Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C204
  Reference Plasmid   CP110033.1
  Reference Plasmid Size   120630
  Reference Plasmid GC Content   0.35
  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
M0148090 GILNKEGI_00034 24682 3 Gut 0.60 protein_coding missense_variant MODERATE 328G>T Ala110Ser
M0148091 GILNKEGI_00034 24726 3 Gut 0.60 protein_coding missense_variant MODERATE 284T>A Phe95Tyr
M0148092 GILNKEGI_00035 25365 3 Gut 0.60 protein_coding synonymous_variant LOW 60G>A Ser20Ser
M0148093 GILNKEGI_00035 25371 3 Gut 0.60 protein_coding synonymous_variant LOW 54C>T Ala18Ala
M0148094 GILNKEGI_00036 25778 3 Gut 0.60 protein_coding missense_variant MODERATE 4G>C Glu2Gln
M0148095 GILNKEGI_00025 25964 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4877A>G None
M0148096 GILNKEGI_00025 26056 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4969C>A None
M0148097 GILNKEGI_00026 26158 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4867C>T None
M0148098 GILNKEGI_00037 26183 3 Gut 0.60 protein_coding missense_variant MODERATE 119A>G Tyr40Cys
M0148099 GILNKEGI_00037 26186 3 Gut 0.60 protein_coding missense_variant MODERATE 116G>A Arg39Gln
M0148100 GILNKEGI_00037 26233 3 Gut 0.60 protein_coding missense_variant MODERATE 69A>C Glu23Asp
M0148101 GILNKEGI_00038 26420 4 Gut 0.80 protein_coding missense_variant MODERATE 2074G>A Val692Met
M0148102 GILNKEGI_00038 26442 4 Gut 0.80 protein_coding synonymous_variant LOW 2052T>C Asn684Asn
M0148103 GILNKEGI_00038 26504 4 Gut 0.80 protein_coding missense_variant MODERATE 1990A>G Thr664Ala
M0148104 GILNKEGI_00038 26511 4 Gut 0.80 protein_coding synonymous_variant LOW 1983C>T Ala661Ala
M0148105 GILNKEGI_00038 26526 4 Gut 0.80 protein_coding synonymous_variant LOW 1968G>T Thr656Thr
M0148106 GILNKEGI_00038 26547 4 Gut 0.80 protein_coding synonymous_variant LOW 1947G>A Thr649Thr
M0148107 GILNKEGI_00038 26637 4 Gut 0.80 protein_coding synonymous_variant LOW 1857G>A Gly619Gly
M0148108 GILNKEGI_00038 26892 4 Gut 0.80 protein_coding synonymous_variant LOW 1602G>A Ala534Ala
M0148109 GILNKEGI_00038 26915 4 Gut 0.80 protein_coding missense_variant MODERATE 1579A>G Thr527Ala
M0148110 GILNKEGI_00038 26973 4 Gut 0.80 protein_coding synonymous_variant LOW 1521C>A Thr507Thr
M0148111 GILNKEGI_00038 27060 4 Gut 0.80 protein_coding synonymous_variant LOW 1434C>T Asn478Asn
M0148112 GILNKEGI_00038 27107 4 Gut 0.80 protein_coding missense_variant MODERATE 1387G>A Ala463Thr
M0148113 GILNKEGI_00038 27174 4 Gut 0.80 protein_coding synonymous_variant LOW 1320C>T Asn440Asn
M0148114 GILNKEGI_00038 27285 3 Gut 0.60 protein_coding synonymous_variant LOW 1209G>A Gly403Gly
M0148115 GILNKEGI_00038 27300 3 Gut 0.60 protein_coding synonymous_variant LOW 1194G>A Gln398Gln
M0148116 GILNKEGI_00038 27314 3 Gut 0.60 protein_coding missense_variant MODERATE 1180A>C Lys394Gln
M0148117 GILNKEGI_00038 27350 3 Gut 0.60 protein_coding missense_variant MODERATE 1144A>T Ile382Phe
M0148118 GILNKEGI_00038 27460 3 Gut 0.60 protein_coding missense_variant MODERATE 1034C>T Thr345Ile
M0148119 GILNKEGI_00038 27476 3 Gut 0.60 protein_coding missense_variant MODERATE 1018C>A Gln340Lys
