Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C128
  Reference Plasmid   CP077327.1
  Reference Plasmid Size   91885
  Reference Plasmid GC Content   0.53
  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
M0144810 IINKGMCE_00034 31774 3 Gut 0.18 protein_coding synonymous_variant LOW 63A>T Ala21Ala
M0144811 IINKGMCE_00034 31775 3 Gut 0.18 protein_coding missense_variant MODERATE 64A>C Ile22Leu
M0144812 IINKGMCE_00031 32458 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -3683T>A None
M0144813 IINKGMCE_00031 32459 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -3684T>G None
M0144814 IINKGMCE_00036 33306 5 Gut 0.29 protein_coding synonymous_variant LOW 42C>T Ala14Ala
M0144815 IINKGMCE_00036 33333 5 Gut 0.29 protein_coding synonymous_variant LOW 15A>C Ile5Ile
M0144816 IINKGMCE_00037 33767 5 Gut 0.29 protein_coding synonymous_variant LOW 318T>C Val106Val
M0144817 IINKGMCE_00037 33871 5 Gut 0.29 protein_coding missense_variant MODERATE 422C>T Ala141Val
M0144818 IINKGMCE_00040 34882 5 Gut 0.29 protein_coding missense_variant MODERATE 34A>G Thr12Ala
M0144819 IINKGMCE_00033 36024 5 Gut 0.29 protein_coding upstream_gene_variant MODIFIER -4849T>A None
M0144820 IINKGMCE_00045 39640 3 Gut 0.18 protein_coding synonymous_variant LOW 1183T>C Leu395Leu
M0144821 IINKGMCE_00045 40028 3 Gut 0.18 protein_coding synonymous_variant LOW 795G>A Gln265Gln
M0144822 IINKGMCE_00045 40217 3 Gut 0.18 protein_coding synonymous_variant LOW 606C>A Ser202Ser
M0144823 IINKGMCE_00045 40246 3 Gut 0.18 protein_coding missense_variant MODERATE 577A>G Asn193Asp
M0144824 IINKGMCE_00045 40322 3 Gut 0.18 protein_coding synonymous_variant LOW 501T>A Val167Val
M0144825 IINKGMCE_00046 41010 3 Gut 0.18 protein_coding synonymous_variant LOW 457T>C Leu153Leu
M0144826 IINKGMCE_00047 42192 3 Gut 0.18 protein_coding synonymous_variant LOW 477T>C Asp159Asp
M0144827 IINKGMCE_00048 42727 3 Gut 0.18 protein_coding missense_variant MODERATE 520A>G Lys174Glu
M0144828 IINKGMCE_00048 43117 3 Gut 0.18 protein_coding missense_variant MODERATE 130A>T Thr44Ser
M0144829 IINKGMCE_00049 45622 3 Gut 0.18 protein_coding synonymous_variant LOW 669T>C Ala223Ala
M0144830 IINKGMCE_00049 45753 3 Gut 0.18 protein_coding missense_variant MODERATE 538A>G Asn180Asp
M0144831 IINKGMCE_00050 46699 3 Gut 0.18 protein_coding synonymous_variant LOW 513A>T Ala171Ala
M0144832 IINKGMCE_00054 49058 3 Gut 0.18 protein_coding missense_variant MODERATE 254T>G Ile85Ser
M0144833 IINKGMCE_00055 49627 3 Gut 0.18 protein_coding missense_variant MODERATE 1019T>C Val340Ala
M0144834 IINKGMCE_00055 49850 3 Gut 0.18 protein_coding synonymous_variant LOW 796C>A Arg266Arg
M0144835 IINKGMCE_00055 49992 3 Gut 0.18 protein_coding synonymous_variant LOW 654C>T Asp218Asp
M0144836 IINKGMCE_00055 49995 3 Gut 0.18 protein_coding synonymous_variant LOW 651C>T Ile217Ile
M0144837 IINKGMCE_00055 50001 3 Gut 0.18 protein_coding synonymous_variant LOW 645T>C Ala215Ala
M0144838 IINKGMCE_00055 50041 3 Gut 0.18 protein_coding missense_variant MODERATE 605A>C Gln202Pro
M0144839 IINKGMCE_00055 50048 3 Gut 0.18 protein_coding missense_variant MODERATE 598A>G Thr200Ala
M0144840 IINKGMCE_00055 50049 3 Gut 0.18 protein_coding synonymous_variant LOW 597T>A Ala199Ala
M0144841 IINKGMCE_00055 50055 3 Gut 0.18 protein_coding synonymous_variant LOW 591A>C Thr197Thr
