Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C603
  Reference Plasmid   NZ_CP035852.1
  Reference Plasmid Size   133955
  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
M0169274 DBPBMMNC_00081 88878 5 Gut 0.24 protein_coding missense_variant MODERATE 82C>A His28Asn
M0169275 DBPBMMNC_00084 91108 5 Gut 0.24 protein_coding missense_variant MODERATE 19G>C Asp7His
M0169276 DBPBMMNC_00049 49569 3 Gut 0.14 protein_coding synonymous_variant LOW 288T>C Ala96Ala
M0169277 DBPBMMNC_00049 49575 3 Gut 0.14 protein_coding synonymous_variant LOW 282C>T His94His
M0169278 DBPBMMNC_00049 49584 3 Gut 0.14 protein_coding synonymous_variant LOW 273T>G Arg91Arg
M0169279 DBPBMMNC_00049 49587 3 Gut 0.14 protein_coding synonymous_variant LOW 270C>T Ser90Ser
M0169280 DBPBMMNC_00049 49602 3 Gut 0.14 protein_coding synonymous_variant LOW 255G>A Pro85Pro
M0169281 DBPBMMNC_00049 49605 3 Gut 0.14 protein_coding synonymous_variant LOW 252A>G Lys84Lys
M0169282 DBPBMMNC_00056 59073 7 Gut 0.33 protein_coding synonymous_variant LOW 963C>A Ala321Ala
M0169283 DBPBMMNC_00054 60168 4 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2826T>G None
M0169284 DBPBMMNC_00054 60222 4 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2880G>A None
M0169285 DBPBMMNC_00075 85006 4 Gut 0.19 protein_coding missense_variant MODERATE 1270G>T Gly424Cys
M0169286 DBPBMMNC_00049 49451 4 Gut 0.19 protein_coding missense_variant MODERATE 406T>G Phe136Val
M0169287 DBPBMMNC_00058 61478 3 Gut 0.14 protein_coding missense_variant MODERATE 347A>G Asp116Gly
M0169288 DBPBMMNC_00059 61867 3 Gut 0.14 protein_coding missense_variant MODERATE 25A>G Ile9Val
M0169289 DBPBMMNC_00060 62904 3 Gut 0.14 protein_coding missense_variant MODERATE 189G>T Glu63Asp
M0169290 DBPBMMNC_00060 64235 3 Gut 0.14 protein_coding missense_variant MODERATE 1520T>C Ile507Thr
M0169291 DBPBMMNC_00061 64897 3 Gut 0.14 protein_coding missense_variant MODERATE 281G>A Ser94Asn
M0169292 DBPBMMNC_00061 64901 3 Gut 0.14 protein_coding synonymous_variant LOW 285T>C Ser95Ser
M0169293 DBPBMMNC_00061 64946 3 Gut 0.14 protein_coding synonymous_variant LOW 330G>A Gly110Gly
M0169294 DBPBMMNC_00061 64962 3 Gut 0.14 protein_coding missense_variant MODERATE 346T>G Tyr116Asp
M0169295 DBPBMMNC_00061 64971 3 Gut 0.14 protein_coding missense_variant MODERATE 355G>A Asp119Asn
M0169296 DBPBMMNC_00061 64972 3 Gut 0.14 protein_coding missense_variant MODERATE 356A>G Asp119Gly
M0169297 DBPBMMNC_00061 64982 3 Gut 0.14 protein_coding synonymous_variant LOW 366A>G Ala122Ala
M0169298 DBPBMMNC_00061 65071 3 Gut 0.14 protein_coding missense_variant MODERATE 455G>A Ser152Asn
M0169299 DBPBMMNC_00061 65088 3 Gut 0.14 protein_coding missense_variant MODERATE 472A>G Lys158Glu
M0169300 DBPBMMNC_00061 65093 3 Gut 0.14 protein_coding synonymous_variant LOW 477T>G Gly159Gly
M0169301 DBPBMMNC_00061 65218 3 Gut 0.14 protein_coding missense_variant MODERATE 602C>A Ala201Glu
M0169302 DBPBMMNC_00061 65273 3 Gut 0.14 protein_coding synonymous_variant LOW 657C>T Asn219Asn
M0169303 DBPBMMNC_00061 65276 3 Gut 0.14 protein_coding synonymous_variant LOW 660C>T Ser220Ser
M0169304 DBPBMMNC_00061 65309 3 Gut 0.14 protein_coding synonymous_variant LOW 693C>T Val231Val
M0169305 DBPBMMNC_00061 65328 3 Gut 0.14 protein_coding missense_variant MODERATE 712G>A Val238Ile
M0169306 DBPBMMNC_00061 65351 3 Gut 0.14 protein_coding synonymous_variant LOW 735C>T Gly245Gly
M0169307 DBPBMMNC_00061 65365 3 Gut 0.14 protein_coding missense_variant MODERATE 749C>T Ala250Val
M0169308 DBPBMMNC_00061 65461 3 Gut 0.14 protein_coding missense_variant MODERATE 845A>G Asp282Gly
M0169309 DBPBMMNC_00061 65508 3 Gut 0.14 protein_coding missense_variant MODERATE 892G>A Gly298Ser
M0169310 DBPBMMNC_00061 65576 3 Gut 0.14 protein_coding synonymous_variant LOW 960C>T Ser320Ser
M0169311 DBPBMMNC_00061 65612 3 Gut 0.14 protein_coding synonymous_variant LOW 996C>T Gly332Gly
M0169312 DBPBMMNC_00061 65662 3 Gut 0.14 protein_coding missense_variant MODERATE 1046G>A Ser349Asn
M0169313 DBPBMMNC_00061 65767 3 Gut 0.14 protein_coding missense_variant MODERATE 1151A>G Asp384Gly
M0169314 DBPBMMNC_00061 65819 3 Gut 0.14 protein_coding synonymous_variant LOW 1203C>T Ala401Ala
M0169315 DBPBMMNC_00061 65873 3 Gut 0.14 protein_coding synonymous_variant LOW 1257T>C Gly419Gly
M0169316 DBPBMMNC_00061 65899 3 Gut 0.14 protein_coding missense_variant MODERATE 1283A>G Gln428Arg
M0169317 DBPBMMNC_00061 66125 3 Gut 0.14 protein_coding synonymous_variant LOW 1509T>C Asn503Asn
M0169318 DBPBMMNC_00062 70995 5 Gut 0.24 protein_coding missense_variant MODERATE 1514T>C Val505Ala
M0169319 DBPBMMNC_00062 71334 5 Gut 0.24 protein_coding missense_variant MODERATE 1853G>A Gly618Glu
M0169320 DBPBMMNC_00066 73339 5 Gut 0.24 protein_coding missense_variant MODERATE 434C>T Ala145Val
M0169321 DBPBMMNC_00065 75271 5 Gut 0.24 protein_coding upstream_gene_variant MODIFIER -2259A>G None






