Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C944
  Reference Plasmid   NZ_CP082832.1
  Reference Plasmid Size   186443
  Reference Plasmid GC Content   0.52
  Reference Plasmid Mobility Type   conjugative





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0189448 OGMPPGGI_00188 145608 10 Gut 0.91 protein_coding missense_variant MODERATE 167T>C Met56Thr
M0189449 OGMPPGGI_00189 146127 10 Gut 0.91 protein_coding missense_variant MODERATE 214A>G Thr72Ala
M0189450 OGMPPGGI_00189 146135 10 Gut 0.91 protein_coding missense_variant MODERATE 206G>T Gly69Val
M0189451 OGMPPGGI_00189 146290 10 Gut 0.91 protein_coding synonymous_variant LOW 51G>A Gly17Gly
M0189452 OGMPPGGI_00190 146735 10 Gut 0.91 protein_coding synonymous_variant LOW 267G>T Gly89Gly
M0189453 OGMPPGGI_00190 146792 10 Gut 0.91 protein_coding synonymous_variant LOW 324G>A Arg108Arg
M0189454 OGMPPGGI_00191 146897 10 Gut 0.91 protein_coding missense_variant MODERATE 509A>C Gln170Pro
M0189455 OGMPPGGI_00191 146946 10 Gut 0.91 protein_coding missense_variant MODERATE 460A>T Arg154Trp
M0189456 OGMPPGGI_00191 147104 10 Gut 0.91 protein_coding missense_variant MODERATE 302T>A Leu101Gln
M0189457 OGMPPGGI_00191 147106 10 Gut 0.91 protein_coding missense_variant MODERATE 300C>A Asp100Glu
M0189458 OGMPPGGI_00191 147115 10 Gut 0.91 protein_coding synonymous_variant LOW 291G>C Leu97Leu
M0189459 OGMPPGGI_00191 147117 10 Gut 0.91 protein_coding missense_variant MODERATE 289C>A Leu97Met
M0189460 OGMPPGGI_00185 147667 9 Gut 0.82 protein_coding upstream_gene_variant MODIFIER -4132A>G None
M0189461 OGMPPGGI_00185 147742 9 Gut 0.82 protein_coding upstream_gene_variant MODIFIER -4207G>A None
M0189462 OGMPPGGI_00193 147778 9 Gut 0.82 protein_coding synonymous_variant LOW 15A>T Thr5Thr
M0189463 OGMPPGGI_00193 147857 9 Gut 0.82 protein_coding missense_variant MODERATE 94G>A Ala32Thr
M0189464 OGMPPGGI_00193 147911 9 Gut 0.82 protein_coding missense_variant MODERATE 148T>C Trp50Arg
M0189465 OGMPPGGI_00193 147940 8 Gut 0.73 protein_coding synonymous_variant LOW 177A>G Gly59Gly
M0189466 OGMPPGGI_00193 147952 8 Gut 0.73 protein_coding synonymous_variant LOW 189T>A Gly63Gly
M0189467 OGMPPGGI_00193 147994 8 Gut 0.73 protein_coding synonymous_variant LOW 231A>G Glu77Glu
M0189468 OGMPPGGI_00193 148069 8 Gut 0.73 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0189469 OGMPPGGI_00193 148087 8 Gut 0.73 protein_coding synonymous_variant LOW 324G>A Lys108Lys
M0189470 OGMPPGGI_00194 148135 8 Gut 0.73 protein_coding missense_variant MODERATE 46G>C Val16Leu
M0189471 OGMPPGGI_00194 148143 8 Gut 0.73 protein_coding synonymous_variant LOW 54T>C Ser18Ser
M0189472 OGMPPGGI_00194 148200 7 Gut 0.64 protein_coding synonymous_variant LOW 111T>G Pro37Pro
M0189473 OGMPPGGI_00194 148221 7 Gut 0.64 protein_coding synonymous_variant LOW 132A>G Ala44Ala
M0189474 OGMPPGGI_00194 148244 7 Gut 0.64 protein_coding missense_variant MODERATE 155G>A Arg52Lys
M0189475 OGMPPGGI_00193 147811 8 Gut 0.73 protein_coding synonymous_variant LOW 48T>C Val16Val






