Table 1.
PTC superfamily
| Gene
|
Cosmida
|
LG
|
Amino acids
|
BLAST Pb
|
SSD Ec
|
PND Ea
|
TM summaryd
|
TMs
|
EST hits
|
|---|---|---|---|---|---|---|---|---|---|
| tra-2 | C15F1.3 | II | 1147 | N.S. | N.S. | N.S. | 1,3,2,1,3,2 | 12 | 4 |
| ptr-1 | C24B5.3 | V | 956 | 2.4E-22 | 7.1E-09 | 1.30E-24 | 1,3,2,1,3,2 | 12 | 0 |
| ptr-2 | C32E8.8 | I | 933 | 7.6E-26 | 1.2E-28 | 1.80E-45 | 1,3,2,1,3,2 | 12 | 16 |
| ptr-3 | C41D7.2 | II | 871 | 2.1E-09 | 7.1E-08 | 5.40E-14 | 3,2,1,3,2 | 11 | 6 |
| ptr-4 | C45B2.7 | X | 1037 | 1.7E-22 | 1.7E-09 | 8.80E-21 | 1,3,2,1,3,2 | 12 | 21 |
| ptr-5 | C53C11.3 | X | 845 | 2.6E-19 | 3.1E-09 | 2.30E-13 | 3,2,1,3,2 | 11 | 11 |
| ptr-6 | C54A12.1 | II | 1015 | 1.8E-33 | 7.4E-14 | 3.60E-32 | 1,3,2,1,3,2 | 12 | 4 |
| scp-1 | D2013.8 | II | 1032 | 1.5E-03 | 3.5E-78 | N.S. | 1,3,2,1,1 | 8 | 20 |
| npc-1 | F02E8.6 | X | 1456 | 2.4E-14 | 2.8E-10 | 3.10E-96 | 1,1,3,2,1,3,2 | 13 | 6 |
| ptd-2 | F07C3.1 | V | 932 | 1.9E-04 | 6.7E-02 | 7.40E-292 | 1,3,2,1,3,2 | 12 | 2 |
| npc-2 | F09G8.4 | III | 915 | 4.5E-07 | 1.8E-06 | 4.80E-23 | 1,1,3,2,1,3,2 | 13 | 2 |
| ptc-2 | F21H12.4 | II | 714 | 0.0 | 2.4E-67 | 7.90E-243 | 3,2,1,3 | 9 | 0 |
| ptr-7 | F31F6.5 | X | 955 | 4.5E-21 | 6.8E-10 | 4.50E-23 | 1,3,2,1,3,2 | 12 | 2 |
| ptr-8 | F44F4.4 | II | 890 | 6.6E-10 | 5.6E-08 | 5.30E-12 | 1,3,2,1,3,2 | 12 | 10 |
| ptr-9 | F54G8.5 | III | 413 | 2.1E-10 | 1.2E-02 | 1.10E-15 | 2,1,3 | 6 | 0 |
| ptr-10 | F55F8.1 | I | 889 | 7.8E-27 | 7.4E-14 | 4.70E-28 | 1,3,2,1,3,2 | 12 | 4 |
| ptr-11 | F56C11.2 | I | 820 | 8.0E-24 | 6.1E-10 | 1.80E-20 | 1,3,2,1,3,2 | 12 | 4 |
| ptd-1 | F45H1.1 | I | 969 | 1.9E-06 | 1.9E-05 | 1.10E-282 | 1,3,2,1,3,2 | 12 | 3 |
| ptr-12 | K07A3.2 | I | 1110 | 4.0E-09 | 2.7E-07 | 6.90E-09 | 1,1,3,2,1,2,2,1 | 13 | 1 |
| ptr-13 | K07C10.1 | II | 690 | 1.9E-17 | 6.9E-11 | 1.60E-21 | 3,2,1,3,2 | 11 | 0 |
| ptr-14 | R09H10.4 | IV | 877 | 5.8E-20 | 2.2E-12 | 2.10E-18 | 1*,3,2,1,3,2 | 12 | 11 |
| ptr-15 | T07H8.6 | V | 880 | 1.1E-21 | 4.4E-15 | 3.70E-32 | 1,3,2,1,3,2 | 12 | 0 |
| ptr-16 | T21H3.2 | V | 881 | 4.8E-17 | 3.6E-21 | 7.50E-21 | 1,3,2,1,3,2 | 12 | 0 |
| ptc-3 | Y110A2AL.8 | II | 1314 | 1.4E-223 | 2.8E-96 | 0 | 1,3,2,1,3,2 | 12 | 12 |
| ptr-17 | Y18D10A.7 | I | 936 | 7.2E-24 | 5.1E-15 | 8.20E-31 | 1,3,2,1,3,2 | 12 | 0 |
| ptr-18 | Y38F1A.3 | II | 800 | 5.1E-21 | 2.4E-22 | 8.20E-32 | 3,2,1,3,2 | 11 | 4 |
| ptr-19 | Y39A1B.2 | III | 1003 | 2.0E-25 | 3.1E-13 | 2.40E-29 | 1,3,2,1,3,2 | 12 | 0 |
| ptr-20 | Y53F4B.28 | II | 860 | 6.9E-15 | 9.2E-19 | 3.80E-27 | 1,3,2,1,3,2 | 12 | 7 |
| ptr-21 | Y65B4BR.3 | I | 909 | 6.3E-13 | 1.8E-08 | 2.60E-05 | 1,3,2,1,3,2 | 12 | 0 |
| ptr-22 | Y80D3A.7 | V | 859 | 2.9E-16 | 1.4E-08 | 2.40E-20 | 1,3*,2,1,3,2 | 12 | 0 |
| ptr-23 | ZK270.1 | I | 983 | 1.1E-13 | 1.5E-08 | 4.30E-10 | 1,3,2,1,3,2 | 12 | 24 |
| ptc-1 | ZK675.1 | II | 1405 | 0.0 | 1.8E-93 | 0 | 1,3,2,1,3,2 | 12 | 2 |
(LG) Linkage group. (*) An uncertainty in assignment. (N.S.) Not significant.
A profile HMM was constructed using HMMER 2.1.1 (http://www.hmmer.wustl.edu/); the seed alignment for the HMM was a Clustal W alignment of all currently identified PTC, NPC1, and DISP homologs (http://cmgm.stanford.edu/∼jefferis/paperdata/PND.aln). PND E-values were derived by using this calibrated HMM (http://cmgm.stanford.edu/∼jefferis/paperdata/PND.shmm) to search the Wormpep 20 database (http://www.sanger.acu.uk/Projects/C_elegans/wormpep/) in best local alignment mode (http://cmgm.stanford.edu/∼jefferis/paperdata/PND.shmms).
BLAST P represents the probability of a match using PTC-1 to search Wormpep 10 using BLASTP algorithm with default parameters.
A profile HMM was constructed for the SSD motif (Carstea et al. 1997) using a Clustal W alignment of all currently identified PTC, NPC1, and SCAP orthologs and a representative selection of SSD containing HMGCoAR proteins. This calibrated HMM was used to search Wormpep 20, and expectation values are tabulated as SSD E.
The TM domains in this family are arranged in a double repeat of the form 2(1,3,2), where each number represents a closely spaced group of TM domains and the commas represent extramembranous regions.