Table 1.
FnrL directly regulated genes based on ChIP-seq signal with corresponding RNA-seq expression change that also contain a consensus binding sequence
| Locus ID | Gene Name | Description | Recognition Sequence | Enrichment | Regulation | Fold Change |
|---|---|---|---|---|---|---|
| COG C: Energy production and conversion | ||||||
| RCC01157 | ccoN | cbb 3-type cytochrome c oxidase subunit I | TTGATCAAGGTCAAb | 25 | + | 1.55 |
| RCC01157 | ccoN | cbb 3-type cytochrome c oxidase subunit I | ATGATGTCGATCAAa | 25 | + | 1.55 |
| RCC00728 | NnrU family protein | NnrU family protein | CTGCCGCAGATCAAa | 4 | + | 1.47 |
| RCC00732 | sdhD | succinate dehydrogenase | ATGATGAGCGTCAAb | 3 | + | 1.41 |
| RCC00022 | Oxidoreductase | oxidoreductase | ATGATTTACCGCAAa | 5 | + | 1.38 |
| COG E: Amino acid transport and metabolism | ||||||
| RCC01724 | speB1 | agmatinase | TTGATCTGCGTCAAb | 10 | + | 1.33 |
| COG F: Nucleotide transport and metabolism | ||||||
| RCC00400 | pyrB | aspartate carbamoyltransferase | CTGACGCAGATCAAa | 10 | + | 1.47 |
| COG G: Carbohydrate transport and metabolism | ||||||
| RCC00731 | sdhC | succinate dehydrogenase, cytochrome b556 subunit | ATGATGAGCGTCAAa | 3 | + | 1.53 |
| COG I: Lipid transport and metabolism | ||||||
| RCC00480 | rpsU | 30S ribosomal protein S21 | CTGATGCAACTCAAb | 4 | + | 1.57 |
| COG J: Translation, ribisomal tructure and biogenesis | ||||||
| RCC01495 | fusA | translation elongation factor G | TTGGCATGGGTCAAb | 17 | + | 3.48 |
| COG L: Replication, recombination and repair | ||||||
| RCC03240 | ATPase AAA | K01144 exodeoxyribonuclease V | ATGCGCCAGATCAAa | 4 | - | -1.34 |
| RCC02193 | DNA-3-methyladenine glycosylase II | K01247 DNA-3-methyladenine glycosylase II | ATGACGCGGATCAAa | 4 | - | –1.97 |
| COG M: Cell wall/membrane/envelope biogenesis | ||||||
| RCC02479 | lipoprotein | lipoprotein | CTGATGCAGCGCAAb | 13 | + | 1.42 |
| COG N: Cell motility | ||||||
| RCC00481 | mcpI | methyl-accepting chemotaxis protein McpI | CTGACCGAGATCAAa | 4 | - | –1.53 |
| RCC03524 | flagellar FlaF family protein | K06602 flagellar protein FlaF | CTGATCGACATCAAa | 4 | - | –1.87 |
| RCC03523 | flbT | flagellin synthesis repressor protein FlbT | CTGATCGACATCAAb | 4 | - | –2.14 |
| COG O: Post-translational modification, protein turnover, and chaperones | ||||||
| RCC01156 | UspA domain-containing protein | UspA domain-containing protein | TTGACGCGGATCAAb | 26 | + | 5.21 |
| RCC01723 | ccpA | cytochrome-c peroxidase | TTGATCTGCGTCAAb | 10 | + | 3.81 |
| RCC02829 | hypothetical protein | K03699 putative hemolysin | TTGACCCTCGTCAAa | 6 | - | –1.64 |
| COG R: General function prediction only | ||||||
| RCC02684 | polyphosphate kinase 2 | polyphosphate kinase 2 | TTGATGCGTGTCAAb | 14 | + | 2.25 |
| RCC02665 | hemolysin-type calcium-binding | hemolysin-type calcium-binding | ATGACCGGCGTCAAa | 9 | + | 1.46 |
| COG S: Function unknown | ||||||
| RCC00435 | hypothetical protein | hypothetical protein | CTGACCCAGATCAAb | 21 | + | 9.19 |
| RCC00901 | hypothetical protein | hypothetical protein | TTGACACGGGTCAAb | 10 | + | 6.87 |
| RCC00747 | hypothetical protein | hypothetical protein | ATGACGCAGATCAAb | 5 | + | 3.78 |
| RCC00424 | hypothetical protein | hypothetical protein | ATGATTCAGATCAAb | 20 | + | 3.51 |
| RCC02321 | hypothetical protein | hypothetical protein | ATGATCCGGATCAAb | 26 | + | 2.17 |
| RCC02988 | hypothetical protein | hypothetical protein | TTGACCCAGATCAAb | 8 | - | –1.41 |
| RCC01027 | hypothetical protein | hypothetical protein | TTGACCAAGGTCAAb | 6 | - | –1.64 |
| COG T: Signal transduction mechanisms | ||||||
| RCC02849 | dorS | DMSO/TMAO-sensor hybrid histidine kinase | TTGATCGGGATCAAa | 26 | + | 4.53 |
| RCC02590 | dksA | DnaK suppressor protein | TTGATTCAGGTCAAb | 28 | + | 1.79 |
| COG X: Photosynthesis | ||||||
| RCC00667 | aerR | regulatory CrtJ antirepressor AerR | ATGCTCGAGTTCAAb | 8 | + | 1.39 |
| RCC00666 | bchF | 2-vinyl bacteriochlorophyllide hydratase | ATGACATGGGTCAAb | 8 | + | 1.39 |
Recognition sequences were determined using MEME server
aSequence is found within the coding region of the gene
bSequence is found in the upstream intergenic or promoter region