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
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BENCHMARK REPORT (Filtered Test Set) [Ensemble: 3 models, method=vote]
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Total Residues Evaluated: 2500818
Overall Accuracy: 0.9855
Overall MCC: 0.9188
Balanced Accuracy: 0.9185
Macro Precision/Recall/F1:0.9299 / 0.9185 / 0.9238
Weighted P/R/F1: 0.9875 / 0.9855 / 0.9865
Micro P/R/F1: 0.9875 / 0.9855 / 0.9865
Classes absent in y_true for this benchmark split: P
Mean Sequence Accuracy: 0.9756
Median Sequence Accuracy: 1.0000
Sequence Exact Match: 0.8535
[Per-Protein Classification]
Protein Accuracy: 0.9879
Protein MCC: 0.9621
Protein Macro P/R/F1: 0.8878 / 0.9375 / 0.9025
Type | Support | Precision | Recall | F1
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GLOBULAR | 4044 | 0.9948 | 0.9953 | 0.9951
SIGNAL | 273 | 0.9672 | 0.9707 | 0.9689
TM | 566 | 0.9715 | 0.9629 | 0.9672
SP+TM | 15 | 0.5600 | 0.9333 | 0.7000
BETA | 63 | 0.9455 | 0.8254 | 0.8814
[Signal Peptide Metrics]
SP Presence Acc/MCC: 0.9966 / 0.9715
SP Presence P/R/F1: 0.9565 / 0.9904 / 0.9731
CS Exact Accuracy (true SP): 0.8103
CS Relaxed@+/-2 (true SP): 0.9196
CS Exact P/R/F1: 0.7826 / 0.8103 / 0.7962
CS Relaxed P/R/F1: 0.8882 / 0.9196 / 0.9036
[Per-Segment Metrics]
Segment | TP | FP | FN | Precision | Recall | F1 | BoundaryMAE
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B | 763 | 68 | 48 | 0.9182 | 0.9408 | 0.9294 | 0.9463
M | 2544 | 1129 | 483 | 0.6926 | 0.8404 | 0.7594 | 1.7750
S | 292 | 38 | 19 | 0.8848 | 0.9389 | 0.9111 | 0.1284
TM | 3307 | 1197 | 531 | 0.7342 | 0.8616 | 0.7929 | 1.5838
[Per-Class Performance (Residue Level)]
Class | Support | Precision | Recall | F1 | MCC | Specificity
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B | 7210 | 0.8504 | 0.8513 | 0.8508 | 0.8504 | 0.9996
I | 2263185 | 0.9953 | 0.9931 | 0.9942 | 0.9395 | 0.9549
M | 64393 | 0.9172 | 0.8404 | 0.8771 | 0.8749 | 0.9980
O | 158275 | 0.9129 | 0.9433 | 0.9278 | 0.9230 | 0.9939
P | 0 | 0.0000 | 0.0000 | 0.0000 | 0.0000 | 0.9980
S | 7755 | 0.9737 | 0.9645 | 0.9691 | 0.9690 | 0.9999
[Confusion Matrix Counts]
B I M O P S
B 6138 181 0 486 405 0
I 247 2247605 2794 9067 3370 102
M 0 5705 54115 4535 0 38
O 833 4742 2067 149306 1265 62
P 0 0 0 0 0 0
S 0 85 24 165 1 7480
[Confusion Matrix Row-Normalized]
B I M O P S
B 0.851 0.025 0.000 0.067 0.056 0.000
I 0.000 0.993 0.001 0.004 0.001 0.000
M 0.000 0.089 0.840 0.070 0.000 0.001
O 0.005 0.030 0.013 0.943 0.008 0.000
P 0.000 0.000 0.000 0.000 0.000 0.000
S 0.000 0.011 0.003 0.021 0.000 0.965
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Last updated: 2026-05-25