Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C62
  Reference Plasmid   CP024249.1
  Reference Plasmid Size   167230
  Reference Plasmid GC Content   0.47
  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
M0143238 CEBACDEP_00095 75675 7 Gut 0.08 protein_coding missense_variant MODERATE 1064T>C Val355Ala
M0143239 CEBACDEP_00096 76072 4 Gut 0.04 protein_coding missense_variant MODERATE 196T>C Ser66Pro
M0143240 CEBACDEP_00173 148232 6 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4929T>C None
M0143241 CEBACDEP_00174 148711 6 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -4886C>A None
M0143242 CEBACDEP_00179 149339 7 Gut 0.08 protein_coding synonymous_variant LOW 603T>C Thr201Thr
M0143243 CEBACDEP_00185 152272 5 Gut 0.05 protein_coding missense_variant MODERATE 742T>C Cys248Arg
M0143244 CEBACDEP_00146 123360 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4310T>C None
M0143245 CEBACDEP_00197 160136 4 Gut 0.04 protein_coding missense_variant MODERATE 136C>G Leu46Val
M0143246 CEBACDEP_00138 117295 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -4795C>T None
M0143247 CEBACDEP_00138 117476 8 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4976G>A None
M0143248 CEBACDEP_00139 117557 5 Gut 0.05 protein_coding upstream_gene_variant MODIFIER -3291T>A None
M0143249 CEBACDEP_00008 7671 3 Gut 0.03 protein_coding missense_variant MODERATE 155A>G Lys52Arg
M0143250 CEBACDEP_00006 8035 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -1104A>G None
M0143251 CEBACDEP_00006 8193 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -1262A>T None
M0143252 CEBACDEP_00006 8199 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -1268A>G None
M0143253 CEBACDEP_00111 92089 10 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -2848T>C None
M0143254 CEBACDEP_00118 92834 10 Gut 0.11 protein_coding synonymous_variant LOW 438G>A Glu146Glu
M0143255 CEBACDEP_00126 99665 10 Gut 0.11 protein_coding synonymous_variant LOW 1633T>C Leu545Leu
M0143256 CEBACDEP_00127 101502 10 Gut 0.11 protein_coding synonymous_variant LOW 2937T>C Leu979Leu
M0143257 CEBACDEP_00127 103318 8 Gut 0.09 protein_coding missense_variant MODERATE 1121T>C Ile374Thr
M0143258 CEBACDEP_00141 115130 8 Gut 0.09 protein_coding missense_variant MODERATE 82G>A Ala28Thr
M0143259 CEBACDEP_00139 118214 9 Gut 0.10 protein_coding upstream_gene_variant MODIFIER -3948A>G None
M0143260 CEBACDEP_00099 82414 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -2794C>A None
M0143261 CEBACDEP_00105 83177 5 Gut 0.05 protein_coding missense_variant MODERATE 614A>C His205Pro
M0143262 CEBACDEP_00106 83437 4 Gut 0.04 protein_coding synonymous_variant LOW 27T>C Ser9Ser
M0143263 CEBACDEP_00107 84143 4 Gut 0.04 protein_coding stop_lost&splice_region_variant HIGH 334T>C Ter112Glnext*?
