Table 1.

Homology between pNL1 proteins and representative homologs

pNL1Functional description of closest relativepNL1a (alignment region)Homologa(alignment region)% IdentitybSourceGenBank access no.c
orf003 Bcr; sulfonamide-bicyclomycin resistance protein394 (1–378)396 (14–390)25 E. coli K-12584831
orf007 CatR; putative regulator of catechol degradative operon283 (33–283)256 (3–256)26 R. opacus1CP2398776
orf015 DesA; fatty acid desaturase309 (27–283)287 (22–268)29 C. caldarium RK1 chloroplast2465769
nrd Nrd; aerobic-microaerobic growth with nitrates439 (3–438)444 (4–442)69 B. japonicumUSDA 1102961296
orf029 YkpB; conserved hypothetical protein310 (3–303)303 (2–297)20 B. subtilis1682633815
ORF58; conserved hypothetical protein310 (4–294)337 (7–322)28 S. aromaticivorans F199 (pNL1)3378270
orf041 ORF1; conserved hypothetical protein136 (1–131)139 (1–131)51 B. cepaciaLB400586492
orf045 YtvB; hypothetical protein94 (18–52)111 (65–99)34 B. subtilis 2293180
orf047 ImdH; probable tartrate dehydrogenase355 (1–353)361 (2–360)60 E. coliK-123024767
DlpA; isocitrate-isopropylmalate dehydrogenase family355 (8–350)615 (9–362)32 L. pneumophila 2497266
orf058 YkpB; thiamin biosynthesis-like hypothetical protein337 (11–335)301 (7–295)28 P. horikoshiiOT33257813
orf064 DapA; putative dihydropicolinate synthase320 (18–317)289 (4–285)25 A. fulgidus 2649690
ppdK PpdK; pyruvate phosphate dikinase888 (21–885)874 (16–871)57 C. symbiosum 1084302
xylB XylB; aryl alcohol dehydrogenase365 (1–365)366 (1–365)51 P. putida(pWW53)731175
bphA2f ORFG6; small subunit174 (23–173)176 (22–175)38 Sphingomonassp. strain RW13618275
bphA1f PahA3; large subunit component naphthalene dioxygenase459 (7–436)449 (8–439)44 P. aeruginosa PaK11255669
orf114 AF010496; conserved hypothetical protein309 (17–306)289 (9–295)32 R. capsulatus SB10033128363
orf121 VceB; putative multidrug resistance pump gene 2509 (21–502)511 (22–504)43 V. cholerae569B2815578
orf132 VceA; putative multidrug resistance pump gene 1381 (19–380)395 (16–376)46 V. cholerae569B2815577
orf140 OprJ; outer membrane component of multidrug resistance efflux pump483 (12–473)479 (12–468)30 P. aeruginosaPAO2497711
orf151 ORF151; conserved hypothetical protein137 (25–135)151 (25–145)32 H. halobium 141254
orf154 BpoA; conserved hypothetical protein247 (2–242)261 (21–259)43 M. tuberculosis H37Rv2104396
orf158 YybA; hypothetical regulator, Marr family148 (24–148)150 (11–135)25 B. subtilis 1682636618
orf181 Y4cG; probable DNA invertase293 (1–292)305 (16–303)45 Rhizobiumsp. strain NGR234(pNGR234α)2497425
orf198 Y4dW; conserved hypothetical protein103 (21–85)204 (91–155)36 Rhizobium sp. strain NGR234(pNGR234α)2496610
repB QsopB;trans-acting replication protein327 (54–299)334 (62–296)28 C. burnetii(QpH1)1075479
repAa RepA; DNA replicase420 (22–412)405 (2–402)32 A. tumefaciens (pTiB6S3)95114
repAb RepA; DNA replicase434 (52–312)307 (29–284)28 R. marinusR-21(pRM21)527643
orf229 ORF248; conserved hypothetical protein280 (103–174)248 (165–239)41 C. burnetii(QpDV)1075477
orf235 R31180_1; conserved hypothetical protein1425 (375–1146)1384 (197–1015)31 H. sapiens 3399676
