Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C3339
  Reference Plasmid   MGYG000298756__MGYG000298756_22
  Reference Plasmid Size   24785
  Reference Plasmid GC Content   0.34
  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
M0136140 IIHOMEJH_00003 1621 3 Oral 0.75 protein_coding synonymous_variant LOW 195C>T His65His
M0136141 IIHOMEJH_00003 1660 3 Oral 0.75 protein_coding synonymous_variant LOW 156G>A Val52Val
M0136142 IIHOMEJH_00004 2048 3 Oral 0.75 protein_coding synonymous_variant LOW 750A>G Leu250Leu
M0136143 IIHOMEJH_00004 2126 3 Oral 0.75 protein_coding synonymous_variant LOW 672A>G Thr224Thr
M0136144 IIHOMEJH_00004 2135 3 Oral 0.75 protein_coding synonymous_variant LOW 663A>G Gln221Gln
M0136145 IIHOMEJH_00004 2141 3 Oral 0.75 protein_coding synonymous_variant LOW 657T>C Ser219Ser
M0136146 IIHOMEJH_00004 2156 3 Oral 0.75 protein_coding synonymous_variant LOW 642T>C Asn214Asn
M0136147 IIHOMEJH_00004 2249 3 Oral 0.75 protein_coding synonymous_variant LOW 549C>T Asp183Asp
M0136148 IIHOMEJH_00004 2252 3 Oral 0.75 protein_coding missense_variant MODERATE 546T>A Phe182Leu
M0136149 IIHOMEJH_00004 2264 3 Oral 0.75 protein_coding synonymous_variant LOW 534T>C Ser178Ser
M0136150 IIHOMEJH_00004 2330 3 Oral 0.75 protein_coding synonymous_variant LOW 468C>A Ile156Ile
M0136151 IIHOMEJH_00004 2354 3 Oral 0.75 protein_coding synonymous_variant LOW 444G>A Glu148Glu
M0136152 IIHOMEJH_00004 2360 3 Oral 0.75 protein_coding synonymous_variant LOW 438C>T Phe146Phe
M0136153 IIHOMEJH_00004 2390 3 Oral 0.75 protein_coding synonymous_variant LOW 408A>G Glu136Glu
M0136154 IIHOMEJH_00004 2465 3 Oral 0.75 protein_coding synonymous_variant LOW 333T>C Asp111Asp
M0136155 IIHOMEJH_00004 2543 3 Oral 0.75 protein_coding synonymous_variant LOW 255C>T Tyr85Tyr
M0136156 IIHOMEJH_00004 2597 3 Oral 0.75 protein_coding synonymous_variant LOW 201T>C Tyr67Tyr
M0136157 IIHOMEJH_00004 2612 3 Oral 0.75 protein_coding synonymous_variant LOW 186C>T Phe62Phe
M0136158 IIHOMEJH_00004 2663 3 Oral 0.75 protein_coding synonymous_variant LOW 135C>T Ser45Ser
M0136159 IIHOMEJH_00004 2672 3 Oral 0.75 protein_coding synonymous_variant LOW 126T>C Ser42Ser
M0136160 IIHOMEJH_00004 2711 3 Oral 0.75 protein_coding synonymous_variant LOW 87G>A Gly29Gly
M0136161 IIHOMEJH_00004 2714 3 Oral 0.75 protein_coding synonymous_variant LOW 84T>C Gly28Gly
M0136162 IIHOMEJH_00005 2828 3 Oral 0.75 protein_coding synonymous_variant LOW 3468G>A Leu1156Leu
M0136163 IIHOMEJH_00005 2933 3 Oral 0.75 protein_coding synonymous_variant LOW 3363T>C Ser1121Ser
M0136164 IIHOMEJH_00005 2948 3 Oral 0.75 protein_coding synonymous_variant LOW 3348C>T Ser1116Ser
M0136165 IIHOMEJH_00005 3129 3 Oral 0.75 protein_coding missense_variant MODERATE 3167C>G Ala1056Gly
M0136166 IIHOMEJH_00005 3146 3 Oral 0.75 protein_coding synonymous_variant LOW 3150T>C His1050His
M0136167 IIHOMEJH_00005 3203 3 Oral 0.75 protein_coding synonymous_variant LOW 3093C>T Asp1031Asp
M0136168 IIHOMEJH_00005 3212 3 Oral 0.75 protein_coding synonymous_variant LOW 3084T>C Asp1028Asp
M0136169 IIHOMEJH_00005 3221 3 Oral 0.75 protein_coding synonymous_variant LOW 3075A>G Leu1025Leu
