Table 2 Genes, Sites, and Specific Fragments Identified in NAH7

Supplemental table. Genes, sites, and specific fragments identified in NAH7

Name / Positiona / Estimated or determinated function of the closest relative / Source bacterium / Protein ID of theclosest relative / Product size ofNAH7/relative / amino acid identity (%)
parA / 1-774 / Putative plasmid partitioning protein ParA / P. putida NCIB9816-4(pDTG1) / AAO64258 / 257/255 / 98
parB / 785-1,711 / Putative plasmid partitioning protein ParB / P. putida NCIB9816-4(pDTG1) / AAO64259 / 308/308 / 97
parR / 1,708-2,055 / Putative partitioning gene repressor protein ParR / P. putida NCIB9816-4(pDTG1) / AAO64260 / 115/113 / 92
parC / 2,052-2,468 / Putative plasmid partitioning protein ParC / P. putida M(pM3) / AAD46125 / 138/141 / 26
rsv / 2,736-3,383 / Putative resolvase / P. putida NCIB9816-4(pDTG1) / AAO64262 / 215/209 / 91
oriV / 3,384-3,837 / Vegetative origin of plasmid replication / P. putida NCIB9816-4(pDTG1) / ---- / ---- / ----
rep / 3,838-4,407 / Plasmid replication-initiation protein Rep / P. putida NCIB9816-4(pDTG1) / AAO64263 / 189/189 / 96
orf1 / 4,447-5,208 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64264 / 253/253 / 90
orf2 / 5,352-5,849 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64265 / 165/165 / 89
orf3 / 5,859-7,127 / Hypothetical protein / P. putida mt-2(pWW0) / CAC86741 / 422/424 / 71
rulB / 7,780-9,063C / Ultraviolet light resistance and DNA polymerase V / P. putida mt-2(pWW0) / CAC86743 / 427/402 / 75
rulA / 9,053-9,481C / Ultraviolet light resistance and DNA polymerase V / P. putida NCIB9816-4(pDTG1) / AAO64309 / 142/131 / 87
orf4 / 9,504-10,079 / Hypothetical protein / P. putida mt-2(pWW0) / CAC86749 / 191/165 / 47
orf5 / 10,076-10,372C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64310 / 98/98 / 94
orf6 / 10,369-10,671C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64311 / 100/100 / 98
orf7 / 10,883-11,101 / Hypothetical protein / P. putida mt-2(pWW0) / CAC86756 / 72/72 / 54
orf8 / 11,692-12,114 / Hypothetical protein / P. putida mt-2(pWW0) / CAC86761 / 140/146 / 40
ssb / 13,489-13,938 / Putative single strand binding protein Ssb / P. putida NCIB9816-4(pDTG1) / AAO64313 / 149/161 / 85
orf9 / 14,193-14,474 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64314 / 93/275 / 94
orf10 / 14,471-15,052 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64314 / 193/275 / 97
orf11 / 15,107-15,529 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64315 / 140/140 / 98
orf12 / 15,553-15,882 / Putative transcriptional regulator protein / P. putida NCIB9816-4(pDTG1) / AAO64316 / 109/109 / 97
orf13 / 16,764-17,129C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64317 / 121/172 / 59
orf14 / 17,273-18,058C / Putative zinc metalloprotease protein / P. putida NCIB9816-4(pDTG1) / AAO64318 / 261/261 / 98
orf15 / 18,196-18,582C / Hypothetical protein / P. putida mt-2(pWW0) / CAC86850 / 128/130 / 67