HsdM; StySKI methylase1425 (121–298)493 (167–373)23 S. enterica 1841495
orf261 AF056496; conserved hypothetical protein379 (100–288)252 (93–252)22 H. pyloriOU145B(pHP0100)3046602
orf271 Rv3749c; hypothetical protein196 (99–177)169 (60–138)35 M. tuberculosis H37Rv2960173
orf277 Rv3750c; hypothetical protein similar to excisionases152 (53–144)130 (23–114)38 M. tuberculosis H37Rv2960174
orf282 ORF1; 20.4-kDa plasmid stabilizing protein705 (119–288)180 (1–168)29 R. meliloti GR446317
ORF2; 38.5-kDa plasmid stabilizing protein705 (310–624)356 (21–324)26 R. melilotiGR446318
AF053947; conserved hypothetical protein705 (4–632)669 (21–624)27 Y. pestis(pMT1)2996364
orf299 AF0450; hypothetical signal transducing His kinase555 (30–128)329 (229–329)31 A. fulgidus 2650174
orf310 ORF382; conserved hypothetical protein127 (5–109)300 (9–118)44 S. aromaticivorans F199(pNL1)3378306
Y4eC; conserved hypothetical protein127 (8–108)307 (9–118)35 Rhizobium sp. strain NGR234(pNGR234α)2496614
matRa MatRb; putative maturase-related protein633 (45–611)571 (3–570)52 S. aromaticivorans F199(pNL1)3378311
MatR; maturase-related protein633 (26–601)599 (26–594)38 L. lactisMG13631296829
orf332 Y4eC; conserved hypothetical protein130 (13–115)307 (137–235)37 Rhizobiumsp. strain NGR234(pNGR234α)2496614
ORF382; conserved hypothetical protein130 (13–118)300 (134–235)37 S. aromaticivorans F199(pNL1)3378306
orf338 XerD; putative phage-type integrase-recombinase463 (202–459)316 (143–346)23 M. leprae 2065218
orf382 Y4eC; conserved hypothetical protein300 (6–292)307 (7–295)56 Rhizobium sp. strain NGR234(pNGR234α)2496614
orf385 Y4eC; conserved hypothetical protein90 (14–90)307 (225–307)36 Rhizobium sp. strain NGR234(pNGR234α)2496614
ORF382; conserved hypothetical protein90 (22–80)300 (235–293)32 S. aromaticivorans F199(pNL1)3378306
matRb MatRa; putative maturase-related protein571 (3–570)633 (45–611)52 S. aromaticivorans F199(pNL1)338301
MatR; maturase related protein571 (6–561)599 (48–594)36 L. lactis MG13631296829
orf447 ORF480; hypothetical protein533 (18–386)507 (14–368)29 S. aromaticivorans F199(pNL1)3378320
orf480 ORF447; hypothetical protein507 (14–368)533 (18–386)29 S. aromaticivorans F199(pNL1)3378317
orf520 Rv3226c; conserved hypothetical protein220 (20–189)252 (1–200)28 M. tuberculosis H37Rv2072693
orf563 HglK; protein involved in glycolipid localization229 (12–206)245 (52–240)33 Synechocystissp. strain PCC68031653115
orf569 RpoE; RNA polymerase sigma-E factor (sigma 24)181 (4–170)202 (11–192)26 E. coliK-12987648
orf583 ORFL1; conjugal transfer region114 (16–113)152 (69–151)43 A. tumefaciens(Ti)ATU43674
ssbR Ssb; homolog of single-strand binding protein111 (3–111)113 (4–104)30 E. aerogenes(R751)1572546
orf597 Ros; repressor of plant conjugal transfer genes159 (2–128)142 (9–137)53 A. tumefaciens (Ti)1710641
tnpC TnpC; type Tn554 transposase homolog218 (18–109)125 (17–106)23 S. aureus 136146
tnpB TnpB; Tn554transposase710 (373–622)630 (336–578)30 S. aureus 135956
tnpA TnpA; type Tn554 transposase homolog404 (24–374)361 (16–347)31 S. aureus 135955
orf630 PHS027; conserved hypothetical protein81 (7–68)74 (6–66)35 P. horikoshiiOT33257321
