Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2360
  Reference Plasmid   1111525849768046_bin.25__k141_90932
  Reference Plasmid Size   45139
  Reference Plasmid GC Content   0.56
  Reference Plasmid Mobility Type   non-mobilizable





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
M0041272 PEAJFNCH_00018 16886 3 Skin 0.38 protein_coding synonymous_variant LOW 1698T>C Ser566Ser
M0041273 PEAJFNCH_00018 16892 3 Skin 0.38 protein_coding synonymous_variant LOW 1704C>G Gly568Gly
M0041274 PEAJFNCH_00018 17093 3 Skin 0.38 protein_coding synonymous_variant LOW 1905T>C Ala635Ala
M0041275 PEAJFNCH_00018 17183 3 Skin 0.38 protein_coding synonymous_variant LOW 1995T>C Asn665Asn
M0041276 PEAJFNCH_00018 17207 3 Skin 0.38 protein_coding synonymous_variant LOW 2019T>G Gly673Gly
M0041277 PEAJFNCH_00018 17288 3 Skin 0.38 protein_coding synonymous_variant LOW 2100T>G Leu700Leu
M0041278 PEAJFNCH_00018 17337 3 Skin 0.38 protein_coding missense_variant MODERATE 2149C>A Leu717Ile
M0041279 PEAJFNCH_00019 18990 3 Skin 0.38 protein_coding synonymous_variant LOW 1287T>G Val429Val
M0041280 PEAJFNCH_00019 19132 4 Skin 0.50 protein_coding missense_variant MODERATE 1429A>G Asn477Asp
M0041281 PEAJFNCH_00019 19239 4 Skin 0.50 protein_coding synonymous_variant LOW 1536C>T Ala512Ala
M0041282 PEAJFNCH_00020 19885 3 Skin 0.38 protein_coding synonymous_variant LOW 570G>A Glu190Glu
M0041283 PEAJFNCH_00020 19996 3 Skin 0.38 protein_coding synonymous_variant LOW 681T>C Asp227Asp
M0041284 PEAJFNCH_00023 20023 3 Skin 0.38 protein_coding upstream_gene_variant MODIFIER -2527C>T None
M0041285 PEAJFNCH_00021 20242 3 Skin 0.38 protein_coding synonymous_variant LOW 969G>A Leu323Leu
M0041286 PEAJFNCH_00021 20248 4 Skin 0.50 protein_coding synonymous_variant LOW 963T>C Gly321Gly
M0041287 PEAJFNCH_00021 20311 3 Skin 0.38 protein_coding synonymous_variant LOW 900C>A Gly300Gly
M0041288 PEAJFNCH_00021 20338 4 Skin 0.50 protein_coding synonymous_variant LOW 873T>C Ile291Ile
M0041289 PEAJFNCH_00021 20341 4 Skin 0.50 protein_coding synonymous_variant LOW 870G>A Glu290Glu
M0041290 PEAJFNCH_00021 20386 4 Skin 0.50 protein_coding synonymous_variant LOW 825A>G Ala275Ala
M0041291 PEAJFNCH_00021 20401 3 Skin 0.38 protein_coding synonymous_variant LOW 810A>G Val270Val
M0041292 PEAJFNCH_00021 20413 3 Skin 0.38 protein_coding synonymous_variant LOW 798G>A Val266Val
M0041293 PEAJFNCH_00021 20423 3 Skin 0.38 protein_coding missense_variant MODERATE 788G>A Ser263Asn
M0041294 PEAJFNCH_00021 20449 4 Skin 0.50 protein_coding synonymous_variant LOW 762G>T Arg254Arg
M0041295 PEAJFNCH_00021 20535 4 Skin 0.50 protein_coding missense_variant MODERATE 676A>C Asn226His
M0041296 PEAJFNCH_00021 20605 4 Skin 0.50 protein_coding synonymous_variant LOW 606A>G Pro202Pro
M0041297 PEAJFNCH_00021 20614 4 Skin 0.50 protein_coding synonymous_variant LOW 597T>C Gly199Gly
M0041298 PEAJFNCH_00021 20662 4 Skin 0.50 protein_coding synonymous_variant LOW 549C>T Ala183Ala
M0041299 PEAJFNCH_00021 20674 4 Skin 0.50 protein_coding synonymous_variant LOW 537T>A Gly179Gly
M0041300 PEAJFNCH_00021 20689 3 Skin 0.38 protein_coding synonymous_variant LOW 522A>T Ile174Ile
M0041301 PEAJFNCH_00021 20761 3 Skin 0.38 protein_coding synonymous_variant LOW 450A>G Glu150Glu
M0041302 PEAJFNCH_00021 20776 4 Skin 0.50 protein_coding synonymous_variant LOW 435A>G Ala145Ala
