Identity
Taxonomy and isolate
- Domain
- Bacteria
- Phylum
- Pseudomonadota
- Class
- Gammaproteobacteria
- Order
- Enterobacterales
- Family
- Enterobacteriaceae
- Genus
- Salmonella
- Species
- enterica
- Strain
- SL1344
- Serovar
- Typhimurium
- Biosafety level
- BL2
Public bacterial data preview
Salmonella enterica SL1344
BMCPR ID: BMCPR_BAC_002355
This public summary contains selected taxonomy and genome information only.
Genome assembly
Assembly facts
- Assembly name
- BMCPR_BAC_002355
- Assembly type
- final
- Assembler
- Trycycler 0.5.0
- Assembly size
- 4,745,344 bp
- Contigs
- 2
- Largest contig
- 4,685,972 bp
- N50
- 4,685,972 bp
- Circular contigs
- 2
Genomic profile
Sequence typing
- MLST scheme
- salmonella
- Sequence type
- 11
- MLST result
- PERFECT
Genome analysis
Genome quality summary
- Completeness
- 100%
- Contamination
- 0.23%
- GC content
- 52%
- Coding sequences
- 4,447
Genome analysis
GTDB-Tk classification
- GTDB genus
- Salmonella
- GTDB species
- enterica
- Closest-reference ANI
- 98.92%
- Marker alignment
- 97.14%
ABRicate analysis
Genome annotation hits
Resistance and virulence annotations identified with the CARD, ResFinder, and VFDB databases.
25CARD
1ResFinder
159VFDB
CARD results25 hits
| Gene | Locus tag | Accession | Coverage | Identity | Classification | Product |
|---|---|---|---|---|---|---|
| AAC(6')-Iy | 03560 | AF144880.1:3541-3979 | 100.0% | 96.8% | aminoglycoside | AAC(6')-Iy is a chromosomal-encoded aminoglycoside acetyltransferase in S. enteritidis and S. enterica. Regulatory mutation required to increase expression of this chromosomally-encoded gene for resistance. In the specific system aminoglycoside resistance was due to a transcriptional fusion secondary to a chromosomal deletion in which the downstream aac(6')-Iy gene was placed under the control of the upstream nmpC promoter. |
| CRP | 01579 | AP009048.1:4154296-4153663 | 100.0% | 87.99% | fluoroquinolone; macrolide; penicillin_beta-lactam | CRP is a global regulator that represses MdtEF multidrug efflux pump expression. |
| Escherichia_coli_acrA | 04590 | U00096.3:485619-484425 | 100.0% | 83.42% | cephalosporin; disinfecting_agents_and_antiseptics; fluoroquinolone; glycylcycline; penicillin_beta-lactam; phenicol; rifamycin; tetracycline | AcrA is a subunit of the AcrAB-TolC multidrug efflux system found in E. coli. |
| H-NS | 03726 | BA000007.3:1738104-1737690 | 100.0% | 88.89% | cephalosporin; fluoroquinolone; macrolide; penicillin_beta-lactam; tetracycline | H-NS is a histone-like protein involved in global gene regulation in Gram-negative bacteria. It is a repressor of the membrane fusion protein genes acrE mdtE and emrK as well as nearby genes of many RND-type multidrug exporters. |
| MdtK | 02957 | CP014358.1:2162750-2161325 | 100.0% | 98.81% | fluoroquinolone | A multidrug and toxic compound extrusions (MATE) transporter conferring resistance to norfloxacin doxorubicin and acriflavine. |
| OmpA | 04086 | FO834906.1:2175099-2173974 | 93.6% | 82.73% | peptide | OmpA is a porin that confers resistance to beta-lactam antibiotics. |
| TolC | 01865 | FJ768952.1:0-1488 | 97.51% | 81.64% | aminocoumarin; aminoglycoside; carbapenem; cephalosporin; disinfecting_agents_and_antiseptics; fluoroquinolone; glycylcycline; macrolide; penicillin_beta-lactam; peptide; phenicol; rifamycin; tetracycline | TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex. |
| YojI | 02705 | U00096.3:2308615-2306971 | 99.7% | 80.41% | peptide | YojI mediates resistance to the peptide antibiotic microcin J25 when it is expressed from a multicopy vector. YojI is capable of pumping out microcin molecules. The outer membrane protein TolC in addition to YojI is required for export of microcin J25 out of the cell. Microcin J25 is thus the first known substrate for YojI. |