orf16 / 18,586-19,305C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64320 / 239/239 / 97
traD / 19,302-19,757C / Putative plasmid transfer protein TraD / P. putida NCIB9816-4(pDTG1) / AAO64321 / 151/151 / 84
oriT / 19,758-20,187 / Putative origin of plasmid transfer / P. putida NCIB9816-4(pDTG1) / ---- / ---- / ----
traA / 20,188-20,580 / Putative plasmid transfer protein TraA / P. putida NCIB9816-4(pDTG1) / AAO64322 / 130/130 / 92
traB / 20,573-22,132 / Putative plasmid transfer protein TraB / P. putida NCIB9816-4(pDTG1) / AAO64323 / 519/518 / 97
traC / 22,143-25,079 / Putative plasmid transfer protein TraC / P. putida NCIB9816-4(pDTG1) / AA064324 / 978/981 / 97
orf17 / 25,155-25,904 / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AA064325 / 249/193 / 63
orf18 / 25,934-26,467C / Putative Nudix hydrolase / P. syringae B728a / AAY37705 / 177/175 / 83
IR1 / 26,470-26,507 / IR of Tn4655 (Tn501-like) / ---- / ---- / ---- / ----
orf19 / 26,564-27,592 / Putative aldo/keto reductase protein / Rubrobacter xylanophilus DSM 9941 / EAN36981 / 342/327 / 45
orf20 / 27,752-28,549 / Putative dehydrogenase/reductase protein / Mesorhizobium sp. BNC1 / EAN06915 / 265/280 / 38
IR2 / 28,676-28,711C / Tn21-like IR / ---- / ---- / ---- / ----
---- / 28,712-29,339C / Highly homologous to P. Putida OUS82 / P. putida OUS82 / ---- / ---- / ----
---- / 29,260-29,359C / Tn501 remnant / ---- / ---- / ---- / ----
---- / 29,408-29,630C / Partial sequence of ISPpu2 / ---- / ---- / ----
nahAa / 29,864-30,850 / Reductase component NahAa of naphthalene dioxygenase / P. putida OUS82 / BAA20389 / 328/328 / 96
nahAb / 30,994-31,317 / Ferredoxin component NahAb of naphthalene dioxygenase / P. putida OUS82 / BAA20390 / 107/104 / 96
nahAc / 31,379-32,728 / Iron sulfur protein large subunit NahAc of napthalene dioxygenase / P. fluorescens / AAL07262 / 449/449 / 98
nahAd / 32,743-33,327 / Iron sulfur protein small subunit NahAd of naphthalene dioxygenase / P. putida NCIB9816-4(pDTG1) / AAO64275 / 194/194 / 94
nahB / 33,397-34,176 / Cis-1, 2-dihydro-1, 2-dihydroxynaphtalene-1, 2-dehydrogenase NahB / Pseudomonas sp. ND6(pND6-1) / AAP44290 / 259/275 / 98
nahF / 34,222-35,673 / Salicylaldehyde dehydrogenase NahF / P. putida OUS82 / BAA20394 / 483/483 / 98
nahC / 35,700-36,608 / 1, 2-dihydroxynaphthalene dioxygenase NahC / P. putida OUS82 / BAA20395 / 302/302 / 99
nahQ / 36,705-37,337 / Hypothetical protein NahQ, no known function / P. putida OUS82 / BAA20396 / 210/211 / 95
nahE / 37,386-38,381 / Trans-o-hydroxybenzylidenepyruvate hydratase-aldolase NahE / P. putida OUS82 / BAA20397 / 331/334 / 98
nahD / 38,646-39,257 / 2-hydroxychromene-2-carboxylate isomerase NahD / P. putida OUS82 / BAA20398 / 203/203 / 94
IR3 / 39,627-39,663 / Tn5046-like IR / Pseudomonas sp. LS46-6(pKLH466) / ---- / ---- / ----
---- / 39,701-42,322C / Tn5046tnpA, truncated in N-terminal (broken) / Pseudomonas sp. LS46-6(pKLH466) / ---- / ---- / ----