orf633 Rv2759c; conserved hypothetical protein129 (4–108)131 (1–115)27 M. tuberculosisH37Rv2624281
orf649 ORF2; putative 27.6-kDa protein495 (261–440)236 (31–212)27 H. pylori(pHPM180)530827
Tca; DNA polymerase495 (31–262)834 (276–528)28 T. aquaticus caldophilus GK242506365
traD TraD; membrane protein involved in DNA export776 (237–726)738 (183–677)30 E. coli(R100)136176
trwC TrwC; DNA helicase1013 (2–955)966 (4–929)31 E. coli(R388)1084124
orf758 ORF4; hypothetical regulatory protein266 (11–201)251 (7–209)24 Acinetobactersp. strain ADP12271498
isAb ORFA; transposase part A ISRm2011-2128 (1–126)135 (1–126)40 R. meliloti20111583631
isAa ORFB; transposase part B ISRm2011-2157 (1–155)201 (45–199)50 R. meliloti20111583632
traG TraG; pilus biosynthesis-mating aggregate stabilization912 (1–830)938 (1–802)21 E. coliK-12 (F)464922
traH TraH; F pilus assembly484 (21–469)458 (10–443)32 E. coli K-12 (F)464925
traF TraF; F pilus assembly270 (48–263)247 (23–241)27 E. coli(R100-1)2226078
traN TraN; stabilization of mating pairs704 (396–695)602 (293–593)29 E. coli K-12 (F)730985
trbC TrbC; F pilus assembly254 (99–221)212 (74–206)27 E. coli(R100-1)2226075
traU TraU; conjugal DNA transfer-F pilus assembly340 (19–340)330 (13–330)44 E. coli K-12 (F)136155
traW TraW; F pilus assembly231 (12–210)210 (5–204)36 E. coli(R100-1)2226072
orf851 TraF; F pilus assembly368 (209–340)177 (9–141)32 E. coli(RK2)549119
TrbI; influences F pilus outgrowth and retraction368 (85–150)128 (56–125)31 Escherichia coli (R100-1)2226071
traC TraC; F pilus assembly856 (5–833)875 (24–851)25 E. coli K-12 (F)136145
dsbC DsbC; protein disulfide-isomerase298 (182–290)235 (110–223)32 E. coli 96548
traB TraB; F pilus assembly458 (36–453)475 (4–406)26 E. coli(ColB2)730990
traK TraK; F pilus assembly264 (32–263)242 (8–241)20 E. coli(ColB2)1293089
traE TraE; F pilus assembly207 (19–183)187 (12–186)22 S. typhi(pED208)136180
traL TraL; F pilus assembly94 (1–79)91 (8–86)31 E. coli(ColB2)136149
orf916 Phbn040; hypothetical regulator177 (80–156)158 (26–93)29 P. horikoshii OT33130383
orf925 YjbJ; conserved hypothetical protein similar to lytic transglycolases265 (103–217)181 (63–177)47 B. subtilis 2633511
orf933 MTH888; hypothetical protein222 (7–203)220 (22–214)32 M. thermoautotrophicum 2621982
ORF938; conserved hypothetical protein222 (2–216)232 (9–226)34 S. aromaticivorans F199(pNL1)3378388
DlpA; isocitrate-isopropylmalate dehydrogenase family222 (6–219)615 (395–611)36 L. pneumophila 2497266
orf938 MTH888; hypothetical protein232 (25–217)220 (33–217)34 M. thermoautotrophicum 2621982
DlpA; isocitrate-isopropylmalate dehydrogenase family232 (1–214)615 (374–595)29 L. pneumophila 2497266
orf942 PH0854; hypothetical protein130 (16–125)137 (27–135)32 P. horikoshii OT33257265
orf946 Slr0619; hypothetical protein336 (53–331)348 (66–334)23 Synechocystissp. strain PCC68031208451
bphA2e BphA2e; small subunit component of a dioxygenase165 (1–165)165 (1–165)72 S. yanoikuyae B1
bphA1e BphA1e; large subunit component of a dioxygenase391 (1–391)391 (1–391)90 S. yanoikuyae B1
