TABLE 2.
Genes and corresponding products isolated from S. herbicidovorans MH
| Plasmid | ORFa | Position (nt)b | Probable function or product | Homologous proteinc | Source | Reference accession no. | % Amino acid identityd | No. of amino acidse |
|---|---|---|---|---|---|---|---|---|
| pMec10 | tnpA | 226-374 | Transposase | TnpA | Ralstonia sp. strain JS705 | CAD60927 | 87 (352/403) | 403/414 |
| rdpA | 1733-2620 | (R)-Dichlorprop/α-ketoglutarate dioxygenase | RdpA | D. acidovorans MCI | AAM90962 | 100 (295/295) | 295/295 | |
| pMec16 | (tnpA) | (1-447) | Transposase (C terminus) | Transposase | Ralstonia sp. JS705 | CAD60927 | 79 (117/148) | -/414 |
| sdpA | 750-1613 | (S)-Dichlorprop/α-ketoglutarate dioxygenase | SdpA | D. acidovorans MCI | AAM90963 | 58 (171/290) | 287/292 | |
| pMec25 | (cadR) | (1-972) | Transcriptional regulator | CadR | Bradyrhizobium sp. HW13 | BAB78520 | 65 (181/276) | -/336 |
| ORF2 | 1062-2627f | Outer membrane receptor protein | COG1629 | Novosphingobium aromaticivorans | ZP_00096178 | 26 (129/488) | 521/743 | |
| tfdB | 2654-4453 | Dichlorophenol hydroxylase | TfdB | D. acidovorans MC1 | AAM76774 | 57 (334/585) | 600/586 | |
| pMec4 (cluster I) | (dccE) | (1-247) | (Partial) maleylacetate reductase | TfdF | Burkholderia cepacia | AAK81685 | 53 (42/78) | -/357 |
| dccAI | 514-1350 | Chlorocatechol 1,2-dioxygenase | TfdC | R. eutropha JMP134(pJP4) | P05403 | 53 (134/255) | 278/255 | |
| dccDI | 1293-2015 | Dienelactone hydrolase | TfdEII | R. eutropha JMP134(pJP4) | P94136 | 47 (106/222) | 240/235 | |
| pMec2 + 12 (cluster II) | tfdK | 595-1968 | Putative transport protein | TfdK | R. eutropha JMP134(pJP4) | AAC44725 | 36 (159/440) | 457/463 |
| (orfB) | 2494-2865g | ISCc3 transposase orfB (C terminus) | ISCc3 transposase OrfB | Caulobacter crescentus CB15 | NP_419441 | 65 (81/123) | -/326 | |
| dccAII | 3320-4087 | Chlorocatechol 1,2-dioxygenase | TfdC | R. eutropha JMP134(pJP4) | BAA74530 | 51 (125/242) | 256/251 | |
| (dccDII) | 4100-(4705) | (Interrupted dienelactone hydrolase) | TfdEII | R. eutropha JMP134(pJP4) | P94136 | 50 (88/173) | -/235 | |
| (tnpA) | (5161-4677) | Transposase (C terminus) | TnpA of IS6100 | Salmonella enterica subsp. | AAG03007 | 100 (156/156) | -/264 |
Incomplete ORFs are set in parentheses.
The position is given respectively to the nucleotides of the plasmid insert.
Given is the most similar protein identified by BLASTX.
The values in parentheses refer to the number of identical amino acids over the aligned region.
The number of amino acids of the protein in S. herbicidovorans MH is given first, and the number of the reference protein is given second.
The exact start position of the ORF could not be determined. Other possible start codons are at nucleotides 969, 1185, and 1290.
The nucleotide region represents the part that is similar to the C terminus of outer membrane proteins, since no start codon was found upstream of position 2494, and at nucleotide 2389, a stop codon is encoded.