| acrB | 04591 | U00096.3:484403-481253 | 99.4% | 85.61% | cephalosporin; disinfecting_agents_and_antiseptics; fluoroquinolone; glycylcycline; penicillin_beta-lactam; phenicol; rifamycin; tetracycline | Protein subunit of AcrA-AcrB-TolC multidrug efflux complex. AcrB functions as a herterotrimer which forms the inner membrane component and is primarily responsible for substrate recognition and energy transduction by acting as a drug/proton antiporter. |
| acrD | 02478 | AP009048.1:2586250-2589364 | 99.97% | 81.89% | aminoglycoside | AcrD is an aminoglycoside efflux pump expressed in E. coli. Its expression can be induced by indole and is regulated by baeRS and cpxAR. |
| bacA | 01845 | U00096.3:3204131-3203309 | 99.39% | 85.84% | peptide | The bacA gene product (BacA) recycles undecaprenyl pyrophosphate during cell wall biosynthesis which confers resistance to bacitracin. |
| cpxA | 00974 | BA000007.3:4905062-4903688 | 99.49% | 85.22% | aminocoumarin; aminoglycoside | CpxA is a membrane-localized sensor kinase that is activated by envelope stress. It starts a kinase cascade that activates CpxR which promotes efflux complex expression. |
| emrA | 02258 | AP009048.1:2810082-2811255 | 99.91% | 82.2% | fluoroquinolone | EmrA is a membrane fusion protein providing an efflux pathway with EmrB and TolC between the inner and outer membranes of E. coli a Gram-negative bacterium. |
| emrB | 02257 | U00096.1:2812615-2814154 | 100.0% | 84.41% | fluoroquinolone | emrB is a translocase in the emrB -TolC efflux protein in E. coli. It recognizes substrates including carbonyl cyanide m-chlorophenylhydrazone (CCCP) nalidixic acid and thioloactomycin. |
| emrR | 02259 | U00096.3:2810769-2811300 | 100.0% | 85.88% | fluoroquinolone | EmrR is a negative regulator for the EmrAB-TolC multidrug efflux pump in E. coli. Mutations lead to EmrAB-TolC overexpression. |
| golS | 00096 | AE006468.2:400860-401325 | 100.0% | 99.57% | carbapenem; cephalosporin; monobactam; penicillin_beta-lactam; phenicol | GolS is a regulator activated by the presence of golD and promotes the expression of the MdsABC efflux pump. |
| kdpE | 04363 | U00096.3:721733-721055 | 99.12% | 81.6% | aminoglycoside | kdpE is a transcriptional activator that is part of the two-component system KdpD/KdpE that is studied for its regulatory role in potassium transport and has been identified as an adaptive regulator involved in the virulence and intracellular survival of pathogenic bacteria. kdpE regulates a range of virulence loci through direct promoter binding. |
| marA | 03465 | AP009048.1:1621287-1621671 | 91.15% | 89.43% | carbapenem; cephalosporin; disinfecting_agents_and_antiseptics; fluoroquinolone; glycylcycline; monobactam; penicillin_beta-lactam; phenicol; rifamycin; tetracycline | In the presence of antibiotic stress E. coli overexpresses the global activator protein MarA which besides inducing MDR efflux pump AcrAB also down- regulates synthesis of the porin OmpF. |
| mdsA | 00098 | AE006468.2:398284-397057 | 100.0% | 98.86% | carbapenem; cephalosporin; monobactam; penicillin_beta-lactam; phenicol | MdsA is the membrane fusion protein of the multidrug and metal efflux complex MdsABC. |
| mdsB | 00099 | AE006468.2:397061-393893 | 100.0% | 99.53% | carbapenem; cephalosporin; monobactam; penicillin_beta-lactam; phenicol | MdsB is the inner membrane transporter of the multidrug and metal efflux complex MdsABC. mdsB corresponds to 1 locus in Pseudomonas aeruginosa PAO1 (gene name: mexQ) and 2 loci in Pseudomonas aeruginosa LESB58. |
| mdsC | 00100 | AE006468.2:393931-392419 | 96.43% | 98.28% | carbapenem; cephalosporin; monobactam; penicillin_beta-lactam; phenicol | MdsC is the outer membrane channel of the multidrug and metal efflux complex MdsABC. |