M0143264 CEBACDEP_00099 84161 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4541T>G None
M0143265 CEBACDEP_00108 85251 3 Gut 0.03 protein_coding synonymous_variant LOW 786G>C Val262Val
M0143266 CEBACDEP_00108 85520 6 Gut 0.07 protein_coding missense_variant MODERATE 517T>C Trp173Arg
M0143267 CEBACDEP_00108 85538 3 Gut 0.03 protein_coding missense_variant MODERATE 499A>G Ile167Val
M0143268 CEBACDEP_00104 87100 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4767T>C None
M0143269 CEBACDEP_00104 87132 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4799C>T None
M0143270 CEBACDEP_00192 160876 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4600A>G None
M0143271 CEBACDEP_00195 162447 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -3536C>T None
M0143272 CEBACDEP_00092 72678 3 Gut 0.03 protein_coding missense_variant MODERATE 16T>C Tyr6His
M0143273 CEBACDEP_00165 132465 5 Gut 0.05 protein_coding synonymous_variant LOW 66A>T Gly22Gly
M0143274 CEBACDEP_00166 133644 4 Gut 0.04 protein_coding synonymous_variant LOW 363T>C His121His
M0143275 CEBACDEP_00114 91169 6 Gut 0.07 protein_coding missense_variant MODERATE 94A>G Lys32Glu
M0143276 CEBACDEP_00119 93697 4 Gut 0.04 protein_coding missense_variant MODERATE 242C>A Thr81Asn
M0143277 CEBACDEP_00120 94004 4 Gut 0.04 protein_coding missense_variant MODERATE 161G>A Arg54His
M0143278 CEBACDEP_00122 95289 5 Gut 0.05 protein_coding missense_variant MODERATE 113A>G Lys38Arg
M0143279 CEBACDEP_00126 99534 4 Gut 0.04 protein_coding synonymous_variant LOW 1764C>T Thr588Thr
M0143280 CEBACDEP_00129 105567 3 Gut 0.03 protein_coding missense_variant MODERATE 127T>C Ser43Pro
M0143281 CEBACDEP_00138 111723 5 Gut 0.05 protein_coding missense_variant MODERATE 778C>T His260Tyr
M0143282 CEBACDEP_00182 150875 3 Gut 0.03 protein_coding missense_variant MODERATE 266A>C Glu89Ala
M0143283 CEBACDEP_00183 151104 4 Gut 0.04 protein_coding synonymous_variant LOW 93G>A Ala31Ala
M0143284 CEBACDEP_00178 152170 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -4409T>C None
M0143285 CEBACDEP_00173 146616 4 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -3313A>G None
M0143286 CEBACDEP_00173 146756 6 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -3453C>T None
M0143287 CEBACDEP_00178 147452 3 Gut 0.03 protein_coding missense_variant MODERATE 310G>A Asp104Asn
M0143288 CEBACDEP_00178 147588 3 Gut 0.03 protein_coding synonymous_variant LOW 174G>A Ser58Ser
M0143289 CEBACDEP_00178 147668 6 Gut 0.07 protein_coding missense_variant MODERATE 94G>A Val32Met
M0143290 CEBACDEP_00173 147776 8 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -4473G>A None
M0143291 CEBACDEP_00173 147875 7 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -4572G>A None
M0143292 CEBACDEP_00173 147881 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4578C>T None
M0143293 CEBACDEP_00173 148005 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4702G>A None
M0143294 CEBACDEP_00173 148184 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4881G>A None
M0143295 CEBACDEP_00172 145486 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4687T>C None
M0143296 CEBACDEP_00031 26364 3 Gut 0.03 protein_coding missense_variant MODERATE 298C>A Gln100Lys
M0143297 CEBACDEP_00034 28015 3 Gut 0.03 protein_coding missense_variant MODERATE 278G>A Gly93Glu
M0143298 CEBACDEP_00175 144468 4 Gut 0.04 protein_coding missense_variant MODERATE 43G>A Val15Met
M0143299 CEBACDEP_00102 80885 3 Gut 0.03 protein_coding stop_lost&splice_region_variant HIGH 146A>G Ter49Trpext*?
