Marker Gene Database
The marker database (data/db/D1_marker/, the bundled mini tier) powers the
default --mode marker identification: blastn maps query contigs against
80 curated reference sequences, and 38 species rules turn the hits into a
verdict. gside is a species-identification engine: every reference is anchored
to a verifiable NCBI/RefSeq accession and was validated by blast against the
291-genome panel. Sub-species typing is gapit's job — the V. cholerae
O1/O139 serogroup database lives there (gapit screen --db vc_serogroup).
How marker identification works
blastnaligns contigs against the pre-builtmarkers_blastdb(evalue 1e-10, word size 11).- Hits pass the global thresholds: identity >= 85% and coverage >= 60%; the best hit per gene is selected among passing hits, so a short high-identity fragment cannot displace a full-length match.
- The best hit per gene feeds the species rules: a rule fires when enough of
its genes (
min_hits) match atmin_identityor better; the rule with the most matched genes wins. - Mean identity of matched genes >= 90% reports high confidence, otherwise medium; near-threshold marker calls suggest an ANI recheck.
See Marker Rules for the rule-file format and Identification Modes for how marker results arbitrate against ANI methods.
Gene roles
| Role | Meaning | Count |
|---|---|---|
primary |
Species-defining marker; a rule's genes draw from these |
46 |
confirm |
Corroborating evidence reported alongside the verdict | 22 |
Gene inventory (80 sequences)
| Gene | Role | Reference |
|---|---|---|
inva |
primary | M90846.1 invasion protein A [Salmonella enterica] |
rpoD |
confirm | M14427.1 rpoD operon region (dnaG-rpoD) [Salmonella enterica] |
iroB |
confirm | PV799927.1 glycosyltransferase iroB [Salmonella enterica] |
uida |
primary | NC_000913.3 beta-D-glucuronidase uidA [Escherichia coli] |
lacy |
primary | NC_000913.3 lactose permease lacY [Escherichia coli] |
gada |
confirm | NC_000913.3 glutamate decarboxylase alpha [Escherichia coli] |
stx1 |
virulence | AF125520.1 Shiga toxin 1 subunit A [Escherichia coli] |
stx2 |
virulence | PZ374831.1 Shiga toxin 2 subunit A (stx2A) [Escherichia coli] |
eae |
virulence | PZ374841.1 intimin (eae) [Escherichia coli] |
ipah |
primary | NC_004337.2 invasion plasmid antigen H ipaH [Shigella flexneri] |
toxr |
primary | NC_004603.1 toxR regulatory protein [Vibrio parahaemolyticus] |
tlh |
confirm | M36437.1 thermolabile hemolysin tlh [Vibrio parahaemolyticus] |
tdh |
virulence | M10069.1 thermostable direct hemolysin [Vibrio parahaemolyticus] |
vvha |
primary | PQ308339.1 hemolysin vvhA [Vibrio vulnificus] |
hly |
primary | M24199.1 listeriolysin O hly [Listeria monocytogenes] |
prs |
confirm | LC700425.1 phosphoribosyl pyrophosphate synthetase prs [Listeria monocytogenes] |
inlj |
confirm | AL592102.1 internalin J inlJ [Listeria monocytogenes] |
nuc |
primary | V01281.1 thermonuclease nuc [Staphylococcus aureus] |
fema |
confirm | X17688.1 methicillin resistance femA [Staphylococcus aureus] |
khe |
primary | PZ143400.1 hemolysin khe [Klebsiella pneumoniae] |
gyrb-kpn |
confirm | PZ127011.1 DNA gyrase subunit B gyrB [Klebsiella pneumoniae] |
oxa51 |
primary | MZ351777.1 beta-lactamase blaOXA-51 [Acinetobacter baumannii] |
rpob-aba |
