Table 2 The performance of the Phyto-LRR prediction program. Sequences from the PDB files were used to examine the performance of the LRR prediction program
From: Identification and characterization of the LRR repeats in plant LRR-RLKs
Protein Name | Species | Uniprot ID | PDB code | Gene accession | Phyto-LRR (Accuracy) | SMART (Accuracy) | Pfam (Accuracy) |
|---|---|---|---|---|---|---|---|
Training dataset of plant LRR-RLK/RLP with crystal structures | |||||||
RGFR1 | Arabidopsis thaliana | C0LGR3 | 5hz1 | At4g26540 | 24 (96%) | 8 (33%) | 10 (42%) |
PXY/TDR | Arabidopsis thaliana | Q9FII5 | 5jfk | At5g61480 | 23 (96%) | 9 (39%) | 10 (43%) |
BRI1 | Arabidopsis thaliana | O22476 | 3rgz | At4g39400 | 25 (100%) | 7 (28%) | 13 (52%) |
BRL1 | Arabidopsis thaliana | Q9ZWC8 | 4j0m | At1g55610 | 24 (100%) | 8 (33%) | 12 (50%) |
PSKR1 | Arabidopsis thaliana | Q9ZVR7 | 4z63 | At2g02220 | 21 (100%) | 6 (29%) | 11 (52%) |
PEPR1 | Arabidopsis thaliana | Q9SSL9 | 5gr8 | At1g73080 | 27 (100%) | 9 (33%) | 13 (48%) |
FLS2 | Arabidopsis thaliana | Q9FL28 | 4mna | At5g46330 | 24 (100%) | 13 (54%) | 13 (54%) |
HAE | Arabidopsis thaliana | P47735 | 5ixo | At4g28490 | 22 (100%) | 8 (36%) | 11 (50%) |
Average accuracy | 99% | 36% | 45.5% | ||||
Test dataset of plant LRR-RLK/RLP with crystal structures | |||||||
SOBIR1 | Arabidopsis thaliana | Q9SKB2 | 6r1h | At2g31880 | 6 (67%) | 0 (0%) | 0 (0%) |
PRK6 | Arabidopsis thaliana | Q3E991 | 5yah | At5g20690 | 6 (100%) | 4 (67%) | 4 (67%) |
SERK2 | Arabidopsis thaliana | Q9XIC7 | 6g3w | At1g34210 | 5 (80%) | 0 (0%) | 3 (60%) |
ERL1 | Arabidopsis thaliana | C0LGW6 | 5xjo | At5g62230 | 20 (100%) | 10 (50%) | 11 (55%) |
TMM | Arabidopsis thaliana | Q9SSD1 | 5xjo | At1g80080 | 10 (91%) | 5 (50%) | 5 (50%) |
TMK1 | Arabidopsis thaliana | P43298 | 4hq1 | At1g66150 | 13 (91%) | 5 (38%) | 8 (62%) |
BIR2 | Arabidopsis thaliana | Q9LSI9 | 6fg7 | At3g28450 | 5 (100%) | 0 (0%) | 4 (80%) |
ERL2 | Arabidopsis thaliana | Q6XAT2 | 5xkn | At5g07180 | 20 (100%) | 9 (45%) | 10 (50%) |
PGIP | Phaseolus vulgaris | P58822 | 1ogq | 9 (90%) | 0 (0%) | 5 (55%) | |
TMK3 | Arabidopsis thaliana | Q9SIT1 | 7brc | At2g01820 | 13 (92%) | 5 (38%) | 7 (54%) |
ERL2 | Arabidopsis thaliana | Q6XAT2 | 5xkn | At5g07180 | 20 (100%) | 9 (45%) | 10 (50%) |
PRK3 | Arabidopsis thaliana | Q9M1L7 | 5wls | At3g42880 | 6 (100%) | 0 (0%) | 4 (67%) |
Average accuracy | 92.6% | 28% | 54% | ||||