Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C350
  Reference Plasmid   NZ_AP014877.1
  Reference Plasmid Size   65140
  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
M0153392 IJHOJKAE_00004 7126 4 Gut 0.29 protein_coding synonymous_variant LOW 3126A>G Thr1042Thr
M0153393 IJHOJKAE_00004 7219 3 Gut 0.21 protein_coding synonymous_variant LOW 3219T>A Ser1073Ser
M0153394 IJHOJKAE_00004 7237 3 Gut 0.21 protein_coding synonymous_variant LOW 3237C>T Asp1079Asp
M0153395 IJHOJKAE_00004 7288 4 Gut 0.29 protein_coding synonymous_variant LOW 3288T>C Ala1096Ala
M0153396 IJHOJKAE_00004 7497 3 Gut 0.21 protein_coding missense_variant MODERATE 3497T>A Leu1166Gln
M0153397 IJHOJKAE_00004 7999 3 Gut 0.21 protein_coding synonymous_variant LOW 3999A>C Thr1333Thr
M0153398 IJHOJKAE_00004 8002 3 Gut 0.21 protein_coding synonymous_variant LOW 4002A>G Pro1334Pro
M0153399 IJHOJKAE_00004 8203 3 Gut 0.21 protein_coding synonymous_variant LOW 4203T>C Thr1401Thr
M0153400 IJHOJKAE_00004 8274 3 Gut 0.21 protein_coding missense_variant MODERATE 4274A>T Gln1425Leu
M0153401 IJHOJKAE_00004 8512 3 Gut 0.21 protein_coding synonymous_variant LOW 4512G>A Ala1504Ala
M0153402 IJHOJKAE_00004 8551 3 Gut 0.21 protein_coding synonymous_variant LOW 4551T>A Ala1517Ala
M0153403 IJHOJKAE_00004 8572 4 Gut 0.29 protein_coding synonymous_variant LOW 4572A>G Gln1524Gln
M0153404 IJHOJKAE_00004 8593 3 Gut 0.21 protein_coding synonymous_variant LOW 4593T>G Ala1531Ala
M0153405 IJHOJKAE_00004 8610 4 Gut 0.29 protein_coding missense_variant MODERATE 4610G>A Arg1537Lys
M0153406 IJHOJKAE_00004 8614 4 Gut 0.29 protein_coding synonymous_variant LOW 4614T>C Ser1538Ser
M0153407 IJHOJKAE_00004 8728 3 Gut 0.21 protein_coding synonymous_variant LOW 4728C>T Gly1576Gly
M0153408 IJHOJKAE_00004 8992 4 Gut 0.29 protein_coding synonymous_variant LOW 4992C>T Arg1664Arg
M0153409 IJHOJKAE_00004 8995 3 Gut 0.21 protein_coding synonymous_variant LOW 4995A>G Ala1665Ala
M0153410 IJHOJKAE_00004 9008 4 Gut 0.29 protein_coding synonymous_variant LOW 5008A>C Arg1670Arg
M0153411 IJHOJKAE_00004 9010 4 Gut 0.29 protein_coding missense_variant MODERATE 5010A>T Arg1670Ser
M0153412 IJHOJKAE_00004 9070 4 Gut 0.29 protein_coding synonymous_variant LOW 5070A>G Glu1690Glu
M0153413 IJHOJKAE_00004 9095 4 Gut 0.29 protein_coding missense_variant MODERATE 5095G>A Ala1699Thr
M0153414 IJHOJKAE_00004 9099 4 Gut 0.29 protein_coding missense_variant MODERATE 5099A>C Asp1700Ala
M0153415 IJHOJKAE_00004 9102 3 Gut 0.21 protein_coding missense_variant MODERATE 5102T>C Ile1701Thr
M0153416 IJHOJKAE_00004 9103 3 Gut 0.21 protein_coding synonymous_variant LOW 5103A>T Ile1701Ile
M0153417 IJHOJKAE_00004 9104 4 Gut 0.29 protein_coding missense_variant MODERATE 5104A>T Thr1702Ser
M0153418 IJHOJKAE_00004 9116 3 Gut 0.21 protein_coding missense_variant MODERATE 5116G>A Ala1706Thr
M0153419 IJHOJKAE_00004 9121 3 Gut 0.21 protein_coding synonymous_variant LOW 5121G>A Ala1707Ala
M0153420 IJHOJKAE_00004 9136 3 Gut 0.21 protein_coding synonymous_variant LOW 5136G>A Val1712Val
M0153421 IJHOJKAE_00004 9146 3 Gut 0.21 protein_coding missense_variant MODERATE 5146T>C Ser1716Pro
M0153422 IJHOJKAE_00004 9156 3 Gut 0.21 protein_coding missense_variant MODERATE 5156A>T Glu1719Val
M0153423 IJHOJKAE_00004 9176 4 Gut 0.29 protein_coding missense_variant MODERATE 5176A>G Ile1726Val
M0153424 IJHOJKAE_00004 9205 3 Gut 0.21 protein_coding synonymous_variant LOW 5205T>A Arg1735Arg