M0148120 GILNKEGI_00038 27489 3 Gut 0.60 protein_coding synonymous_variant LOW 1005C>T Asn335Asn
M0148121 GILNKEGI_00038 27498 3 Gut 0.60 protein_coding synonymous_variant LOW 996A>G Thr332Thr
M0148122 GILNKEGI_00038 27537 3 Gut 0.60 protein_coding synonymous_variant LOW 957T>C Thr319Thr
M0148123 GILNKEGI_00038 27538 3 Gut 0.60 protein_coding missense_variant MODERATE 956C>T Thr319Ile
M0148124 GILNKEGI_00038 27553 3 Gut 0.60 protein_coding missense_variant MODERATE 941A>G Asn314Ser
M0148125 GILNKEGI_00038 27612 3 Gut 0.60 protein_coding synonymous_variant LOW 882T>C Leu294Leu
M0148126 GILNKEGI_00038 27660 3 Gut 0.60 protein_coding synonymous_variant LOW 834T>C Val278Val
M0148127 GILNKEGI_00038 27668 3 Gut 0.60 protein_coding missense_variant MODERATE 826T>C Ser276Pro
M0148128 GILNKEGI_00038 27678 3 Gut 0.60 protein_coding synonymous_variant LOW 816G>A Glu272Glu
M0148129 GILNKEGI_00038 27774 3 Gut 0.60 protein_coding synonymous_variant LOW 720G>A Glu240Glu
M0148130 GILNKEGI_00038 27987 3 Gut 0.60 protein_coding synonymous_variant LOW 507T>C Ile169Ile
M0148131 GILNKEGI_00038 28230 3 Gut 0.60 protein_coding synonymous_variant LOW 264A>G Val88Val
M0148132 GILNKEGI_00038 28262 3 Gut 0.60 protein_coding missense_variant MODERATE 232C>T His78Tyr
M0148133 GILNKEGI_00038 28263 3 Gut 0.60 protein_coding synonymous_variant LOW 231A>G Thr77Thr
M0148134 GILNKEGI_00038 28341 3 Gut 0.60 protein_coding synonymous_variant LOW 153G>A Lys51Lys
M0148135 GILNKEGI_00038 28347 3 Gut 0.60 protein_coding synonymous_variant LOW 147C>T Thr49Thr
M0148136 GILNKEGI_00112 89163 3 Gut 0.60 protein_coding synonymous_variant LOW 1536T>C Ser512Ser
M0148137 GILNKEGI_00112 89208 3 Gut 0.60 protein_coding synonymous_variant LOW 1491C>T Ser497Ser
M0148138 GILNKEGI_00112 89232 3 Gut 0.60 protein_coding synonymous_variant LOW 1467A>G Ala489Ala
M0148139 GILNKEGI_00112 89265 3 Gut 0.60 protein_coding synonymous_variant LOW 1434G>A Gly478Gly
M0148140 GILNKEGI_00112 89295 3 Gut 0.60 protein_coding synonymous_variant LOW 1404C>T Asn468Asn
M0148141 GILNKEGI_00112 89300 3 Gut 0.60 protein_coding synonymous_variant LOW 1399C>T Leu467Leu
M0148142 GILNKEGI_00112 89316 3 Gut 0.60 protein_coding missense_variant MODERATE 1383T>A Asn461Lys
M0148143 GILNKEGI_00112 89319 3 Gut 0.60 protein_coding synonymous_variant LOW 1380C>A Arg460Arg
M0148144 GILNKEGI_00112 89320 3 Gut 0.60 protein_coding missense_variant MODERATE 1379G>C Arg460Pro
M0148145 GILNKEGI_00112 89325 3 Gut 0.60 protein_coding synonymous_variant LOW 1374T>G Leu458Leu
M0148146 GILNKEGI_00112 89327 3 Gut 0.60 protein_coding missense_variant MODERATE 1372C>T Leu458Phe
M0148147 GILNKEGI_00112 89328 3 Gut 0.60 protein_coding synonymous_variant LOW 1371G>C Thr457Thr
M0148148 GILNKEGI_00112 89334 3 Gut 0.60 protein_coding missense_variant MODERATE 1365A>C Leu455Phe
M0148149 GILNKEGI_00112 89336 3 Gut 0.60 protein_coding synonymous_variant LOW 1363T>C Leu455Leu
M0148150 GILNKEGI_00112 89340 3 Gut 0.60 protein_coding synonymous_variant LOW 1359C>T Asn453Asn
M0148151 GILNKEGI_00112 89343 3 Gut 0.60 protein_coding synonymous_variant LOW 1356G>A Leu452Leu