---- / 42,323-42,790 / Tn5046tnpR, truncated in N-terminal (broken) / Pseudomonas sp. LS46-6(pKLH466) / ---- / ---- / ----
IR4 / 42,793-42,830C / Tn5046-like IR / Pseudomonas sp. LS46-6(pKLH466) / ---- / ---- / ----
---- / 42,835-43,056C / N-terminal sequence of Tnp from IS1328 / ---- / ---- / ---- / ----
nahR / 43,220-44,344C / LysR-type transcriptional activator NahR / P. fluorescens / AAM18544 / 374/300 / 98
nahG / 44,492-45,796 / Salicylate hydroxylase NahG / P. putida NCIB9816-4(pDTG1) / AAO64307 / 434/438 / 92
nahT / 46,293-46,619 / Chloroplast-type ferredoxin NahT / P. putida NCIB9816-4(pDTG1) / AAO64306 / 108/105 / 90
nahH / 46,628-47,551 / Catechol-2, 3-dioxygenase NahH / P. putida NCIB9816-4(pDTG1) / AAO64305 / 307/307 / 92
nahI / 47,586-49,046 / 2-hydroxymuconic semialdehyde dehydrogenase NahI / P. putida NCIB9816-4(pDTG1) / AAO64304 / 486/486 / 95
nahN / 49,054-49,935 / 2-hydroxymuconic semialdehyde hydrolase NahN / P. putida NCIB9816-4(pDTG1) / AAO64303 / 293/293 / 92
nahL / 49,950-50,735 / 2-oxypent-4-enoate hydratase NahL / P. putida NCIB9816-4(pDTG1) / AAO64302 / 261/261 / 98
nahO / 50,755-51,678 / Acetaldehyde dehydrogenase NahO / P. putida NCIB9816-4(pDTG1) / AAO64301 / 307/307 / 97
nahM / 51,690-52,730 / 4-hydroxy-2-oxovalerate aldolase NahM / P. putida NCIB9816-4(pDTG1) / AAO64300 / 346/346 / 97
nahK / 52,727-53,521 / 4-oxalocrotonate decarboxylase NahK / P. putida NCIB9816-4(pDTG1) / AAO64299 / 264/264 / 99
nahJ / 53,576-53,767 / 4-oxalocrotonate tautomerase NahJ / P. putida NCIB9816-4(pDTG1) / AAO64298 / 63/63 / 96
nahX / 53,775-54,197 / Hypothetical protein NahX, no known function / P. putida K82 / AAR03452 / 140/143 / 66
nahY / 54,319-55,935 / Methyl-accepting chemotaxis protein NahY / P. putida NCIB9816-4(pDTG1) / AAO64297 / 538/538 / 95
IR5 / 56,011-56,048 / Tn4653-like IR / P. putida mt-2(pWW0) / ---- / ---- / ----
orf21 / 56,202-56,606 / Hypothetical protein, truncated ORF41 of pWW0 / P. putida mt-2(pWW0) / CAC86771 / 134/226 / 90
orf22 / 56,603-57,187 / Putative transcriptional regulator protein, ORF43 of pWW0 / P. putida mt-2(pWW0) / CAC86772 / 194/194 / 96
---- / 57,277-57,362 / N-terminal sequence of pWW0 ORF44 / P. putida mt-2(pWW0) / ---- / ---- / ----
---- / 57,363-57,880 / C-terminal sequence of pCAR1 ORF76 / P. resinovorans CA10(pCAR1) / ---- / ---- / ----
orf23 / 57,999-58,694 / Putative serine/theronine protein phosphatase / P. resinovorans CA10(pCAR1) / BAC41595 / 262/262 / 93
attI / 58,833-58,951 / Site-specific recombination site / P. resinovorans CA10(pCAR1) / ---- / ---- / ----
orf24 / 59,010-59,417 / Hypothetical protein / P. putida NCIB9816-4 (pDTG1) / AAO64270 / 135/135 / 89
tnpI / 59,414-60,661 / Tyrosine recombinase TnpI / P. resinovorans CA10(pCAR1) / BAC41593 / 416/419 / 96
---- / 60,763-62,034C / pCAR1 ORF72 (broken) / P. resinovorans CA10(pCAR1) / ---- / ---- / ----
---- / 62,124-62,846C / Partial sequence of pCAR1 tnpAa / P. resinovorans CA10(pCAR1) / ---- / ---- / ----