M0153425 IJHOJKAE_00004 9256 3 Gut 0.21 protein_coding synonymous_variant LOW 5256A>C Thr1752Thr
M0153426 IJHOJKAE_00006 10133 3 Gut 0.21 protein_coding synonymous_variant LOW 42G>A Lys14Lys
M0153427 IJHOJKAE_00006 10385 3 Gut 0.21 protein_coding synonymous_variant LOW 294T>C Cys98Cys
M0153428 IJHOJKAE_00006 10508 3 Gut 0.21 protein_coding synonymous_variant LOW 417T>C Ala139Ala
M0153429 IJHOJKAE_00012 13652 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -150C>T None
M0153430 IJHOJKAE_00012 13655 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -147C>A None
M0153431 IJHOJKAE_00012 13727 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -75A>G None
M0153432 IJHOJKAE_00014 15225 3 Gut 0.21 protein_coding synonymous_variant LOW 126C>T Thr42Thr
M0153433 IJHOJKAE_00014 15767 3 Gut 0.21 protein_coding missense_variant MODERATE 668A>G His223Arg
M0153434 IJHOJKAE_00076 63486 3 Gut 0.21 protein_coding synonymous_variant LOW 1602C>G Arg534Arg
M0153435 IJHOJKAE_00076 63600 3 Gut 0.21 protein_coding synonymous_variant LOW 1716A>C Thr572Thr
M0153436 IJHOJKAE_00076 63606 3 Gut 0.21 protein_coding synonymous_variant LOW 1722T>C Gly574Gly
M0153437 IJHOJKAE_00076 63615 3 Gut 0.21 protein_coding synonymous_variant LOW 1731T>C Ser577Ser
M0153438 IJHOJKAE_00076 63618 3 Gut 0.21 protein_coding synonymous_variant LOW 1734G>C Thr578Thr
M0153439 IJHOJKAE_00076 63624 3 Gut 0.21 protein_coding synonymous_variant LOW 1740C>T Ser580Ser
M0153440 IJHOJKAE_00076 64080 3 Gut 0.21 protein_coding synonymous_variant LOW 2196A>G Thr732Thr
M0153441 IJHOJKAE_00076 64107 3 Gut 0.21 protein_coding synonymous_variant LOW 2223T>G Ala741Ala
M0153442 IJHOJKAE_00076 64116 3 Gut 0.21 protein_coding synonymous_variant LOW 2232A>C Ala744Ala
M0153443 IJHOJKAE_00076 64137 3 Gut 0.21 protein_coding synonymous_variant LOW 2253T>C Ser751Ser
M0153444 IJHOJKAE_00076 64155 3 Gut 0.21 protein_coding synonymous_variant LOW 2271T>C Asp757Asp
M0153445 IJHOJKAE_00076 64190 3 Gut 0.21 protein_coding missense_variant MODERATE 2306A>G His769Arg
M0153446 IJHOJKAE_00076 64194 3 Gut 0.21 protein_coding synonymous_variant LOW 2310G>A Ala770Ala
M0153447 IJHOJKAE_00076 64224 3 Gut 0.21 protein_coding synonymous_variant LOW 2340C>T Asn780Asn
M0153448 IJHOJKAE_00076 64233 3 Gut 0.21 protein_coding synonymous_variant LOW 2349A>G Ser783Ser
M0153449 IJHOJKAE_00076 64260 3 Gut 0.21 protein_coding synonymous_variant LOW 2376G>T Ala792Ala
M0153450 IJHOJKAE_00076 64266 3 Gut 0.21 protein_coding synonymous_variant LOW 2382A>G Ala794Ala
M0153451 IJHOJKAE_00043 40974 3 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -80A>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
IJHOJKAE_00045 VFG001445 TraJ 100 6e-116 1 200 0.8772 0.995 Invasion unknown protein experiment
IJHOJKAE_00045 VFG001445 TraJ 100 4.5e-115 1 200 0.8772 0.995 Invasion unknown 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
IJHOJKAE_00015 ARO:3000873 100 5.12e-208 1 286 1.0000 1.0000 monobactam TEM beta-lactamase antibiotic inactivation
IJHOJKAE_00016 ARO:3000316 99.7 2.87e-217 1 301 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation
IJHOJKAE_00017 ARO:3003839 100 4.74e-272 1 412 1.0000 1.0000 macrolide antibiotic macrolide phosphotransferase (MPH) antibiotic inactivation






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
IJHOJKAE_00020 PHI:3113 stbA 98.8 2.5e-183 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
IJHOJKAE_00043 QDD24054.1|GH23 100 2.34e-156 1 215 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