Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C655
  Reference Plasmid   NZ_CP042248.1
  Reference Plasmid Size   102714
  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
M0170329 AFBHDIDO_00048 49390 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -107T>C None
M0170330 AFBHDIDO_00048 49395 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -112G>A None
M0170331 AFBHDIDO_00048 49397 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -114C>T None
M0170332 AFBHDIDO_00048 49441 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -158G>A None
M0170333 AFBHDIDO_00048 49442 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -159C>T None
M0170334 AFBHDIDO_00048 49443 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -160A>G None
M0170335 AFBHDIDO_00048 49455 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -172T>C None
M0170336 AFBHDIDO_00048 49462 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -179T>C None
M0170337 AFBHDIDO_00048 49477 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -194A>C None
M0170338 AFBHDIDO_00048 49484 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -201A>G None
M0170339 AFBHDIDO_00048 49486 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -203T>C None
M0170340 AFBHDIDO_00048 49552 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -269T>A None
M0170341 AFBHDIDO_00048 49556 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -273C>T None
M0170342 AFBHDIDO_00048 49674 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -391G>C None
M0170343 AFBHDIDO_00049 49914 3 Gut 0.60 protein_coding missense_variant MODERATE 52G>A Val18Ile
M0170344 AFBHDIDO_00049 49931 3 Gut 0.60 protein_coding synonymous_variant LOW 69T>C Ala23Ala
M0170345 AFBHDIDO_00049 49943 3 Gut 0.60 protein_coding synonymous_variant LOW 81C>T Ile27Ile
M0170346 AFBHDIDO_00049 50006 3 Gut 0.60 protein_coding synonymous_variant LOW 144A>G Ala48Ala
M0170347 AFBHDIDO_00049 50030 3 Gut 0.60 protein_coding synonymous_variant LOW 168C>T Ser56Ser
M0170348 AFBHDIDO_00049 50063 3 Gut 0.60 protein_coding synonymous_variant LOW 201T>C Cys67Cys
M0170349 AFBHDIDO_00049 50105 3 Gut 0.60 protein_coding synonymous_variant LOW 243G>A Ala81Ala
M0170350 AFBHDIDO_00049 50110 3 Gut 0.60 protein_coding missense_variant MODERATE 248G>A Arg83Lys
M0170351 AFBHDIDO_00049 50132 3 Gut 0.60 protein_coding synonymous_variant LOW 270C>T Asp90Asp
M0170352 AFBHDIDO_00049 50147 3 Gut 0.60 protein_coding synonymous_variant LOW 285C>T Asp95Asp
M0170353 AFBHDIDO_00049 50279 3 Gut 0.60 protein_coding synonymous_variant LOW 417T>G Leu139Leu
M0170354 AFBHDIDO_00049 50299 3 Gut 0.60 protein_coding missense_variant MODERATE 437T>C Ile146Thr
M0170355 AFBHDIDO_00049 50312 3 Gut 0.60 protein_coding synonymous_variant LOW 450G>A Gly150Gly
M0170356 AFBHDIDO_00049 50366 3 Gut 0.60 protein_coding synonymous_variant LOW 504C>T Cys168Cys
M0170357 AFBHDIDO_00049 50372 3 Gut 0.60 protein_coding synonymous_variant LOW 510G>T Leu170Leu
M0170358 AFBHDIDO_00049 50375 3 Gut 0.60 protein_coding synonymous_variant LOW 513T>C Gly171Gly
M0170359 AFBHDIDO_00049 50380 3 Gut 0.60 protein_coding missense_variant MODERATE 518A>G Lys173Arg
M0170360 AFBHDIDO_00049 50474 3 Gut 0.60 protein_coding synonymous_variant LOW 612G>T Pro204Pro
M0170361 AFBHDIDO_00049 50511 3 Gut 0.60 protein_coding synonymous_variant LOW 649A>C Arg217Arg
M0170362 AFBHDIDO_00049 50515 3 Gut 0.60 protein_coding missense_variant MODERATE 653A>G Asn218Ser
M0170363 AFBHDIDO_00049 50624 3 Gut 0.60 protein_coding synonymous_variant LOW 762C>T His254His
M0170364 AFBHDIDO_00049 50687 3 Gut 0.60 protein_coding synonymous_variant LOW 825A>T Pro275Pro
M0170365 AFBHDIDO_00050 50827 3 Gut 0.60 protein_coding missense_variant MODERATE 312G>T Arg104Ser
M0170366 AFBHDIDO_00050 50852 3 Gut 0.60 protein_coding missense_variant MODERATE 287C>T Ala96Val
M0170367 AFBHDIDO_00050 50879 3 Gut 0.60 protein_coding missense_variant MODERATE 260C>T Pro87Leu
M0170368 AFBHDIDO_00050 50880 3 Gut 0.60 protein_coding missense_variant MODERATE 259C>A Pro87Thr
