TABLE 2.
MHC domains’ motifs of SARS-COV-2 virus proteins
| Protein | Domain | Alias | Motif | Start | End |
|---|---|---|---|---|---|
| S | MHC_I_2 | A | CEFQFCNDPFLGVYYHKNNKSWMESE | 131 | 156 |
| B | WPWYIW | 1212 | 1217 | ||
| MHC_I_C | A | KWPWYIWLGFIAGLIAIVMVTIMLCCM | 1211 | 1237 | |
| MHC_II_alpha | A | CEFQFCNDPFLGVYYHKNNKSWMESEFRVYSS | 131 | 162 | |
| B | QIPFAMQMAYR | 895 | 905 | ||
| C | LGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSC | 1203 | 1243 | ||
| MHC_II_beta | A | WFHAIHVSGTNGTKRFD | 64 | 80 | |
| B | VIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMD | 127 | 178 | ||
| C | FAMQMAYRFN | 898 | 907 | ||
| D | KMSECV | 1028 | 1033 | ||
| E | YVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQR | 1067 | 1107 | ||
| F | DLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPV | 1199 | 1264 | ||
| MHC_I-like_Ag-recog | A | VTWFHAIH | 62 | 69 | |
| B | VIKVCEFQFCNDPFLGVYYHKNNKSWMESEFRVYSSANNCTFEYVSQPFLMDLEGKQGNFKNLREFVF | 127 | 194 | ||
| C | RFASVYAWNRKRISNCVADYSVLYNSASFSTFKCYGV | 346 | 382 | ||
| D | SNKKFLPFQQFGRDIADTTDAVRDPQTLE | 555 | 583 | ||
| E | NCTEVPVAIHADQLTPTWRVYSTGSNVFQTRAGCLIGAEHVNNSYECDIPIGAGICASYQT | 616 | 676 | ||
| F | IPFAMQMAYR | 896 | 905 | ||
| G | RAAEIRASANLAATKMSECVLGQSKRVDFCGKGYHLMSFPQSAPHGVVFLHVTYVPAQEKNFTTAPAICHDGKAHFPREGVFVSNGTHWFVTQRNFYEPQI | 1014 | 1114 | ||
| H | QPELDSFKEELDKY | 1142 | 1155 | ||
| I | ESLIDLQELGKYEQYIKWPWYIWLGFIAGLIAIVMVTIMLCCMTSCCSCLKGCCSCGSCCKFDEDDSEPVLKGVKLHYT | 1195 | 1273 | ||
| MHC2-interact | A | APAICHDGKAHFPRE | 1078 | 1092 | |
| B | WPWYIW | 1212 | 1217 | ||
| C | IVMVTIMLCCMTSCCSCLKGCC | 1227 | 1248 | ||
| MHCassoc_trimer | A | YYHKNNKSWMESEFRVYSS | 144 | 162 | |
| B | AHFPREGVFVSNGTHW | 1087 | 1102 | ||
| C | ELGKYEQYIKWPWYIW | 1202 | 1217 | ||
| E | MHC_II_alpha | A | TLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLN | 30 | 66 |
| MHC_II_beta | A | FVVFLLVTLAILTALRLCAYCCNIVNVSLVKPSFYVYSRVKNLNSSRVPD | 23 | 72 | |
| MHC_I-like_Ag-recog | A | ALRLCAYCCNI | 36 | 46 | |
| MHCassoc_trimer | A | CAYCCNI | 40 | 46 | |
| M | MHC_II_alpha | A | RCDIKDLPKE | 158 | 167 |
| MHC_II_beta | A | EELKKLLEQWN | 11 | 21 | |
| B | SMWSFNPETN | 108 | 117 | ||
| C | HHLGRCDIKDLPKEITVATSRTLSYYKLGASQRVAGDSGFAAYSRYRIGNYKLNTDHSSSSDN | 154 | 216 | ||
| MHC_I-like_Ag-recog | A | GHHLGRCDIKD | 153 | 163 | |
| N | MHC_II_alpha | A | DQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHI | 82 | 146 |
| B | TDYKHWPQIAQFAPSASAFFGMSRIGMEVT | 296 | 325 | ||
