TABLE 1.
Gene clusters detected as significantly associated with Psychrobacter ecotype based on a pangenome-wide association analysisa
| Gene cluster | Paralogsb | Predicted gene name | KEGG KO | COG category | eggNOG annotation | No. of FE strains | No. of RE strains | % FE strains | % RE strains |
|---|---|---|---|---|---|---|---|---|---|
| GC00000020 | GC00000020_1 | merA | K00382, K00383, K00520 | C | Mercuric reductase | 0 | 1 | 0 | 2 |
| GC00000020 | GC00000020_2 | merA | K00382, K00383, K00520 | C | Mercuric reductase | 4 | 4 | 15 | 7 |
| GC00000020 | GC00000020_3 | lpd | K00382 | C | Dihydrolipoamide dehydrogenase | 2 | 1 | 8 | 2 |
| GC00000020 | GC00000020_4 | lpd | K00382 | C | Dihydrolipoamide dehydrogenase | 1 | 0 | 4 | 0 |
| GC00000020 | GC00000020_5 | lpd | K00382 | C | Dihydrolipoamide dehydrogenase | 25 | 59 | 96 | 100 |
| GC00000020 | GC00000020_6*** | lpdA | K00382, K00383 | C | Dihydrolipoamide dehydrogenase | 9 | 53 | 35 | 90 |
| GC00000020 | GC00000020_7 | K00383 | C | Pyridine nucleotide-disulfide oxidoreductase | 0 | 3 | 0 | 5 | |
| GC00000020 | GC00000020_8 | sthA | K00322, K00382, K17883 | C | Conversion of NADPH to NADH | 26 | 59 | 100 | 100 |
| GC00000020 | GC00000020_9 | gor | K00383 | O | Glutathione reductase | 23 | 46 | 88 | 78 |
| GC00000020 | GC00000020_10 | lpdG | K00382 | C | Dihydrolipoyl dehydrogenase | 26 | 59 | 100 | 100 |
| GC00001343 | GC00001343_1 | K16137 | K | TetR family transcriptional regulator | 0 | 1 | 0 | 2 | |
| GC00001343 | GC00001343_2 | K16137 | K | Transcriptional regulator | 0 | 1 | 0 | 2 | |
| GC00001343 | GC00001343_3 | K16137 | K | TetR family transcriptional regulator | 3 | 0 | 12 | 0 | |
| GC00001343 | GC00001343_4 | K16137, K19335 | K | Transcriptional regulator TetR family | 1 | 0 | 4 | 0 | |
| GC00001343 | GC00001343_5 | K16137, K19335 | K | Transcriptional regulator TetR family | 5 | 16 | 19 | 27 | |
| GC00001343 | GC00001343_6*** | K16137, K19335 | K | Transcriptional regulator TetR family | 5 | 52 | 19 | 88 | |
| GC00001837 | GC00001837_1*** | S | Ig domain protein group 1 domain protein | 1 | 11 | 4 | 19 | ||
| GC00001837 | GC00001837_r1_1 | S | Ig domain protein group 1 domain protein | 1 | 0 | 4 | 0 | ||
| GC00001837 | GC00001837_r1_r1_1 | S | Ig domain protein group 1 domain protein | 12 | 26 | 46 | 44 | ||
| GC00001839 | GC00001839_1 | X | 1 | 0 | 4 | 0 | |||
| GC00001839 | GC00001839_r1_1*** | X | 6 | 47 | 23 | 80 | |||
a
Gene cluster refers to a group of protein-coding gene sequences with distant sequence homology which may be either orthologs or paralogs, while paralog refers to subsets within the gene cluster identified as exact gene matches.
b
***, the paralogs identified as significantly associated with ecotype by the pangenome-wide association software treeWAS.