Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C605
  Reference Plasmid   NZ_CP035863.1
  Reference Plasmid Size   83626
  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
M0169407 IPHBNGFD_00027 20085 3 Gut 0.30 protein_coding missense_variant MODERATE 2120T>C Val707Ala
M0169408 IPHBNGFD_00028 20229 3 Gut 0.30 protein_coding synonymous_variant LOW 30T>C Ala10Ala
M0169409 IPHBNGFD_00028 21342 3 Gut 0.30 protein_coding synonymous_variant LOW 1143G>A Thr381Thr
M0169410 IPHBNGFD_00028 21372 3 Gut 0.30 protein_coding synonymous_variant LOW 1173C>A Ser391Ser
M0169411 IPHBNGFD_00028 21450 3 Gut 0.30 protein_coding synonymous_variant LOW 1251T>C Ala417Ala
M0169412 IPHBNGFD_00028 21519 3 Gut 0.30 protein_coding synonymous_variant LOW 1320C>G Gly440Gly
M0169413 IPHBNGFD_00028 21522 3 Gut 0.30 protein_coding synonymous_variant LOW 1323T>A Gly441Gly
M0169414 IPHBNGFD_00028 21525 3 Gut 0.30 protein_coding synonymous_variant LOW 1326A>C Ala442Ala
M0169415 IPHBNGFD_00028 21540 3 Gut 0.30 protein_coding synonymous_variant LOW 1341A>G Glu447Glu
M0169416 IPHBNGFD_00028 21573 3 Gut 0.30 protein_coding synonymous_variant LOW 1374A>G Glu458Glu
M0169417 IPHBNGFD_00028 21600 3 Gut 0.30 protein_coding synonymous_variant LOW 1401C>T Ala467Ala
M0169418 IPHBNGFD_00028 21609 3 Gut 0.30 protein_coding synonymous_variant LOW 1410C>T Arg470Arg
M0169419 IPHBNGFD_00028 21615 3 Gut 0.30 protein_coding synonymous_variant LOW 1416A>G Ser472Ser
M0169420 IPHBNGFD_00028 21813 3 Gut 0.30 protein_coding synonymous_variant LOW 1614A>G Gly538Gly
M0169421 IPHBNGFD_00028 21852 3 Gut 0.30 protein_coding synonymous_variant LOW 1653A>G Lys551Lys
M0169422 IPHBNGFD_00028 21951 3 Gut 0.30 protein_coding synonymous_variant LOW 1752A>T Ala584Ala
M0169423 IPHBNGFD_00028 22059 3 Gut 0.30 protein_coding synonymous_variant LOW 1860A>G Thr620Thr
M0169424 IPHBNGFD_00028 22076 3 Gut 0.30 protein_coding missense_variant MODERATE 1877T>A Leu626His
M0169425 IPHBNGFD_00028 22080 3 Gut 0.30 protein_coding synonymous_variant LOW 1881G>T Pro627Pro
M0169426 IPHBNGFD_00028 22086 3 Gut 0.30 protein_coding synonymous_variant LOW 1887A>G Val629Val
M0169427 IPHBNGFD_00028 22095 3 Gut 0.30 protein_coding synonymous_variant LOW 1896C>T Thr632Thr
M0169428 IPHBNGFD_00028 22098 3 Gut 0.30 protein_coding synonymous_variant LOW 1899C>A Ala633Ala
M0169429 IPHBNGFD_00028 22104 3 Gut 0.30 protein_coding synonymous_variant LOW 1905G>A Ser635Ser
M0169430 IPHBNGFD_00028 22152 3 Gut 0.30 protein_coding synonymous_variant LOW 1953C>T Arg651Arg
M0169431 IPHBNGFD_00028 22159 3 Gut 0.30 protein_coding missense_variant MODERATE 1960C>A Leu654Met
M0169432 IPHBNGFD_00028 22319 3 Gut 0.30 protein_coding missense_variant MODERATE 2120A>C Gln707Pro
M0169433 IPHBNGFD_00028 22350 3 Gut 0.30 protein_coding synonymous_variant LOW 2151T>A Arg717Arg
M0169434 IPHBNGFD_00028 22365 3 Gut 0.30 protein_coding synonymous_variant LOW 2166A>G Gly722Gly
M0169435 IPHBNGFD_00028 22371 3 Gut 0.30 protein_coding synonymous_variant LOW 2172C>T Ile724Ile
M0169436 IPHBNGFD_00028 22425 3 Gut 0.30 protein_coding synonymous_variant LOW 2226G>A Glu742Glu
M0169437 IPHBNGFD_00028 22428 3 Gut 0.30 protein_coding synonymous_variant LOW 2229C>T Asp743Asp
M0169438 IPHBNGFD_00028 22452 3 Gut 0.30 protein_coding synonymous_variant LOW 2253A>G Gly751Gly
M0169439 IPHBNGFD_00028 22480 3 Gut 0.30 protein_coding missense_variant MODERATE 2281G>A Gly761Arg
M0169440 IPHBNGFD_00028 22482 3 Gut 0.30 protein_coding synonymous_variant LOW 2283G>C Gly761Gly
M0169441 IPHBNGFD_00028 22682 3 Gut 0.30 protein_coding missense_variant MODERATE 2483T>C Val828Ala
M0169442 IPHBNGFD_00029 25753 3 Gut 0.30 protein_coding synonymous_variant LOW 264A>G Pro88Pro
M0169443 IPHBNGFD_00029 25780 3 Gut 0.30 protein_coding synonymous_variant LOW 291A>G Gly97Gly
M0169444 IPHBNGFD_00029 25926 3 Gut 0.30 protein_coding missense_variant MODERATE 437T>C Val146Ala
M0169445 IPHBNGFD_00032 27318 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -60T>C None
M0169446 IPHBNGFD_00032 27562 3 Gut 0.30 protein_coding missense_variant MODERATE 185G>A Arg62Lys
M0169447 IPHBNGFD_00033 27985 3 Gut 0.30 protein_coding missense_variant MODERATE 38T>G Leu13Arg
M0169448 IPHBNGFD_00033 28143 3 Gut 0.30 protein_coding missense_variant MODERATE 196G>A Glu66Lys
M0169449 IPHBNGFD_00034 28182 3 Gut 0.30 protein_coding upstream_gene_variant MODIFIER -13A>G None
M0169450 IPHBNGFD_00034 28235 3 Gut 0.30 protein_coding missense_variant MODERATE 41T>C Val14Ala






