Table 1. Genes required for M. xanthus fruiting body development.
| MXAN Locus Tag | Protein Product | Function | Codon Bias1 | Phylogeny2 | Code3 |
| 0581 | InfC | Translation initiation factor | 0.038 | Delta Proteobacteria | S |
| 0733 | RodK | Sensor histidine kinase | Delta Proteobacteria | S | |
| 1014 | SdeK | Sensor histidine kinase | Delta Proteobacteria | S | |
| 1020 | Hypothetical | Delta Proteobacteria | |||
| 1078 | Nla19 | Sigma 54-dependent response regulator | Delta Proteobacteria | S | |
| 1167 | Nla28 | Sigma 54 dependent response regulator | Delta Proteobacteria | S | |
| 1294 | CsgA | C-signal | Delta Proteobacteria | S | |
| 1402 | LadA | Transcription factor | Actinobacteria | S | |
| Planctomyces | |||||
| 1450 | Oar | TonB-dependent receptor | Delta Proteobacteria | S | |
| 2044 | Pph1 | Ser/Thr protein phosphatase | Delta Proteobacteria | S | |
| 2670 | AsgA | A-signal production | Alpha Proteobacteria | S | |
| Cyanobacteria | |||||
| 2778 | PhoP2 | DNA binding response regulator | Delta Proteobacteria | S | |
| 2779 | PhoR2 | Sensor histidine kinase | Delta Proteobacteria | S | |
| 2905 | DofA | Hypothetical | Unique | ||
| 2913 | AsgB | DNA binding protein | Delta Proteobacteria | S | |
| 3117 | FruA | CsgA-dependent response regulator | Delta Proteobacteria | S | |
| 3204 | RelA | Stringent response | Delta Proteobacteria | ||
| 3213 | ActA | CsgA regulator | Delta Proteobacteria | S | |
| 3214 | ActB | Sigma 54-dependent response regulator | Delta Proteobacteria | S | |
| 3225 | FrgA | Polysaccharide export | Delta Proteobacteria | ||
| 3692 | Nla18 | Sigma 54-dependent response regulator | Delta Proteobacteria | S | |
| 3993 | BsgA/Lon | ATP-dependent protease | Delta Proteobacteria | S | |
| 4016 | Pfk1 | 6-phosphofructokinase | Delta Proteobacteria | E | |
| 4017 | Pkn4 | Ser/The protein kinase | Delta Proteobacteria | S | |
| 4042 | Nla6 | Sigma 54 dependent response regulator | Delta Proteobacteria | S | |
| 4138 | FrzF | Protein methyl transferase | Delta Proteobacteria | S | |
| 4139 | FrzG | Protein methyl esterase | Delta Proteobacteria | S | |
| 4140 | FrzE | Chemotaxis histidine kinase | Delta Proteobacteria | S | |
| 4141 | FrzCD | Chemotaxis receptor | Delta Proteobacteria | S | |
| 4142 | FrzB | Hypothetical | Unique | ||
| 4143 | FrzA | Hypothetical | Delta Proteobacteria | ||
| 4144 | FrzZ | Response regulator | Delta Proteobacteria | S | |
| 4146 | AldA | Alanine dehydrogenase | Firmicutes | E | |
| 4149 | FrzS | Response regulator | Delta Proteobacteria | S | |
| 4486 | FruE | Hypothetical | 0.064 | Unique | |
| 4564 | Esg | Branched chain keto acid dehydrogenase | Delta Proteobacteria | E | |
| 4565 | Esg | Branched chain keto acid dehydrogenase | Delta Proteobacteria | E | |
| 4621 | RfbC/SasA | Glycosyl transferase | Actinobacteria | E | |
| Firmicutes | |||||
| 4778 | PhoR1 | Sensor histidine kinase | Delta Proteobacteria | S | |
| 4787 | PhoP4 | DNA-binding response regulator | Unclassified Proteobacteria | S | |
| 5123 | MrpA | Sensor histidine kinase | Delta Proteobacteria | S | |
| 5124 | MrpB | Sigma 54-dependent response regulator | Delta Proteobacteria | S | |
| 5125 | MrpC | Transcription factor | Planctomyces | S | |
| Actinobacteria | |||||
