Table S1:
Table columns:
Query ID
Subject ID
-log(Exp) = normalized expectation (-log(Exp))
% identity = percent of identity
# perfect matches = number of perfect matches
length of alignment
hit number for primary alignment (1 is the best first hit)
hit number for alternative alignment
First query = first position of the "Query" sequence in the alignment
Last query = last position of the "Query" sequence in the alignme
First subj = first position of the "Subject" sequence in the alignment
Last subj = last position of the "Subject" sequence in the alignment
Query ID / Subject ID / -log(Exp) / % identity / # perfect matches / length of alignment / hit number for primary alignment / hit number for alternative alignment / First query / Last query / First subj / Last subjContig1 / NP_957176.1| poly A binding protein, cytoplasmic 1 b [Danio rerio] / 1 / 100 / 184 / 184 / 1 / 2 / 5 / 556 / 5 / 188
Contig2 / AAP22046.1| ferritin heavy subunit [Oreochromis mossambicus] / 0.63 / 80 / 117 / 145 / 1 / 2 / 275 / 709 / 1 / 145
Contig3 / CAC29154.1| complement component C3 [Anarhichas minor] / 0.79 / 71 / 148 / 206 / 1 / 2 / 8 / 622 / 1169 / 1374
Contig4 / XP_001135183.1| PREDICTED: similar to ubiquitin A-52 residue ribosomal protein fusion product 1 [Pan troglodytes] / 0.69 / 99 / 129 / 130 / 1 / 3 / 6 / 395 / 92 / 221
Contig5 / AAG24633.1|AF300706_1 serum amyloid A protein [Holothuria glaberrima] / 0.37 / 69 / 75 / 108 / 2 / 2 / 104 / 424 / 15 / 122
Contig7 / CAH57700.1| 60S ribosomal protein L5 [Platichthys flesus] / 0.74 / 84 / 138 / 164 / 1 / 3 / 6 / 497 / 65 / 228
Contig8 / AAG30030.1|AF281355_1 differentially regulated trout protein 1 [Oncorhynchus mykiss] / 0.07 / 38 / 29 / 75 / 3 / 3 / 105 / 326 / 16 / 88
Contig9 / Q9IA79|BI1_PAROL Probable Bax inhibitor 1 (BI-1) / 0.75 / 77 / 144 / 185 / 1 / 2 / 71 / 625 / 1 / 185
Contig10 / CAL92184.1| ceruloplasmin [Chionodraco rastrospinosus] / 1 / 86 / 222 / 257 / 1 / 2 / 5 / 775 / 657 / 913
Contig11 / XP_533253.2| PREDICTED: similar to HRAS-like suppressor 3 (H-rev 107 protein homolog) (HREV107-3) isoform 1 [Canis familiaris] / 0.39 / 62 / 79 / 127 / 3 / 3 / 153 / 533 / 7 / 133
Contig13 / ABH07676.1| cold-shock domain protein [Scophthalmus maximus] / 0.58 / 64 / 128 / 200 / 1 / 1 / 139 / 738 / 1 / 198
Contig14 / AAU00798.1| hepcidin 5 precursor [Acanthopagrus schlegelii] / 0.19 / 87 / 49 / 56 / 1 / 2 / 89 / 256 / 1 / 56
Contig15 / NP_001018426.1| nuclear import 7 homolog [Danio rerio] / 0.65 / 84 / 107 / 126 / 1 / 1 / 7 / 384 / 4 / 129
Contig16 / Q04604|TYRO_RANNI Tyrosinase precursor (Monophenol monooxygenase) / 0.27 / 41 / 73 / 175 / 1 / 2 / 8 / 505 / 273 / 443
Contig17 / AAS66305.1| hepcidin-like precursor [Pagrus major] / 0.18 / 59 / 53 / 89 / 1 / 3 / 90 / 353 / 1 / 88
Contig18 / XP_622598.2| PREDICTED: similar to Lipopolysaccharide-induced TNF factor [Mus musculus] / 0.11 / 48 / 18 / 37 / 4 / 1 / 277 / 387 / 89 / 125
Contig19 / NP_958880.1| plasminogen [Danio rerio] / 0.43 / 74 / 58 / 78 / 1 / 1 / 7 / 240 / 350 / 426
Contig20 / AAQ94564.1| ribosomal protein S3 [Danio rerio] / 0.84 / 71 / 181 / 252 / 2 / 3 / 18 / 752 / 1 / 242