| MHC_II_beta | A | SWFTALTQHGKEDLKFPRGQGVPIN | 51 | 75 | |
| B | QIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIV | 83 | 158 | ||
| C | EQTQGNFGDQELIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPK | 280 | 369 | ||
| MHC_I-like_Ag-recog | A | RRPQGLPNNTASWFTALTQHGKEDL | 40 | 64 | |
| B | DDQIGYYRRATRRIRGGDGKMKDLSPRWYFYYLGTGPEAGLPYGANKDGIIWVATEGALNTPKDHIGTRNPANNAAIVLQLPQGTTLPKGFY | 81 | 172 | ||
| C | LIRQGTDYKHWPQIAQFAPSASAFFGMSRIGMEVTPSGTWLTYTGAIKLDDKDPNFKDQVILLNKHIDAYKTFPPTEPKKD | 291 | 371 | ||
| MHC2-interact | A | RWYFYYL | 107 | 113 | |
| MHCassoc_trimer | A | WYFYYL | 108 | 113 | |
| ORF3a | MHC_I_2 | A | NFVRIIMRLWLCW | 119 | 131 |
| MHC_II_alpha | A | RIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPYN | 122 | 161 | |
| MHC_II_beta | A | MDLFMR | 1 | 6 | |
| B | NFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIP | 119 | 159 | ||
| MHC_I-like_Ag-recog | A | INFVRIIMRLWLCWKCRSKNPLLYDANYFLCWHTNCYDYCIPY | 118 | 160 | |
| B | YNKIVDEPEEHVQIH | 233 | 247 | ||
| C | NPVMEP | 257 | 262 | ||
| MHC2-interact | A | YFLCWHTNC | 145 | 153 | |
| MHCassoc_trimer | A | IMRLWLCWKCRSKNP | 124 | 138 | |
| B | DANYFLCWHTNCYDYCIPYN | 142 | 161 | ||
| ORF6 | MHC_II_alpha | A | DFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKYSQ | 6 | 51 |
| MHC_II_beta | A | MFHLVDFQVTIAEILLIIMRTFKVSIWNLDYIINLIIKNLSKSLTENKY | 1 | 49 | |
| MHC_I-like_Ag-recog | A | MFHLVD | 1 | 6 | |
| B | TFKVSIWNLDYIINLIIKNLSKSLTENKYSQ | 21 | 51 | ||
| ORF7a | MHC_II_alpha | A | YEGNSPFH | 40 | 47 |
| MHC_II_beta | A | GTTVLLKEPCSSGTYEGNSPFHPLADNKFALTCFSTQFAFACPDGVKHVYQLRARSVSPKLFIRQEEVQELYSPIFLIVAAIVFI | 26 | 110 | |
| MHC_I-like_Ag-recog | A | CELYHYQECVRG | 15 | 26 | |
| B | YEGNSPFHPLADNK | 40 | 53 | ||
| C | CPDGVKHVY | 67 | 75 | ||
| ORF7b | MHC_II_alpha | A | DHNETCHA | 36 | 43 |
| MHC_II_beta | A | CFLAFLLFLVLIMLIIFWFSLELQDHNETCH | 12 | 42 | |
| MHC_I-like_Ag-recog | A | FYLCFLAFLLFLVLIMLIIFWFSLELQDHNETCHA | 9 | 43 | |
| MHCassoc_trimer | A | MLIIFWFSLELQDHNETCH | 24 | 42 | |
| ORF8 | MHC_II_alpha | A | TTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLI | 11 | 58 |
| MHC_II_beta | A | TVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKSAPLIELCVDEAGSKSPIQYIDIGNYTVSCLPFTINC | 12 | 90 | |
| MHC_I-like_Ag-recog | A | ITTVAAFHQECSLQSCTQHQPYVVDDPCPIHFYSKWYIRVGARKS | 10 | 54 | |
| B | DEAGSKSPIQYIDI | 63 | 76 | ||
| C | NYTVSCLPFTINCQEPK | 78 | 94 | ||
| MHCassoc_trimer | A | DDPCPIHFYSKW | 34 | 45 | |
| ORF10 | MHC_I_2 | A | AFPFTIYSLLLCRMNSRNYIAQVDVVN | 8 | 34 |