M0148152 GILNKEGI_00112 89472 3 Gut 0.60 protein_coding synonymous_variant LOW 1227A>C Gly409Gly
M0148153 GILNKEGI_00112 89485 3 Gut 0.60 protein_coding missense_variant MODERATE 1214C>T Ala405Val
M0148154 GILNKEGI_00112 89556 3 Gut 0.60 protein_coding synonymous_variant LOW 1143G>A Ala381Ala
M0148155 GILNKEGI_00112 89614 3 Gut 0.60 protein_coding missense_variant MODERATE 1085T>A Val362Glu
M0148156 GILNKEGI_00112 89791 3 Gut 0.60 protein_coding missense_variant MODERATE 908T>A Val303Glu
M0148157 GILNKEGI_00112 89979 3 Gut 0.60 protein_coding synonymous_variant LOW 720C>T Thr240Thr
M0148158 GILNKEGI_00112 90092 3 Gut 0.60 protein_coding missense_variant MODERATE 607A>G Thr203Ala
M0148159 GILNKEGI_00112 90237 3 Gut 0.60 protein_coding synonymous_variant LOW 462A>G Ala154Ala
M0148160 GILNKEGI_00113 90791 3 Gut 0.60 protein_coding synonymous_variant LOW 393T>C Thr131Thr
M0148161 GILNKEGI_00113 90804 3 Gut 0.60 protein_coding missense_variant MODERATE 380C>T Pro127Leu
M0148162 GILNKEGI_00113 90961 3 Gut 0.60 protein_coding missense_variant MODERATE 223A>G Lys75Glu
M0148163 GILNKEGI_00108 91330 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4706A>T None
M0148164 GILNKEGI_00114 91397 3 Gut 0.60 protein_coding synonymous_variant LOW 405T>C Asp135Asp
M0148165 GILNKEGI_00114 91415 3 Gut 0.60 protein_coding synonymous_variant LOW 387G>A Lys129Lys
M0148166 GILNKEGI_00114 91539 3 Gut 0.60 protein_coding missense_variant MODERATE 263A>C Asn88Thr
M0148167 GILNKEGI_00114 91574 3 Gut 0.60 protein_coding synonymous_variant LOW 228T>C Asn76Asn
M0148168 GILNKEGI_00114 91603 3 Gut 0.60 protein_coding missense_variant MODERATE 199C>A Pro67Thr
M0148169 GILNKEGI_00114 91658 3 Gut 0.60 protein_coding synonymous_variant LOW 144A>G Glu48Glu
M0148170 GILNKEGI_00114 91661 3 Gut 0.60 protein_coding synonymous_variant LOW 141G>A Val47Val
M0148171 GILNKEGI_00114 91705 3 Gut 0.60 protein_coding missense_variant MODERATE 97G>A Asp33Asn
M0148172 GILNKEGI_00109 91809 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3737A>G None
M0148173 GILNKEGI_00109 91851 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3779G>C None
M0148174 GILNKEGI_00109 91853 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3781G>A None
M0148175 GILNKEGI_00109 91929 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -3857T>C None
M0148176 GILNKEGI_00109 92143 3 Gut 0.60 protein_coding upstream_gene_variant MODIFIER -4071A>G None
M0148177 GILNKEGI_00116 92191 3 Gut 0.60 protein_coding missense_variant MODERATE 605G>A Ser202Asn
M0148178 GILNKEGI_00116 92640 3 Gut 0.60 protein_coding synonymous_variant LOW 156A>G Glu52Glu
M0148179 GILNKEGI_00116 92775 3 Gut 0.60 protein_coding synonymous_variant LOW 21A>G Leu7Leu
M0148180 GILNKEGI_00117 92925 3 Gut 0.60 protein_coding missense_variant MODERATE 2150C>T Ser717Phe
M0148181 GILNKEGI_00117 92987 3 Gut 0.60 protein_coding synonymous_variant LOW 2088A>T Thr696Thr
M0148182 GILNKEGI_00117 92994 3 Gut 0.60 protein_coding missense_variant MODERATE 2081T>C Ile694Thr
M0148183 GILNKEGI_00117 93017 3 Gut 0.60 protein_coding synonymous_variant LOW 2058C>T Ala686Ala
M0148184 GILNKEGI_00117 93019 3 Gut 0.60 protein_coding missense_variant MODERATE 2056G>A Ala686Thr