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
DBPBMMNC_00060 VFG042382 EtpA 99.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB experiment
DBPBMMNC_00061 VFG034541 EtpA 93.6 0 1 1526 1.0 0.9916 Adherence Two-partner secreted adhesin EtpA experiment
DBPBMMNC_00060 VFG042382 EtpA 99.7 0 1 603 1.0 1 Adherence two-partner secretion transporter EtpB prediction
DBPBMMNC_00061 VFG034541 EtpA 93.6 0 1 1526 1.0 0.9916 Adherence Two-partner secreted adhesin EtpA prediction
DBPBMMNC_00074 VFG033834 Pic 98.2 0 1 1364 1.0 0.9985 Effector delivery system Pic serine protease precursor, autotransporter prediction
DBPBMMNC_00081 VFG041000 AAI/SCI-II T6SS 91.5 3.1e-98 1 188 1.0 1 Effector delivery system hypothetical protein prediction
DBPBMMNC_00090 VFG017870 Icm/dot type IVB locus 77.9 1e-89 1 208 0.9905 0.9952 Effector delivery system ParA family protein 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






        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
DBPBMMNC_00035 SPE00673.1|GH23 100 1.33e-115 1 161 1 1
DBPBMMNC_00062 ATB16983.1|GT41 99.7 0 1 636 1 0.9984





        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
DBPBMMNC_00001 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
DBPBMMNC_00018 3.A.7.10.1 74.3 4.2e-138 1 319 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
DBPBMMNC_00020 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
DBPBMMNC_00023 3.A.7.10.1 77.8 7.9e-176 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
DBPBMMNC_00024 3.A.7.10.1 96.7 1.1e-121 1 214 0.9683 2.2292 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
DBPBMMNC_00025 3.A.7.10.1 98.7 8.7e-86 1 152 1.0000 1.5833 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
DBPBMMNC_00060 1.B.20.3.3 99.7 0 1 603 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
DBPBMMNC_00063 9.B.127.1.3 98.2 3.6e-93 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family
DBPBMMNC_00130 3.A.7.10.1 79.7 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
DBPBMMNC_00132 3.A.7.10.1 76.6 2.2e-190 1 401 0.9032 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