Contig23 / XP_001380249.1| PREDICTED: similar to Inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein) [Monodelphis domestica] / 0.8 / 49 / 160 / 322 / 5 / 2 / 5 / 949 / 175 / 496
Contig24 / BAD15059.1| chitinase1 [Paralichthys olivaceus] / 0.82 / 73 / 151 / 206 / 1 / 3 / 6 / 617 / 29 / 232
Contig25 / AAD30201.1| complement C3 precursor alpha chain [Protopterus aethiopicus] / 0.63 / 39 / 144 / 368 / 5 / 3 / 9 / 1097 / 534 / 888
Contig26 / ABN14356.1| MHC class I antigen [Gasterosteus aculeatus] / 0.12 / 69 / 36 / 52 / 1 / 1 / 43 / 198 / 1 / 52
Contig27 / BAA13148.1| ferritin H-3 [Oncorhynchus mykiss] / 0.86 / 85 / 150 / 176 / 2 / 1 / 67 / 594 / 1 / 176
Contig28 / XP_001599434.1| PREDICTED: similar to polyubiquitin [Nasonia vitripennis] / 1 / 98 / 220 / 224 / 1 / 1 / 406 / 1077 / 160 / 383
Contig29 / AAY21009.1| zona pellucida protein Ba [Sparus aurata] / 0.82 / 67 / 147 / 219 / 1 / 3 / 3 / 656 / 188 / 406
Contig30 / ABA33614.1| fetuin-B [Carassius auratus gibelio] / 0.1 / 46 / 35 / 75 / 2 / 1 / 4 / 222 / 402 / 475
Contig32 / XP_001343030.1| PREDICTED: similar to novel carboxylesterase domain containing protein, partial [Danio rerio] / 0.18 / 37 / 52 / 140 / 2 / 2 / 5 / 382 / 235 / 362
Contig34 / ABQ41317.1| fibrinogen beta chain precursor [Paralichthys olivaceus] / 1 / 79 / 214 / 269 / 1 / 1 / 187 / 990 / 39 / 307
Contig35 / NP_001027892.1| apolipoprotein A-IV3 [Takifugu rubripes] / 0.77 / 84 / 127 / 151 / 1 / 3 / 90 / 542 / 14 / 164
Contig36 / NP_998697.1| cAMP responsive element binding protein 3-like 3 [Danio rerio] / 0.29 / 50 / 71 / 141 / 2 / 3 / 6 / 428 / 196 / 332
Contig37 / BAC23057.1| complement component C5-1 [Cyprinus carpio] / 0.75 / 41 / 144 / 343 / 2 / 2 / 23 / 1042 / 1351 / 1691
Contig38 / AAP94279.1| transferrin [Pagrus major] / 1 / 69 / 176 / 252 / 1 / 1 / 109 / 837 / 440 / 691
Contig39 / NP_957371.1| formiminotransferase cyclodeaminase [Danio rerio] / 0.27 / 68 / 61 / 89 / 2 / 3 / 6 / 272 / 435 / 523
Contig40 / YP_001105845.1| NAD-dependent epimerase/dehydratase [Saccharopolyspora erythraea NRRL 2338] / 0.26 / 35 / 79 / 220 / 4 / 2 / 29 / 676 / 1 / 209
Contig41 / AAA92556.1| complement regulatory plasma protein [Paralabrax nebulifer] / 0.74 / 60 / 129 / 215 / 1 / 2 / 5 / 643 / 141 / 352
Contig42 / AAG28030.1| chemotaxin [Oncorhynchus mykiss] / 0.42 / 77 / 82 / 106 / 3 / 1 / 160 / 477 / 51 / 156
Contig43 / XP_573464.2| PREDICTED: similar to complement component factor H [Rattus norvegicus] / 0.27 / 30 / 88 / 289 / 1 / 3 / 111 / 920 / 420 / 666
Contig44 / CAE45343.1| TPA: C1 inhibitor precursor [Paralichthys olivaceus] / 0.63 / 62 / 121 / 193 / 1 / 1 / 4 / 582 / 147 / 339
Contig45 / CAA67765.1| pentraxin [Salmo salar] / 0.43 / 46 / 94 / 202 / 2 / 2 / 161 / 760 / 26 / 225
Contig46 / NP_001026846.1| poly A binding protein, cytoplasmic 1 a [Danio rerio] / 1 / 88 / 184 / 209 / 2 / 2 / 2 / 628 / 56 / 264
Contig47 / AAS66305.1| hepcidin-like precursor [Pagrus major] / 0.13 / 77 / 41 / 53 / 1 / 3 / 90 / 245 / 1 / 53
Contig48 / CAD45003.1| complement component C4 [Takifugu rubripes] / 0.76 / 60 / 142 / 236 / 1 / 1 / 4 / 705 / 1324 / 1544
