Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C2042
  Reference Plasmid   1111525849737189_bin.2__k141_5069
  Reference Plasmid Size   23552
  Reference Plasmid GC Content   0.63
  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
M0023283 LHMAHOPM_00011 9974 4 Skin 0.08 protein_coding synonymous_variant LOW 369C>T Arg123Arg
M0023284 LHMAHOPM_00013 13617 9 Skin 0.18 protein_coding missense_variant MODERATE 386G>A Gly129Asp
M0023285 LHMAHOPM_00019 18038 19 Skin 0.39 protein_coding synonymous_variant LOW 589C>T Leu197Leu
M0023286 LHMAHOPM_00021 19836 3 Skin 0.06 protein_coding missense_variant MODERATE 786G>C Glu262Asp
M0023287 LHMAHOPM_00018 20779 6 Skin 0.12 protein_coding upstream_gene_variant MODIFIER -3764G>A None
M0023288 LHMAHOPM_00023 21301 8 Skin 0.16 protein_coding missense_variant MODERATE 5C>T Ser2Phe
M0023289 LHMAHOPM_00023 21432 4 Skin 0.08 protein_coding missense_variant MODERATE 136G>C Ala46Pro
M0023290 LHMAHOPM_00023 21433 4 Skin 0.08 protein_coding missense_variant MODERATE 137C>T Ala46Val
M0023291 LHMAHOPM_00023 21488 7 Skin 0.14 protein_coding synonymous_variant LOW 192C>G Leu64Leu
M0023292 LHMAHOPM_00011 9902 3 Skin 0.06 protein_coding synonymous_variant LOW 297C>T Thr99Thr
M0023293 LHMAHOPM_00011 9948 4 Skin 0.08 protein_coding missense_variant MODERATE 343G>A Ala115Thr
M0023294 LHMAHOPM_00004 87 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2968T>C None
M0023295 LHMAHOPM_00004 88 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2967C>A None
M0023296 LHMAHOPM_00004 101 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2954A>G None
M0023297 LHMAHOPM_00004 106 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2949A>G None
M0023298 LHMAHOPM_00004 133 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2922T>C None
M0023299 LHMAHOPM_00004 142 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2913G>A None
M0023300 LHMAHOPM_00004 143 15 Skin 0.31 protein_coding upstream_gene_variant MODIFIER -2912A>G None
M0023301 LHMAHOPM_00004 184 14 Skin 0.29 protein_coding upstream_gene_variant MODIFIER -2871A>G None
M0023302 LHMAHOPM_00004 219 17 Skin 0.35 protein_coding upstream_gene_variant MODIFIER -2836G>A None
M0023303 LHMAHOPM_00004 229 16 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -2826C>G None
M0023304 LHMAHOPM_00004 233 16 Skin 0.33 protein_coding upstream_gene_variant MODIFIER -2822C>T None
M0023305 LHMAHOPM_00001 262 15 Skin 0.31 protein_coding synonymous_variant LOW 144G>A Ala48Ala
M0023306 LHMAHOPM_00001 370 10 Skin 0.20 protein_coding synonymous_variant LOW 36T>C Gly12Gly
M0023307 LHMAHOPM_00002 1285 20 Skin 0.41 protein_coding missense_variant MODERATE 128G>A Arg43Lys
M0023308 LHMAHOPM_00002 1287 20 Skin 0.41 protein_coding synonymous_variant LOW 126C>T Asp42Asp
M0023309 LHMAHOPM_00002 1394 13 Skin 0.27 protein_coding missense_variant MODERATE 19T>C Phe7Leu
M0023310 LHMAHOPM_00003 1918 11 Skin 0.22 protein_coding missense_variant MODERATE 938C>G Pro313Arg
