Table 1.
Major Proteins of the Magellania venosa Shell Matrix
| Contig ID | Protein ID | BLAST Hits | Interpro Domains; Transmembrane Helices; Disordered Domains; Phosphorylation | % of Total Identified Dorsal Proteome 2/24 h | % of Total Identified Ventral Proteome 2/24 h | pI | SS | Anomalous Amino Acid Contents |
|---|---|---|---|---|---|---|---|---|
| 12373 | R20074237 | Uncharacterized | 2 TMH; DI | 13.8/8.4 | 11.6/8.0 | 4.34 | Y | Asp 12.1% |
| 10941 | F20065642 | Uncharacterized | — | 7.8/13.4 | 7.9/13.6 | 8.88 | N | — |
| 13662 | R30081972 | Uncharacterized | — | 9.6/8.3 | 5.0/8.3 | 9.34 | N | — |
| 8496 | F20050972 | Uncharacterized | — | 7.8/14.4 | 6.4/13.2 | 5.7 | Y | — |
| 16167 | R20097001 | Uncharacterized | TIMP like OB fold | 6.8/9.8 | 6.1/10.4 | 9.96 | N | — |
| 9860 | F30059157 | Uncharacterized | Phosphorylation: S174 (90%) | 4.8/0.6 | 4.4/0.6 | 9.71 | N | Gly 29.3% |
| 10182 | R10061090 | Uncharacterized | DI | 3.2/4.5 | 5.0/4.4 | 4.37 | Y | Asp 15.4% |
| 14565 | R20087389 | Similar to mesenchyme-specific cell surface glycoprotein/calcium and integrin-binding family member 2 | WD40/YVTN repeat like; DI | 4.5/5.3 | 3.1/5.2 | 9.19 | N | — |
| 13892 | R30083352 | Uncharacterized | — | 2.9/3.2 | 3.5/3.0 | 11.38 | Y | — |
| 481 | R20002885 | Uncharacterized | — | 2.8/0.1 | 3.0/0.1 | 9.88 | N | Gly 17.3% |
| 10544 | R20063263 | Uncharacterized | Phosphorylation: S73 (4%) | 2.4/2.7 | 2.9/2.5 | 6.64 | N | Ser 10.4% |
| 21084 a | R10126502 | Uncharacterized | FAD linked oxidase N term | 2.1/<0.01 | 2.9/0.0 | 10.35 | Y | — |
| 6089 b | F10036529 | Similar to complement receptor type 1 | Sushi/SCR/CCP (8×) | 2.4/5.6 | 2.3/5.8 | 6.28 | Y | — |
| 8840 | F20053036 | Uncharacterized | 2 TMH | 2.0/2.2 | 2.6/1.9 | 9.63 | Y | — |
| 25732 | R10154390 | Uncharacterized | — | 1.8/1.4 | 1.2/1.2 | 9.85 | Y | — |
| 17985 c | F20107906 | Similar to peroxidasin | Haem peroxidase, TSP1 repeat | 1.3/0.0 | 1.2/0.0 | 9.12 | N | — |
| 17302 | R20103811 | Uncharacterized | 2 TMH | 1.0/0.1 | 1.1/0.1 | 6.01 | N | Ala 11.8% |
| 16240 d | R10097438 | Uncharacterized | FAD linked oxidase N term, berberine; 3 TMH | 0.5/0.0 | 1.3/0.0 | 9.64 | N | — |
| 8882 | F20053288 | Uncharacterized | 1 TMH | 0.8/0.6 | 1.0/0.7 | 9.99 | Y | Gly 14.5% |
| 10588 | R10063526 | Uncharacterized | DI; phosphorylation: S272 (1%), S277 (9%), doubly phosphorylated peptide (69%) | 0.6/0.0 | 1.2/0.0 | 4.48 | Y | Gly 19.4%, Ser 22.6% |
| 17072 | R30102432 | Uncharacterized | — | 0.7/0.6 | 0.8/0.5 | 9.14 | Y | — |
| 1404 | R10008422 | Uncharacterized | DI | 0.8/1.1 | 0.6/1.3 | 9.49 | N | Ser 10.6% |
| 3349 | F10020089 | Uncharacterized | DI | 0.6/0.0 | 0.8/0.0 | 4.29 | N | Glu 19.5%, Ser 11.9% |