| mdtB | 02835 | U00096.1:2155262-2158385 | 99.97% | 81.39% | aminocoumarin | MdtB is a transporter that forms a heteromultimer complex with MdtC to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. |
| mdtC | 02834 | U00096.1:2158385-2161463 | 99.03% | 81.36% | aminocoumarin | MdtC is a transporter that forms a heteromultimer complex with MdtB to form a multidrug transporter. MdtBC is part of the MdtABC-TolC efflux complex. In the absence of MdtB MdtC can form a homomultimer complex that results in a functioning efflux complex with a narrower drug specificity. mdtC corresponds to 3 loci in Pseudomonas aeruginosa PAO1 (gene name: muxC/muxB) and 3 loci in Pseudomonas aeruginosa LESB58. |
| msbA | 04130 | U00096.3:966620-968369 | 100.0% | 84.96% | nitroimidazole | MsbA is a multidrug resistance transporter homolog from E. coli and belongs to a superfamily of transporters that contain an adenosine triphosphate (ATP) binding cassette (ABC) which is also called a nucleotide-binding domain (NBD). MsbA is a member of the MDR-ABC transporter group by sequence homology. MsbA transports lipid A a major component of the bacterial outer cell membrane and is the only bacterial ABC transporter that is essential for cell viability. |
| sdiA | 03954 | AE006468.2:2040377-2039654 | 100.0% | 99.31% | cephalosporin; disinfecting_agents_and_antiseptics; fluoroquinolone; glycylcycline; penicillin_beta-lactam; phenicol; rifamycin; tetracycline | SdiA is a cell division regulator that is also a positive regulator of AcrAB only when it's expressed from a plasmid. When the sdiA gene is on the chromosome it has no effect on expression of acrAB. |
RESFINDER results1 hit
| Gene | Locus tag | Accession | Coverage | Identity | Classification | Product |
|---|---|---|---|---|---|---|
| aac(6')-Iaa_1 | 03560 | NC_003197 | 100.0% | 96.35% | Amikacin; Tobramycin | aac(6')-Iaa |
VFDB results159 hits
| Gene | Locus tag | Accession | Coverage | Identity | Classification | Product |
|---|---|---|---|---|---|---|
| STM0266 | 00166 | NP_459263 | 100.0% | 98.67% | (STM0266) hypothetical protein [SCI (Salmonella centrisome island)/SPI-6 T6SS (VF0974) - Effector delivery system (VFC0086)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| acrB | 04591 | WP_002892069 | 99.4% | 83.82% | (acrB) acriflavine resistance protein B [AcrAB (VF0568) - Antimicrobial activity/Competitive advantage (VFC0325)] [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044] | |
| allB | 04540 | WP_012737535 | 99.93% | 82.17% | (allB) allantoinase [Allantion utilization (VF0572) - Nutritional/Metabolic factor (VFC0272)] [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044] | |
| avrA | 02205 | NP_461786 | 95.38% | 99.65% | (avrA) type III secretion system effector AvrA acetyltransferease [TTSS-1 secreted effectors (VF0949) - Effector delivery system (VFC0086)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| bapA | 02314 | WP_001237694 | 100.0% | 100.0% | (bapA) biofilm-associated protein BapA [BapA (VF0971) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Enteritidis str. P125109] | |
| cheB | 03923 | WP_003859716 | 100.0% | 85.14% | (cheB) protein-glutamate methylesterase/protein-glutamine glutaminase [Flagella (VF1400) - Motility (VFC0204)] [Enterobacter cloacae strain M12X01451] | |
| cheR | 03924 | WP_008500429 | 100.0% | 81.31% | (cheR) protein-glutamate O-methyltransferase CheR [Flagella (VF1400) - Motility (VFC0204)] [Enterobacter cloacae strain M12X01451] | |
| cheW | 03926 | WP_013096054 | 96.83% | 81.35% | (cheW) chemotaxis protein CheW [Flagella (VF1400) - Motility (VFC0204)] [Enterobacter cloacae strain M12X01451] | |
| cheY | 03922 | WP_008500431 | 100.0% | 84.87% | (cheY) chemotaxis response regulator CheY [Flagella (VF1400) - Motility (VFC0204)] [Enterobacter cloacae strain M12X01451] | |
