Table 3.
Conserved motifs that predict the specificity.
| Specificity | TRBV | Shared TCR | TRBJ | Motif |
|---|---|---|---|---|
| CMV-pp50VTE | 9 | CASSVGQGSSYEQYF | 2-7 | S xGQG |
| CMV-pp65YSE | 9 | CASSVTGGTDTQYF | 2-3 | VTGGT |
| CMV-pp65NLV | 7-6 | CASSLAPGATNEKLFF | 1-4 | LAPG |
| CMV-IE1VLE | 9 | CASSLGQGGVETQYF | 2-5 | GQGGV |
| CMV-pp65TPR | 7-9 | CASSLIGVSSYNEQFF | 2-1 | SLIG xS |
| CMV-pp65RPH | 4-3 | CASSPQRNTEAFF | 1-1 | P xRNT |
| CMV-IE1QIK | 9 | CASSVQRQTANTGELFF | 2-2 | V xR xxANT |
| CMV-IE1ELR | 27 | CASSSYRTDLNTEAFF | 1-1 | TDLN |
| EBV-LMP2FLY | 6-5 | CASSYQGGNYGYTF | 1-2 | S xQGG |
| EBV-LMP2CLG | 10-2 | CASSEDGMNTEAFF | 1-1 | DGMN |
| 5-1 | CASSLEGQASSYEQYF | 2-7 | EGQ xxS | |
| EBV-EBNA3CLLD | 19 | CASSIALASEQYF | 2-7 | IAL |
| EBV-BMLF1GLC | 20-1 | CSARDRVGNTIYF | 1-3 | RDR(V/T)G |
| 29-1 | CSVGTGGTNEKLFF | 1-4 | G xGGTN | |
| EBV-BRLF1YVL | 20-1 | CSAIGGSYNEQFF | 2-1 | AIGGS |
| EBV-EBNA3ARPP | 4-1 | CASSQDRLTGGYTF | 1-2 | RLTG |
| EBV-BZLF1RAK | 27 | CASSSLNTEAFF | 2-1 | SSSLN |
| 20-1 | CSARDRGAENTGELFF | 2-2 | RDR xxEN | |
| EBV-EBNA3AFLR | 7-8 | CASSLGQAYEQYF | 2-7 | S xGQA |
| EBV-EBNA3AQAK | 5-1 | CASSLETGGYGYTF | 1-2 | LET(A/G) |
| AdV-HEXONTDL | 20-1 | CSAPGQGTDTQYF | 2-3 | (A/V)PGQ |
| AdV-E1ALLD | 20-1 | CSARPGLADEQFF | 2-1 | AR xGLA |
| AdV-HEXONKPY | 10-3 | CAINPGTAYGYTF | 1-2 | INP |
We investigated which regions of PUB-I or PUB-HS CDR3β AA-sequences were predictive for the specificity. We searched for each motif in our library of 2355 CDR3β AA-sequences to determine what part of the junctional regions were unique for each specificity, without being present in any other specificity. Underscores with an x represent any of the 20 AAs. Some motifs contain two possible AAs that can be part of the motif which are shown between brackets. The minimum motifs are also shown in bold font in the original CDR3β AA-sequences.