Contig49 / AAA92556.1| complement regulatory plasma protein [Paralabrax nebulifer] / 0.61 / 41 / 135 / 324 / 2 / 3 / 177 / 1103 / 310 / 627
Contig50 / AAG24633.1|AF300706_1 serum amyloid A protein [Holothuria glaberrima] / 0.38 / 71 / 77 / 108 / 2 / 2 / 104 / 424 / 15 / 122
Contig53 / AAF87767.1| haptoglobin [Oncorhynchus mykiss] / 0.26 / 79 / 55 / 69 / 3 / 1 / 148 / 354 / 40 / 108
Contig54 / AAA73954.1| serine protease inhibitor / 0.87 / 56 / 137 / 241 / 4 / 3 / 177 / 896 / 36 / 276
Contig56 / AAG24633.1|AF300706_1 serum amyloid A protein [Holothuria glaberrima] / 0.18 / 67 / 48 / 71 / 1 / 2 / 95 / 307 / 15 / 81
Contig57 / BAE92861.1| Tributyltin binding protein type 1 [Paralichthys olivaceus] / 0.07 / 26 / 56 / 209 / 5 / 1 / 25 / 591 / 2 / 202
Contig58 / ABA41374.1| type III antifreeze protein [Lycodichthys dearborni] / 0.38 / 96 / 83 / 86 / 2 / 3 / 72 / 329 / 1 / 86
Contig59 / AAT09138.1| hepcidin-like precursor [Lateolabrax japonicus] / 0.39 / 87 / 75 / 86 / 1 / 1 / 85 / 342 / 1 / 86
Contig60 / NP_001027888.1| 14kDa apolipoprotein [Takifugu rubripes] / 0.32 / 48 / 69 / 143 / 3 / 2 / 44 / 472 / 1 / 143
Contig61 / ABA41374.1| type III antifreeze protein [Lycodichthys dearborni] / 0.38 / 95 / 82 / 86 / 3 / 2 / 59 / 316 / 1 / 86
Contig62 / CAH59609.1| apolipoprotein AI precursor [Platichthys flesus] / 0.84 / 59 / 156 / 263 / 1 / 3 / 15 / 803 / 1 / 263
Contig63 / BAD98538.1| warm-temperature-acclimation-related-65 [Oryzias latipes] / 1 / 67 / 285 / 421 / 1 / 3 / 9 / 1268 / 12 / 427
Contig64 / ABA41374.1| type III antifreeze protein [Lycodichthys dearborni] / 0.39 / 97 / 84 / 86 / 2 / 2 / 71 / 328 / 1 / 86
Contig65 / AAP94279.1| transferrin [Pagrus major] / 1 / 75 / 410 / 546 / 1 / 3 / 24 / 1658 / 1 / 546
Contig66 / Q9DD65|LYSC_PAROL Lysozyme C precursor (1,4-beta-N-acetylmuramidase C) / 0.61 / 84 / 106 / 126 / 1 / 1 / 70 / 447 / 18 / 143
Contig67 / ABA41374.1| type III antifreeze protein [Lycodichthys dearborni] / 0.4 / 97 / 85 / 87 / 1 / 3 / 72 / 332 / 1 / 87
Contig68 / CAC29154.1| complement component C3 [Anarhichas minor] / 1 / 84 / 661 / 779 / 1 / 1 / 1 / 2331 / 884 / 1662
Contig69 / ABA41374.1| type III antifreeze protein [Lycodichthys dearborni] / 0.4 / 96 / 84 / 87 / 2 / 1 / 70 / 330 / 1 / 87
Sequence1 / AAH75758.1| Snx5 protein [Danio rerio] / 0.48 / 85 / 90 / 105 / 3 / 2 / 5 / 319 / 63 / 167
Sequence2 / XP_001501102.1| PREDICTED: similar to NADH-cytochrome b5 reductase isoform 1 [Equus caballus] / 0.09 / 46 / 37 / 79 / 5 / 3 / 6 / 242 / 1993 / 2070
Sequence3 / EDL01088.1| chloride channel 4-2, isoform CRA_b [Mus musculus] / 0.11 / 86 / 31 / 36 / 4 / 1 / 7 / 114 / 52 / 87
Sequence4 / BAE48202.1| proteasome alpha 2 [Paralichthys olivaceus] / 0.1 / 59 / 36 / 61 / 1 / 1 / 25 / 204 / 151 / 211
Sequence5 / O73672|PSA2_CARAU Proteasome subunit alpha type 2 / 0.09 / 58 / 34 / 58 / 3 / 1 / 25 / 195 / 159 / 216
Sequence6 / AAR87007.1| complement component C9 [Fundulus heteroclitus] / 0.17 / 52 / 45 / 86 / 3 / 1 / 7 / 261 / 492 / 577
Sequence7 / CAE53703.1| fibrinogen alpha chain [Platichthys flesus] / 0.27 / 77 / 51 / 66 / 1 / 1 / 7 / 204 / 17 / 82