M0023311 LHMAHOPM_00003 1926 12 Skin 0.24 protein_coding synonymous_variant LOW 930C>T Asp310Asp
M0023312 LHMAHOPM_00003 1944 13 Skin 0.27 protein_coding synonymous_variant LOW 912T>G Pro304Pro
M0023313 LHMAHOPM_00003 1965 13 Skin 0.27 protein_coding synonymous_variant LOW 891T>C Leu297Leu
M0023314 LHMAHOPM_00003 2052 10 Skin 0.20 protein_coding synonymous_variant LOW 804G>A Thr268Thr
M0023315 LHMAHOPM_00003 2628 5 Skin 0.10 protein_coding synonymous_variant LOW 228C>A Ala76Ala
M0023316 LHMAHOPM_00003 2796 10 Skin 0.20 protein_coding synonymous_variant LOW 60C>T Phe20Phe
M0023317 LHMAHOPM_00003 1704 11 Skin 0.22 protein_coding synonymous_variant LOW 1152T>C Arg384Arg
M0023318 LHMAHOPM_00002 801 12 Skin 0.24 protein_coding synonymous_variant LOW 612G>A Ala204Ala
M0023319 LHMAHOPM_00003 1530 10 Skin 0.20 protein_coding synonymous_variant LOW 1326A>G Gly442Gly
M0023320 LHMAHOPM_00003 2676 16 Skin 0.33 protein_coding synonymous_variant LOW 180C>A Ile60Ile
M0023321 LHMAHOPM_00004 3307 4 Skin 0.08 protein_coding missense_variant MODERATE 253C>A His85Asn
M0023322 LHMAHOPM_00004 3308 4 Skin 0.08 protein_coding missense_variant MODERATE 254A>G His85Arg
M0023323 LHMAHOPM_00004 3348 4 Skin 0.08 protein_coding synonymous_variant LOW 294C>T Ala98Ala
M0023324 LHMAHOPM_00004 3897 9 Skin 0.18 protein_coding missense_variant MODERATE 843A>G Ile281Met
M0023325 LHMAHOPM_00004 3909 9 Skin 0.18 protein_coding synonymous_variant LOW 855G>C Gly285Gly
M0023326 LHMAHOPM_00005 4236 13 Skin 0.27 protein_coding synonymous_variant LOW 129T>A Arg43Arg
M0023327 LHMAHOPM_00003 2148 10 Skin 0.20 protein_coding synonymous_variant LOW 708A>G Val236Val
M0023328 LHMAHOPM_00004 3175 5 Skin 0.10 protein_coding missense_variant MODERATE 121T>C Ser41Pro
M0023329 LHMAHOPM_00004 3177 5 Skin 0.10 protein_coding synonymous_variant LOW 123G>T Ser41Ser
M0023330 LHMAHOPM_00004 3186 5 Skin 0.10 protein_coding synonymous_variant LOW 132A>C Pro44Pro
M0023331 LHMAHOPM_00004 3204 5 Skin 0.10 protein_coding synonymous_variant LOW 150A>C Ala50Ala
M0023332 LHMAHOPM_00004 3210 5 Skin 0.10 protein_coding synonymous_variant LOW 156A>C Leu52Leu
M0023333 LHMAHOPM_00005 4158 5 Skin 0.10 protein_coding synonymous_variant LOW 51A>G Gln17Gln
M0023334 LHMAHOPM_00005 4387 9 Skin 0.18 protein_coding missense_variant MODERATE 280A>C Lys94Gln
M0023335 LHMAHOPM_00005 4416 10 Skin 0.20 protein_coding synonymous_variant LOW 309C>A Gly103Gly
M0023336 LHMAHOPM_00006 4539 9 Skin 0.18 protein_coding synonymous_variant LOW 2109C>T Cys703Cys
M0023337 LHMAHOPM_00002 735 11 Skin 0.22 protein_coding synonymous_variant LOW 678C>T Ser226Ser
M0023338 LHMAHOPM_00002 762 9 Skin 0.18 protein_coding synonymous_variant LOW 651C>T His217His
M0023339 LHMAHOPM_00018 20898 7 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3883G>A None
M0023340 LHMAHOPM_00018 20900 7 Skin 0.14 protein_coding upstream_gene_variant MODIFIER -3885A>C None
M0023341 LHMAHOPM_00022 20956 6 Skin 0.12 protein_coding missense_variant MODERATE 7C>T Pro3Ser