---- / 62,850-62,999C / C-terminal sequence of pcar1 tnpRa / P. resinovorans CA10(pCAR1) / ---- / ---- / ----
---- / 63,000-63,320C / N-terminal sequence of pWW0 ORF45 / P. putida mt-2(pWW0) / ---- / ---- / ----
orf25 / 63,321-64,097C / Putative reductase protein, ORF44 of pWW0 / P. putida mt-2(pWW0) / CAC86773 / 258/258 / 98
orf26 / 64,158-64,742C / Putative transcriptional regulator protein, ORF43 of pWW0 / P. putida mt-2(pWW0) / CAC86772 / 194/194 / 99
orf27 / 64,739-65,419C / Hypothetical protein, ORF41 of pWW0 / P. putida mt-2(pWW0) / CAC86771 / 226/226 / 98
IR6 / 65,548-65,585 / IR of Tn4655 (Tn4653-like) / P. putida mt-2(pWW0) / ---- / ---- / ----
orf28 / 65,681-66,532C / Hypothetical protein / Pseudomonas sp. R9 / AAD47991 / 283/283 / 64
orf29 / 66,544-68,031C / Putative sulfate permease protein / Pseudomonas sp. R9 / AAD47994 / 495/495 / 87
orf30 / 68,550-68,846C / Hypothetical protein / Listeria innocua / CAC96046 / 98/876 / 37
orf31 / 68,860-69,498C / Putative nuclease protein / P. putida NCIB9816-4(pDTG1) / AAO64326 / 212/212 / 95
orf32 / 69,546-70,028C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64327 / 160/160 / 96
orf33 / 70,043-70,648C / Putative nuclease protein / P. putida NCIB9816-4(pDTG1) / AAO64328 / 201/201 / 96
orf34 / 70,638-70,967C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64329 / 109/109 / 91
mpfJ / 70,997-71,902C / Putative mating pair formation protein MpfJ / P. putida NCIB9816-4(pDTG1) / AAO64330 / 301/301 / 88
mpfI / 71,886-72,914C / Putative mating pair formation protein MpfI / P. putida NCIB9816-4(pDTG1) / AAO64331 / 342/342 / 99
mpfH / 72,924-74,207C / Putative mating pair formation protein MpfH / P. putida NCIB9816-4(pDTG1) / AAO64332 / 427/427 / 93
mpfG / 74,210-75,001C / Putative mating pair formation protein MpfG / P. putida NCIB9816-4(pDTG1) / AAO64333 / 263/263 / 95
mpfF / 75,026-75,691C / Putative mating pair formation protein MpfF / P. putida NCIB9816-4(pDTG1) / AAO64334 / 221/221 / 94
mpfE / 75,695-76,558C / Putative mating pair formation protein MpfE / P. putida NCIB9816-4(pDTG1) / AAO64335 / 287/287 / 97
orf35 / 76,546-76,950C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64336 / 134/134 / 91
orf36 / 76,943-77,155C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64337 / 70/70 / 98
mpfD / 77,183-77,866C / Putative mating pair formation protein MpfD / P. putida NCIB9816-4(pDTG1) / AAO64338 / 227/229 / 94
mpfC / 77,866-80,550C / Putative mating pair formation protein MpfC / P. putida NCIB9816-4(pDTG1) / AAO64339 / 894/894 / 98
mpfB / 80,537-80,830C / Putative mating pair formation protein MpfB / P. putida NCIB9816-4(pDTG1) / AAO64340 / 97/97 / 94
mpfA / 80,834-81,295C / Putative mating pair formation protein MpfA / P. putida NCIB9816-4(pDTG1) / AAO64341 / 153/153 / 96
orf37 / 81,312-81,659C / Hypothetical protein / P. putida NCIB9816-4(pDTG1) / AAO64342 / 115/115 / 97

a The letter C indicates that the gene is on the complementary strand.