M0041303 PEAJFNCH_00021 20803 4 Skin 0.50 protein_coding synonymous_variant LOW 408T>C Pro136Pro
M0041304 PEAJFNCH_00021 21016 4 Skin 0.50 protein_coding synonymous_variant LOW 195A>C Arg65Arg
M0041305 PEAJFNCH_00019 19119 3 Skin 0.38 protein_coding synonymous_variant LOW 1416C>T Asp472Asp
M0041306 PEAJFNCH_00021 21074 3 Skin 0.38 protein_coding missense_variant MODERATE 137G>T Arg46Leu
M0041307 PEAJFNCH_00021 21205 3 Skin 0.38 protein_coding synonymous_variant LOW 6C>T His2His
M0041308 PEAJFNCH_00022 21639 3 Skin 0.38 protein_coding synonymous_variant LOW 777G>C Leu259Leu
M0041309 PEAJFNCH_00022 21654 4 Skin 0.50 protein_coding synonymous_variant LOW 762A>C Ile254Ile
M0041310 PEAJFNCH_00022 21888 4 Skin 0.50 protein_coding synonymous_variant LOW 528T>G Leu176Leu
M0041311 PEAJFNCH_00022 21954 4 Skin 0.50 protein_coding synonymous_variant LOW 462A>G Ala154Ala
M0041312 PEAJFNCH_00022 22194 4 Skin 0.50 protein_coding synonymous_variant LOW 222C>G Leu74Leu
M0041313 PEAJFNCH_00023 22882 3 Skin 0.38 protein_coding synonymous_variant LOW 333T>G Pro111Pro
M0041314 PEAJFNCH_00024 23463 3 Skin 0.38 protein_coding synonymous_variant LOW 660T>C Arg220Arg
M0041315 PEAJFNCH_00024 23532 3 Skin 0.38 protein_coding synonymous_variant LOW 591T>G Leu197Leu
M0041316 PEAJFNCH_00024 23740 4 Skin 0.50 protein_coding missense_variant MODERATE 383G>A Arg128Gln
M0041317 PEAJFNCH_00025 24175 3 Skin 0.38 protein_coding synonymous_variant LOW 687G>A Gly229Gly
M0041318 PEAJFNCH_00025 24187 4 Skin 0.50 protein_coding synonymous_variant LOW 675G>T Gly225Gly
M0041319 PEAJFNCH_00025 24190 4 Skin 0.50 protein_coding synonymous_variant LOW 672A>G Leu224Leu
M0041320 PEAJFNCH_00025 24196 4 Skin 0.50 protein_coding synonymous_variant LOW 666T>G Leu222Leu
M0041321 PEAJFNCH_00025 24205 3 Skin 0.38 protein_coding synonymous_variant LOW 657A>G Ala219Ala
M0041322 PEAJFNCH_00025 24283 3 Skin 0.38 protein_coding synonymous_variant LOW 579C>T Phe193Phe
M0041323 PEAJFNCH_00025 24456 3 Skin 0.38 protein_coding synonymous_variant LOW 406C>T Leu136Leu
M0041324 PEAJFNCH_00025 24457 3 Skin 0.38 protein_coding synonymous_variant LOW 405A>G Gly135Gly
M0041325 PEAJFNCH_00025 24601 4 Skin 0.50 protein_coding synonymous_variant LOW 261A>G Leu87Leu
M0041326 PEAJFNCH_00017 15070 3 Skin 0.38 protein_coding synonymous_variant LOW 576A>G Pro192Pro
M0041327 PEAJFNCH_00018 15232 3 Skin 0.38 protein_coding missense_variant MODERATE 44T>C Val15Ala
M0041328 PEAJFNCH_00018 15273 3 Skin 0.38 protein_coding missense_variant MODERATE 85C>A Leu29Met
M0041329 PEAJFNCH_00018 15683 3 Skin 0.38 protein_coding synonymous_variant LOW 495T>C Ser165Ser
M0041330 PEAJFNCH_00018 16097 3 Skin 0.38 protein_coding synonymous_variant LOW 909A>G Gly303Gly
M0041331 PEAJFNCH_00018 16160 3 Skin 0.38 protein_coding synonymous_variant LOW 972T>G Pro324Pro
M0041332 PEAJFNCH_00018 16424 3 Skin 0.38 protein_coding synonymous_variant LOW 1236T>C Tyr412Tyr
M0041333 PEAJFNCH_00018 16490 3 Skin 0.38 protein_coding synonymous_variant LOW 1302A>G Leu434Leu
M0041334 PEAJFNCH_00024 23706 3 Skin 0.38 protein_coding synonymous_variant LOW 417T>C Pro139Pro
M0041335 PEAJFNCH_00025 24763 3 Skin 0.38 protein_coding missense_variant MODERATE 99G>A Met33Ile
M0041336 PEAJFNCH_00025 24769 3 Skin 0.38 protein_coding synonymous_variant LOW 93T>C Ala31Ala
M0041337 PEAJFNCH_00025 24772 3 Skin 0.38 protein_coding synonymous_variant LOW 90C>G Val30Val