Sequence8 / NP_955865.1| ubiquitin-conjugating enzyme E2D 2 [Danio rerio] / 0.27 / 90 / 57 / 63 / 1 / 3 / 6 / 194 / 85 / 147
Sequence9 / XP_001069684.1| PREDICTED: similar to Protein transport protein SEC61 gamma subunit [Rattus norvegicus] / 0.13 / 92 / 37 / 40 / 3 / 2 / 14 / 133 / 68 / 107
Sequence10 / AAK95140.1| ribosomal protein L13a [Ictalurus punctatus] / 0.25 / 74 / 63 / 85 / 1 / 3 / 6 / 260 / 117 / 201
Sequence11 / AAL84163.1| alpha-amylase [Lates calcarifer] / 0.37 / 52 / 95 / 180 / 1 / 3 / 105 / 620 / 155 / 317
Sequence12 / AAH98591.1| Ribosomal protein L14 [Danio rerio] / 0.64 / 84 / 116 / 137 / 3 / 2 / 11 / 421 / 1 / 137
Sequence13 / NP_001007998.1| proteasome (prosome macropain) subunit alpha type 4 [Xenopus tropicalis] / 0.78 / 95 / 134 / 140 / 3 / 3 / 132 / 551 / 1 / 140
Sequence14 / AAP20169.1| elongation factor 1-alpha [Pagrus major] / 0.67 / 84 / 127 / 150 / 3 / 2 / 14 / 463 / 311 / 460
Sequence15 / AAR01921.1| tyrosinase [Xenopus laevis] / 0.33 / 37 / 75 / 198 / 2 / 3 / 66 / 605 / 2 / 199
Sequence16 / AAH67696.1| Bcdo2l protein [Danio rerio] / 0.26 / 55 / 52 / 94 / 5 / 2 / 2 / 283 / 166 / 258
Sequence17 / P83271|HBA2_ANAMI Hemoglobin subunit alpha-2 (Hemoglobin alpha-2 chain) (Alpha-2-globin) / 0.71 / 94 / 135 / 143 / 1 / 2 / 11 / 439 / 1 / 143
Sequence18 / NP_148754.1| cytochrome c oxidase subunit II [Arctoscopus japonicus] / 0.6 / 70 / 126 / 180 / 5 / 1 / 4 / 543 / 5 / 183
Sequence19 / AAT68082.1| pan-epithelial glycoprotein [Danio rerio] / 0.26 / 45 / 64 / 140 / 5 / 1 / 10 / 429 / 162 / 300
Sequence20 / EDM10084.1| WD repeat domain 41 (predicted), isoform CRA_a [Rattus norvegicus] / 0.37 / 52 / 64 / 121 / 5 / 3 / 21 / 377 / 56 / 175
Sequence21 / XP_001087801.1| PREDICTED: lysosomal-associated membrane protein 1 isoform 2 [Macaca mulatta] / 0.2 / 39 / 60 / 152 / 5 / 1 / 13 / 465 / 213 / 362
Sequence22 / NP_001004986.1| growth arrest and DNA-damage-inducible, gamma [Xenopus tropicalis] / 0.31 / 58 / 47 / 81 / 5 / 2 / 254 / 493 / 59 / 138
Sequence23 / BAF51913.1| cytochrome c oxidase subunit III [Kentrocapros aculeatus] / 0.84 / 77 / 148 / 190 / 1 / 2 / 5 / 574 / 13 / 202
Sequence24 / AAH63960.1| Sepp1a protein [Danio rerio] / 0.32 / 55 / 67 / 121 / 2 / 3 / 6 / 368 / 66 / 185
Sequence25 / EDL14450.1| IMP4, U3 small nucleolar ribonucleoprotein, homolog (yeast) [Mus musculus] / 0.77 / 74 / 136 / 183 / 5 / 3 / 84 / 632 / 24 / 206
Sequence26 / AAP20183.1| ribosomal protein L18a [Pagrus major] / 0.83 / 84 / 152 / 179 / 1 / 2 / 11 / 547 / 5 / 183
Sequence27 / AAC28309.1| cytochrome P450 monooxygenase CYP2K1v2 [Oncorhynchus mykiss] / 0.27 / 60 / 61 / 101 / 4 / 3 / 102 / 404 / 38 / 138
Sequence28 / BAA34707.1| complement factor B/C2B [Cyprinus carpio] / 0.37 / 48 / 75 / 156 / 3 / 3 / 18 / 485 / 684 / 833
Sequence29 / NP_997940.1| tubulin folding cofactor B [Danio rerio] / 0.52 / 60 / 101 / 168 / 3 / 2 / 92 / 589 / 1 / 168
Sequence30 / AAI07516.1| Ribosomal protein L7 [Danio rerio] / 0.85 / 74 / 153 / 205 / 4 / 1 / 13 / 627 / 4 / 208
Sequence31 / XP_698851.2| PREDICTED: similar to Cytochrome b5 type A (microsomal) [Danio rerio] / 0.27 / 52 / 73 / 140 / 2 / 3 / 3 / 389 / 182 / 321
