Table 1.
Comparison of 9 topology prediction algorithms to evaluate prediction accuracy.
| A. Major Facilitator (MFS): Sugar Porter Family (84 Proteins) | # Proteins predicted to have the specified #s of TMSs | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| TC# 2.A.1.1 (Actual: 12 TMSs) | #TMSs: | 6 | N/A | 7 | 8 | 9 | 10 | 11 | 12 | 13 |
| HMMTOP | 0 | 0 | 0 | 0 | 0 | 4 | 3 | 77 | 0 | |
| SVMTOP | 0 | 0 | 0 | 0 | 0 | 5 | 27 | 49 | 3 | |
| TMHMM | 0 | 0 | 0 | 2 | 4 | 14 | 10 | 54 | 0 | |
| DAS | 0 | 0 | 1 | 1 | 4 | 6 | 28 | 36 | 8 | |
| SOSUI | 2 | 0 | 1 | 3 | 4 | 13 | 31 | 29 | 1 | |
| TOPCONS | 0 | 0 | 0 | 0 | 1 | 7 | 3 | 75 | 0 | |
| PHOBIUS | 1 | 0 | 1 | 3 | 20 | 61 | 0 | 0 | 0 | |
| MEMSAT | 0 | 0 | 0 | 0 | 2 | 2 | 2 | 78 | 0 | |
| SPOCTUPUS | 0 | 0 | 0 | 0 | 1 | 0 | 3 | 80 | 0 | |
| B. Amino Acid-Polyamine-Organocation (APC) (91 Proteins) | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| TC # 2.A.3 (Actual: 12 TMSs1) | # TMSs: | 8 | N/A | 9 | 10 | 11 | 12 | 13 | 14 | 15 |
| HMMTOP | 0 | 0 | 0 | 4 | 5 | 69 | 6 | 6 | 1 | |
| SVMTOP | 1 | 0 | 0 | 5 | 10 | 52 | 16 | 6 | 1 | |
| TMHMM | 0 | 0 | 1 | 9 | 17 | 55 | 3 | 5 | 1 | |
| DAS | 0 | 0 | 0 | 5 | 13 | 44 | 22 | 6 | 1 | |
| SOSUI | 0 | 0 | 3 | 6 | 28 | 39 | 10 | 5 | 0 | |
| TOPCONS | 0 | 0 | 0 | 6 | 1 | 74 | 3 | 7 | 0 | |
| PHOBIUS | 0 | 0 | 1 | 9 | 6 | 62 | 5 | 7 | 1 | |
| MEMSAT | 1 | 0 | 1 | 4 | 4 | 70 | 4 | 2 | 5 | |
| SPOCTUPUS | 0 | 0 | 1 | 6 | 4 | 61 | 4 | 15 | 0 | |
| C. Mitochondrial Carrier (MC) (88 Proteins) | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| TC # 2.A.29 (Actual: 6 TMSs) | # TMSs: | 0 | N/A | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 9 |
| HMMTOP | 9 | 0 | 2 | 7 | 8 | 25 | 12 | 23 | 2 | 0 | |
| SVMTOP | 55 | 0 | 0 | 2 | 6 | 9 | 8 | 6 | 1 | 1 | |
| TMHMM | 50 | 0 | 7 | 13 | 11 | 5 | 2 | 0 | 0 | 0 | |
| DAS | 22 | 0 | 23 | 16 | 18 | 6 | 2 | 1 | 0 | 0 | |
| SOSUI | 73 | 0 | 1 | 8 | 3 | 3 | 0 | 0 | 0 | 0 | |
| TOPCONS | 66 | 0 | 0 | 3 | 8 | 8 | 2 | 1 | 0 | 0 | |
| PHOBIUS | 46 | 0 | 11 | 15 | 10 | 4 | 1 | 1 | 0 | 0 | |
| MEMSAT | 0 | 0 | 1 | 2 | 0 | 5 | 12 | 68 | 0 | 0 | |
| SPOCTUPUS | 0 | 0 | 3 | 1 | 1 | 0 | 4 | 79 | 0 | 0 |
| D. Potassium Transporter (Trk) (20 Proteins) | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| TC # 2.A.38 (Actual: 8 TMSs2) | # TMSs: | 3 | 6 | 7 | 8 | 9 | 10 | 11 | 12 |
| HMMTOP | 0 | 0 | 0 | 3 | 3 | 6 | 4 | 4 | |
| SVMTOP | 1 | 0 | 0 | 0 | 0 | 6 | 7 | 6 | |
| TMHMM | 0 | 0 | 0 | 3 | 5 | 8 | 3 | 1 | |
| DAS | 0 | 0 | 0 | 0 | 2 | 6 | 7 | 5 | |
| SOSUI | 0 | 0 | 1 | 1 | 2 | 10 | 3 | 3 | |
| TOPCONS | 0 | 0 | 0 | 2 | 3 | 8 | 5 | 0 | |
| PHOBIUS | 0 | 0 | 0 | 1 | 3 | 6 | 6 | 4 | |
| MEMSAT | 0 | 3 | 3 | 7 | 1 | 5 | 1 | 0 | |
| SPOCTUPUS | 0 | 0 | 4 | 10 | 2 | 6 | 0 | 0 | |
1
Four members of the APC superfamily in TCDB are believe to have 10 TMSs, 6 have 14 TMSs, and 1 has 15 TMSs (See APC family description).
2
One member of the Trk family in TCDB (2.A.38.1.5) is believed to have 10 TMSs, with 2 extra N-terminal TMSs preceding the four repeats.