TABLE 2.

Biologically relevant reading frames

Gene nameCoordinates and directionaSize (no. of residues)GC (%)Most closely related gene product (EMBL accession no. of sequence)bProduct identity (%)Proposed function
istA-1 434-143833454IstA of IS1326, e.g., on Tn21 (AF071413 )100Transposition, 5′ truncated, presumed inactive
istB-1 1425-221026150IstB of IS1326, e.g., on Tn21 (AF071413 )100Transposition, presumed inactive
orf5 2386-2886 c16665Orf5 in 3′ conserved region of integron, e.g., In2 on Tn21 (AF071413 )100Not known; conserved in integrons
sul1 3014-3853 c27962Sul1 in 3′ conserved region of integron, e.g., In2 on Tn21 (AF071413 )100Sulfonamide resistance, conserved in integrons
qacEΔ12847-4194 c11550QacEΔ1 in 3′ conserved region of integron, e.g., In2 on Tn21 (AF071413 )100Minimal resistance to quaternary ammonium compounds
aadA5 4400-5188 c26258AadA5, integron cassette (e.g., AF137361 )100Streptomycin and spectinomycin resistance
aac(3)-I 5293-5757 c15455Aac(3)-I, integron cassette (AF318077 )95Gentamicin resistance
intI1 5909-692233761IntI1 in 5′ conserved region of integron, e.g., In2 on Tn21 (AF071413 )100Gene cassette integration
tnpA-1 7270-7836 c18867DNA recombinase of composite transposon on pFBAOT6 (CR376602 )c100Transposition
ofn10 7935-81868363Unannotated open reading frame on pFBAOT6 (CR376602 )100Unknown
ofn11 8347-8769 c14063No significant protein matchesUnknown
ofn12 8766-9248 c1605672% DNA identity to region of Xylella fastidiosa (AE003901 )-Unknown
repB 9366-10238, 30756-30944 c35365C-terminus of polyprotein of pRAS3.2 (AY043299 ); equivalent to RepB in other IncQ-like plasmids97Primase of IncQ replicon; not required by Rms149, interrupted by Tn1011
istB-2 10370-11110 c24657IstB on pB4 (AJ431260 )52Transposition
istA-2 11107-12657 c51659IstA on pB4 (AJ431260 )45Transposition
ofn15 13350-1435133358No significant matchesUnknown
tnpA-2 14727-15707 c32660Transposases, e.g., TnpA3 of ISPre2 on pCAR-1 (AB088420 )95Transposition
hlyB 14559-14579, 15776-1791471961Hemolysin export, ABC transporter protein of Photorhabdus luminescens subsp. laumondii (BX571861 )80Toxin secretion ABC transporter protein-ISPa16 insertion, presumed inactive
hlyD 17911-1932647163Hemolysin export, membrane fusion protein of Photorhabdus luminescens subsp. laumondii (BX571861 )64Toxin secretion, presumed inactive
hlyH 19362-2066943556Probable glycosyltransferase of Chromobacterium violaceum (AE016911 )62Possible glycosyltransferase, presumed inactive
hlyI 20656-2142925743No significant matchesToxin pathway related? presumed inactive
hlyJ 21414-30608306458Putative hemolysin, Ralstonia solanacearum (AL646058 ) (after removing annotated IS)41Putative hemolysin, presumed inactive
mobA 30687-32492 c60161N-terminus of polyprotein of pRAS3.2 (AY043299 ); equivalent to MobA in other IncQ-like plasmids87Mobilization presumed functional; reads in to Tn1011
mobB 32542-32853 c10358MobB, IncQ-like plasmids, e.g. pTF-FC2 (M57717 ) (unannotated in this plasmid)92Mobilization
mobC 33165-3352111855MobC, IncQ-like plasmids, e.g., pRAS3.2 (AY043299 )98Mobilization
mobD 33534-3421722753MobD, IncQ-like plasmids, e.g., pRAS3.2 (AY043299 )99Mobilization
mobE 34210-3485121360MobE, IncQ-like plasmids, e.g., pTF-FC2 (M57717 )93Mobilization
orfX 34848-35300, 44177-4440822855OrfX, IncQ-like plasmids, e.g., pRAS3.2 (AY043299 ) (unannotated in this plasmid)97Mobilization?, possibly inactive due to Tn1012 insertion
