TABLE 2.
Genes, sites, and specific fragments on pLB1
| Gene | Positiona | Determined or estimated function | % Amino acid identityb | Source | Protein identification no. of closest relative |
|---|---|---|---|---|---|
| repA | 1-783 | Replication protein | 33 (83/245) | Agrobacterium tumefaciens K84 plasmid pAgK84 | YP_086770.1 |
| orf1 | 895-1776 | Putative primase | 38 (111/291) | Novosphingobium aromaticivorans DSM 12444 | ZP_00873452.1 |
| orf2 | 1863-2360 | Putative nuclease | 29 (45/151) | Nitrobacter hamburgensis X14 | ZP_00626575.1 |
| parB1 | 3079-4854 | Putative plasmid stabilization protein | 29 (190/638) | A. tumefaciens K84 plasmid pAgK84 | YP_086769.1 |
| orf3 | 5293-6165 | ArdC-like antirestriction protein | 51 (152/294) | Nitrobacter hamburgensis X14 | ZP_00627826.1 |
| orf4 | 6577-7857 | Fic-like filamentation protein | 37 (70/187) | Xyielia fastidiosa Dixon | ZP_00653050.1 |
| orf5 | 8186-8575 | Conserved hypothetical protein | 35 (47/132) | Rhodobacter sphaeroides 2.4.1 | ABA81614.1 |
| tnpA | 10065-12956C | Tn3 family transposase | 92 (888/964) | Acetobacter aceti plasmid pAC5 | AAF20014.1 |
| —c | 13082-13186 | Resolvase N-terminal fragment | 94 (33/35) | Xanthomonas campestris pv. Vesicatoria strain 85-10 | YP_364058.1 |
| — | 13220-13639 | IS6100 transposase N-terminal fragment | 100 (140/140) | Salmonella entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| — | 13694-14074C | IS6100 transposase C-terminal fragment | 100 (126/126) | S. entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| tnp | 14131-14925C | IS6100 transposase | 100 (264/264) | S. entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| linB | 15264-16154 | 1,4-TCDNd halidohydrolase | 100 (296/296) | Sphingobium indicum B90A | AAR05978.1 |
| tnp | 16314-17108C | IS6100 transposase | 100 (264/264) | S. entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| linB | 17447-18337 | 1,4-TCDN halidohydrolase | 100 (296/296) | S. indicum B90A | AAR05978.1 |
| tnp | 18497-19291C | IS6100 transposase | 100 (264/264) | S. entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| — | 19324-19866 | Resolvase C-terminal fragment | 75 (131/174) | Zymomonas mobilis subsp. mobilisZM4 | AAV90079.1 |
| orf6 | 19898-20206 | Putative inner membrane protein | 56 (55/97) | S. entericaserovar Typhimurium LT2 | NP_463387.1 |
| orf7 | 20187-20519 | Hypothetical protein | 52 (45/86) | Escherichia coli B7A | ZP_00714508.1 |
| — | 20981-21688C | IS4 transposase gene remnant | 67 (161/238) | N. hamburgensis X14 | ZP_00627545.1 |
| orf8 | 22076-22762C | Hypothetical protein | 34 (29/85) | Synechococcus sp. strain CC9605 | YP_381146.1 |
| orf9 | 22790-23551C | Short-chain dehydrogenase | 53 (136/253) | S. indicum B90A | AAR05964.1 |
| tnpA | 23816-26773C | Tn3 family transposase | 69 (682/985) | Gluconobacter oxydans 621H plasmid pG0X1 | YP_190365.1 |
| tnpR | 26832-27506 | Resolvase | 70 (141/199) | Uncultured bacterium plasmid pTB11 | YP_112363.1 |
| — | 27519-28349C | Putative ring-hydroxylating dioxygenase gene remnant | 41 (110/265) | Burkholderia sp. strain 383 | YP_366455.1 |
| tnp | 28381-29175 | IS6100 transposase | 100 (264/264) | S. entericaserovar Typhimurium G8430 plasmid pU302L | AAR05758.1 |
| — | 29230-29751 | Resolvase gene remnant | 89 (150/168) | Pseudomonas syringae pv. Syringae A2 plasmid pPSR1 | NP_940689.1 |
| orf10 | 29754-30278 | Putative acetyltransferase | 29 (47/158) | P. fluorescens Pf-5 | YP_260527.1 |
| — | 30344-30655 | LexA gene remnant | 47 (47/100) | Rhodoferax ferrireducens DSM 15236 | ZP_00695279.1 |
| orf11 | 30666-31928 | Putative UV protection protein | 41 (176/422) | Magnetococcus sp. strain MC-1 | ZP_00607746.1 |
| orf12 | 32290-35097C | Hypothetical protein | 68 (641/935) | Aurantimonas sp. strain SI85-9A1 | ZP_01227946.1 |
