Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C775
  Reference Plasmid   NZ_CP060803.1
  Reference Plasmid Size   46541
  Reference Plasmid GC Content   0.35
  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
M0177463 HAHMPLJO_00006 7147 3 Gut 1.00 protein_coding synonymous_variant LOW 93T>C Asn31Asn
M0177464 HAHMPLJO_00006 7228 3 Gut 1.00 protein_coding synonymous_variant LOW 12T>G Thr4Thr
M0177465 HAHMPLJO_00007 7283 3 Gut 1.00 protein_coding synonymous_variant LOW 189T>A Ile63Ile
M0177466 HAHMPLJO_00007 7303 3 Gut 1.00 protein_coding missense_variant MODERATE 169A>C Lys57Gln
M0177467 HAHMPLJO_00007 7355 3 Gut 1.00 protein_coding synonymous_variant LOW 117T>C Ile39Ile
M0177468 HAHMPLJO_00007 7394 3 Gut 1.00 protein_coding synonymous_variant LOW 78G>A Gly26Gly
M0177469 HAHMPLJO_00007 7400 3 Gut 1.00 protein_coding synonymous_variant LOW 72T>A Ile24Ile
M0177470 HAHMPLJO_00007 7468 3 Gut 1.00 protein_coding missense_variant MODERATE 4G>A Val2Ile
M0177471 HAHMPLJO_00002 7495 3 Gut 1.00 protein_coding upstream_gene_variant MODIFIER -4667G>A None
M0177472 HAHMPLJO_00008 7629 3 Gut 1.00 protein_coding synonymous_variant LOW 831T>C Ser277Ser
M0177473 HAHMPLJO_00008 7668 3 Gut 1.00 protein_coding synonymous_variant LOW 792C>A Gly264Gly
M0177474 HAHMPLJO_00008 7781 3 Gut 1.00 protein_coding missense_variant MODERATE 679A>G Thr227Ala
M0177475 HAHMPLJO_00008 7920 3 Gut 1.00 protein_coding synonymous_variant LOW 540C>T Val180Val






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







        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
HAHMPLJO_00001 ARO:3002931 100 8.08e-256 1 364 1.0000 0.9479 glycopeptide antibiotic vanS antibiotic target alteration
HAHMPLJO_00002 ARO:3002919 100 7.79e-171 1 231 1.0000 1.0000 glycopeptide antibiotic glycopeptide resistance gene cluster antibiotic target alteration
HAHMPLJO_00010 ARO:3000375 97.2 4.23e-124 12 187 0.9412 0.7097 macrolide antibiotic Erm 23S ribosomal RNA methyltransferase antibiotic target alteration
HAHMPLJO_00046 ARO:3002962 100 5.6e-107 1 161 1.0000 1.0000 glycopeptide antibiotic vanZ antibiotic target alteration
HAHMPLJO_00047 ARO:3002955 98.7 1.31e-220 25 326 0.9264 0.9967 glycopeptide antibiotic vanY antibiotic target alteration
HAHMPLJO_00048 ARO:3002949 100 2.99e-156 1 202 1.0000 1.0000 glycopeptide antibiotic vanX antibiotic target alteration
HAHMPLJO_00049 ARO:3000010 100 1.24e-252 7 349 0.9828 1.0000 glycopeptide antibiotic glycopeptide resistance gene cluster antibiotic target alteration






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






        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
HAHMPLJO_00032 QNP36482.1|GH23 100 7.99e-273 1 369 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
HAHMPLJO_00024 3.A.7.14.1 77 1e-96 1 237 1.0000 1.5410 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
HAHMPLJO_00026 3.A.7.14.1 98.4 6e-169 1 322 1.0000 1.7596 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
HAHMPLJO_00027 3.A.7.14.1 92.3 1.7e-152 1 310 1.0000 1.6940 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
HAHMPLJO_00028 3.A.7.14.1 86.9 5.9e-150 1 306 0.9967 1.6721 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
HAHMPLJO_00029 3.A.7.14.1 98.7 1.60000000000001e-310 1 551 1.0000 3.0109 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
HAHMPLJO_00030 3.A.7.14.1 97.9 1.8e-69 1 143 1.0000 0.7814 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
HAHMPLJO_00031 3.A.7.14.1 96.2 1.1e-90 1 183 1.0000 1.0000 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
HAHMPLJO_00032 3.A.7.14.1 98.1 1.3e-212 1 369 1.0000 2.0164 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
HAHMPLJO_00033 3.A.7.14.1 99.1 4.7e-244 1 450 1.0000 2.4590 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
HAHMPLJO_00034 3.A.7.14.1 98 0 1 653 1.0000 3.5683 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
HAHMPLJO_00035 3.A.7.14.1 98.4 4.4e-104 23 212 0.8962 1.0383 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
HAHMPLJO_00038 3.A.7.14.1 97.7 0 1 654 1.0000 3.5738 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