| MHC_II_beta | A | MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFNLT | 1 | 38 | |
| MHC_I-like_Ag-recog | A | MGYINVFAFPFTIYSLLLCRMNSRNYIAQVDVVNFN | 1 | 36 | |
| MHC2-interact | A | MGYINVFAFPFTIYSLLLC | 1 | 19 | |
| MHCassoc_trimer | A | MGYINVFAFPFTIYSLLLCRMNSRNYIA | 1 | 28 | |
| nsp2 | MHC_II_alpha | A | RGVYCCREHEHEIAW | 46 | 60 |
| MHC_II_beta | A | DTKRGVYCCREHEHEIAWYTERSEKSYELQTPF | 43 | 75 | |
| MHC_II_beta | B | DGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQT | 114 | 153 | |
| MHC_I-like_Ag-recog | A | FIDTKRGVYCCREHEHEIAWYTERSEKSYELQTPFEI | 41 | 77 | |
| MHC_I-like_Ag-recog | B | KLDGFMGRIRSVYPVASPNECNQMCLSTLMKCDHCGETSWQTGDFVKATCEFCGTENLTKEGATTCGYLPQNA | 112 | 184 | |
| MHC_I-like_Ag-recog | C | CPACHNSEVGPEHSLAEYHN | 190 | 209 | |
| nsp3 | MHC_II_beta | A | DYKHYTPSFKKGAKLLHKPIVWHVNNATNKATYKPNTWCIRCLWS | 1153 | 1197 |
| MHC_II_beta | B | IMQLFFSYFAVHFISNSWLMWLIINLVQMAPISAMVRMYIFFASFYYVWKSYVHVVDGCNSSTCMMCYKRNRATRVECT | 1528 | 1606 | |
| MHC_II_beta | C | CSARHIN | 1876 | 1882 | |
| MHC_I-like_Ag-recog | A | ASHMYCSFYPPDEDEEEGDCEEEEF | 99 | 123 | |
| MHC_I-like_Ag-recog | B | QPEEEQEEDW | 152 | 161 | |
| MHC_I-like_Ag-recog | C | NEKQEILGTVSWNLREMLAHAEETR | 544 | 568 | |
| MHC_I-like_Ag-recog | D | WCIRCLW | 1190 | 1196 | |
| MHC_I-like_Ag-recog | E | SWLMWLIINLVQMAPISAMVRMYIFFASFYYVW | 1544 | 1576 | |
| MHC_I-like_Ag-recog | F | RRSFYVYANGGKGFCKLHNWNCVNCDT | 1613 | 1639 | |
| nsp4 | MHC_I_2 | A | QWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRR | 364 | 401 |
| MHC_II_alpha | A | QWMVMFTPLVPFWI | 364 | 377 | |
| MHC_II_beta | A | EYCRHGTCER | 219 | 228 | |
| MHC_II_beta | B | HIQWMVMFTPLVPFWITIAYIICISTKHFYWFFSNYLKRR | 362 | 401 | |
| MHC_I-like_Ag-recog | A | PVHVMSKHTDFSSEIIGYKAIDGGVTRDIASTDTCFANKHADFDTWFSQR | 29 | 78 | |
| MHC_I-like_Ag-recog | B | FYLTNDVSFLAHIQWMVMFTPLVPFWITIAYIICISTKHFYWF | 351 | 393 | |
| nsp6 | MHC_II_beta | A | QSTQWSLFFFLYENAFLPFAMGIIAMSAFAMMFVKH | 27 | 62 |
| MHC_II_beta | B | WVMRIMTWLDM | 90 | 100 | |
| MHC_I-like_Ag-recog | A | SWVMRIMTWLDM | 89 | 100 | |
| MHC2-interact | A | MVYMPASWVMRIMTWLDM | 83 | 100 | |
| MHCassoc_trimer | A | GTHHWL | 9 | 14 | |
| nsp7 | MHC_I-like_Ag-recog | A | WAQCVQLHND | 29 | 38 |
| nsp8 | MHC_I-like_Ag-recog | A | KSEFDRDAAMQRKLEKMADQAMTQMYKQARSEDKRAKVTSAMQTM | 46 | 90 |
| nsp10 | MHC_II_beta | A | NMDQESFGGASCCLYCRCHIDHPNP | 62 | 86 |
| MHC_II_beta | B | WKGYGCSCDQLREPMLQ | 123 | 139 | |
| MHC_I-like_Ag-recog | A | TPEANMDQESFGGASCCLYCRCHIDHPN | 58 | 85 | |