| 25890 | F30155337 | Uncharacterized | DI | 0.6/0.5 | 0.8/0.4 | 12.18 | N | — |
| 12037 | F10072217 | Similar to collagen α5 (VI), nontriple helical region | — | 0.7/0.2 | 0.7/0.2 | 10.01 | Y | Gly 11.5% |
| 1290 | R30007740 | Uncharacterized | VWA | 0.7/0.0 | 0.4/0.0 | 10.14 | N | — |
| 24592 | R20147551 | Uncharacterized | — | 0.4/0.0 | 0.6/0.0 | 9.6 | N | Lys 11.0% |
| 13443 | F30080655 | Uncharacterized | 1 TMH | 0.5/0.2 | 0.5/0.1 | 9.59 | Y | — |
| 3937 | R10023620 | Similar to CRE-TYR-3 | Tyrosinase | 0.3/0.0 | 0.6/0.0 | 9.06 | N | Cys 9.6%, Gly 10.9% |
| 3968 | F10023803 | Similar to mesenchyme-specific cell surface glycoprotein | WD40/YVTN repeat like/cytochrome cd1 (cyt cd1) nitrite reductase like, haem d1; DI | 0.4/1.5 | 0.4/1.7 | 6.47 | N | — |
| 6648 | R30039888 | Similar to lactadherin | Galactose binding like/coagulation factor 5/8 C | 0.3/0.8 | 0.6/0.7 | 9.41 | N | — |
| 12090 | F10072535 | Uncharacterized | DI | 0.4/1.0 | 0.3/1.2 | 8.85 | N | Gly 10.2% |
| 14281 | F10085681 | Similar to hemagglutinin family protein | DI | 0.5/0.4 | 0.3/0.4 | 5.12 | N | Ser 11.3% |
| 23379 | F20140270 | Uncharacterized | — | 0.5/1.9 | 0.3/1.9 | 10.42 | N | Gly 12.8% |
| 10375 | R10062248 | Uncharacterized | 3 TMH; DI | 0.5/0.7 | 0.3/0.8 | 10.91 | Y | Ala 11.2% |
| 22890 | R30137340 | Uncharacterized | ConA-like lectin | 0.1/0.0 | 0.6/0.0 | 9.72 | Y | — |
| 20588 | R20123527 | Uncharacterized | 1 TMH | 0.3/0.3 | 0.4/0.3 | 9.47 | N | — |
| 26985 | F30161907 | Uncharacterized | — | 0.3/0.0 | 0.3/0.0 | 9 | N | Ser 13.7% |
| 14828 e | R20088967 | Similar to complement receptor type 1 | — | 0.3/0.8 | 0.2/0.9 | 6.85 | Y | Gly 10.4% |
| 16143 | F30096855 | Uncharacterized | — | 0.4/0.4 | 0.3/0.4 | 9.02 | Y | — |
| 4638 | R30027828 | Uncharacterized | DOMON, SEA | 0.3/0.3 | 0.1/0.5 | 4.84 | N | — |
| 8473f | R10050836 | Uncharacterized/similar to peroxinectin | Haem peroxidase 3 | 0.1/<0.01 | 0.2/0.0 | 9.25 | N | — |
| 10638 | F10063823 | Uncharacterized | Sushi/SCR/CCP (8×); 1 TMH; DI | 0.2/1.1 | 0.2/1.1 | 9.39 | N | — |
| 14771 | F20088622 | Uncharacterized | 1 TMH; DI | 0.2/0.4 | 0.2/0.4 | 10.07 | N | — |
| 17017 | R20102101 | Similar to noelin-2 | Olfactomedin like | 0.1/0.0 | 0.3/0.0 | 9.14 | N | — |
| 19193 | R30115158 | Uncharacterized | CUB; 1 TMH | 0.3/0.3 | 0.2/0.4 | 8.66 | N | — |
| 19686 | F20118112 | Uncharacterized | — | 0.0/0.0 | 0.3/0.0 | 5.26 | N | — |
| 22374 | F30134241 | Uncharacterized | — | 0.0/0.1 | 0.4/0.1 | 8.91 | N | Cys 8.2%, Gly 18.9% |
| 22496 | F10134971 | Uncharacterized | — | 0.3/0.0 | 0.1/0.0 | 9.3 | N | — |
