Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C340
  Reference Plasmid   NC_020208.1
  Reference Plasmid Size   214319
  Reference Plasmid GC Content   0.36
  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
M0153302 PHFLKNOO_00137 111217 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -2203A>C None
M0153303 PHFLKNOO_00137 111261 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -2159C>T None
M0153304 PHFLKNOO_00134 111313 4 Gut 0.08 protein_coding stop_lost&splice_region_variant HIGH 253T>C Ter85Glnext*?
M0153305 PHFLKNOO_00134 111563 4 Gut 0.08 protein_coding start_lost HIGH 3G>A Met1?
M0153306 PHFLKNOO_00134 111566 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1T>C None
M0153307 PHFLKNOO_00135 111697 4 Gut 0.08 protein_coding missense_variant MODERATE 462T>G Ser154Arg
M0153308 PHFLKNOO_00135 111806 4 Gut 0.08 protein_coding missense_variant MODERATE 353G>A Arg118His
M0153309 PHFLKNOO_00136 112430 4 Gut 0.08 protein_coding missense_variant MODERATE 501T>G Ile167Met
M0153310 PHFLKNOO_00136 112628 4 Gut 0.08 protein_coding synonymous_variant LOW 303T>C Pro101Pro
M0153311 PHFLKNOO_00134 112939 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1374G>A None
M0153312 PHFLKNOO_00134 113267 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1702T>A None
M0153313 PHFLKNOO_00134 113291 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1726A>G None
M0153314 PHFLKNOO_00134 113311 5 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -1746T>A None
M0153315 PHFLKNOO_00134 113337 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1772T>C None
M0153316 PHFLKNOO_00137 113836 4 Gut 0.08 protein_coding synonymous_variant LOW 417A>G Lys139Lys
M0153317 PHFLKNOO_00138 114187 4 Gut 0.08 protein_coding missense_variant MODERATE 326A>T Lys109Met
M0153318 PHFLKNOO_00140 115991 4 Gut 0.08 protein_coding synonymous_variant LOW 669A>G Val223Val
M0153319 PHFLKNOO_00142 117048 4 Gut 0.08 protein_coding missense_variant MODERATE 401C>T Thr134Met
M0153320 PHFLKNOO_00142 117111 4 Gut 0.08 protein_coding missense_variant MODERATE 464T>C Val155Ala
M0153321 PHFLKNOO_00142 117203 4 Gut 0.08 protein_coding missense_variant MODERATE 556G>T Ala186Ser
M0153322 PHFLKNOO_00142 117224 4 Gut 0.08 protein_coding missense_variant MODERATE 577T>C Phe193Leu
M0153323 PHFLKNOO_00142 117429 4 Gut 0.08 protein_coding missense_variant MODERATE 782C>T Ala261Val
M0153324 PHFLKNOO_00142 118154 4 Gut 0.08 protein_coding missense_variant MODERATE 1507A>G Ser503Gly
M0153325 PHFLKNOO_00142 118159 4 Gut 0.08 protein_coding synonymous_variant LOW 1512C>T Tyr504Tyr
M0153326 PHFLKNOO_00142 118249 4 Gut 0.08 protein_coding synonymous_variant LOW 1602G>A Thr534Thr
M0153327 PHFLKNOO_00143 118395 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -101A>G None
M0153328 PHFLKNOO_00143 119599 4 Gut 0.08 protein_coding synonymous_variant LOW 1104C>T Tyr368Tyr
M0153329 PHFLKNOO_00144 120119 4 Gut 0.08 protein_coding synonymous_variant LOW 195G>A Glu65Glu
M0153330 PHFLKNOO_00145 120674 4 Gut 0.08 protein_coding missense_variant MODERATE 457A>T Ser153Cys
M0153331 PHFLKNOO_00145 120814 4 Gut 0.08 protein_coding synonymous_variant LOW 597A>G Lys199Lys
M0153332 PHFLKNOO_00145 121059 4 Gut 0.08 protein_coding missense_variant MODERATE 842C>T Thr281Met
M0153333 PHFLKNOO_00211 180075 3 Gut 0.06 protein_coding missense_variant MODERATE 209C>A Ala70Asp
M0153334 PHFLKNOO_00148 124131 3 Gut 0.06 protein_coding missense_variant MODERATE 92A>G Glu31Gly
M0153335 PHFLKNOO_00146 124249 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -1824A>T None
M0153336 PHFLKNOO_00150 126868 6 Gut 0.12 protein_coding synonymous_variant LOW 1629G>A Leu543Leu
M0153337 PHFLKNOO_00150 127009 6 Gut 0.12 protein_coding missense_variant MODERATE 1770T>G Ile590Met
M0153338 PHFLKNOO_00148 128853 7 Gut 0.14 protein_coding upstream_gene_variant MODIFIER -4631A>G None
M0153339 PHFLKNOO_00153 129411 3 Gut 0.06 protein_coding missense_variant MODERATE 326T>C Ile109Thr
M0153340 PHFLKNOO_00153 129508 3 Gut 0.06 protein_coding stop_lost&splice_region_variant HIGH 423A>C Ter141Cysext*?