tnpA-3 35336-38305 c98965Transposase of Tn3 family transposon on pFBAOT6 (CR376602 )95Transposition
ofn30 38541-39077 c17863Transposase-like protein of apparent insertion into mobile genome island TNCP23 on plasmid pKLC102 from P. aeruginosa (AY257539 )100Transposition?
ofn31 39089-39484 c13162Hypothetical protein of apparent insertion into mobile genome island TNCP23 on plasmid pKLC102 from P. aeruginosa (AY257539 )100Unknown
ofn32 39481-39732 c8362Hypothetical protein of apparent insertion into mobile genome island TNCP23 on plasmid pKLC102 from P. aeruginosa (AY257539 )100Unknown
tnpA-4 39914-4048018867Recombinase of apparent insertion into mobile genome island TNCP23 on plasmid pKLC102 from P. aeruginosa (AY257539 )c100Transposition
ofn34 40615-409059663Putative nucleotidyltransferase of Tn3 family transposon on pFBAOT6 (CR376602 )98Unknown
ofn35 40902-4133914561Hypothetical protein of Tn3 family transposon on pFBAOT6 (CR376602 ) (C-terminus affected by insertion/deletion, majority is 92% identical)87Unknown
invA 41333-4189018563Recombinase of Tn3 family transposon on pFBAOT6 (CR376602 )95Transposition
gipA 41987-43105 c37255Peyer's patch-specific virulence factor of lysogenic phage Gifsy-1, Salmonella enterica (AF246666 )72Transposition
blaA 43233-4411429360β-Lactamase, Aeromonas hydrophila (U14748 )58Carbenicillin resistance
tnpA-5 44471-45298 c27564Hypothetical exonuclease in bacteriophage 186 (U32222 )45Transposition (putative)
kfrA 45684-46574 c29673KfrA of IncP-1 plasmids, e.g., pB4 (AJ431260 )38Replication/partition associated
ofn41 47109-48023 c30462C-terminal (major) part of hypothetical proteins, e.g., of Pseudomonas aeruginosa (AE004827 )58Unknown
ofn42 48062-48352 c9660N-terminal (minor) part of hypothetical proteins, e.g., of Pseudomonas aeruginosa (AE004827 )41Unknown
ofn43 48470-48850 c12664Conserved hypothetical protein of Tn3 family transposon on pFBAOT6 (CR376602 )d84Unknown
ofn44 48847-49173 c10863Conserved hypothetical protein of Tn3 family transposon on pFBAOT6 (CR376602 )d94Unknown
ofn45 49197-49532 c11159Putative transposase repressor of unmarked transposon on plasmid pND6-1 (AY208917 )100Unknown
ofn46 49547-49882 c11158Hypothetical protein of unmarked transposon on plasmid pND6-1 (AY208917 )100Unknown
ofn47 49863-50186 c10759Hypothetical protein of unmarked transposon on plasmid pND6-1 (AY208917 )100Unknown
tnpR-6 50399-5103421164Resolvase of unmarked transposon on plasmid pND6-1 (AY208917 )100Transposition
tnpA-6 51018-54047100961Transposase of unmarked transposon on plasmid pND6-1 (AY208917 )100Transposition
repA 54559-55920 c45366Putative replication protein of broad-host-range IncU plasmid pFBAOT6 (CR376602 )71Replication
parC 56086-56472 c12854Hypothetical protein of pRA2, Pseudomonas alcaligenes (U88088 )98Partitioning
parB 56509-56727 c7361Partitioning protein ParB of pRA2, Pseudomonas alcaligenes (U88088 )100Partitioning
parA 56749-57121, 1-266 c21164Partitioning protein ParA of pRA2, Pseudomonas alcaligenes (U88088 )100Partitioning
  • a c indicates the ORF is present on the complementary strand.

  • b Where similar strength matches are found in multiple genera, organism names are not given.

  • c TnpA-1 and TnpA-4 are identical. Different matches are given to represent the different contexts.

  • d The DNA sequence covering ofn43 and ofn44 is highly conserved in an unmarked transposon on plasmid pND6-1, but these reading frames are not annotated in favor of an open reading frame in the opposite direction.