INCFinder

GenBank ID	CP117349.1
Plasmid name	pRM101_1
Classification	C1
Length	180 389 bp
GC content	51%
Organism	Salmonella enterica subsp. enterica serovar Heidelberg strain RM101
Curation	Automatic annotation

Plasmid map

Characteristic genes

Gene name	Length	Location	Length of alignment	Identity (%)	Coverage (%)
repA	1101	1 - 1101 (+)	1101	100	100
ORF1832	5499	65093 - 70591 (+)	5499	100	100
RHS1	4254	154133 - 158386 (+)	4254	100	100
AriB	1156	33094 - 34249 (+)	1156	100	44
AriB	640	24214 - 24853 (+)	640	100	24

Antimicrobial resistance genes

Type match	Model name	Model type	Location	E-value	Identity
Strict	APH(6)-Id	protein homolog model	31435 - 32271(-)	0	99.64 %
APH(6) AMR Gene Family Phosphorylation of streptomycin on the hydroxyl group at position 6 streptomycin Antibiotic Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Strict	APH(3'')-Ib	protein homolog model	32271 - 33074(-)	0	99.63 %
APH(3'') AMR Gene Family Phosphorylation of streptomycin on the hydroxyl group at position 3'' streptomycin Antibiotic Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Perfect	sul2	protein homolog model	33135 - 33950(-)	0	100 %
sulfonamide resistant sul AMR Gene Family The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide. sulfadiazine Antibiotic Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfadimidine Antibiotic Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides. sulfadoxine Antibiotic Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfamethoxazole Antibiotic Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides. sulfisoxazole Antibiotic Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfacetamide Antibiotic Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability. mafenide Antibiotic Mafenide is a sulfonamide used topically for treating burns. sulfasalazine Antibiotic Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis. sulfamethizole Antibiotic Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase. sulfonamide antibiotic Drug Class Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway. antibiotic target replacement Resistance Mechanism Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.
Perfect	CMY-2	protein homolog model	62291 - 63436(+)	0	100 %
CMY beta-lactamase AMR Gene Family CMY beta-lactamases are plasmid-mediated class C beta-lactamases that encodes for resistance to cephamycins. cefoxitin Antibiotic Cefoxitin is a cephamycin antibiotic often grouped with the second generation cephalosporins. Cefoxitin is bactericidal and acts by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. Cefoxitin's 7-alpha-methoxy group and 3' leaving group make it a poor substrate for most beta-lactamases. ceftazidime Antibiotic Ceftazidime is a third-generation cephalosporin antibiotic. Like other third-generation cephalosporins, it has broad spectrum activity against Gram-positive and Gram-negative bacteria. Unlike most third-generation agents, it is active against Pseudomonas aeruginosa, however it has weaker activity against Gram-positive microorganisms and is not used for such infections. cephalosporin Drug Class Cephalosporins are a class of beta-lactam antibiotics, containing the beta-lactam ring fused with a dihydrothiazolidine ring. Together with cephamycins they belong to a sub-group called cephems. Cephalosporin are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. cephamycin Drug Class Cephamycins are a group of beta-lactam antibiotics, very similar to cephalosporins. Together with cephalosporins, they form a sub-group of antibiotics known as cephems. Cephamycins are bactericidal, and act by inhibiting the synthesis of the peptidoglycan layer of bacterial cell walls. The peptidoglycan layer is important for cell wall structural integrity, especially in Gram-positive organisms. The 7-alpha-methoxy group increases resistance to beta-lactamases. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Strict	aadA22	protein homolog model	97724 - 98515(+)	4.35414e-176	90.49 %
ANT(3'') AMR Gene Family Nucleotidylylation of streptomycin at the hydroxyl group at position 3'' spectinomycin Antibiotic Spectinomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Spectinomycin works by binding to the bacterial 30S ribosomal subunit inhibiting translation. streptomycin Antibiotic Streptomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Streptomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Perfect	sul1	protein homolog model	100967 - 101806(+)	0	100 %
sulfonamide resistant sul AMR Gene Family The sul genes encode forms of dihydropteroate synthase that confer resistance to sulfonamide. sulfadiazine Antibiotic Sulfadiazine is a potent inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfadimidine Antibiotic Sulfadimidine is an alkaline sulfonamide antibiotic that inhibits dihydropteroate synthase, and enzyme in the tetrahydrofolic acid biosynthesis pathway. This interferes with the production of folate, which is a precursor to many amino acids and nucleotides. sulfadoxine Antibiotic Sulfadoxine is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfamethoxazole Antibiotic Sulfamethoxazole is a sulfonamide antibiotic usually taken with trimethoprim, a diaminopyrimidine antibiotic. Sulfamethoxazole inhibits dihydropteroate synthase, essential to tetrahydrofolic acid biosynthesis. This pathway generates compounds used in the synthesis of many amino acids and nucleotides. sulfisoxazole Antibiotic Sulfisoxazole is an inhibitor of dihydropteroate synthase, interfering with the tetrahydrofolic biosynthesis pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor to many nucleotides and amino acids. sulfacetamide Antibiotic Sulfacetamide is a very soluable sulfonamide antibiotic previously used to treat urinary tract infections. Its relatively low activity and toxicity to those with Stevens-Johnson syndrome have reduced its use and availability. mafenide Antibiotic Mafenide is a sulfonamide used topically for treating burns. sulfasalazine Antibiotic Sulfasalazine is a derivative of the early sulfonamide sulfapyridine (salicylazosulfapyridine). It was developed to increase water solubility and is taken orally for ulcerative colitis. sulfamethizole Antibiotic Sulfamethizole is a short-acting sulfonamide that inhibits dihydropteroate synthetase. sulfonamide antibiotic Drug Class Sulfonamides are broad spectrum, synthetic antibiotics that contain the sulfonamide group. Sulfonamides inhibit dihydropteroate synthase, which catalyzes the conversion of p-aminobenzoic acid to dihydropteroic acid as part of the tetrahydrofolic acid biosynthetic pathway. Tetrahydrofolic acid is essential for folate synthesis, a precursor of many nucleotides and amino acids. Many sulfamides are taken with trimethoprim, an inhibitor of dihydrofolate reductase, also disturbing the trihydrofolic acid synthesis pathway. antibiotic target replacement Resistance Mechanism Replacement or substitution of antibiotic action target, which process will result in antibiotic resistance.