| orf13 | 35106-38039C | Putative Type III restriction-modification enzyme | 45 (447/972) | Thermoplasma volcanium GSS1 | NP_111994.1 |
| — | 38039-39613C | Adenine-specific DNA methylase C-terminal fragment | 50 (270530) | Azotobacter vinelandii AvOP | ZP_00416345.1 |
| tnp | 39630-40952C | IS5 family transposase | 62 (260/418) | Desulfovibrio desulfuricans G20 | YP_390215.1 |
| — | 41057-41551C | Adenine-specific DNA methylase N-terminal fragment | 49 (90/183) | A. vinelandii AvOP | ZP_00416345.1 |
| orf14 | 41607-41945C | Plasmid maintenance system antidote protein | 85 (87/102) | Rhodospirillum rubrum | ZP_00270380.1 |
| orf15 | 41949-42239C | Plasmid maintenance system killer protein | 82 (79/96) | N. hamburgensisX14 | ZP_00624977.1 |
| orf16 | 44188-44445C | XRE family transcriptional regulator | 41 (25/60) | Rhizobium sp. strain NGR234 plasmid pNGR234a | NP_443819.1 |
| — | 44697-44897 | RNA polymerase sigma 70 factor fragment | 44 (30/67) | Thermosynechococcus elongatus BP-1 | NP_681289.1 |
| rsv | 45325-46023 | Resolvase | 70 (153/217) | Plasmid RP4 | AAA26414.1 |
| ssb | 46417-46731 | Single-strand binding protein | 50 (52/103) | N. hamburgensis X14 | ZP_00627857.1 |
| orf17 | 46789-47091 | Putative transcriptional regulator | 40 (34/85) | Sphingopyxis alaskensis RB2256 | ZP_00579357.1 |
| parA | 47479-48237 | ParA-like partition protein | 28 (67/235) | Sinorhizobium meliloti MBA19 plasmid pMBA19a | AAX19280.1 |
| parB2 | 48234-49253 | ParB-like partition protein | 30 (73/242) | Bradyrhizobium sp. strain BTAi1 | ZP_00864437.1 |
| oriT | 49254-49443 | Putative oriT region | |||
| mobC | 49444-49995 | MobC-like protein | 28 (47/163) | Bradyrhizobium sp. strain BTAi1 | ZP_00864438.1 |
| virD2 | 49982-51049 | Relaxase | 32 (104/320) | Aeromonas punctata HGB5 plasmid pFBAOT6 | YP_067824.1 |
| orf18 | 51526-52734C | Putative DNA primase | 28 (58/202) | X. fastidiosa 9a5c plasmid pXF51 | NP_061673.1 |
| virD4 | 52724-54640C | VirD4 type IV secretion protein | 45 (257/569) | Bradyrhizobium sp. strain BTAi1 | ZP_00864242.1 |
| virB11 | 54618-55610C | VirB11 type IV secretion protein | 62 (201/324) | Bradyrhizobium sp. strain BTAi1 | ZP_00864241.1 |
| virB10 | 55607-56782C | VirB10 type IV secretion protein | 38 (143/371) | Mesorhizobium sp. strain BNC1 | ZP_00614245.1 |
| virB9 | 56877-57719C | VirB9 type IV secretion protein | 38 (108/279) | R. etli CFN42 plasmid p42d | NP_659886.1 |
| virB8 | 57716-58399C | VirB8 type IV secretion protein | 44 (97/220) | S. meliloti 1021 plasmid pSymA | NP_435958.1 |
| orf19 | 58447-58620C | Hypothetical protein | |||
| virB6 | 58740-59756C | VirB6 type IV secretion protein | 28 (95/336) | A. tumefaciensstrain C58 plasmid AT | NP_535541.1 |
| orf20 | 59797-60102C | Hypothetical protein | |||
| virB5 | 60105-60818C | VirB5 type IV secretion protein | 36 (80/217) | R. etli CFN42 plasmid p42d | NP_659890.1 |
| virB4 | 60832-63216C | VirB4 type IV secretion protein | 51 (402/777) | R. etli CFN42 plasmid p42d | NP_659891.1 |
| virB3 | 63203-63547C | VirB3 type IV secretion protein | 43 (42/96) | Bartonella henselae strain Houston-1 | YP_034052.1 |
| virB2 | 63554-63895C | VirB2 type IV secretion protein | 38 (38/99) | Mesorhizobium sp. strain BNC1 | ZP_00614254.1 |
| virB1 | 63917-64582C | VirB1 type IV secretion protein | 47 (80/169) | X. fastidiosa 9a5c plasmid pXF51 | NP_061658.1 |
| orf21 | 64597-64920C | Hypothetical protein | 48 (38/79) | S. meliloti 1021 plasmid pSymA | NP_435966.1 |
| oriV | 64921-65998 | Putative oriV region |
a
The letter C indicates that the gene is carried on the complementary strand.
b
Values in parentheses refer to numbers of identical amino acids per the number examined.
c
—, probable gene remnant.
d
TCDN, 1,3,4,6-tetrachloro-1,4-cyclohexadiene.