Sequence32 / CAF22027.2| complement component C8 gamma [Oncorhynchus mykiss] / 0.53 / 67 / 100 / 149 / 1 / 1 / 4 / 444 / 73 / 221
Sequence33 / AAX43793.1| ribosomal protein L38 [synthetic construct] / 0.17 / 72 / 50 / 69 / 3 / 3 / 45 / 251 / 1 / 69
Sequence34 / 2D85|A Chain A, Solution Structure Of The Fourth Ch Domain From Human L- Plastin / 0.12 / 39 / 46 / 117 / 3 / 1 / 7 / 357 / 40 / 119
Sequence35 / AAG11410.1|AF140783_1 apolipoprotein CII [Oncorhynchus mykiss] / 0.23 / 50 / 56 / 112 / 4 / 1 / 16 / 312 / 1 / 112
Sequence36 / AAQ17065.1| nucleolin 3 [Cyprinus carpio] / 0.59 / 61 / 105 / 170 / 5 / 3 / 6 / 515 / 304 / 468
Sequence37 / XP_531475.2| PREDICTED: solute carrier family 37 member 1 isoform 6 [Pan troglodytes] / 0.33 / 54 / 78 / 142 / 4 / 1 / 280 / 678 / 1 / 142
Sequence38 / AAP20169.1| elongation factor 1-alpha [Pagrus major] / 0.66 / 64 / 139 / 214 / 3 / 2 / 146 / 778 / 1 / 213
Sequence39 / XP_855343.1| PREDICTED: similar to statin-like [Canis familiaris] / 0.66 / 60 / 139 / 228 / 2 / 2 / 101 / 763 / 266 / 487
Sequence40 / ABD67515.1| microsomal glutathione S-transferase 3 [Cyprinus carpio] / 0.54 / 79 / 102 / 129 / 2 / 2 / 164 / 550 / 1 / 129
Sequence41 / ABE98240.1| ring finger protein 128-like [Oreochromis mossambicus] / 0.83 / 76 / 149 / 196 / 1 / 3 / 90 / 677 / 111 / 306
Sequence42 / ABC69047.1| chemokine CC-like protein [Scophthalmus maximus] / 0.06 / 51 / 29 / 56 / 1 / 1 / 94 / 261 / 57 / 111
Sequence43 / ABJ98546.1| fibrinogen beta chain precursor [Pseudosciaena crocea] / 0.39 / 87 / 67 / 77 / 2 / 1 / 97 / 327 / 320 / 396
Sequence44 / AAI50465.1| Ambpl protein [Danio rerio] / 0.12 / 34 / 25 / 72 / 5 / 3 / 180 / 395 / 233 / 304
Sequence45 / NP_956366.1| lectin, galactoside-binding, soluble, 9 (galectin 9)-like 1 [Danio rerio] / 0.52 / 54 / 105 / 192 / 4 / 1 / 109 / 648 / 1 / 191
Sequence46 / AAI50465.1| Ambpl protein [Danio rerio] / 0.56 / 59 / 107 / 179 / 4 / 2 / 170 / 706 / 3 / 181
Sequence47 / NP_001002151.1| calumenin [Danio rerio] / 0.37 / 64 / 55 / 85 / 2 / 3 / 147 / 401 / 3 / 87
Sequence48 / AAH63811.1| Ribosomal protein L4 [Rattus norvegicus] / 0.81 / 80 / 151 / 187 / 4 / 1 / 139 / 699 / 156 / 342
Sequence49 / BAA86980.1| novel member of chitinase family [Homo sapiens] / 0.66 / 61 / 114 / 184 / 4 / 2 / 95 / 640 / 113 / 296
Sequence50 / AAG13292.1|AF266172_1 60S acidic ribosomal protein P1 [Gillichthys mirabilis] / 0.26 / 98 / 61 / 62 / 2 / 2 / 221 / 406 / 1 / 62
Sequence51 / Q07598|NLTP_CHICK Nonspecific lipid-transfer protein (Propanoyl-CoA C-acyltransferase) (NSL-TP) (Sterol carrier protein 2) (SCP-2) (Sterol carrier protein X) (SCP-X) (SCP-chi) (SCPX) / 0.87 / 76 / 135 / 177 / 4 / 3 / 90 / 620 / 173 / 349
Sequence52 / CAC45059.1| type I keratin S8 [Oncorhynchus mykiss] / 0.79 / 71 / 156 / 219 / 1 / 1 / 100 / 750 / 215 / 433
Sequence53 / NP_001007924.1| fatty acid binding protein 2, intestinal [Gallus gallus] / 0.49 / 67 / 89 / 132 / 4 / 1 / 139 / 534 / 1 / 132
Sequence54 / AAA97879.1| fibrinogen gamma subunit [Rana sylvatica] / 0.7 / 59 / 134 / 226 / 4 / 1 / 10 / 681 / 23 / 248
Sequence55 / AAH84690.1| Macrophage stimulating 1 (hepatocyte growth factor-like) [Danio rerio] / 1 / 82 / 193 / 235 / 2 / 2 / 8 / 703 / 132 / 363