M0023342 LHMAHOPM_00004 3435 3 Skin 0.06 protein_coding synonymous_variant LOW 381C>T His127His
M0023343 LHMAHOPM_00006 5091 6 Skin 0.12 protein_coding synonymous_variant LOW 1557C>T Leu519Leu
M0023344 LHMAHOPM_00006 5124 5 Skin 0.10 protein_coding missense_variant MODERATE 1524C>G Phe508Leu
M0023345 LHMAHOPM_00005 4191 5 Skin 0.10 protein_coding synonymous_variant LOW 84C>G Arg28Arg
M0023346 LHMAHOPM_00022 21006 4 Skin 0.08 protein_coding synonymous_variant LOW 57A>C Ala19Ala
M0023347 LHMAHOPM_00022 21012 4 Skin 0.08 protein_coding synonymous_variant LOW 63T>C Val21Val
M0023348 LHMAHOPM_00023 21970 3 Skin 0.06 protein_coding missense_variant MODERATE 674A>G His225Arg
M0023349 LHMAHOPM_00023 21971 3 Skin 0.06 protein_coding missense_variant MODERATE 675T>G His225Gln
M0023350 LHMAHOPM_00023 22100 5 Skin 0.10 protein_coding synonymous_variant LOW 804T>C Ser268Ser
M0023351 LHMAHOPM_00023 22109 5 Skin 0.10 protein_coding synonymous_variant LOW 813C>T Arg271Arg
M0023352 LHMAHOPM_00023 22124 5 Skin 0.10 protein_coding synonymous_variant LOW 828T>C Tyr276Tyr
M0023353 LHMAHOPM_00023 22178 6 Skin 0.12 protein_coding missense_variant MODERATE 882T>A Asp294Glu
M0023354 LHMAHOPM_00023 22183 6 Skin 0.12 protein_coding missense_variant MODERATE 887T>C Val296Ala
M0023355 LHMAHOPM_00023 22195 6 Skin 0.12 protein_coding missense_variant MODERATE 899G>C Ser300Thr
M0023356 LHMAHOPM_00023 23003 3 Skin 0.06 protein_coding synonymous_variant LOW 1707T>C Thr569Thr
M0023357 LHMAHOPM_00021 19989 3 Skin 0.06 protein_coding synonymous_variant LOW 633G>C Ala211Ala
M0023358 LHMAHOPM_00018 20707 4 Skin 0.08 protein_coding upstream_gene_variant MODIFIER -3692C>T None
M0023359 LHMAHOPM_00018 21216 3 Skin 0.06 protein_coding upstream_gene_variant MODIFIER -4201A>G None
M0023360 LHMAHOPM_00023 22274 3 Skin 0.06 protein_coding synonymous_variant LOW 978G>A Gln326Gln
M0023361 LHMAHOPM_00002 495 5 Skin 0.10 protein_coding synonymous_variant LOW 918G>A Ala306Ala
M0023362 LHMAHOPM_00002 516 5 Skin 0.10 protein_coding synonymous_variant LOW 897G>A Gln299Gln
M0023363 LHMAHOPM_00002 525 5 Skin 0.10 protein_coding synonymous_variant LOW 888C>G Pro296Pro
M0023364 LHMAHOPM_00002 546 5 Skin 0.10 protein_coding synonymous_variant LOW 867C>T Ile289Ile
M0023365 LHMAHOPM_00006 4824 6 Skin 0.12 protein_coding synonymous_variant LOW 1824T>C Gly608Gly
M0023366 LHMAHOPM_00006 4845 6 Skin 0.12 protein_coding synonymous_variant LOW 1803T>C Ile601Ile
M0023367 LHMAHOPM_00006 5174 5 Skin 0.10 protein_coding missense_variant MODERATE 1474G>A Ala492Thr
M0023368 LHMAHOPM_00006 5277 8 Skin 0.16 protein_coding synonymous_variant LOW 1371C>A Gly457Gly
M0023369 LHMAHOPM_00006 5283 8 Skin 0.16 protein_coding synonymous_variant LOW 1365G>A Lys455Lys
M0023370 LHMAHOPM_00006 6060 6 Skin 0.12 protein_coding synonymous_variant LOW 588G>C Gly196Gly
M0023371 LHMAHOPM_00006 6138 12 Skin 0.24 protein_coding synonymous_variant LOW 510A>G Ala170Ala
M0023372 LHMAHOPM_00006 6297 11 Skin 0.22 protein_coding synonymous_variant LOW 351A>C Ala117Ala