confirm | QB079536.1 RNA polymerase beta rpoB [Acinetobacter baumannii] |
ecfx |
primary | AE004091.2 sigma factor ECF ecfX [Pseudomonas aeruginosa] |
gyrb-pae |
confirm | PZ521782.1 DNA gyrase subunit B gyrB [Pseudomonas aeruginosa] |
ddl-ef |
primary | QB064932.1 D-alanine-D-alanine ligase ddl [Enterococcus faecalis] |
ddl-efm |
primary | PZ904265.1 D-alanine-D-alanine ligase ddl [Enterococcus faecium] |
lyta |
primary | PP971805.1 autolysin lytA [Streptococcus pneumoniae] |
psaa |
confirm | AF030366.1 manganese transport psaA [Streptococcus pneumoniae] |
cfb |
primary | PP475782.1 CAMP factor cfb [Streptococcus agalactiae] |
ctra |
primary | AY336258.1 outer membrane protein ctrA [Neisseria meningitidis] |
sodc |
confirm | PP471286.1 superoxide dismutase sodC [Neisseria meningitidis] |
pora |
primary | M21289.1 porin protein A porA [Neisseria gonorrhoeae] |
tcda |
primary | M30307.1 toxin A tcdA [Clostridioides difficile] |
tcdb |
confirm | PQ863731.1 toxin B tcdB [Clostridioides difficile] |
rpob-cs |
primary | MW380341.1 RNA polymerase beta rpoB [Cronobacter sakazakii] |
aera |
primary | PQ871546.1 aerolysin aerA [Aeromonas hydrophila] |
ahh1 |
confirm | PZ301496.1 hemolysin ahh1 [Aeromonas hydrophila] |
ail |
primary | M29945.1 attachment invasion locus ail [Yersinia enterocolitica] |
yada |
confirm | X13881.1 Yersinia adhesin yadA [Yersinia enterocolitica] |
nheb |
virulence | Z11886.1 non-hemolytic enterotoxin B nheB [Bacillus cereus] |
ces |
virulence | AF110410.1 cereulide synthetase ces [Bacillus cereus] |
cpe |
virulence | L43549.1 enterotoxin cpe [Clostridium perfringens] |
mip |
primary | PX526202.1 macrophage infectivity potentiator mip [Legionella pneumophila] |
dota |
confirm | MW092166.1 dotA [Legionella pneumophila] |
cards |
confirm | AF390408.1 CARDS toxin [Mycoplasma pneumoniae] |
ompa-cp |
primary | Z31593.1 major outer membrane protein [Chlamydia pneumoniae] |
ompa-cps |
primary | PZ860298.1 major outer membrane protein ompA [Chlamydia psittaci] |
urea |
primary | M60398.1 urease subunit alpha [Helicobacter pylori] |
urec |
confirm | M60398.1 urease subunit gamma/ureC [Helicobacter pylori] |
caga |
virulence | AB015416.1 cytotoxin-associated gene A [Helicobacter pylori] |
ptxs1 |
confirm | M13223.1 pertussis toxin S1 subunit [Bordetella pertussis] |
tox |
primary | KX703000.1 diphtheria toxin tox [Corynebacterium diphtheriae] |
hpd |
primary | U32723.1 hemoglobin-binding protein D [Haemophilus influenzae] |
gdh |
primary | MT542692.1 glutamate dehydrogenase gdh [Streptococcus suis] |
bimabp |
primary | AF505187.1 bacterial actin motility BimA(Bp) [Burkholderia pseudomallei] |
tts1 |
confirm | AY089501.1 type III secretion system 1 [Burkholderia pseudomallei] |
lipl32 |
primary | PZ599989.1 lipoprotein lipL32 [Leptospira interrogans] |
tpp47 |
primary | AE000520.1:622266-623570 47 kDa membrane lipoprotein tpp47 [Treponema pallidum] |
gyrb-ps |
primary | AB015801.1 DNA gyrase subunit B [Plesiomonas shigelloides] |
eacf |
primary | CP099906.1:3631386-3634232 intimin eae [Escherichia albertii] |
toxrf |
primary | OR123876.1 transmembrane regulatory protein toxR [Vibrio fluvialis] |
bontA |
primary | M30171.1 botulinum neurotoxin type A [Clostridium botulinum] |
bontB |
typing | M81186.1 botulinum neurotoxin type B [Clostridium botulinum] |
bontE |