M0041338 PEAJFNCH_00025 24778 3 Skin 0.38 protein_coding synonymous_variant LOW 84T>C Val28Val
M0041339 PEAJFNCH_00025 24790 3 Skin 0.38 protein_coding synonymous_variant LOW 72C>T Thr24Thr
M0041340 PEAJFNCH_00025 24793 3 Skin 0.38 protein_coding synonymous_variant LOW 69G>C Leu23Leu
M0041341 PEAJFNCH_00025 24796 3 Skin 0.38 protein_coding synonymous_variant LOW 66C>T Phe22Phe
M0041342 PEAJFNCH_00025 24799 3 Skin 0.38 protein_coding synonymous_variant LOW 63C>T Gly21Gly
M0041343 PEAJFNCH_00025 24808 3 Skin 0.38 protein_coding synonymous_variant LOW 54A>T Ile18Ile
M0041344 PEAJFNCH_00026 25371 3 Skin 0.38 protein_coding synonymous_variant LOW 309T>C Gly103Gly
M0041345 PEAJFNCH_00027 25819 3 Skin 0.38 protein_coding missense_variant MODERATE 727C>G Pro243Ala
M0041346 PEAJFNCH_00027 26249 3 Skin 0.38 protein_coding synonymous_variant LOW 297A>G Pro99Pro
M0041347 PEAJFNCH_00028 26944 3 Skin 0.38 protein_coding missense_variant MODERATE 170T>C Ile57Thr






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
PEAJFNCH_00015 VFG002413 ECP 77.1 4.3e-77 1 179 0.9944 0.9944 Adherence regulator protein EcpR experiment
PEAJFNCH_00016 VFG002414 ECP 91.3 5.5e-94 1 195 1.0 1 Adherence E. coli common pilus structural subunit EcpA experiment
PEAJFNCH_00017 VFG002412 ECP 82.4 1.3e-102 1 222 1.0 1 Adherence E. coli common pilus chaperone EcpB experiment
PEAJFNCH_00018 VFG002415 ECP 86.2 0 1 841 1.0 1 Adherence E. coli common pilus usher EcpC experiment
PEAJFNCH_00019 VFG002416 ECP 87.9 5.7e-290 1 547 1.0 1 Adherence polymerized tip adhesin of ECP fibers experiment
PEAJFNCH_00020 VFG002417 ECP 76.2 1.5e-106 1 231 1.0 0.9788 Adherence E. coli common pilus chaperone EcpE experiment
PEAJFNCH_00015 VFG034392 ECP 78.2 2.9e-77 1 179 0.9944 0.9944 Adherence regulator protein EcpR prediction
PEAJFNCH_00016 VFG002414 ECP 91.3 4.1e-93 1 195 1.0 1 Adherence E. coli common pilus structural subunit EcpA prediction
PEAJFNCH_00017 VFG002412 ECP 82.4 9.4e-102 1 222 1.0 1 Adherence E. coli common pilus chaperone EcpB prediction
PEAJFNCH_00018 VFG034475 ECP 86.7 0 1 841 1.0 1 Adherence E. coli common pilus usher EcpC prediction
PEAJFNCH_00019 VFG018221 ECP 88.3 8.6e-290 1 547 1.0 1 Adherence polymerized tip adhesin of ECP fibers prediction
PEAJFNCH_00020 VFG034514 ECP 76.6 1.3e-106 1 231 1.0 0.9788 Adherence E. coli common pilus chaperone EcpE 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





        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
PEAJFNCH_00006 1.B.1.1.2 85.2 1.7e-177 1 350 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.1 The General Bacterial Porin (GBP) Family
PEAJFNCH_00029 2.A.3.1.10 92.8 3.8e-249 1 469 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family
PEAJFNCH_00031 3.A.1.17.1 88.8 5.1e-160 1 320 1.0000 1.1636 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PEAJFNCH_00032 3.A.1.17.1 88.6 1.7e-126 1 255 1.0000 0.9273 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PEAJFNCH_00033 3.A.1.17.1 86.5 1.3e-127 1 275 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
PEAJFNCH_00040 9.A.18.1.1 86.5 1.7e-205 1 406 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.A Recognized transporters of unknown biochemical mechanism 9.A.18 The Peptide Uptake Permease (PUP) Family
PEAJFNCH_00043 9.B.382.1.1 80 3.1e-27 1 65 0.9701 0.9286 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.382 The DUF2754 domain or YaiZ (DUF2754) Family