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
IPHBNGFD_00044 VFG034574 Dispersin 94.8 1.5e-59 1 116 1.0 1 Others dispersin experiment
IPHBNGFD_00049 VFG042382 EtpA 99.8 0 1 598 1.0 0.9917 Adherence two-partner secretion transporter EtpB experiment
IPHBNGFD_00050 VFG034541 EtpA 93.7 0 1 1526 1.0 0.9916 Adherence Two-partner secreted adhesin EtpA experiment
IPHBNGFD_00044 VFG034574 Dispersin 94.8 1.1e-58 1 116 1.0 1 Others dispersin prediction
IPHBNGFD_00049 VFG042382 EtpA 99.8 0 1 598 1.0 0.9917 Adherence two-partner secretion transporter EtpB prediction
IPHBNGFD_00050 VFG034541 EtpA 93.7 0 1 1526 1.0 0.9916 Adherence Two-partner secreted adhesin EtpA prediction
IPHBNGFD_00062 VFG041000 AAI/SCI-II T6SS 92.6 3.7e-99 1 188 1.0 1 Effector delivery system hypothetical 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
IPHBNGFD_00063 PHI:3113 stbA 97.9 2.8e-182 1 326 1.0000 1.0000 rodents neonatal meningitis stability protein for the plasmid reduced virulence






        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
IPHBNGFD_00051 ATB16983.1|GT41 100 0 1 636 1 0.9984
IPHBNGFD_00088 UUX86900.1|GH23 99.4 1.45e-122 1 169 1 0.786





        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
IPHBNGFD_00049 1.B.20.3.3 99.8 0 1 598 1.0000 0.9917 1 Channels/Pores 1.B β-Barrel Porins 1.B.20 The Two-Partner Secretion (TPS) Family
IPHBNGFD_00052 9.B.127.1.3 98.8 1.2e-93 1 164 1.0000 1.0000 9 Incompletely Characterized Transport Systems 9.B Putative transport proteins 9.B.127 The DUF2919 (PF11143) Family