nahE NahE; 2-hydroxy-benzalpyruvate aldolase328 (1–327)333 (1–327)83 S. yanoikuyaeB1
xylL XylL; cis-(methyl)benzoate dihydrodiol dehydrogenase262 (7–262)263 (8–263)76 S. yanoikuyae B1
bphA4 BphA4; reductase component of a dioxygenase408 (1–408)407 (1–407)72 S. yanoikuyae B1
bphR BphR; regulatory protein546 (1–542)543 (1–541)61 S. yanoikuyaeB1
bphR BphR; regulatory protein546 (1–542)543 (1–541)61 S. yanoikuyaeB1
bphA1a BphA1a; large subunit component of a dioxygenase450 (5–450)448 (3–448)82 S. yanoikuyae B1
bpha2a BphA2a; small subunit component of a dioxygenase175 (1–175)175 (1–175)65 S. yanoikuyae B1
bphA1b BphA1b; large subunit component of a dioxygenase455 (1–455)455 (1–455)89 S. yanoikuyae B1
bphA2b BphA2b; small subunit component of a dioxygenase183 (1–183)183 (1–183)80 S. yanoikuyae B1
orf1038 ORF1217; conserved hypothetical protein135 (1–135)832 (1–135)79 S. aromaticivorans F199(pNL1)3378429
orf1042 ORF1217; conserved hypothetical protein705 (1–705)832 (152–832)72 S. aromaticivorans F199(pNL1)3378429
xylM XylM; reductase component of xylene monooxygenase367 (1–363)375 (1–371)67 S. yanoikuyae B1
xylA XylA; oxygenase component of xylene monooxygenase346 (1–343)346 (1–343)63 S. yanoikuyae B1
bphB BphB; cis-biphenyl dihydrodiol dehydrogenase266 (1–265)266 (1–265)80 S. yanoikuyae B1
xylC XylC; benzylaldehyde dehydrogenase501 (1–501)499 (1–499)89 S. yanoikuyae B1
xylT XylT; ferredoxin, plant-type93 (3–92)92 (2–91)68 S. yanoikuyae B1
xylH XylH; 4-oxalocrotonoate tautomerase80 (1–69)70 (1–69)79 S. yanoikuyaeB1
xylI XylI; 4-oxalocrotonate decarboxylase256 (1–256)256 (1–256)85 S. yanoikuyae B1
xylK XylK; 4-hydroxy-2-oxovalerate aldolase343 (1–342)343 (1–342)90 S. yanoikuyaeB1
xylQ XylQ; acetaldehyde dehydrogenase (acylating)312 (1–312)312 (1–312)82 S. yanoikuyae B1
xylJ XylJ; 2-hydroxypent-2,4-dienoate hydratase264 (1–264)264 (1–264)91 Pseudomonassp. strain DJ772315998
xylG XylG; 2-hydroxymuconic semialdehyde dehydrogenase505 (12–505)494 (1–494)96 Sphingomonassp. strain HV3(pSKY4)2293079
cmpX CmpX; conserved hypothetical protein143 (1–143)143 (1–143)97 Sphingomonassp. strain HV3(pSKY4)2293078
xylE XylE; catechol 2,3-dioxygenase307 (1–307)307 (1–307)95 Sphingomonassp. strain HV3(pSKY4)2293077
xylF XylF; 2-hydroxymuconic semialdehyde hydrolase283 (1–282)292 (1–282)93 Sphingomonassp. strain HV3(pSKY4)2293079
bphK BphK; glutathioneS-transferase201 (1–201)201 (1–201)97 S. yanoikuyae B1
bphA2d BphA2d; small subunit component of a dioxygenase162 (7–162)159 (4–159)76 S. yanoikuyae B1
bphA1d BphA1d; large subunit component of a dioxygenase426 (1–426)424 (1–424)80 S. yanoikuyae B1
Orf1158 ORF2; conserved hypothetical protein330 (9–327)330 (7–325)87 S. yanoikuyaeB1
xylY XylY; small subunit component of benzene dioxygenase164 (1–164)164 (1–164)69 S. yanoikuyae B1
xylX XylX; large subunit component of benzene dioxygenase471 (1–462)470 (1–462)73 S. yanoikuyae B1
bphC BphC; 2,3-dihydroxybiphenyl 1,2-dioxygenase299 (1–298)299 (1–298)87 S. yanoikuyae B1115106
bphA3 PhnR; ferredoxin component of phenanthrene dioxygenase108 (1–108)108 (1–108)97 Pseudomonassp. strain DJ772316014
bphA2c BphA2c; small subunit component of a dioxygenase162 (1–162)162 (1–162)67 S. yanoikuyae B1
