ProtTM tool predicts protein transmembrane topology and supports both transmembrane alpha-helix and beta-barrel systems, without species restrictions. It accepts multiple FASTA sequences and is suitable for batch pre-screening of candidate proteins, membrane protein expression planning, and joint evaluation of signal peptides with transmembrane regions.
The model output includes global class prediction, residue-level topology labels, transmembrane segment boundaries, and signal peptide cleavage sites. Note: this tool is intended for topology inference and is not a direct subcellular localization predictor.
1. Protein Sequences (up to 10 FASTA entries):
Parsed sequences: 0, total residues: 0
Label Definitions (Residue Level)
- B: Beta Strand (TM), transmembrane beta-sheet strand
- I: Inside (Cytoplasm), inner/cytoplasmic side of membrane
- O: Outside (Extracellular), outer/extracellular side of membrane
- M: Alpha Helix (TM), transmembrane alpha-helix
- P: Periplasm, periplasmic space region
- S: Signal Peptide, signal peptide region
Model Performance Metrics
[k-fold Per-Class Performance (Residue Level)]
Class | Support | Precision | Recall | F1 | MCC
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B | 1458 | 0.8206 | 0.8409 | 0.8306 | 0.8291
I | 108316 | 0.9876 | 0.9971 | 0.9924 | 0.9765
M | 5651 | 0.8990 | 0.8614 | 0.8798 | 0.8758
O | 40637 | 0.9688 | 0.9627 | 0.9657 | 0.9542
P | 2183 | 0.8512 | 0.6422 | 0.7321 | 0.7364
S | 2922 | 0.9878 | 0.9706 | 0.9791 | 0.9788
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BENCHMARK REPORT (Filtered Test Set)
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Total Residues Evaluated: 2500818
Overall Accuracy: 0.9838
Overall MCC: 0.9087
Balanced Accuracy: 0.8893
Macro Precision/Recall/F1:0.9133 / 0.8893 / 0.9005
Weighted P/R/F1: 0.9856 / 0.9838 / 0.9846
Micro P/R/F1: 0.9856 / 0.9838 / 0.9847
Classes absent in y_true for this benchmark split: P
Mean Sequence Accuracy: 0.9719
Median Sequence Accuracy: 1.0000
Sequence Exact Match: 0.8406
[Per-Protein Classification]
Protein Accuracy: 0.9806
Protein MCC: 0.9402
Protein Macro P/R/F1: 0.8568 / 0.9384 / 0.8799
Type | Support | Precision | Recall | F1
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GLOBULAR | 4044 | 0.9940 | 0.9879 | 0.9909
SIGNAL | 273 | 0.9464 | 0.9707 | 0.9584
TM | 566 | 0.9360 | 0.9558 | 0.9458
SP+TM | 15 | 0.5000 | 1.0000 | 0.6667
BETA | 63 | 0.9074 | 0.7778 | 0.8376
[Signal Peptide Metrics]
SP Presence Acc/MCC: 0.9950 / 0.9590
SP Presence P/R/F1: 0.9307 / 0.9936 / 0.9611
CS Exact Accuracy (true SP): 0.8167
CS Relaxed@±2 (true SP): 0.9068
CS Exact P/R/F1: 0.7651 / 0.8167 / 0.7900
CS Relaxed P/R/F1: 0.8494 / 0.9068 / 0.8771
[Per-Segment Metrics]
Segment | TP | FP | FN | Precision | Recall | F1 | BoundaryMAE
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B | 700 | 256 | 111 | 0.7322 | 0.8631 | 0.7923 | 1.3743
M | 2359 | 1725 | 668 | 0.5776 | 0.7793 | 0.6635 | 1.9532
S | 287 | 70 | 24 | 0.8039 | 0.9228 | 0.8593 | 0.1498
TM | 3059 | 1981 | 779 | 0.6069 | 0.7970 | 0.6891 | 1.8207
[Per-Class Performance (Residue Level)]
Class | Support | Precision | Recall | F1 | MCC | Specificity
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B | 7210 | 0.7967 | 0.7456 | 0.7703 | 0.7701 | 0.9994
I | 2263185 | 0.9945 | 0.9931 | 0.9938 | 0.9355 | 0.9480
M | 64393 | 0.9080 | 0.8096 | 0.8560 | 0.8539 | 0.9978
O | 158275 | 0.8990 | 0.9331 | 0.9157 | 0.9101 | 0.9929
P | 0 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.9981
S | 7755 | 0.9683 | 0.9649 | 0.9666 | 0.9665 | 0.9999
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