M0143300 CEBACDEP_00095 75099 3 Gut 0.03 protein_coding missense_variant MODERATE 488A>G Gln163Arg
M0143301 CEBACDEP_00172 145721 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4922T>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
CEBACDEP_00152 VFG002039 Heat-stable toxin (ST) 100 7.4e-36 1 72 1.0 1 Exotoxin heat stable enterotoxin I experiment
CEBACDEP_00195 VFG036068 Heat-labile toxin (LT) 100 4.8e-67 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) experiment
CEBACDEP_00196 VFG036066 Heat-labile toxin (LT) 99.5 5.3e-130 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) experiment
CEBACDEP_00126 VFG035429 AAI/SCI-II T6SS 88.5 0 1 842 1.0 0.9918 Effector delivery system type VI secretion system ATPase TssH prediction
CEBACDEP_00127 VFG035428 AAI/SCI-II T6SS 79.8 0 1 1045 1.0 0.9215 Effector delivery system hypothetical protein prediction
CEBACDEP_00128 VFG035422 AAI/SCI-II T6SS 76 1.7e-82 31 226 0.8673 1 Effector delivery system DotU family type IV/VI secretion system protein prediction
CEBACDEP_00130 VFG035409 AAI/SCI-II T6SS 84.7 2.4e-229 1 451 0.9934 0.9596 Effector delivery system type VI secretion system baseplate subunit TssK prediction
CEBACDEP_00131 VFG035404 AAI/SCI-II T6SS 85.8 4.4e-89 1 183 1.0 1 Effector delivery system type VI secretion lipoprotein TssJ prediction
CEBACDEP_00132 VFG035399 AAI/SCI-II T6SS 81.5 1.5e-128 1 276 1.0 0.7709 Effector delivery system type VI secretion system protein TssA prediction
CEBACDEP_00134 VFG035394 AAI/SCI-II T6SS 89.9 6.6e-47 1 99 1.0 1 Effector delivery system PAAR domain-containing protein prediction
CEBACDEP_00135 VFG035389 AAI/SCI-II T6SS 77.1 1.1e-67 1 153 0.9871 0.9871 Effector delivery system hypothetical protein prediction
CEBACDEP_00136 VFG035384 AAI/SCI-II T6SS 80.4 3.8e-264 1 565 1.0 0.8561 Effector delivery system type VI secretion system tip protein VgrG prediction
CEBACDEP_00138 VFG035379 AAI/SCI-II T6SS 87.1 3.7e-160 10 319 0.9718 1 Effector delivery system type VI secretion system baseplate subunit TssG prediction
CEBACDEP_00139 VFG035374 AAI/SCI-II T6SS 87 0 1 600 1.0 1 Effector delivery system type VI secretion system baseplate subunit TssF prediction
CEBACDEP_00140 VFG035369 AAI/SCI-II T6SS 87.9 1.8e-66 1 140 1.0 1 Effector delivery system hypothetical protein prediction
CEBACDEP_00144 VFG035354 AAI/SCI-II T6SS 92.4 2.7e-79 1 158 1.0 1 Effector delivery system type VI secretion system contractile sheath small subunit prediction
CEBACDEP_00152 VFG002039 Heat-stable toxin (ST) 100 5.5e-35 1 72 1.0 1 Exotoxin heat stable enterotoxin I prediction
CEBACDEP_00173 VFG042515 Adhesive fimbriae 96.5 0 1 834 0.9988 0.9988 Adherence FotD prediction
CEBACDEP_00174 VFG042514 Adhesive fimbriae 83 6.8e-64 1 147 1.0 1 Adherence FotC prediction
CEBACDEP_00175 VFG042513 Adhesive fimbriae 71.9 1.6e-94 7 234 0.962 0.9913 Adherence FotB prediction
CEBACDEP_00195 VFG036068 Heat-labile toxin (LT) 100 3.6e-66 1 124 1.0 1 Exotoxin enterotoxin subunit B (from human) prediction
CEBACDEP_00196 VFG036065 Heat-labile toxin (LT) 100 1.1e-129 1 218 1.0 0.845 Exotoxin heat-labile enterotoxin A prepeptide (from human) 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
CEBACDEP_00195 PHI:699 CtxB 78.2 1.9e-51 1 124 1.0000 1.0000 primates cholera Cholera toxin (CT) reduced virulence
CEBACDEP_00196 PHI:698 CtxA 80.7 2.9e-106 1 218 1.0000 0.8450 primates cholera Cholera toxin (CT) 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
CEBACDEP_00071 QJS03103.1|GH23 100 1e-123 1 169 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
CEBACDEP_00196 1.C.72.4.1 99.5 3.1e-129 1 218 1.0000 0.8450 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.72 The Pertussis Toxin (PTX) Family