Sequence56 / ABA54278.1| DnaJ-like subfamily B member 11 [Paralichthys olivaceus] / 0.3 / 94 / 63 / 67 / 1 / 1 / 91 / 291 / 294 / 360
Sequence57 / AAT77220.1| C type lectin receptor A [Salmo salar] / 0.61 / 52 / 128 / 243 / 2 / 1 / 103 / 822 / 1 / 238
Sequence58 / XP_001364180.1| PREDICTED: similar to IQ motif and WD repeats 1 isoform 1 [Monodelphis domestica] / 0.23 / 87 / 57 / 65 / 3 / 1 / 97 / 291 / 815 / 879
Sequence59 / AAF78087.1|AF274502_2 protein disulfide isomerase ER-60 [Takifugu rubripes] / 0.3 / 71 / 43 / 60 / 2 / 3 / 9 / 188 / 60 / 119
Sequence60 / AAH25681.1| Insulin-like growth factor binding protein, acid labile subunit [Homo sapiens] / 0.18 / 35 / 61 / 171 / 5 / 1 / 1 / 444 / 436 / 605
Sequence62 / AAH44541.1| DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 19 (DBP5 homolog, yeast) [Danio rerio] / 0.68 / 93 / 128 / 137 / 1 / 3 / 6 / 416 / 350 / 486
Sequence63 / AAL08417.1| multiple inositol polyphosphate phosphatase 1 [Takifugu rubripes] / 0.45 / 58 / 90 / 153 / 4 / 2 / 143 / 571 / 293 / 445
Sequence64 / |T02955 probable cytochrome P450 monooxygenase - maize (fragment) / 0.25 / 58 / 71 / 122 / 3 / -1 / 610 / 251 / 26 / 143
Sequence65 / AAG13337.1|AF266217_1 peptidyl-proline isomerase [Gillichthys mirabilis] / 0.5 / 83 / 101 / 121 / 3 / 1 / 142 / 504 / 1 / 119
Sequence66 / AAH95051.1| RNA terminal phosphate cyclase-like 1 [Danio rerio] / 0.35 / 83 / 71 / 85 / 3 / 1 / 34 / 288 / 283 / 367
Sequence67 / NP_957307.2| adhesion regulating molecule 1b [Danio rerio] / 0.19 / 64 / 50 / 77 / 2 / 1 / 25 / 237 / 290 / 366
Sequence68 / NP_001005981.1| kininogen 1 [Danio rerio] / 0.05 / 28 / 38 / 134 / 2 / 2 / 8 / 400 / 240 / 330
Sequence69 / NP_083968.1| uridine phosphorylase 2 [Mus musculus] / 0.34 / 78 / 71 / 91 / 5 / 1 / 4 / 276 / 224 / 314
Sequence70 / NP_956381.1| thioredoxin interacting protein [Danio rerio] / 0.37 / 91 / 43 / 47 / 1 / 3 / 159 / 299 / 112 / 158
Sequence71 / AAQ14272.1|AF255348_1 cytochrome c oxidase subunit VIc precursor [Thunnus obesus] / 0.21 / 68 / 52 / 76 / 1 / 1 / 61 / 288 / 1 / 76
Sequence72 / ABB29989.1| FBP32 precursor [Morone saxatilis] / 0.44 / 61 / 87 / 141 / 3 / 2 / 5 / 412 / 28 / 168
Sequence73 / ABK78762.1| flavin-containing monooxygenase FMO1 [Oncorhynchus mykiss] / 0.3 / 71 / 57 / 80 / 3 / 3 / 147 / 386 / 1 / 80
Sequence74 / EDL24912.1| RIKEN cDNA 5730469M10, isoform CRA_b [Mus musculus] / 0.14 / 37 / 55 / 147 / 5 / 2 / 122 / 562 / 8 / 104
Sequence75 / AAX29203.1| ribosomal protein S20 [synthetic construct] / 0.59 / 97 / 116 / 119 / 5 / 1 / 91 / 447 / 1 / 119
Sequence76 / XP_534566.1| PREDICTED: similar to epoxide hydrolase 2, cytoplasmic isoform 1 [Canis familiaris] / 0.43 / 58 / 61 / 105 / 5 / 1 / 151 / 465 / 326 / 427
Sequence77 / ABQ08618.1| cytochrome oxidase subunit 1 [Anarhichas minor] / 0.67 / 97 / 127 / 130 / 1 / 3 / 6 / 395 / 387 / 516
Sequence78 / AAI25050.1| Keratin associated protein 10-4 [Homo sapiens] / 0.06 / 31 / 42 / 135 / 1 / 3 / 6 / 365 / 275 / 396
Sequence79 / AAC83698.1| complement factor Bf-2 [Oncorhynchus mykiss] / 0.43 / 43 / 104 / 238 / 5 / 3 / 6 / 686 / 477 / 711
