Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C502
  Reference Plasmid   NZ_CP024238.1
  Reference Plasmid Size   274465
  Reference Plasmid GC Content   0.50
  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
M0167502 CGLHMGKM_00029 25099 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4802C>T None
M0167503 CGLHMGKM_00029 25121 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4824C>T None
M0167504 CGLHMGKM_00037 26000 3 Gut 0.09 protein_coding missense_variant MODERATE 1912C>A Arg638Ser
M0167505 CGLHMGKM_00037 27096 3 Gut 0.09 protein_coding synonymous_variant LOW 816A>G Gln272Gln
M0167506 CGLHMGKM_00037 27474 3 Gut 0.09 protein_coding missense_variant MODERATE 438T>A Asp146Glu
M0167507 CGLHMGKM_00034 28356 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4326A>G None
M0167508 CGLHMGKM_00043 32556 3 Gut 0.09 protein_coding synonymous_variant LOW 970C>T Leu324Leu
M0167509 CGLHMGKM_00039 33324 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -3856A>C None
M0167510 CGLHMGKM_00046 34069 3 Gut 0.09 protein_coding missense_variant MODERATE 169G>A Glu57Lys
M0167511 CGLHMGKM_00047 34539 3 Gut 0.09 protein_coding synonymous_variant LOW 42T>C Tyr14Tyr
M0167512 CGLHMGKM_00048 35509 3 Gut 0.09 protein_coding missense_variant MODERATE 108G>T Leu36Phe
M0167513 CGLHMGKM_00044 36111 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -2857G>A None
M0167514 CGLHMGKM_00151 121037 4 Gut 0.11 protein_coding synonymous_variant LOW 402T>C Ile134Ile
M0167515 CGLHMGKM_00151 121103 4 Gut 0.11 protein_coding synonymous_variant LOW 336T>C Ala112Ala
M0167516 CGLHMGKM_00151 121268 4 Gut 0.11 protein_coding synonymous_variant LOW 171G>C Gly57Gly
M0167517 CGLHMGKM_00151 121271 4 Gut 0.11 protein_coding synonymous_variant LOW 168C>T Phe56Phe
M0167518 CGLHMGKM_00152 121652 4 Gut 0.11 protein_coding synonymous_variant LOW 1806C>T Ala602Ala
M0167519 CGLHMGKM_00152 122777 3 Gut 0.09 protein_coding synonymous_variant LOW 681G>A Val227Val
M0167520 CGLHMGKM_00156 125279 4 Gut 0.11 protein_coding synonymous_variant LOW 456G>A Pro152Pro
M0167521 CGLHMGKM_00156 125384 4 Gut 0.11 protein_coding synonymous_variant LOW 351A>C Ile117Ile
M0167522 CGLHMGKM_00156 125582 4 Gut 0.11 protein_coding synonymous_variant LOW 153G>T Arg51Arg
M0167523 CGLHMGKM_00156 125585 4 Gut 0.11 protein_coding synonymous_variant LOW 150C>T Asn50Asn
M0167524 CGLHMGKM_00157 126021 4 Gut 0.11 protein_coding synonymous_variant LOW 1122G>A Glu374Glu
M0167525 CGLHMGKM_00157 126105 4 Gut 0.11 protein_coding synonymous_variant LOW 1038A>G Pro346Pro
M0167526 CGLHMGKM_00157 126384 4 Gut 0.11 protein_coding synonymous_variant LOW 759G>A Arg253Arg
M0167527 CGLHMGKM_00158 127242 5 Gut 0.14 protein_coding synonymous_variant LOW 183T>C Ala61Ala
M0167528 CGLHMGKM_00207 168730 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1365A>G None
M0167529 CGLHMGKM_00207 168833 3 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -1468T>A None
M0167530 CGLHMGKM_00210 169012 3 Gut 0.09 protein_coding missense_variant MODERATE 841T>G Ser281Ala
M0167531 CGLHMGKM_00210 169250 3 Gut 0.09 protein_coding synonymous_variant LOW 603C>G Val201Val
M0167532 CGLHMGKM_00210 169442 3 Gut 0.09 protein_coding synonymous_variant LOW 411T>C Asp137Asp
M0167533 CGLHMGKM_00239 194420 3 Gut 0.09 protein_coding missense_variant MODERATE 13G>A Ala5Thr
M0167534 CGLHMGKM_00239 194496 3 Gut 0.09 protein_coding missense_variant MODERATE 89C>T Thr30Ile
M0167535 CGLHMGKM_00213 171358 3 Gut 0.09 protein_coding missense_variant MODERATE 136T>C Tyr46His
M0167536 CGLHMGKM_00216 172923 3 Gut 0.09 protein_coding synonymous_variant LOW 228T>C Ala76Ala
M0167537 CGLHMGKM_00216 172998 3 Gut 0.09 protein_coding synonymous_variant LOW 153T>A Ala51Ala
M0167538 CGLHMGKM_00216 173010 3 Gut 0.09 protein_coding synonymous_variant LOW 141G>A Ala47Ala
M0167539 CGLHMGKM_00216 173013 3 Gut 0.09 protein_coding synonymous_variant LOW 138G>A Lys46Lys






