TABLE 1.
sox genes of P. pantotrophus and genes thought to be involved in sulfur oxidation in other thiobacteria
| Organism | Gene | No. of amino acids | % Identity to P. pantotrophusa | Signal peptide with twin arginine motif | Putative function | Reference(s) | Accession no. |
|---|---|---|---|---|---|---|---|
| P. pantotrophus | orf1 | 149 | −c | Transcriptional regulator | 20 | X79242PDSOXf | |
| R. palustris | orf685 | 124 | 47.1 (104) | −c | RRPA00685d | ||
| P. pantotrophus | orf2 | 142 | − | Thioredoxin | This study | ||
| R. palustris | orf708 | 142 | 41.4 (116) | − | RRPA00708d | ||
| P. pantotrophus | shxV | 245 | − | Reductant transporter | 20 | X79242PDSOXf | |
| R. palustris | orf618 | 247 | 46.4 (237) | − | RRPA00618d | ||
| P. pantotrophus | shxW | 186 | − | Thioredoxin | 20 | X79242PDSOXf | |
| R. palustris | orf651 | 197 | 42.0 (176) | − | RRPA00651d | ||
| M. extorquens | orf239b | 119b | 47.6 (105) | + (TRRQFLA) | RMQ00239d | ||
| P. pantotrophus | soxX | 157 | − | Cytochrome c | 20 | X79242PDSOXf | |
| R. palustris | orf625 | 247 | 47.5 (40) | − | RRPA00625d | ||
| C. tepidum | orf1709 | 118 | 29.7 (37) | − | RCL01709d | ||
| A. vinosum | soxX | 135 | 32.5 (80) | − | 13 | ||
| M. extorquens | orf2551b,g | 158bg | 47.2 (125) | − | RMQ02551dg | ||
| P. pantotrophus | soxY | 140 | + (SRREALW) | Sulfur covalently binding protein | 20 | X79242PDSOXf | |
| R. palustris | orf660 | 154 | 44.5 (146) | + (SRREALA) | RRPA00660d | ||
| R. palustris | orf2261 | 156 | 34.9 (140) | ? (DRRQMLI) | RRPA02261d | ||
| C. tepidum | orf1710g | 153g | 37.5 (120) | + (SRRDFCR) | RCL01710dg | ||
| A. aeolicus | aq1810 | 150 | 30.1 (136) | + (TRRDFLK) | 14 | AE000757e | |
| M. extorquens | orf2552 | 152 | 56.7 (60) | + (NRRQALA) | RMQ02552d | ||
| P. pantotrophus | soxZ | 109 | −c | Sulfur compound chelating protein | 20 | X79242PDSOXf | |
| R. palustris | orf674 | 109 | 54.1 (109) | −c | RRPA00674d | ||
| R. palustris | orf2280 | 111 | 36.1 (108) | −c | RRPA02280d | ||
| C. tepidum | orf1711 | 101 | 37.0 (81) | −c | RCL01711d | ||
| A. aeolicus | aq1809 | 110 | 36.4 (110) | −c | 14 | AE000757e | |
| M. extorquens | orf2553 | 109 | 49.5 (107) | −c | RMQ02553d | ||
| P. salicylatoxidans | soxZb | 33b | 62.5 (32) | ? | 43 | ||
| P. pantotrophus | soxA | 290 | − | Cytochrome c (diheme) | 20 | X79242PDSOXf | |
| R. palustris | orf637 | 273 | 28.5 (144) | − | Cytochrome c (monoheme) | RRPA00637d | |
| R. palustris | orf2737 | 341 | 22.5 (120) | −c | Cytochrome c (diheme) | RRPA02737d | |
| C. tepidum | orf1712 | 286 | 29.5 (176) | − | Cytochrome c (monoheme) | RCL01712d | |
| A. vinosum | soxA | 281 | 30.0 (207) | − | Cytochrome c (monoheme) | 13 | |
| A. aeolicus | aq1807 | 267 | 29.2 (178) | − | Cytochrome c (diheme) | 14 | AE000757e |
| P. salicylatoxidans | soxA | 286 | 46.0 (276) | − | Cytochrome c (diheme) | 43 | AJ404005 |
| P. pantotrophus | soxB | 564 | + (TRREFIQ) | Sulfate thiol esterase | 20, 69 | X79242PDSOXf | |
| R. palustris | orf525 | 565 | 59.8 (565) | + (SRREFLQ) | RPA00525d | ||
| C. tepidum | orf1714g | 584g | 47.9 (376) | + (SRREFLR) | RCL01714dg | ||
| A. vinosum | soxB | 522b | 49.9 (519) | + (SRREFVR) | 13 | ||
| A. aeolicus | orf724 | 592 | 40.5 (551) | + (TRRDFLE) | Quinol-oxidase polypeptide 1 | 14 | AE000757e |
| M. extorquens | orf2550b | 374b | 65.7 (370) | ? | RMQ02550d | ||
| S. novella | soxBb | 309b | 62.3 (308) | ? | AF139113e | ||
| P. salicylatoxidans | soxBb | 7b | 85.7 (7) | + (SRREF..) | 43 | ||
| P. pantotrophus | soxC | 430 | + (SRRAFLR) | Sulfur dehydrogenase | 70 | X79242PDSOXf | |
| R. palustris | orf545 | 431 | 61.3 (408) | + (NRRRFLG) | RRPA00545d | ||