| 5766 | TPR domain protein | Delta Proteobacteria | |||
| 5772 | PilQ | Type IV pilus | Delta Proteobacteria | ||
| 5775 | PilN | Type IV pilus | Delta Proteobacteria | ||
| 5776 | PilM | Type IV pilus | Delta Proteobacteria | ||
| 5780 | PilI | Efflux ABC permease | Delta Proteobacteria | ||
| 5786 | PilC | Type IV pilus assembly protein | Delta Proteobacteria | ||
| 5788 | PilB | Type IV pilus assembly ATPase | Delta Proteobacteria | ||
| 5870 | SigE | Sigma factor | Delta Proteobacteria | ||
| 6307 | FbdB | Chloride channel | Delta Proteobacteria | ||
| 6413 | PhoP3 | DNA binding response regulator | Delta Proteobacteria | S | |
| 6414 | PhoR3 | Sensor histidine kinase | Delta Proteobacteria | S | |
| 6692 | DifE | Chemosensory histidine kinase | Delta Proteobacteria | S | |
| 6694 | DifC | CheW-like coupling protein | Delta Proteobacteria | S | |
| 6696 | DifA | Chemotaxis receptor | Delta Proteobacteria | S | |
| 6699 | FbdA | Thiol oxidoreductase | Gamma Proteobacteria | E | |
| 6704 | Acetyl transferase | Delta Proteobacteria | E | ||
| 6855 | MokA | Hybrid sensor kinase/response regulator | Delta Proteobacteria | S | |
| 6889 | HthA | LuxR family transcriptional regulator | Delta Proteobacteria | S | |
| 6890 | HthB | DNA-binding protein | Delta Proteobacteria | S | |
| 6996 | AsgD | Sensor histidine kinase/response regulator | Delta Proteobacteria | S | |
| 7261 | DevS | Hypothetical | Cyanobacteria | ||
| 7262 | DevR | Hypothetical | Spirochetes | ||
| 7263 | DevT | Hypothetical | Cyanobacteria | ||
| Spirochetes | |||||
| 7324 | FapA | Hypothetical | Unique | ||
| 7415 | EpsZ | Glycosyl transferase | Delta Proteobacteria | E | |
| 7421 | EpsV | Chain length determinant family protein | Delta Proteobacteria | ||
| 7422 | EpsU | Glycosyl transferase | Chloroflexi | E | |
| 7433 | EpsO | Von Willebrand factor type A domain protein | Alpha Proteobacteria | ||
| 7438 | EpsK | Metal resistance protein | Gamma Proteobacteria | ||
| 7440 | EpsI/Nla24 | Sigma 54-dependent response regulator | Delta Proteobacteria | S | |
| 7441 | EpsH | Glycosyl transferase | Alpha Proteobacteria | E | |
| 7445 | EpsE | Glycosyl transferase | Alpha Proteobacteria | E | |
| 7448 | EpsD | Glycosyl transferase | Delta Proteobacteria | E | |
| 7450 | EpsB | Glycosyl hydrolase | Firmicutes | E | |
| 7451 | EpsA | Glycosyl transferase | Delta Proteobacteria | E |
1
Codon bias was determined using the software available at the Computational Microbiology Laboratory http://www.cmbl.uga.edu/software.html. The larger the number the greater the deviation from normal M. xanthus codon usage. Genes with no entries have a codon bias consistent with other M. xanthus genes.
2
tBLASTn algorithm was used to identify the four most closely related homologs. Each gene was classified as δ Proteobacteria if at least one of the four top homologs belongs to an organism in that group. Gene was classified as unique based on a 1e−10 cutoff. Gene was classified as ‘other’ if the closest four homologs belonged to another phylogenetic group.
3
Code refers to the classification category. Proteins known to be involved in signal production or sensory transduction are denoted with an ‘S’. The remaining genes were examined for a putative enzymatic function in the annotation, which is indicated by an ‘E’