M0144842 IINKGMCE_00055 50088 3 Gut 0.18 protein_coding synonymous_variant LOW 558G>A Gln186Gln
M0144843 IINKGMCE_00055 50108 3 Gut 0.18 protein_coding missense_variant MODERATE 538T>C Ser180Pro
M0144844 IINKGMCE_00056 50968 3 Gut 0.18 protein_coding missense_variant MODERATE 656G>A Arg219Gln
M0144845 IINKGMCE_00059 53566 3 Gut 0.18 protein_coding synonymous_variant LOW 3204A>G Glu1068Glu
M0144846 IINKGMCE_00059 53675 3 Gut 0.18 protein_coding missense_variant MODERATE 3095A>T Glu1032Val
M0144847 IINKGMCE_00059 53746 3 Gut 0.18 protein_coding missense_variant MODERATE 3024A>C Gln1008His
M0144848 IINKGMCE_00059 53970 3 Gut 0.18 protein_coding missense_variant MODERATE 2800A>C Ile934Leu
M0144849 IINKGMCE_00059 54538 3 Gut 0.18 protein_coding synonymous_variant LOW 2232T>G Val744Val
M0144850 IINKGMCE_00059 54639 3 Gut 0.18 protein_coding missense_variant MODERATE 2131A>G Thr711Ala
M0144851 IINKGMCE_00059 54988 3 Gut 0.18 protein_coding synonymous_variant LOW 1782C>A Thr594Thr
M0144852 IINKGMCE_00059 55029 3 Gut 0.18 protein_coding missense_variant MODERATE 1741A>G Lys581Glu
M0144853 IINKGMCE_00064 59953 3 Gut 0.18 protein_coding synonymous_variant LOW 897A>G Gln299Gln
M0144854 IINKGMCE_00073 69626 3 Gut 0.18 protein_coding missense_variant MODERATE 220A>C Ile74Leu
M0144855 IINKGMCE_00074 70802 3 Gut 0.18 protein_coding synonymous_variant LOW 684G>A Gly228Gly
M0144856 IINKGMCE_00078 75085 3 Gut 0.18 protein_coding synonymous_variant LOW 639T>C Arg213Arg
M0144857 IINKGMCE_00031 31980 3 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -3205A>T None
M0144858 IINKGMCE_00033 35462 3 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4287A>G None
M0144859 IINKGMCE_00033 35775 3 Gut 0.18 protein_coding upstream_gene_variant MODIFIER -4600C>T None
M0144860 IINKGMCE_00043 36210 3 Gut 0.18 protein_coding missense_variant MODERATE 1445G>A Arg482Gln






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
IINKGMCE_00024 ARO:3002660 99.6 5.98e-177 15 257 0.9455 0.8741 aminoglycoside antibiotic APH(6) antibiotic inactivation
IINKGMCE_00027 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
IINKGMCE_00028 ARO:3002639 99.6 5.98e-202 1 267 1.0000 1.0000 aminoglycoside antibiotic APH(3'') antibiotic inactivation
IINKGMCE_00029 ARO:3000412 100 4.11e-186 1 271 1.0000 1.0000 sulfonamide antibiotic sulfonamide resistant sul 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






        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
IINKGMCE_00068 SPE00673.1|GH23 100 1.33e-115 1 161 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
IINKGMCE_00031 3.A.7.10.1 79.6 0 1 724 0.9439 7.5417 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
IINKGMCE_00033 3.A.7.10.1 76.1 1.1e-189 1 401 0.9282 4.1771 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
IINKGMCE_00042 1.E.53.1.10 100 2e-18 8 50 0.8600 1.0000 1 Channels/Pores 1.E Holins 1.E.53 The Toxic Hok/Gef Protein (Hok/Gef) Family
IINKGMCE_00056 3.A.7.10.1 74.6 4.2e-138 1 324 1.0000 3.4063 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
IINKGMCE_00058 3.A.7.10.1 73.3 1.9e-40 1 116 1.0000 1.1979 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
IINKGMCE_00061 3.A.7.10.1 77.8 1.7e-175 1 379 0.9921 3.9479 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
IINKGMCE_00062 3.A.7.10.1 77.9 6.6e-124 1 271 0.9748 2.8021 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