TABLE 1.
ORFs in the virulence plasmid p33701 of R. equi ATCC 33701
| Designation | Function or comments (gene designation)a | Reference organism (accession no.)b (% homology) | Orientation | Location (bp) | Number of amino acids |
|---|---|---|---|---|---|
| ORF1 | Lysyl-tRNA synthetase (lsr2) | M. tuberculosis (Z95557) (63) | + | 795–1154 | 119 |
| ORF2 | R. equi Vap protein (vapG) | R. equi (D21236) | − | 2059–1541 | 172 |
| ORF3 | Unknown | E. coli hypothetical protein (U82598) (35) | − | 4706–3951 | 251 |
| ORF4 | LysR family transcriptional regulator | B. subtilis (Z99124) (54) | + | 4993–5829 | 278 |
| ORF5 | Bicyclomycin (sulfonamide) resistance protein | E. coli (P43531) (48) | + | 6322–7230 | 302 |
| ORF6 | R. equi Vap protein (vapH) | R. equi (AF118813) | + | 7367–7930 | 187 |
| ORF7 | Unknown | + | 7982–8419 | 145 | |
| ORF8 | Two-component response regulator | B. subtilis (P35163) (55) | + | 8534–9292 | 252 |
| ORF9 | Unknown | + | 10278–10505 | 75 | |
| ORF10 | Unknown | + | 10574–10759 | 61 | |
| ORF11 | Unknown | + | 10963–11325 | 120 | |
| ORF12 | R. equi Vap protein (vapA) | R. equi (JC4072) | + | 12546–13115 | 189 |
| ORF13 | Unknown | + | 13356–13598 | 80 | |
| ORF14 | R. equi Vap protein (vapC) | R. equi (AF118813) | + | 13970–14494 | 174 |
| ORF15 | R. equi Vap protein (vapD) | R. equi (AF118814) | + | 14835–15329 | 164 |
| ORF16 | Unknown | + | 15897–16367 | 156 | |
| ORF17 | Unknown | − | 16906–16484 | 140 | |
| ORF18 | Unknown | − | 17856–17572 | 94 | |
| ORF19 | R. equi Vap protein (vapE) | R. equi (AF118815) | + | 19108–19728 | 206 |
| ORF20 | R. equi Vap protein (vapF) | R. equi (JC4072) | + | 19874–20326 | 150 |
| ORF21 | Possible chorismate mutase, involved in phenylalanine biosynthesis (Pfam) | M. tuberculosis hypothetical protein (Z97193) (49) | − | 21400–20927 | 157 |
| ORF22 | DNA invertase (invA) | Acetobacter pasteurianus (AF015307) (68) | + | 22223–22801 | 192 |
| ORF23 | Unknown | + | 23106–23630 | 174 | |
| ORF24 | Unknown | + | 23683–23994 | 103 | |
| ORF25 | Unknown | − | 24826–24388 | 145 | |
| ORF26 | Putative methylase or helicase | Hypothetical methylase gene homologue, A. tumefaciens (AB016260) (41) | + | 25511–35200 | 3,229 |
| ORF27 | Unknown | M. tuberculosis hypothetical protein (Z96072) (42) | + | 36778–37767 | 329 |
| ORF28 | Unknown | + | 38402–38869 | 155 | |
| ORF29 | Unknown | − | 39305–39006 | 99 | |
| ORF30 | Conjugal transfer protein (traA) | Rhizobium sp. (AE000069) (19) | + | 39644–43747 | 1,367 |
| ORF31 | Unknown | + | 43797–44849 | 350 | |
| ORF32 | Type 1 DNA topoisomerase (topA) | Salmonella enterica serovar Typhi (AAF14809) (38) | − | 47409–44935 | 789 |
| ORF33 | Unknown | S. coelicolor hypothetical protein (AL049645) (26) | − | 48102–47485 | 205 |
| ORF34 | Conjugative transfer gene complex (trsK) | S. coelicolor hypothetical protein (AL049645) (47); S. aureus trsK (L11998-12) (30) | − | 50117–48105 | 670 |
| ORF35 | Unknown | − | 50679–50134 | 181 | |
| ORF36 | Peptidase, M23/M37 family, possible Gly-Gly endopeptidase (Pfam) | S. coelicolor (AL132662) (33) | − | 52331–50691 | 546 |
| ORF37 | Unknown | − | 52627–52328 | 99 | |
| ORF38 | Unknown | S. coelicolor putative ATP-binding protein (AL049661) (23) | − | 54399–52624 | 591 |
| ORF39 | Unknown | S. coelicolor putative integral membrane protein (AL049661) (34) | − | 55914–54412 | 500 |
| ORF40 | Transfer gene complex (trbL) | Plasmid RP4 (M93696-12) (17) | − | 55867–56911 | 318 |
| ORF41 | Unknown | + | 57004–57417 | 137 | |
| ORF42 | Unknown | − | 58330–57491 | 279 | |
| ORF43 | Unknown | − | 58938–58327 | 203 | |
| ORF44 | Unknown | − | 59333–58935 | 132 | |
| ORF45 | Unknown | + | 59392–60114 | 240 | |
| ORF46 | Unknown | − | 61000–60233 | 255 | |
| ORF47 | Unknown | − | 62157–60997 | 386 | |
| ORF48 | Unknown | − | 63374–62223 | 383 | |
| ORF49 | Possible biopterin-dependent aromatic amino acid hydroxylase (Pfam) | − | 64669–63401 | 422 | |
| ORF50 | Repressor protein (trbA) | Rhodococcus sp. plasmid (AF059700) (49) | + | 65230–65676 | 148 |
| ORF51 | Chromosome-partitioning ATPase (parA) | Deinococcus radiodurans (AE001826) (41) | + | 66207–66911 | 234 |
| ORF52 | Unknown | Unknown | + | 66904–67386 | 160 |
| ORF53 | Unknown, putative phage excisionase | Mycobacteriophage TM4 gp82 (AF068845) (50) | + | 67898–69046 | 382 |
| ORF54 | Unknown | + | 69581–70498 | 305 | |
| ORF55 | Unknown | + | 70526–71326 | 266 | |
| ORF56 | Regulatory protein (DNA binding helix-turn-helix protein) (Pfam) | + | 71674–72045 | 123 | |
| ORF57 | Unknown | + | 72456–73454 | 332 | |
| ORF58 | Unknown | + | 74042–74563 | 173 | |
| ORF59 | Unknown | + | 74892–75185 | 97 | |
| ORF60 | DnaB-like helicase protein (Pfam) | + | 75258–75827 | 189 | |
| ORF61 | DNA transposon resolvase (resA) | Corynebacterium glutamicum (AF121000) (34) | + | 75874–76458 | 194 |
| ORF62 | Chromosome partitioning protein (parB) | Deinococcus radiodurans (AE001865) (28) | + | 77971–79521 | 516 |
| ORF63 | Unknown | + | 80202–80567 | 121 | |
| ORF64 | Unknown | − | 184–80267 | 175 |
a
ORFs were assigned a putative function based on criteria outlined in Results and Discussion. (Pfam) indicates that the designated putative function is based on a protein domain search.
b
Highest amino acid homology of the R. equi ORF with characterized genes from the organism listed (GenBank accession number).