Sequence80 / CAD58653.1| C1 inhibitor [Oncorhynchus mykiss] / 0.13 / 40 / 48 / 120 / 3 / 1 / 88 / 435 / 1 / 120
Sequence81 / ABU63968.1| Ca2+-dependent complex C1R/C1S subunit [Perca flavescens] / 0.17 / 79 / 38 / 48 / 1 / 1 / 4 / 147 / 415 / 462
Sequence82 / AAH64000.1| Ceruloplasmin [Danio rerio] / 0.64 / 63 / 102 / 160 / 4 / 3 / 6 / 485 / 124 / 283
Sequence83 / NP_989261.1| transmembrane emp24 domain containing 3 [Xenopus tropicalis] / 0.68 / 88 / 121 / 136 / 4 / 3 / 60 / 467 / 27 / 162
Sequence84 / NP_001008187.1| solute carrier family 2 (facilitated glucose/fructose transporter), member 5 [Xenopus tropicalis] / 0.67 / 67 / 117 / 173 / 3 / 1 / 4 / 522 / 306 / 478
Sequence85 / BAE97362.1| nephrosin [Oryzias latipes] / 0.45 / 50 / 93 / 186 / 5 / 3 / 135 / 689 / 40 / 223
Sequence86 / BAD93097.1| spectrin, alpha, non-erythrocytic 1 (alpha-fodrin) variant [Homo sapiens] / 0.65 / 87 / 120 / 137 / 1 / 3 / 6 / 416 / 1953 / 2089
Sequence87 / P06682|CO9_ONCMY Complement component C9 / 0.13 / 47 / 41 / 86 / 4 / 2 / 8 / 265 / 83 / 163
Sequence88 / NP_001002207.1| acetyl-Coenzyme A acyltransferase 1 [Danio rerio] / 0.38 / 65 / 60 / 91 / 1 / 3 / 105 / 356 / 1 / 91
Sequence89 / AAT01914.1| complement component C8 beta chain [Pseudopleuronectes americanus] / 0.87 / 84 / 159 / 188 / 3 / 3 / 3 / 566 / 4 / 191
Sequence90 / BAD96725.1| nuclear prelamin A recognition factor-like variant [Homo sapiens] / 0.54 / 73 / 77 / 105 / 4 / 1 / 10 / 324 / 5 / 109
Sequence91 / XP_001092860.1| PREDICTED: similar to 60S ribosomal protein L29 (Cell surface heparin-binding protein HIP) [Macaca mulatta] / 0.23 / 94 / 52 / 55 / 3 / 3 / 12 / 176 / 16 / 70
Sequence92 / AAP80678.1| fibronectin variant 3 [Danio rerio] / 0.86 / 82 / 134 / 162 / 2 / 1 / 7 / 489 / 189 / 350
Sequence93 / BAC54021.1| C-type lectin 2 [Anguilla japonica] / 0.3 / 45 / 59 / 130 / 5 / 2 / 65 / 454 / 29 / 158
Sequence94 / AAB04654.1| beta-2 microglobulin / 0.33 / 56 / 65 / 116 / 5 / 2 / 44 / 391 / 1 / 116
Sequence95 / AAH88067.1| Tetraspanin 8 [Xenopus tropicalis] / 0.05 / 28 / 34 / 118 / 4 / 1 / 4 / 354 / 100 / 207
Sequence96 / AAA92556.1| complement regulatory plasma protein [Paralabrax nebulifer] / 0.55 / 50 / 105 / 206 / 1 / 2 / 44 / 658 / 852 / 1053
Sequence97 / AAH56717.1| Prosaposin [Danio rerio] / 0.51 / 68 / 88 / 129 / 3 / 1 / 121 / 507 / 391 / 519
Sequence98 / ABU54857.1| 40s ribosomal protein S7 [Perca flavescens] / 0.86 / 96 / 163 / 169 / 1 / 2 / 128 / 634 / 1 / 169
Sequence99 / CAJ83333.1| aldehyde dehydrogenase 1 family, member L1 [Xenopus tropicalis] / 0.83 / 85 / 147 / 171 / 5 / 3 / 108 / 620 / 554 / 724
Sequence100 / CAN88468.1| novel protein similar to vertebrate eukaryotic translation initiation factor 4A, isoform 2 (EIF4A2, zgc:63783) [Danio rerio] / 0.92 / 86 / 177 / 205 / 4 / 3 / 99 / 710 / 176 / 380
Sequence101 / AAD19876.1| sterol 12-alpha-hydroxylase CYP8B1 [Mus musculus] / 0.16 / 48 / 29 / 60 / 4 / 2 / 101 / 280 / 73 / 132
Sequence102 / EAA36404.2| 60S ribosomal protein L11 [Neurospora crassa OR74A] / 0.33 / 64 / 50 / 78 / 3 / 3 / 240 / 473 / 44 / 120