typing | X62089.1 botulinum neurotoxin type E [Clostridium botulinum] |
paga |
primary | M22504.1 protective antigen pagA [Bacillus anthracis] |
capb |
confirm | M64091.1 capsule biosynthesis capB [Bacillus anthracis] |
caf1 |
primary | X13880.1 F1 capsule antigen caf1 [Yersinia pestis] |
pla |
confirm | PX130171.1 plasminogen activator pla pPCP1 [Yersinia pestis] |
trh |
virulence | AB663491.1 thermostable direct hemolysin-related trh [Vibrio parahaemolyticus] |
p1 |
primary | U00089.2:180858-185741 P1 adhesin operon mgpA [Mycoplasma pneumoniae] |
is481 |
primary | MK841515.1 insertion sequence IS481 transposase [Bordetella pertussis] |
cadf |
primary | GCF_000009085.1 cadf [Campylobacter jejuni] |
ceue |
primary | GCF_009730395.1 ceue [Campylobacter coli] |
hipo |
primary | GCF_000009085.1 hipo [Campylobacter jejuni] |
mapa |
primary | GCF_000009085.1 mapa [Campylobacter jejuni] |
speb |
primary | GCF_000006785.1 speb [Streptococcus pyogenes] |
ompw |
primary | X51948.1 outer membrane protein W [Vibrio cholerae] |
cpa |
primary | PV804807.1 phospholipase C alpha toxin (cpa/plc) [Clostridium perfringens] |
safC |
typing | NC_003197.2:343560-346076 saf atypical fimbrial operon [Salmonella enterica] |
Species coverage (38 rules)
| Species | Rule genes | min hits | min identity |
|---|---|---|---|
| Salmonella | inva |
1 | 90% |
| V parahaemolyticus | tlh |
1 | 90% |
| Listeria monocytogenes | hly |
1 | 90% |
| Vibrio cholerae | ompw |
1 | 90% |
| Vibrio vulnificus | vvha |
1 | 90% |
| Staphylococcus aureus | nuc |
1 | 90% |
| Klebsiella pneumoniae | khe |
1 | 90% |
| Acinetobacter baumannii | oxa51 |
1 | 90% |
| Pseudomonas aeruginosa | ecfx |
1 | 90% |
| Enterococcus faecalis | ddl-ef |
1 | 90% |
| Enterococcus faecium | ddl-efm |
1 | 90% |
| Streptococcus pneumoniae | lyta |
1 | 90% |
| Streptococcus pyogenes | speb |
1 | 90% |
| Streptococcus agalactiae | cfb |
1 | 90% |
| Neisseria meningitidis | ctra |
1 | 90% |
| Neisseria gonorrhoeae | pora |
1 | 90% |
| Clostridioides difficile | tcda, tcdb |
1 | 90% |
| Cronobacter sakazakii | rpob-cs |
1 | 95% (excludes speb) |
| Legionella pneumophila | mip |
1 | 90% |
| Mycoplasma pneumoniae | p1 |
1 | 90% |
| Helicobacter pylori | urea, urec |
1 | 90% |
| Bordetella pertussis | is481, ptxs1 |
1 | 90% |
| Corynebacterium diphtheriae | tox |
1 | 90% |
| Haemophilus influenzae | hpd |
1 | 90% |
| Streptococcus suis | gdh |
1 | 90% |
| Burkholderia pseudomallei | tts1, bimabp |
1 | 90% |
| Leptospira interrogans | lipl32 |
1 | 90% |
| Treponema pallidum | tpp47 |
1 | 90% |
| Bacillus anthracis | paga, capb |
2 | 90% |
| Yersinia pestis | caf1, pla |
2 | 90% |
| Yersinia enterocolitica | ail, yada |
1 | 90% |
| Aeromonas hydrophila | aera, ahh1 |
1 | 90% |
| Clostridium botulinum | bontA, bontB, bontE |
1 | 90% |
| Clostridium perfringens | cpa |
1 | 90% |
| DEC | uida, lacy, gada |
2 | 95% |
| Shigella EIEC | ipah |
1 | 95% |
| Campylobacter jejuni | mapa, hipo, cadf |
2 | 90% |
| Campylobacter coli | ceue |
1 | 90% (excludes mapa, hipo, cadf) |
Customizing
Edit data/db/D1_marker/marker_rules.yaml (fields documented in
Marker Rules), then rebuild the BLAST database
after changing markers.fasta:
makeblastdb -in data/db/D1_marker/markers.fasta -dbtype nucl -out data/db/D1_marker/markers_blastdb