| 26237 | F30157419 | Uncharacterized | — | 0.2/0.1 | 0.2/0.1 | 7.89 | N | — |
| 1954 | F20011720 | Neutral ceramidase B | Neutral/alkaline nonlysosomal ceramidase | 0.2/0.2 | 0.2/0.2 | 8.26 | Y | — |
| 24553 | R10147316 | Uncharacterized | TSP1 | 0.3/0.1 | 0.2/0.2 | 8 | Y | Cys 10.0%, Gly 11.0% |
| 26581 | F10159481 | Uncharacterized | DI | 0.2/0.1 | 0.2/0.1 | 11.96 | Y | — |
| 1953 | R10011716 | Neutral/alkaline nonlysosomal ceramidase | Neutral/alkaline nonlysosomal ceramidase; 1 TMH | 0.1/0.2 | 0.1/0.2 | 7.77 | N | — |
| 3405 | F30020427 | Similar to cysteine-rich secretory protein LCCL domain-containing 2 | CAP | 0.2/0.0 | 0.1/0.0 | 7.92 | N | — |
| 14004 | R10084022 | Uncharacterized | — | 0.1/0.1 | 0.1/0.1 | 9.27 | N | — |
| 20189 | F20121130 | Uncharacterized | — | 0.1/0.0 | 0.1/0.0 | 9.67 | N | Lys 10.1% |
| 20189 | F30121131 | Uncharacterized | DI | 0.1/0.0 | 0.2/0.0 | 9.69 | N | — |
| 21060 | R20126359 | Similar to MAM domain-containing glycosylphosphatidylinositol anchor protein 1 | ConA like lectin/MAM, peptidase S1 | 0.1/0.2 | 0.1/0.1 | 8.38 | N | — |
| 21061 | R30126366 | Similar to atrial natriuretic peptide-converting enzyme | LDLRA 2, SCRC 2, Peptidase S1/trypsin | 0.1/0.2 | 0.1/0.2 | 8.46 | N | — |
| 14224 | F10085339 | Uncharacterized | EGF; DI | 0.1/0.1 | 0.0/0.1 | 7.04 | Y | — |
| 18776 | R30112656 | Uncharacterized | CUB; 1 TMH | 0.1/0.1 | 0.1/0.1 | 8.02 | Y | — |
| 21109 | F30126651 | Uncharacterized | — | 0.0/0.2 | 0.0/0.2 | 6.69 | N | — |
| 27260 | F20163556 | Similar to SCO-spondin/hemicentin-1 | TSP-1 | 0.0/0.3 | 0.0/0.3 | 8.4 | N | Cys 14.8%, Ser 11.8% |
| 24557 | R30147342 | Uncharacterized | 1 TMH | 0.1/0.8 | <0.010/0.8 | 5.52 | Y | Cys 11.2%, Gly 12.1% |
| 17584 | R20105503 | Uncharacterized | Trypsin inhibitor like Cys-rich | 0.0/0.6 | <0.01/1.1 | 10.03 | Y | Cys 7.6%, Gly 16.0% |
Note.—Major proteins were arbitrarily defined as proteins occurring with an average percentage of ≥0.1 in either D1–3 and V1–3 (2 h) or D4–6 and V4–6 (24 h) or both. Known intracellular proteins or membrane proteins with predominantly intracellular function, some of which showed high percentages in samples treated with hypochlorite for 2 h only, are not included. DI, predicted disordered structure; TMH, predicted transmembrane helices; SS, predicted secretion signal peptide.
aPossibly a fragment of the same protein as peptide R10097438.
bPossibly the same protein as contig 14828 (R20088967), possibly the N-terminal half.
cShares two peptides with R10050836.
dPossibly a fragment of the same protein as peptide R10126502.
ePossibly the same protein as contig 6089 (F10036529)—possibly the C-terminal half.
fShares peptides with F20107906.