| M. extorquens | orf3760b,g | 403bg | 45.6 (410) | + (NRRAFLR) | RMQ03760dg | ||
| A. aeolicus | aq979 | 200 | 25.2 (119) | −c | 14 | AE000716c | |
| S. novella | soxC | 427 | 61.2 (428) | + (DRRRFLN) | AF139113c | ||
| S. novella | sorA | 405 | 26.5 (385) | + (NRRQILK) | Sulfite-cytochrome c oxidoreductase subunit A | 28 | AF154565e |
| S. solfataricus | 209 | 37.0 (100) | + (NRRDFLK) | J. van der Oost | |||
| P. pantotrophus | soxD | 384 | − | Cytochrome c | 70 | X79242PDSOXf | |
| R. palustris | orf644 | 251 | 52.7 (201) | − | RRPA00644d | ||
| M. extorquens | orf3759b,g | 190bg | 47.2 (176) | − | RMQ03789d, g | ||
| S. novella | soxDb | 84b | 55.2 (67) | − | AF139113e | ||
| S. novella | sorB | 108 | 60.0 (10) | − | c-type heme subunit of sorA | 28 | AF154565e |
| P. pantotrophus | soxE | 236 | − | Cytochrome c | 70 | X79242PDSOXf | |
| R. palustris | orf701 | 139 | 49.4 (77) | − | RRPA00701d | ||
| M. extorquens | orf3227 | 305 | 43.0 (107) | − | RMQ03227d | ||
| P. pantotrophus | soxF | 420 | + (TRRSLIA) | Flavoprotein | 51a, 70 | X79242PDSOXf | |
| R. palustris | orf554 | 421 | 57.1 (422) | + (NRRDVFK) | RRPA00554d | ||
| R. palustris | orf566 | 430 | 48.1 (420) | + (SRRGMIR) | RPA00566d | ||
| C. tepidum | orf1707g | 430g | 40.2 (420) | + (SRRTFNR) | RCL01707d, g | ||
| C. tepidum | orf258 | 458 | 46.3 (382) | + (SRRDFNK) | RCL00258d | ||
| A. aeolicus | dhsU | 436 | 30.5 (410) | + (NRRDVFK) | Flavocytochrome c sulfide dehydrogenase | 14 | AE000679e |
| A. aeolicus | fccB | 417 | 30.1 (379) | + (DRRNLLL) | Sulfide dehydrogenase, flavoprotein subunit | 14 | AE000679e |
| R. capsulatus | orf443 | 340 | 26.7 (318) | + (TRRHLAL) | RCL00443d | ||
| P. pantotrophus | soxG | 303 | + (SRRHFLA) | Thiol esterase | 51a | X79242PDSOXf | |
| M. extorquens | orf2512b | 145b | 32.7 (113) | ? | RMQ02512d | ||
| P. pantotrophus | soxH | 317 | ? (MRRLILC) | Thiol esterase | 51a | X79242PDSOXf | |
| A. aeolicus | cphA1 | 326 | 27.2 (268) | − | beta-Lactamase precursor | 14 | AE000757e |
| R. palustris | orf708 | 142 | − | Thiol-disulfide isomerase and thioredoxins | RRPA00708d | ||
| A. aeolicus | rhdA2 | 293 | − | Thiosulfate sulfur transferase | 14 | AE000757c | |
| A. aeolicus | aq1806 | 206 | − | 14 | AE000757c | ||
| A. aeolicus | trxA2 | 135 | − | Thioredoxin | 14 | AE000757c | |
| C. tepidum | orf717b | 444b | ? | Sulfide-quinone oxidoreductase | RCL00717d | ||
| C. tepidum | orf540 | 390 | − | Sulfide-quinone oxidoreductase | RCL00540d | ||
| A. aeolicus | sqr | 430 | − | Sulfide-quinone reductase | 14 | AE000777e | |
| R. capsulatus | sqr | 427 | − | Sulfide-quinone reductase | 53, 54 | X97478f |
a
The numbers in parentheses indicate the sizes of the amino acid overlaps.
b
The ORF is incomplete.
c
There is no signal peptide.
d
IGwit database accession number.
e
GenBank database accession number.
f
EMBL data library accession number.
g
Based on our analysis, we concluded that some sequences contain errors which affect the lengths of the ORFs, as follows: in orf1710 of C. tepidum the predicted start is 72 nucleotides upstream of the designated start; in orf1714 of C. tepidum the predicted start is 96 nucleotides downstream of the designated start; in orf3760 of M. extorquens the predicted start is at nucleotide 1838 due to a frameshift aound position 1426 upstream of the designated start at nucleotide 1384; in orf3759 of M. extorquens the predicted start is at nucleotide 639 due to a frameshift around position 505 downstream of the designated start at nucleotide 518; and in orf1707 of C. tepidum the predicted start is 90 nucleotides upstream of the designated start.