M0136170 IIHOMEJH_00005 3305 3 Oral 0.75 protein_coding synonymous_variant LOW 2991G>A Lys997Lys
M0136171 IIHOMEJH_00005 3326 3 Oral 0.75 protein_coding synonymous_variant LOW 2970T>C Ser990Ser
M0136172 IIHOMEJH_00005 3377 3 Oral 0.75 protein_coding synonymous_variant LOW 2919G>A Lys973Lys
M0136173 IIHOMEJH_00005 3413 3 Oral 0.75 protein_coding synonymous_variant LOW 2883C>T Ala961Ala
M0136174 IIHOMEJH_00005 3416 3 Oral 0.75 protein_coding synonymous_variant LOW 2880G>A Lys960Lys
M0136175 IIHOMEJH_00005 3470 3 Oral 0.75 protein_coding synonymous_variant LOW 2826C>T Asp942Asp
M0136176 IIHOMEJH_00005 3494 3 Oral 0.75 protein_coding synonymous_variant LOW 2802T>G Thr934Thr
M0136177 IIHOMEJH_00005 3506 3 Oral 0.75 protein_coding synonymous_variant LOW 2790A>G Ser930Ser
M0136178 IIHOMEJH_00005 3578 3 Oral 0.75 protein_coding synonymous_variant LOW 2718T>A Pro906Pro
M0136179 IIHOMEJH_00005 3604 3 Oral 0.75 protein_coding synonymous_variant LOW 2692T>C Leu898Leu
M0136180 IIHOMEJH_00005 3608 3 Oral 0.75 protein_coding synonymous_variant LOW 2688T>C Ile896Ile
M0136181 IIHOMEJH_00005 3617 3 Oral 0.75 protein_coding synonymous_variant LOW 2679C>T Asp893Asp
M0136182 IIHOMEJH_00005 3653 3 Oral 0.75 protein_coding synonymous_variant LOW 2643A>C Ile881Ile
M0136183 IIHOMEJH_00005 3695 3 Oral 0.75 protein_coding synonymous_variant LOW 2601C>T Ser867Ser
M0136184 IIHOMEJH_00005 3796 3 Oral 0.75 protein_coding missense_variant MODERATE 2500G>A Ala834Thr
M0136185 IIHOMEJH_00005 3889 3 Oral 0.75 protein_coding synonymous_variant LOW 2407T>C Leu803Leu
M0136186 IIHOMEJH_00005 3944 3 Oral 0.75 protein_coding synonymous_variant LOW 2352C>A Ile784Ile
M0136187 IIHOMEJH_00005 3947 3 Oral 0.75 protein_coding synonymous_variant LOW 2349T>C Val783Val
M0136188 IIHOMEJH_00005 4013 3 Oral 0.75 protein_coding synonymous_variant LOW 2283C>T Tyr761Tyr
M0136189 IIHOMEJH_00005 4043 3 Oral 0.75 protein_coding synonymous_variant LOW 2253T>C Ile751Ile
M0136190 IIHOMEJH_00005 4072 3 Oral 0.75 protein_coding missense_variant MODERATE 2224G>A Gly742Ser
M0136191 IIHOMEJH_00005 4094 3 Oral 0.75 protein_coding synonymous_variant LOW 2202T>C Thr734Thr
M0136192 IIHOMEJH_00005 4103 3 Oral 0.75 protein_coding synonymous_variant LOW 2193T>G Leu731Leu
M0136193 IIHOMEJH_00005 4121 3 Oral 0.75 protein_coding synonymous_variant LOW 2175G>A Ala725Ala
M0136194 IIHOMEJH_00005 4160 3 Oral 0.75 protein_coding synonymous_variant LOW 2136T>C Asp712Asp
M0136195 IIHOMEJH_00005 4188 3 Oral 0.75 protein_coding missense_variant MODERATE 2108G>A Arg703Lys
M0136196 IIHOMEJH_00005 4205 3 Oral 0.75 protein_coding synonymous_variant LOW 2091A>G Ala697Ala
M0136197 IIHOMEJH_00005 4226 3 Oral 0.75 protein_coding synonymous_variant LOW 2070G>A Gln690Gln
M0136198 IIHOMEJH_00005 4286 3 Oral 0.75 protein_coding synonymous_variant LOW 2010A>C Ile670Ile
M0136199 IIHOMEJH_00005 4337 3 Oral 0.75 protein_coding synonymous_variant LOW 1959G>A Lys653Lys
M0136200 IIHOMEJH_00005 4340 3 Oral 0.75 protein_coding synonymous_variant LOW 1956C>T Thr652Thr
M0136201 IIHOMEJH_00005 4409 3 Oral 0.75 protein_coding synonymous_variant LOW 1887T>C Ile629Ile