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
CGLHMGKM_00061 VFG034541 EtpA 70.8 0 1 1513 0.9967 0.9831 Adherence Two-partner secreted adhesin EtpA experiment
CGLHMGKM_00062 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
CGLHMGKM_00140 VFG001445 TraJ 100 6e-116 1 200 0.8772 0.995 Invasion unknown protein experiment
CGLHMGKM_00278 VFG036068 Heat-labile toxin (LT) 99.2 1.4e-66 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
CGLHMGKM_00279 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
CGLHMGKM_00302 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
CGLHMGKM_00303 VFG036068 Heat-labile toxin (LT) 98.2 5.8e-60 1 114 0.8976 0.9194 Exotoxin enterotoxin subunit B (from human) experiment
CGLHMGKM_00061 VFG034541 EtpA 70.8 0 1 1513 0.9967 0.9831 Adherence Two-partner secreted adhesin EtpA prediction
CGLHMGKM_00062 VFG042382 EtpA 98.8 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
CGLHMGKM_00070 VFG035930 Dispersin 100 8.1e-235 15 428 0.9673 1 Others AatD prediction
CGLHMGKM_00079 VFG035924 Dispersin 77.8 1.7e-89 1 207 0.9952 0.9952 Others ATP-binding protein AatC prediction
CGLHMGKM_00080 VFG035917 Dispersin 99.6 7.5e-143 3 257 0.9922 1 Others AatB prediction
CGLHMGKM_00081 VFG035910 Dispersin 100 2.4e-220 1 400 1.0 1 Others outer membrane protein AatA prediction
CGLHMGKM_00082 VFG035903 Dispersin 99.7 4.7e-194 4 379 0.9921 1 Others permease AatP prediction
CGLHMGKM_00140 VFG001445 TraJ 100 4.5e-115 1 200 0.8772 0.995 Invasion unknown protein prediction
CGLHMGKM_00278 VFG036068 Heat-labile toxin (LT) 99.2 1e-65 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
CGLHMGKM_00279 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
CGLHMGKM_00291 VFG043747 Heat-stable toxin (ST) 98.6 1.2e-34 1 72 1.0 1 Exotoxin unknown protein prediction
CGLHMGKM_00302 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) prediction
CGLHMGKM_00303 VFG036068 Heat-labile toxin (LT) 98.2 4.3e-59 1 114 0.8976 0.9194 Exotoxin enterotoxin subunit B (from human) prediction
CGLHMGKM_00312 VFG042480 Adhesive fimbriae 97.3 4.5e-205 1 372 1.0 0.9973 Adherence CS5 fimbrial minor pilin subunit prediction
CGLHMGKM_00313 VFG042479 Adhesive fimbriae 92.9 1.7e-114 1 225 1.0 1.0045 Adherence hypothetical protein prediction
CGLHMGKM_00314 VFG042478 Adhesive fimbriae 90.6 3.9e-102 1 203 1.0 1 Adherence hypothetical protein prediction
CGLHMGKM_00315 VFG042477 Adhesive fimbriae 95.5 0 1 815 1.0 1.0012 Adherence hypothetical protein prediction
CGLHMGKM_00316 VFG042476 Adhesive fimbriae 94.6 4.8e-122 1 223 1.0 0.9955 Adherence hypothetical protein prediction
CGLHMGKM_00317 VFG001433 Adhesive fimbriae 99.5 1.9e-104 1 203 1.0 1 Adherence CS7 fimbria major subunit CsvA precursor 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






        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






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
CGLHMGKM_00278 PHI:699 CtxB 79 3e-52 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
CGLHMGKM_00279 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
CGLHMGKM_00302 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) reduced virulence
CGLHMGKM_00303 PHI:699 CtxB 79.8 4.2e-49 1 114 0.8976 1.0000 primates cholera Cholera toxin (CT) reduced virulence






        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
CGLHMGKM_00059 APG37925.1|GT41 99.8 0 1 465 1 0.73
CGLHMGKM_00142 CCA64278.1|GH23 99.5 7.84e-155 1 215 1 1
CGLHMGKM_00260 APG37898.1|GH23 100 4.96e-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
CGLHMGKM_00040 8.B.24.2.1 100 1.8e-68 1 127 1.0000 1.0000 8 Accessory Factors Involved in Transport 8.B Ribosomally synthesized protein/peptide toxins/agonists that target channels and carriers 8.B.24 The Colicin Immunity Protein (ColIP) Functional Family
CGLHMGKM_00058 9.B.127.1.3 100 1.4e-94 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
CGLHMGKM_00062 1.B.20.3.3 98.8 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
CGLHMGKM_00279 1.C.72.4.1 99.5 3.1e-129 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family
CGLHMGKM_00302 1.C.72.4.1 99.5 3.1e-129 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family
CGLHMGKM_00329 9.B.40.1.2 99.4 0 1 722 1.0000 0.9691 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.40 The DotA/TraY (DotA/TraY) Family
CGLHMGKM_00335 1.E.53.1.10 90.7 4.1e-16 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
CGLHMGKM_00337 3.A.7.10.1 99.8 4.2e-244 1 402 1.0000 4.1875 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
CGLHMGKM_00338 3.A.7.10.1 98.9 1.8e-206 1 356 1.0000 3.7083 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
CGLHMGKM_00339 3.A.7.10.1 99.8 2.3e-300 1 504 0.9882 5.2500 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
CGLHMGKM_00340 3.A.7.10.1 100 2.9e-136 1 241 1.0000 2.5104 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family