKTWSKGNFSNDE
126
+ ILEMEELFRLYFLGFVKEVQELVSDFQLEYPFEIQGIAGCELHSGGAIVSFLMGAIEGLHFMSINNYSCLPAPEGGTRAQ
127
+ KFCALILQYKGICDIVENLLTKVCPRYLMSVLEAGKAALQKHVKPEAWLSQGPSPEPGYLQLVCHVSGFYPKPVWVMWMR
128
+ GEQEQPETQRGDVLPNPDDTWYLRATLDVVAKEATGLSCRVKHSSLGGQDIILYWGNSSIGWIILAVFVSCLIVLLFYVL
129
+ WFYKHWSYQDIL
130
+ >Q9QZZ2|reviewed|T-cell surface glycoprotein CD1b1|taxID:10141
131
+ MLLVALALLAFLFPAGDTQNALQWPTSVHGIQISSFFNHTMAQSRCSGWLGNMELGSFDSDTGTIIFKKPWSKANFSNEE
132
+ VLELEELFQVYMLGFIREVQERMSDFQMEYPFEIQGIAGCELISGGTIDFFLRGALEGLDFLSIKNSTCWPAPEGGTKAK
133
+ KFCTLILQYKGIWDIMENLLTKTCPRYVLSVLESGKPDIQKQVKPDAWLSQGPSPGPGLLQLVCHVSGFYPKPVWVMWMR
134
+ GEQEQPETQKGDVLPNADETWYLQVTLDVAAEEAAGLSCRVKHSSLEGQDIILYWGHSISIGWIILAVLVPCLIVLVLFV
135
+ LWFYRRWSYEDIL
136
+ >Q9XS72|reviewed|T-cell surface glycoprotein CD1a|taxID:9823
137
+ MLFLQLPLLLVLLPGGDSEEGFQEPISFQIIWISSFYNRSWEEEVCSAWLGELQTHRREGKSDIVIYRQPWSKGNFSRED
138
+ LMESEHILRMFFVRFVQAFFNHASQWKLEYPFDVQIAGGCDLYHGETSVGFVRIAYQGSDFASFQNNSWLPSPKGGTRAQ
139
+ LVCKLFNLYQGTLEIIHKLLSDTCPRFVLGLLDAGKADLQRQVRPEAWLSSGPNPSPGHLMLVCHVSGFYPKPIWVMWMR
140
+ DEQEQPGTQQGDILPNADGTWYLRVTLDVAAGEASGLSCRVKHSSLGGQDIILYWEQHSSVGWILLAVIVPLVLLTGLAF
141
+ WHRKHWKHCDPSSALHRLE