M0136202 IIHOMEJH_00005 4430 3 Oral 0.75 protein_coding synonymous_variant LOW 1866G>A Lys622Lys
M0136203 IIHOMEJH_00005 4433 3 Oral 0.75 protein_coding synonymous_variant LOW 1863C>T Ala621Ala
M0136204 IIHOMEJH_00005 4550 3 Oral 0.75 protein_coding synonymous_variant LOW 1746A>G Lys582Lys
M0136205 IIHOMEJH_00005 4622 3 Oral 0.75 protein_coding synonymous_variant LOW 1674C>T Ser558Ser
M0136206 IIHOMEJH_00005 4652 3 Oral 0.75 protein_coding synonymous_variant LOW 1644A>G Ala548Ala
M0136207 IIHOMEJH_00005 4703 3 Oral 0.75 protein_coding synonymous_variant LOW 1593C>T Gly531Gly
M0136208 IIHOMEJH_00005 4881 3 Oral 0.75 protein_coding missense_variant MODERATE 1415C>G Ala472Gly
M0136209 IIHOMEJH_00005 4982 3 Oral 0.75 protein_coding synonymous_variant LOW 1314T>C Ile438Ile
M0136210 IIHOMEJH_00005 5102 3 Oral 0.75 protein_coding synonymous_variant LOW 1194T>C Ile398Ile
M0136211 IIHOMEJH_00005 5105 3 Oral 0.75 protein_coding synonymous_variant LOW 1191C>T Asn397Asn
M0136212 IIHOMEJH_00005 5236 3 Oral 0.75 protein_coding synonymous_variant LOW 1060C>T Leu354Leu
M0136213 IIHOMEJH_00005 5308 3 Oral 0.75 protein_coding missense_variant MODERATE 988A>G Asn330Asp
M0136214 IIHOMEJH_00005 5309 3 Oral 0.75 protein_coding synonymous_variant LOW 987T>C Ser329Ser
M0136215 IIHOMEJH_00005 5342 3 Oral 0.75 protein_coding synonymous_variant LOW 954C>T Ala318Ala
M0136216 IIHOMEJH_00005 5381 3 Oral 0.75 protein_coding synonymous_variant LOW 915C>T Asn305Asn
M0136217 IIHOMEJH_00005 5663 3 Oral 0.75 protein_coding synonymous_variant LOW 633T>C Asp211Asp
M0136218 IIHOMEJH_00005 5708 3 Oral 0.75 protein_coding synonymous_variant LOW 588C>T Thr196Thr
M0136219 IIHOMEJH_00005 5831 3 Oral 0.75 protein_coding synonymous_variant LOW 465T>C Ser155Ser
M0136220 IIHOMEJH_00005 5840 3 Oral 0.75 protein_coding synonymous_variant LOW 456G>A Leu152Leu
M0136221 IIHOMEJH_00005 5846 3 Oral 0.75 protein_coding synonymous_variant LOW 450C>T Phe150Phe
M0136222 IIHOMEJH_00005 5876 3 Oral 0.75 protein_coding synonymous_variant LOW 420C>T Ser140Ser
M0136223 IIHOMEJH_00005 5882 3 Oral 0.75 protein_coding synonymous_variant LOW 414T>C Gly138Gly
M0136224 IIHOMEJH_00005 5942 3 Oral 0.75 protein_coding synonymous_variant LOW 354A>G Lys118Lys
M0136225 IIHOMEJH_00005 6148 3 Oral 0.75 protein_coding missense_variant MODERATE 148A>G Ile50Val
M0136226 IIHOMEJH_00005 6185 3 Oral 0.75 protein_coding synonymous_variant LOW 111A>G Pro37Pro
M0136227 IIHOMEJH_00005 6224 3 Oral 0.75 protein_coding synonymous_variant LOW 72C>T Thr24Thr
M0136228 IIHOMEJH_00005 6242 3 Oral 0.75 protein_coding synonymous_variant LOW 54T>C His18His






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







        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
IIHOMEJH_00003 3.A.23.3.1 82.7 1.1e-79 1 168 0.9711 1.2923 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.23 The Type VI Symbiosis/Virulence Secretory System (T6SS) Family
IIHOMEJH_00009 3.A.23.3.1 76.7 1.2e-224 1 482 1.0000 3.7231 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.23 The Type VI Symbiosis/Virulence Secretory System (T6SS) Family