M0170369 AFBHDIDO_00050 51004 3 Gut 0.60 protein_coding synonymous_variant LOW 135C>T Ile45Ile
M0170370 AFBHDIDO_00050 51058 3 Gut 0.60 protein_coding synonymous_variant LOW 81C>T Leu27Leu
M0170371 AFBHDIDO_00050 51061 3 Gut 0.60 protein_coding synonymous_variant LOW 78T>C Asp26Asp
M0170372 AFBHDIDO_00050 51073 3 Gut 0.60 protein_coding synonymous_variant LOW 66A>G Ser22Ser
M0170373 AFBHDIDO_00050 51108 3 Gut 0.60 protein_coding missense_variant MODERATE 31G>T Asp11Tyr
M0170374 AFBHDIDO_00050 51127 3 Gut 0.60 protein_coding synonymous_variant LOW 12T>G Ala4Ala
M0170375 AFBHDIDO_00048 51218 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1935G>T None
M0170376 AFBHDIDO_00048 51250 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -1967C>T None
M0170377 AFBHDIDO_00048 51313 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -2030A>G None
M0170378 AFBHDIDO_00048 51337 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -2054A>C None
M0170379 AFBHDIDO_00052 51843 3 Gut 0.60 protein_coding synonymous_variant LOW 135G>A Pro45Pro
M0170380 AFBHDIDO_00052 51844 3 Gut 0.60 protein_coding missense_variant MODERATE 136C>T His46Tyr
M0170381 AFBHDIDO_00052 51885 3 Gut 0.60 protein_coding synonymous_variant LOW 177T>C Arg59Arg
M0170382 AFBHDIDO_00052 51972 3 Gut 0.60 protein_coding synonymous_variant LOW 264T>C His88His
M0170383 AFBHDIDO_00052 51981 3 Gut 0.60 protein_coding synonymous_variant LOW 273T>A Thr91Thr
M0170384 AFBHDIDO_00052 51996 3 Gut 0.60 protein_coding synonymous_variant LOW 288C>T Ala96Ala
M0170385 AFBHDIDO_00052 52029 3 Gut 0.60 protein_coding synonymous_variant LOW 321A>T Ala107Ala
M0170386 AFBHDIDO_00052 52260 3 Gut 0.60 protein_coding synonymous_variant LOW 552A>C Ser184Ser
M0170387 AFBHDIDO_00052 52480 3 Gut 0.60 protein_coding missense_variant MODERATE 772C>A His258Asn
M0170388 AFBHDIDO_00052 52662 3 Gut 0.60 protein_coding synonymous_variant LOW 954G>A Val318Val
M0170389 AFBHDIDO_00052 52722 3 Gut 0.60 protein_coding synonymous_variant LOW 1014A>C Ala338Ala
M0170390 AFBHDIDO_00052 52787 3 Gut 0.60 protein_coding missense_variant MODERATE 1079T>C Leu360Pro
M0170391 AFBHDIDO_00052 52814 3 Gut 0.60 protein_coding missense_variant MODERATE 1106G>A Arg369Gln
M0170392 AFBHDIDO_00052 52838 3 Gut 0.60 protein_coding missense_variant MODERATE 1130T>A Leu377Gln






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
AFBHDIDO_00007 VFG043980 Colicin Ib 98.7 0 13 635 0.9811 0.9952 Exotoxin colicin-like pore-forming protein prediction
AFBHDIDO_00014 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
AFBHDIDO_00087 QDX42089.1|GH23 100 2.05e-138 1 186 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
AFBHDIDO_00007 1.C.1.1.2 99 0 13 635 0.9811 0.9952 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.1 The Channel-forming Colicin (Colicin) Family
AFBHDIDO_00008 8.B.24.2.1 97.3 4.6e-55 1 110 0.9565 0.8661 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
AFBHDIDO_00053 3.A.7.10.1 100 0 1 763 1.0000 7.9479 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
AFBHDIDO_00054 3.A.7.10.1 99.7 1.2e-207 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
AFBHDIDO_00055 3.A.7.10.1 99.5 2.1e-243 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
AFBHDIDO_00062 9.B.40.1.2 86.3 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
AFBHDIDO_00073 3.A.7.10.1 100 6.1e-185 1 327 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
AFBHDIDO_00074 3.A.7.10.1 99.6 3.3e-129 1 230 1.0000 2.3958 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
AFBHDIDO_00075 3.A.7.10.1 100 1.3e-57 1 115 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
AFBHDIDO_00078 3.A.7.10.1 97.9 1.3e-55 1 96 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
AFBHDIDO_00079 3.A.7.10.1 100 3.3e-222 1 382 1.0000 3.9792 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
AFBHDIDO_00080 3.A.7.10.1 98.9 3.6e-159 1 272 1.0000 2.8333 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
AFBHDIDO_00081 3.A.7.10.1 98.7 2.5e-85 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