M0153341 PHFLKNOO_00159 133682 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -433A>G None
M0153342 PHFLKNOO_00159 134321 4 Gut 0.08 protein_coding synonymous_variant LOW 207A>C Gly69Gly
M0153343 PHFLKNOO_00162 136180 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -258A>C None
M0153344 PHFLKNOO_00162 136300 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -138G>A None
M0153345 PHFLKNOO_00163 136605 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -242A>G None
M0153346 PHFLKNOO_00150 126274 3 Gut 0.06 protein_coding synonymous_variant LOW 1035G>A Lys345Lys
M0153347 PHFLKNOO_00150 126469 3 Gut 0.06 protein_coding synonymous_variant LOW 1230G>A Leu410Leu
M0153348 PHFLKNOO_00090 74586 3 Gut 0.06 protein_coding missense_variant MODERATE 1823T>C Phe608Ser
M0153349 PHFLKNOO_00034 26646 3 Gut 0.06 protein_coding synonymous_variant LOW 207A>G Glu69Glu
M0153350 PHFLKNOO_00031 22847 3 Gut 0.06 protein_coding missense_variant MODERATE 628G>A Gly210Arg
M0153351 PHFLKNOO_00157 131135 3 Gut 0.06 protein_coding missense_variant MODERATE 295C>A Pro99Thr
M0153352 PHFLKNOO_00157 131714 3 Gut 0.06 protein_coding synonymous_variant LOW 874T>C Leu292Leu
M0153353 PHFLKNOO_00158 132883 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -299G>T None
M0153354 PHFLKNOO_00159 133415 4 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -700A>G None
M0153355 PHFLKNOO_00157 131600 3 Gut 0.06 protein_coding missense_variant MODERATE 760G>A Glu254Lys
M0153356 PHFLKNOO_00159 133614 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -501G>T None
M0153357 PHFLKNOO_00159 133782 3 Gut 0.06 protein_coding upstream_gene_variant MODIFIER -333T>C 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
PHFLKNOO_00081 VFG042989 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 1.2e-125 1 223 1.0 1 Adherence putative housekeeping sortase prediction
PHFLKNOO_00082 VFG042988 PilA-type pili (PGS1, pilin gene clusters 1) 99.1 0 1 658 1.0 1 Adherence PilA prediction
PHFLKNOO_00083 VFG042987 PilA-type pili (PGS1, pilin gene clusters 1) 98.8 7e-138 1 250 1.0 1 Adherence putative pilus-dedicated sortase prediction
PHFLKNOO_00084 VFG042986 PilA-type pili (PGS1, pilin gene clusters 1) 100 2.4e-133 1 251 1.0 1 Adherence cell wall-associated LPXTG-like protein prediction
PHFLKNOO_00085 VFG042985 PilA-type pili (PGS1, pilin gene clusters 1) 97.7 1.4e-37 1 86 1.0 1 Adherence hypothetical hydrophobic peptide prediction
PHFLKNOO_00086 VFG042984 PilA-type pili (PGS1, pilin gene clusters 1) 99.6 0 1 696 1.0 1 Adherence minor pilin subunit 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
PHFLKNOO_00022 Copper (Cu), Cobalt (Co) 99.2 3.5e-309 1 527 1.0000 1.0000 prediction






        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
PHFLKNOO_00015 PHI:5205 HMPREF0351_10118 (WxL locusC) 99.7 1.1e-225 1 392 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
PHFLKNOO_00186 PHI:8586 mntH1 77.6 3.1e-223 17 530 0.9607 0.9737 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity






        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
PHFLKNOO_00055 CCO10203.2|GH1 85.9 4.33e-181 2 299 0.9967 0.7641
PHFLKNOO_00097 AGE31386.1|GH73 100 2.13e-275 1 401 1 1
PHFLKNOO_00143 QZK92746.1|GH1 100 0 1 468 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
PHFLKNOO_00142 4.A.3.1.1 71.7 4.4e-239 1 568 1.0000 0.9965 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.3 The PTS Lactose-N,N'-Diacetylchitobiose-β-glucoside (Lac) Family
PHFLKNOO_00188 1.C.24.1.10 94.4 9.5e-27 1 54 1.0000 0.7606 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.24 The Pediocin (Pediocin) Family