Table 2. Annotated genes that are absent or possibly pseudogenes in the other genome.
| Category | Genbank accession | Gene length (AA) | Annotation | Function description |
|---|---|---|---|---|
| UCYN-A1 genes that are possible pseudogenes in UCYN-A2 | YP_003421868 | 159 | Peroxiredoxin | Protein related to alkyl hydroperoxide reductase |
| YP_003421145 | 167 | Restriction endonuclease | Defense | |
| YP_003421558 | 207 | HAS barrel domain protein | Domain in ATP synthases | |
| YP_003421659 | 398 | NurA domain-containing protein | NurA domain, endo- and exonucleases | |
| YP_003421689 | 103 | NifZ domain-containing protein | N2 fixation, nif operon | |
| YP_003422000 | 318 | Transcriptional regulator, GntR family | Transcription factors, possibly regulation of primary metabolism | |
| YP_003422259 | 554 | Predicted ATPase | Function unknown | |
| YP_003422147 | 462 | NAD-dependent aldehyde dehydrogenase | 17 Kegg pathways, aldehyde substrates, various functions | |
| YP_003421484 (3) | 369 | Glycerol dehydrogenase-like oxidoreductase | Glycerolipid metabolism, possibly involved in fermentation | |
| YP_003421571 (2) | 236 | Phosphopantetheinyl transferase | Pantothenate and CoA biosynthesis | |
| YP_003421341 (2) | 812 | Uncharacterized domain HDIG-containing protein | Predicted membrane-associated HD superfamily hydrolase | |
| YP_003421605 (2) | 1081 | Carbamoyl-phosphate synthase large subunit | Pyrimidine synthesis | |
| YP_003421764 (5) | 884 | Fe-S oxidoreductase | Diverse reactions, energy production/conversion | |
| YP_003422257 (2) | 457 | Predicted membrane protein | Function unknown | |
| YP_003421792 (3) | 749 | Copper/silver-translocating P-type ATPase | Transmembrane protein, inorganic ion transport and metabolism | |
| YP_003422189 (2) | 514 | Lysyl-tRNA synthetase (class II) | Translation, ribosomal structure and biogenesis | |
| UCYN-A2 genes absent in UCYN-A1 | KFF41946 | 371 | Predicted membrane protein | Function unknown |
| KFF42131 | 430 | Glucosylglycerol phosphatase (EC 3.1.3.69) | Osmoprotectant synthesis | |
| KFF41831 | 236 | Tellurite resistance protein | Contains C-terminal domain of Mo-dependent nitrogenase | |
| KFF41325 | 208 | Thymidylate kinase | Pyrimidine metabolism, DNA synthesis | |
| KFF41279 | 347 | Cell shape-determining protein, MreB/Mrl family | Cytoskeleton synthesis, cell shape determination | |
| KFF41280 | 248 | Rod shape-determining protein MreC | Cytoskeleton synthesis, cell shape determination | |
| KFF41281 | 186 | Rod shape-determining protein MreD | Cytoskeleton synthesis, cell shape determination | |
| KFF41062 | 427 | Folate/biopterin transporter | Membrane transport | |
| KFF40998 | 165 | 2TM domain | Function unclear, transmembrane alpha helixes | |
| KFF41013 | 56 | Sigma-70, region 4 | DNA directed RNA polymerase | |
| KFF41656 | 344 | Folate-binding protein YgfZ | Predicted aminomethyltransferase, possibly glycine synthesis | |
| KFF41014 | 63 | Sigma-70 region 3 | DNA directed RNA polymerase | |
| KFF40922 | 215 | Peroxiredoxin | Detoxification of active oxygen species such as H2O2 | |
| KFF41590 | 231 | Zn-dependent hydrolases, including glyoxylases | Pyruvate metabolism | |
| KFF40927 | 277 | Tetratricopeptide repeat/TPR repeat | Unclear function- involved in chaperone, cell-cycle, transciption, and protein transport complexes | |
| KFF41183 | 94 | RNA-binding proteins (RRM domain) | Function unclear | |
| UCYN-A2 genes that match | KFF41758 | 38 | Cytochrome B6-F complex subunit 5 | Photosynthesis, connects PSI and PSII in e- transport chain |
| unannotated ORFs in UCYN-A1 | KFF41141 | 64 | LSU ribosomal protein L33P | Structural constituent of ribosome |
| KFF41382 | 470 | Hemolysins and related proteins containing CBS domains | Membrane protein, regulate activity of associated enzymatic transporters | |
| UCYN-A2 genes that are possible pseudogenes in UCYN-A1 | KFF41284 | 211 | Uncharacterized protein, similar to the N-terminal domain of Lon protease | Proteolysis |
| KFF41208 | 165 | Predicted RNA-binding protein | General function prediction only | |
| KFF41109 | 86 | Glutaredoxin-like domain (DUF836) | Domain of unknown function | |
| KFF41037 | 267 | Helix-turn-helix domain | DNA binding, gene expression regulation | |
| KFF40997 (2) | 461 | Domain of unknown function (DUF697) | Function unknown | |
| KFF41565 (2) | 301 | CAAX protease self-immunity | Probably protease, transmembrane protein | |
| KFF41236 (2) | 396 | Glycosyltransferases involved in cell wall biogenesis | Cell wall/membrane/envelope biogenesis | |
| KFF42055 (2) | 350 | UDP-N-acetylglucosamine-N-acetylmuramylpentapeptide N-acetylglucosamine transferase | Cell wall/membrane/envelope biogenesis | |
| KFF41265 (2) | 294 | Competence/damage-inducible protein CinA C-terminal domain | Transformation | |
| KFF41488 (2) | 196 | Putative translation factor (SUA5) | Translation, ribosomal structure and biogenesis | |
| KFF41875 (2) | 140 | Predicted endonuclease involved in recombination (possible Holliday junction resolvase in Mycoplasma and Bacillus subtilis) | Replication, recombination and repair | |
| KFF41338 (2) | 600 | Subtilisin-like serine proteases | Proteolysis or cell motility | |
| KFF42033 (2) | 385 | Phosphate ABC transporter substrate-binding protein, PhoT family (TC 3.A.1.7.1) | Inorganic ion transport and metabolism |
The table also shows three annotated genes in UCYN-A2 that match unannotated regions in UCYN-A1. This table does not list hypothetical proteins, which account for another 25 UCYN-A1 genes that match pseudogenes in UCYN-A2, 15 genes unique in UCYN-A2, 13 genes that match pseudogenes in UCYN-A1 and 2 genes that match unannotated open reading frames in UCYN-A1 (Supplementary Table 1). Where given, the numbers in brackets next to the gene IDs depict the number of consecutive annotated partial genes in the other genome aligned to this particular gene sequence.