| cheZ | 03921 | WP_013096065 | 99.38% | 83.15% | (cheZ) protein phosphatase CheZ [Flagella (VF1400) - Motility (VFC0204)] [Enterobacter cloacae strain M12X01451] | |
| csgA | 03073 | NP_460115 | 100.0% | 98.9% | (csgA) curlin major subunit CsgA [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgB | 03072 | NP_460114 | 100.0% | 99.56% | (csgB) minor curlin subunit precursor curli nucleator protein CsgB [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgC | 03074 | NP_460116 | 100.0% | 100.0% | (csgC) curli assembly protein CsgC [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgD | 03070 | NP_460113 | 100.0% | 99.69% | (csgD) DNA-binding transcriptional regulator CsgD [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgE | 03069 | NP_460112 | 100.0% | 100.0% | (csgE) curli production assembly/transport protein CsgE [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgF | 03068 | NP_460111 | 100.0% | 100.0% | (csgF) curli production assembly/transport protein CsgF [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| csgG | 03067 | NP_460110 | 100.0% | 99.64% | (csgG) curli production assembly/transport protein CsgG [Agf (VF0103) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| entA | 04471 | WP_000348393 | 97.46% | 80.5% | (entA) 23-dihydro-23-dihydroxybenzoate dehydrogenase EntA [Enterobactin (VF0228) - Nutritional/Metabolic factor (VFC0272)] [Escherichia coli CFT073] | |
| entB | 04472 | WP_004210873 | 98.94% | 80.77% | (entB) 23-dihydro-23-dihydroxybenzoate synthetase isochroismatase [Ent (VF0562) - Nutritional/Metabolic factor (VFC0272)] [Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044] | |
| fepG | 04478 | WP_000640938 | 91.54% | 80.53% | (fepG) iron-enterobactin ABC transporter permease [Enterobactin (VF0228) - Nutritional/Metabolic factor (VFC0272)] [Escherichia coli CFT073] | |
| fimA | 04519 | NP_459538 | 100.0% | 99.1% | (fimA) type-1 fimbrial protein subunit A [Type 1 fimbriae (VF0102) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| fimC | 04517 | NP_459540 | 100.0% | 98.99% | (fimC) chaperone protein FimC [Type 1 fimbriae (VF0102) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| fimD | 04516 | NP_459541 | 100.0% | 99.0% | (fimD) usher protein FimD [Type 1 fimbriae (VF0102) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| fimF | 04514 | NP_459543 | 100.0% | 99.23% | (fimF) type I fimbriae adaptor protein FimF [Type 1 fimbriae (VF0102) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] | |
| fimH | 04515 | NP_459542 | 100.0% | 98.21% | (fimH) type I fimbriae minor fimbrial subunit FimH adhesin [Type 1 fimbriae (VF0102) - Adherence (VFC0001)] [Salmonella enterica subsp. enterica serovar Typhimurium str. LT2] |
This public preview shows the first 25 of 159 hits.
geNomad analysis
Mobile genetic element predictions
Prophage and plasmid predictions identified from the submitted genome assembly.
3Prophage predictions
1Plasmid predictions
Prophage predictions3 results
| Sequence | Length | Topology | Coordinates | Genes | Taxonomy |
|---|---|---|---|---|---|
| BMCPR_BAC_002355_1|provirus_3082424_3148145 | 65,722 bp | Provirus | 3082424-3148145 | 84 | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; |
| BMCPR_BAC_002355_1|provirus_3685904_3698959 | 13,056 bp | Provirus | 3685904-3698959 | 21 | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; |
| BMCPR_BAC_002355_1|provirus_3916047_3942637 | 26,591 bp | Provirus | 3916047-3942637 | 37 | Viruses;Duplodnaviria;Heunggongvirae;Uroviricota;Caudoviricetes;; |
Plasmid predictions1 result
| Sequence | Length | Topology | Genes | Score | Conjugation genes | AMR genes |
|---|---|---|---|---|---|---|
| BMCPR_BAC_002355_2 | 59,372 bp | No terminal repeats | 76 | 1.0 | F_traV;F_traK;F_traE;F_traL |
Detailed collection and experimental records remain accessible only to authorised users.