Strict	APH(3')-Ia	protein homolog model	124133 - 124948(+)	0	98.89 %
APH(3') AMR Gene Family Phosphorylation of 2-deoxystreptamine aminoglycosides on the hydroxyl group at position 3' neomycin Antibiotic Neomycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Neomycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. ribostamycin Antibiotic Ribostamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Ribostamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. kanamycin A Antibiotic Kanamycin is an aminoglycoside antibiotic used to treat different types of bacterial infections. Kanamycin works by binding to the bacterial 30S ribosomal subunit, causing misreading of mRNA and leaving the bacterium unable to synthesize proteins vital to its growth. G418 Antibiotic A gentamicin class aminoglycoside antibiotic often used in mammalian cell culture work as a selectable marker for the neo cassette (APH3'). paromomycin Antibiotic An aminoglycoside antibiotic used for the treatment of parasitic infections. It is similar to neomycin sharing a similar spectrum of activity, but its hydroxyl group at the 6'-position instead of an amino group makes it resistant to AAC(6') modifying enzymes. lividomycin A Antibiotic Lividomycin A is a pentasaccharide antibiotic which interferes with bacterial protein synthesis. lividomycin B Antibiotic Lividomycin B is a derivative of lividomycin A with a removed mannose group (demannosyllividomycin A). Livodomycins interfere with bacterial protein synthesis. aminoglycoside antibiotic Drug Class Aminoglycosides are a group of antibiotics that are mostly effective against Gram-negative bacteria. These molecules consist of aminated sugars attached to a dibasic cyclitol. Aminoglycosides work by binding to the bacterial 30S ribosomal subunit (some work by binding to the 50S subunit), inhibiting the translocation of the peptidyl-tRNA from the A-site to the P-site and also causing misreading of mRNA, leaving the bacterium unable to synthesize proteins vital to its growth. antibiotic inactivation Resistance Mechanism Enzymatic inactivation of antibiotic to confer drug resistance.
Strict	tetO	protein homolog model	128066 - 129985(-)	0	99.06 %
tetracycline-resistant ribosomal protection protein AMR Gene Family A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein. tetracycline Antibiotic Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome. doxycycline Antibiotic Doxycycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome. minocycline Antibiotic Minocycline is second generation semi-synthetic derivative of the tetracycline group of antibiotics. It inhibits bacterial protein synthesis by binding to the 30S subunit of the bacterial ribosome and preventing the aminotransferase-tRNA from associating with the ribosome. chlortetracycline Antibiotic Chlortetracycline was an early, first-generation tetracycline antibiotic developed in the 1940's. It inhibits bacterial protein synthesis by binding to the 30S subunit of bacterial ribosomes, preventing the aminoacyl-tRNA from binding to the ribosome. demeclocycline Antibiotic Demeclocycline is a tetracycline analog with 7-chloro and 6-methyl groups. Due to its fast absorption and slow excretion, it maintains higher effective blood levels compared to other tetracyclines. oxytetracycline Antibiotic Oxytetracycline is a derivative of tetracycline with a 5-hydroxyl group. Its activity is similar to other tetracyclines. tetracycline antibiotic Drug Class These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes. antibiotic target protection Resistance Mechanism Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance.
Strict	tet(B)	protein homolog model	142476 - 143681(+)	0	99.25 %
major facilitator superfamily (MFS) antibiotic efflux pump AMR Gene Family Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient. tetracycline Antibiotic Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome. tetracycline antibiotic Drug Class These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes. efflux pump complex or subunit conferring antibiotic resistance Efflux Component Efflux proteins that pump antibiotic out of a cell to confer resistance. antibiotic efflux Resistance Mechanism Antibiotic resistance via the transport of antibiotics out of the cell.
Strict	tetR	protein overexpression model	141771 - 142394(-)	1.15596e-155	99.52 %
major facilitator superfamily (MFS) antibiotic efflux pump AMR Gene Family Directed pumping of antibiotic out of a cell to confer resistance. Major facilitator superfamily (MFS) transporters and ABC transporters comprise the two largest and most functionally diverse of the transporter superfamilies. However, MFS transporters are distinct from ABC transporters in both their primary sequence and structure and in the mechanism of energy coupling. As secondary transporters they are, like RND and SMR transporters, energized by the electrochemical proton gradient. tetracycline Antibiotic Tetracycline is a broad-spectrum polyketide antibiotic produced by many Streptomyces. It works by inhibiting action of the prokaryotic 30S ribosome. tetracycline antibiotic Drug Class These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes. efflux pump complex or subunit conferring antibiotic resistance Efflux Component Efflux proteins that pump antibiotic out of a cell to confer resistance. protein(s) and two-component regulatory system modulating antibiotic efflux Efflux Regulator Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux. antibiotic target alteration Resistance Mechanism Mutational alteration or enzymatic modification of antibiotic target which results in antibiotic resistance. antibiotic efflux Resistance Mechanism Antibiotic resistance via the transport of antibiotics out of the cell.

Plasmid genes

AMR genes

Plasmid map

Characteristic genes

Antimicrobial resistance genes