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition
OGMPPGGI_00182 VFG001827 ShET2 99.7 7.9e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
OGMPPGGI_00182 VFG036084 Enterotoxin SenB/TieB 100 1.2e-224 1 391 1.0 1 Exotoxin enterotoxin production-related protein TieB prediction







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group
OGMPPGGI_00157 Benzylkonium Chloride (BAC) [class: Quaternary Ammonium Compounds (QACs)], Ethidium Bromide [class: Phenanthridine], Acriflavine [class: Acridine], Chlorhexidine [class: Biguanides], Pyronin Y [class: Xanthene], Rhodamine 6G [class: Xanthene], Methyl Viologen [class: Paraquat], Tetraphenylphosphonium (TPP) [class: Quaternary Ammonium Compounds (QACs)], 4,6-diamidino-2-phenylindole (DAPI) [class: Diamindine], Acridine Orange [class: Acridine], Sodium Dodecyl Sulfate (SDS) [class: Organo-sulfate], Sodium Deoxycholate (SDC) [class: Acid], Crystal Violet [class: Triarylmethane], Cetrimide (CTM) [class: Quaternary Ammonium Compounds (QACs)], Cetylpyridinium Chloride (CPC) [class: Quaternary Ammonium Compounds (QACs)], Dequalinium [class: Quaternary Ammonium Compounds (QACs)] 100 1.1e-60 1 115 1.0000 1.0000 experiment






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism
OGMPPGGI_00145 ARO:3000165 99.7 7.17e-278 1 390 0.9774 0.9198 tetracycline antibiotic major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
OGMPPGGI_00149 ARO:3000316 100 1e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
OGMPPGGI_00150 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
OGMPPGGI_00156 ARO:3000410 100 2.94e-199 1 279 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul antibiotic target replacement
OGMPPGGI_00157 ARO:3005010 100 2.01e-78 1 115 1.0000 1.0000 disinfecting agents and antiseptics major facilitator superfamily (MFS) antibiotic efflux pump antibiotic efflux
OGMPPGGI_00158 ARO:3002605 100 9.47e-192 1 262 1.0000 1.0000 aminoglycoside antibiotic ANT(3'') antibiotic inactivation
OGMPPGGI_00159 ARO:3002860 99.4 1.04e-111 43 199 0.7889 1.0000 diaminopyrimidine antibiotic trimethoprim resistant dihydrofolate reductase dfr antibiotic target replacement






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant
OGMPPGGI_00160 PHI:9804 int 100 4e-14 1 37 0.1098 1.0000 rodents gastroenteritis integrase reduced virulence
OGMPPGGI_00182 PHI:10795 senB 100 4.2e-225 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
OGMPPGGI_00183 PHI:10794 cjrC 100 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
OGMPPGGI_00184 PHI:10793 cjrB 100 1.7e-137 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
OGMPPGGI_00185 PHI:10792 cjrA 100 5.6e-166 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage
OGMPPGGI_00079 AKD26598.1|GH23 100 3.49e-124 1 169 1 1





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term
OGMPPGGI_00119 1.E.53.1.11 98.5 2.5e-32 1 68 1.0000 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
OGMPPGGI_00144 2.A.7.3.67 100 1.8e-159 1 294 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.7 The Drug/Metabolite Transporter (DMT) Superfamily
OGMPPGGI_00145 2.A.1.2.4 100 2.4e-223 1 399 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.1 The Major Facilitator Superfamily (MFS)
OGMPPGGI_00154 2.A.51.1.7 99.5 5.1e-210 1 376 0.9377 0.9666 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.51 The Chromate Ion Transporter (CHR) Family
OGMPPGGI_00183 1.B.14.7.1 100 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
OGMPPGGI_00184 2.C.1.1.3 100 3.7e-137 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
OGMPPGGI_00205 2.A.108.2.10 100 5e-101 3 175 0.9886 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family
OGMPPGGI_00206 2.A.108.2.10 99.8 0 1 646 1.0000 3.7341 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.108 The Iron/Lead Transporter (ILT) Family