| MHC2-interact | A | YCRCHIDHPNPKGFCD | 76 | 91 | |
| RNA-dependent RNA polymerase | MHC_II_alpha | A | RKHTTCCSLSHRFYR | 640 | 654 |
| MHC_II_alpha | B | YWEPEF | 915 | 920 | |
| MHC_II_beta | A | ERLKLFDRYFKYWDQTYHPNCVNCLDDRCILH | 278 | 309 | |
| MHC_II_beta | B | YSDVENPHLMGWDYPKCDRAMPNMLRIMA | 606 | 634 | |
| MHC_II_beta | C | HPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVM | 872 | 906 | |
| MHC_II_beta | D | SRYWEPEFYEAMYT | 913 | 926 | |
| MHC_I-like_Ag-recog | A | SNYQHEETIYNLLKDCPAVAKHDFFKFRIDGDMVPHISRQRL | 78 | 119 | |
| MHC_I-like_Ag-recog | B | FDRYFKYWDQTYHPNCVNCLDDRCILH | 283 | 309 | |
| MHC_I-like_Ag-recog | C | KFYGGWHNMLKTVYSDVENPHLMGWDYPKCDRAMPNMLRIMASLVLARKHTTCCSLSHRFYRLANECAQVLSEMVMCGGS | 593 | 672 | |
| MHC_I-like_Ag-recog | D | KCWTETDLTKGPHEFCSQHTMLVKQGDDY | 798 | 826 | |
| MHC_I-like_Ag-recog | E | LMIERFVSLAIDAYPLTKHPNQEYADVFHLYLQYIRKLHDELTGHMLDMYSVMLTNDNTSRYWEPEFYEAMYTPHT | 854 | 929 | |
| 2′-O-ribose methyltransferase | MHC_II_alpha | A | TEHSWNADLYKLMGHFAWW | 172 | 190 |
| MHC_II_beta | A | PREQIDGYVMHANYIFWRNT | 215 | 234 | |
| MHC_I-like_Ag-recog | A | HSWNADLYKLMGHFAWWT | 174 | 191 | |
| MHC_I-like_Ag-recog | B | PREQIDGYVMHANYIFWR | 215 | 232 | |
| MHC2-interact | A | MGHFAWWTAF | 184 | 193 | |
| MHCassoc_trimer | A | MGHFAWW | 184 | 190 | |
| 3C-like proteinase | MHC_II_beta | A | YMHHMEL | 161 | 167 |
| MHC_I-like_Ag-recog | A | YDCVSFCYMHHME | 154 | 166 | |
| 3′-to-5′ exonuclease | MHC_I_2 | A | CWHHSIGFDYVYNPFMIDVQQW | 226 | 247 |
| MHC_II_beta | A | EGLCVDIPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATRE | 36 | 99 | |
| MHC_II_beta | B | CWHHSIGFDYVYNPFMIDVQQW | 226 | 247 | |
| MHC_II_beta | C | AVCRHHANEYRLYLDAYNMMISAGFSLWVYKQ | 482 | 513 | |
| MHC_I-like_Ag-recog | A | IPGIPKDMTYRRLISMMGFKMNYQVNGYPNMFITREEAIRHVRAWIGFDVEGCHATR | 42 | 98 | |
| MHC_I-like_Ag-recog | B | DTYACWHHSIGFDYVYNPFMIDVQQWGFTGNLQSNHDLYCQVHGNAHVASCDAIMTRCLAVHECFVKRVDWTIEYPIIGDELKINAACRKVQHM | 222 | 315 | |
| MHC_I-like_Ag-recog | C | CRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNLWNTF | 484 | 523 | |
| endoRNAse | MHC_I-like_Ag-recog | A | RNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHI | 198 | 235 |
| helicase | MHC_I-like_Ag-recog | A | RPFLCCKCCYDHVISTSH | 22 | 39 |
| MHC_I-like_Ag-recog | B | EPEYFNSVCRLMKTIGPDMFLGTCRR | 418 | 443 | |
| MHC_I-like_Ag-recog | C | REFLTRNPAWRKAVFISPYNSQNA | 497 | 520 |
MHC indicates major histocompatibility complex; SARS-COV-2, severe acute respiratory syndrome coronavirus 2.