Sequence103 / NP_001026768.1| poly(A) binding protein, cytoplasmic 1 [Gallus gallus] / 0.39 / 72 / 89 / 123 / 3 / 2 / 98 / 460 / 329 / 448
Sequence104 / AAH66576.1| Cyclin G1 [Danio rerio] / 0.07 / 86 / 26 / 30 / 4 / 3 / 6 / 95 / 270 / 299
Sequence105 / NP_956341.1| ribosomal protein L7a [Danio rerio] / 0.63 / 88 / 121 / 136 / 2 / 3 / 54 / 461 / 17 / 152
Sequence106 / AAP36470.1| Homo sapiens adaptor-related protein complex 2, sigma 1 subunit [synthetic construct] / 0.53 / 87 / 99 / 113 / 3 / 1 / 121 / 459 / 1 / 113
Sequence107 / NP_001068813.1| retinol dehydrogenase 13 (all-trans/9-cis) [Bos taurus] / 0.37 / 59 / 80 / 135 / 3 / 2 / 5 / 409 / 149 / 282
Sequence108 / NP_001001983.1| phosphatidylinositol 4-kinase, catalytic, alpha polypeptide [Mus musculus] / 0.88 / 93 / 136 / 146 / 5 / 3 / 6 / 443 / 1860 / 2005
Table S2: Codon usage table for the sequences included in the codeml analysis. The table highlights the differential codon usage in the three positions: high A/G in position 1, bias towards T (and C or A) in position 2, and strong C / G bias in position 3.
Codon position / T / C / A / G1 / 0.10345 / 0.19540 / 0.36925 / 0.33190
2 / 0.42529 / 0.25287 / 0.23707 / 0.08477
3 / 0.13937 / 0.32328 / 0.15805 / 0.37931
Figure S1: From our data we can confirm the presence of unique peptides (in red): RD2 (monomer) with peptides: AEVVTPMGIPAEDIPR (at 2+ and 3+), EVVTPMGIPAEDIPR (2+) (see Supplementary Figure 2 for the annotated spectra), RD3-B (dimer) with peptides: AEVVTPMGIPAEEIPNLVGMQVNR (2+ and 3+), GIPAEEIPNLVGMQVNR (2+ and 3+) and IPAEEIPNLVGMQVNR (2+), and the multimer with peptides: NYEDVTTCPGFK (2+) and YEDVTTCPGFK (2+). Additionally, there is one peptide (AEVVTPMGIPAEEIPK) that is shared between the RD1 (monomer) and the RD3-A (dimer), and while not unique to either isoform, it is not present in any other isoform (in purple).
RD1 MKSVVLTGLLFVLLCVDHMSSANKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPKLVGMQVNRAVPLGTTLMPDMVKNYEK
RD2 MKSVVLTGLLFVLLCVDHMSSANKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEDIPRIIGMQVNRAVPLGTTLMPDMVKNYEK
RD3-B MKSVVLTGLLFVLLCVDHMSSANKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPNLVGMQVNRAVPLGTTLMPDMVKNYED
SVVANQLIPINTALTLVMMKAEEVSPKGIPSEEISKLVGMQVNRAVPLGTTLMPDMVKNYEK
RD3-A MKSVVLTGLLFVLLCVDHMSSANKASVVANQLIPINTALTLIMMKAEVVTPMGIPAEEIPKLVGMQVNRAVPLGTTLMPDMVKNYED
SVVANQLIPINTALTLVMMKAEEVSPKGIPAEEIPKLVGMQVNRAVYLDQTLMPDMVKNYEK
MULTI MKSVVLTGLLFVLLCVDHMSSANKASVVANQLIPINTALTLIMMKAKVVTPMGIPAEDIPRIIGMQVNRAVPLGTTLMPDMVKNYED
VTTCPGFKSVVANQLIPINTALTLVMMKAEEVSPKGIPAEEIPKLVGMQVNRAVYLDQTLMPDMVKNYED
GTTCPGIKSVVANQLIPINTALTLVMMKAEEVSPKGIPAEEIPKLVGMQVNRAVYLDQTLMPDMVKNYED
GTTCPGIKSVVANQLIPINTALTLVMMKAEEVSPKGIPAEEIPKLVGMQVNRAVYLDQTLMPDMVKNYED...
Figure S2: Annotated spectra for peptide (a) NYEDVTTCPGFK and (b) AEVVTPMGIPAEDIPR
a)
b)
Figure S3: Maximum-likelihood tree of the phylogenetic relationship between the DNA sequence from the 5 different monomers (labeled with -1, -2, or -3 to distinguish between sequence variants), 2 first units of the dimers and the first unit of the multimer. Bootstrap support is shown at all nodes for which majority consensus is 50% or greater.