bphA1c BphA1c; large subunit component of a dioxygenase420 (18–415)419 (19–415)79 S. yanoikuyae B1
nahD NahD; 2-hydroxychromene-2-carboxylate isomerase197 (1–197)197 (1–197)79 S. yanoikuyaeB1
orf1201 ORF1217; conserved hypothetical protein726 (10–726)832 (19–832)26 S. aromaticivorans F199(pNL1)3378429
orf1201 ORF1217; conserved hypothetical protein726 (10–726)832 (19–832)26 S. aromaticivorans F199(pNL1)3378429
orf1217 ORF1042; conserved hypothetical protein832 (152–832)705 (1–705)72 S. aromaticivorans F199(pNL1)3378402
gabD GabD; succinic semialdehyde dehydrogenase490 (8–484)482 (3–482)57 E. coliK-12120777
orf1244 YclB; phenylacrylic acid decarboxylase homolog204 (3–190)204 (14–200)50 B. subtilis168 trpC21805434
pchFa PchF; flavoprotein subunit, p -cresol methyl-hydroxylase519 (5–479)530 (9–487)42 P. putida NCIMB 9866294369
nahF Ydh; vanillin: NAD+oxidoreductase479 (1–473)482 (1–475)41 P. fluorescens AN1033116018
orf1272 YclC; conserved hypothetical protein486 (17–457)473 (7–448)47 B. subtilis 168 trpC21805435
orf1280 YclD; conserved hypothetical protein74 (6–62)229 (4–57)32 B. subtilis 168 trpC21805436
pchFb PchFa; flavoprotein subunit, p -cresol methyl-hydroxylase488 (2–486)519 (9–504)37 S. aromaticivorans F199(pNL1)3378433
PchF; flavoprotein subunit, p -cresol methyl-hydroxylase519 (39–463)530 (57–487)32 P. putida NCIMB 9866294369
pchC PchC; cytochromec subunit, p -cresol methyl-hydroxylase121 (10–115)101 (10–101)29 P. putida NCIMB 9866294349
orf1300 FadE19; acyl-CoA dehydrogenase76 (12–83)394 (53–124)36 M. tuberculosis H37Rv2113933
orf1303 Rv3548c; hypothetical dehydrogenase123 (1–49)304 (210–256)32 M. tuberculosis H37Rv1666112
orf1307 Rv0148; steroid dehydrogenase200 (9–170)286 (9–169)66 M. tuberculosis H37Rv1877273
Rv3548c; hypothetical dehydrogenase200 (5–169)304 (4–178)42 M. tuberculosis H37Rv1666112
orf1313 NKe; hypothetical protein201 (42–182)159 (5–142)30 P. aeruginosaPAO177647
bphD BphDd; 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoate hydrolase286 (1–283)285 (1–284)60 Rhodococcussp. strain RHA1 (390-kb plasmid)1906778
bphE BphEd; 2-hydroxypenta-2,4-dienoate hydratase271 (11–270)267 (7–266)66 Rhodococcussp. strain RHA1 (390-kb plasmid)1906779
bphF BphFd; 4-hydroxy-2-oxovalerate aldolase262 (1–243)258 (1–243)55 Rhodococcussp. strain RHA1 (390-kb plasmid)1906780
orf1338 BaiF; conserved hypothetical protein388 (18–281)381 (5–273)38 E. coli 1799782
  • e NK, no gene name designated.

  • a Values in parentheses describe the portion of protein used in the alignment.

  • b Percentage of amino acids in aligned region that are identical when the sequences are aligned with BLASTP2.

  • c Accession number 1163200 describing ORFL has been removed from GenBank. The accession number listed refers to the DNA sequence from which the corresponding ORF can be derived. Sequences for S. yanoikuyae B1 genes were derived from the DNA sequences provided by Gerben Zylstra where not available in GenBank.

  • d The gene designation refers to those assigned by Masai et al. (56). In GenBank the same genes are designated etbDEF.