M0023373 LHMAHOPM_00006 6315 11 Skin 0.22 protein_coding synonymous_variant LOW 333C>T Ser111Ser
M0023374 LHMAHOPM_00007 6848 4 Skin 0.08 protein_coding missense_variant MODERATE 9A>T Glu3Asp
M0023375 LHMAHOPM_00007 6884 4 Skin 0.08 protein_coding synonymous_variant LOW 45A>G Glu15Glu
M0023376 LHMAHOPM_00002 1059 7 Skin 0.14 protein_coding synonymous_variant LOW 354G>C Ala118Ala
M0023377 LHMAHOPM_00002 1080 8 Skin 0.16 protein_coding synonymous_variant LOW 333C>G Arg111Arg
M0023378 LHMAHOPM_00006 4938 9 Skin 0.18 protein_coding synonymous_variant LOW 1710A>G Ser570Ser
M0023379 LHMAHOPM_00007 7068 7 Skin 0.14 protein_coding missense_variant MODERATE 229T>G Ser77Ala
M0023380 LHMAHOPM_00008 7883 9 Skin 0.18 protein_coding synonymous_variant LOW 987A>G Ser329Ser
M0023381 LHMAHOPM_00008 8735 7 Skin 0.14 protein_coding synonymous_variant LOW 135T>C Ser45Ser
M0023382 LHMAHOPM_00008 8788 8 Skin 0.16 protein_coding missense_variant MODERATE 82G>C Val28Leu
M0023383 LHMAHOPM_00007 7266 5 Skin 0.10 protein_coding missense_variant MODERATE 427A>G Asn143Asp
M0023384 LHMAHOPM_00008 8297 4 Skin 0.08 protein_coding synonymous_variant LOW 573T>C Arg191Arg
M0023385 LHMAHOPM_00008 8301 4 Skin 0.08 protein_coding missense_variant MODERATE 569G>A Arg190His
M0023386 LHMAHOPM_00008 8313 4 Skin 0.08 protein_coding missense_variant MODERATE 557G>A Gly186Glu
M0023387 LHMAHOPM_00008 8348 4 Skin 0.08 protein_coding synonymous_variant LOW 522G>A Leu174Leu
M0023388 LHMAHOPM_00008 8472 3 Skin 0.06 protein_coding missense_variant MODERATE 398C>A Ala133Glu
M0023389 LHMAHOPM_00008 8474 3 Skin 0.06 protein_coding synonymous_variant LOW 396A>G Ala132Ala
M0023390 LHMAHOPM_00008 8477 3 Skin 0.06 protein_coding synonymous_variant LOW 393C>T Gly131Gly
M0023391 LHMAHOPM_00009 8938 7 Skin 0.14 protein_coding synonymous_variant LOW 102T>C Ala34Ala
M0023392 LHMAHOPM_00006 5400 6 Skin 0.12 protein_coding synonymous_variant LOW 1248C>T Leu416Leu
M0023393 LHMAHOPM_00006 5478 5 Skin 0.10 protein_coding synonymous_variant LOW 1170A>C Leu390Leu
M0023394 LHMAHOPM_00006 5487 5 Skin 0.10 protein_coding synonymous_variant LOW 1161G>C Val387Val
M0023395 LHMAHOPM_00007 7196 4 Skin 0.08 protein_coding synonymous_variant LOW 357T>C Gly119Gly
M0023396 LHMAHOPM_00010 9040 4 Skin 0.08 protein_coding stop_lost&splice_region_variant HIGH 453A>G Ter151Trpext*?
M0023397 LHMAHOPM_00010 9042 4 Skin 0.08 protein_coding stop_lost&splice_region_variant HIGH 451T>C Ter151Argext*?
M0023398 LHMAHOPM_00009 8893 3 Skin 0.06 protein_coding synonymous_variant LOW 147T>A Ala49Ala
M0023399 LHMAHOPM_00016 15242 3 Skin 0.06 protein_coding missense_variant MODERATE 460C>G Leu154Val
M0023400 LHMAHOPM_00023 21798 3 Skin 0.06 protein_coding missense_variant MODERATE 502A>G Thr168Ala
M0023401 LHMAHOPM_00023 21800 3 Skin 0.06 protein_coding synonymous_variant LOW 504T>C Thr168Thr
M0023402 LHMAHOPM_00008 8042 3 Skin 0.06 protein_coding synonymous_variant LOW 828C>T Ile276Ile






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