M0148185 GILNKEGI_00117 93020 3 Gut 0.60 protein_coding synonymous_variant LOW 2055G>A Ser685Ser
M0148186 GILNKEGI_00117 93038 3 Gut 0.60 protein_coding synonymous_variant LOW 2037C>A Pro679Pro
M0148187 GILNKEGI_00117 93041 3 Gut 0.60 protein_coding synonymous_variant LOW 2034G>A Thr678Thr
M0148188 GILNKEGI_00117 93047 3 Gut 0.60 protein_coding missense_variant MODERATE 2028T>A Ser676Arg
M0148189 GILNKEGI_00117 93239 3 Gut 0.60 protein_coding synonymous_variant LOW 1836A>G Glu612Glu
M0148190 GILNKEGI_00117 93245 3 Gut 0.60 protein_coding synonymous_variant LOW 1830A>G Gly610Gly
M0148191 GILNKEGI_00117 93269 3 Gut 0.60 protein_coding synonymous_variant LOW 1806A>G Ser602Ser
M0148192 GILNKEGI_00117 93303 3 Gut 0.60 protein_coding missense_variant MODERATE 1772C>T Ala591Val
M0148193 GILNKEGI_00117 93389 3 Gut 0.60 protein_coding synonymous_variant LOW 1686T>G Val562Val
M0148194 GILNKEGI_00117 93428 3 Gut 0.60 protein_coding synonymous_variant LOW 1647C>T Gly549Gly
M0148195 GILNKEGI_00117 93554 3 Gut 0.60 protein_coding synonymous_variant LOW 1521G>A Gln507Gln
M0148196 GILNKEGI_00117 93563 3 Gut 0.60 protein_coding synonymous_variant LOW 1512G>T Gly504Gly
M0148197 GILNKEGI_00117 93599 3 Gut 0.60 protein_coding synonymous_variant LOW 1476A>G Gly492Gly
M0148198 GILNKEGI_00117 93614 3 Gut 0.60 protein_coding synonymous_variant LOW 1461A>T Gly487Gly
M0148199 GILNKEGI_00117 93647 3 Gut 0.60 protein_coding synonymous_variant LOW 1428A>G Ser476Ser
M0148200 GILNKEGI_00117 93695 3 Gut 0.60 protein_coding synonymous_variant LOW 1380T>A Arg460Arg
M0148201 GILNKEGI_00117 93914 3 Gut 0.60 protein_coding missense_variant MODERATE 1161T>A Asp387Glu
M0148202 GILNKEGI_00117 93941 3 Gut 0.60 protein_coding synonymous_variant LOW 1134G>A Thr378Thr
M0148203 GILNKEGI_00117 93980 3 Gut 0.60 protein_coding synonymous_variant LOW 1095A>G Glu365Glu
M0148204 GILNKEGI_00117 94085 3 Gut 0.60 protein_coding synonymous_variant LOW 990A>G Ser330Ser
M0148205 GILNKEGI_00117 94319 3 Gut 0.60 protein_coding synonymous_variant LOW 756G>A Ser252Ser
M0148206 GILNKEGI_00117 94334 3 Gut 0.60 protein_coding synonymous_variant LOW 741G>A Glu247Glu
M0148207 GILNKEGI_00117 94384 3 Gut 0.60 protein_coding synonymous_variant LOW 691T>C Leu231Leu
M0148208 GILNKEGI_00117 94397 3 Gut 0.60 protein_coding missense_variant MODERATE 678C>G Asp226Glu
M0148209 GILNKEGI_00117 94490 3 Gut 0.60 protein_coding missense_variant MODERATE 585T>A Asp195Glu
M0148210 GILNKEGI_00117 94512 3 Gut 0.60 protein_coding missense_variant MODERATE 563A>T Gln188Leu
M0148211 GILNKEGI_00117 94513 3 Gut 0.60 protein_coding stop_gained HIGH 562C>T Gln188*
M0148212 GILNKEGI_00117 94673 3 Gut 0.60 protein_coding synonymous_variant LOW 402A>G Pro134Pro






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
GILNKEGI_00022 VFG002162 BSH 73.9 5.1e-105 5 242 0.9835 0.7323 Stress survival bile salt hydrolase experiment
GILNKEGI_00057 VFG002164 AS 96.9 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 experiment
GILNKEGI_00094 VFG002162 BSH 73.8 1.9e-147 1 324 1.0 0.9969 Stress survival bile salt hydrolase experiment
GILNKEGI_00128 VFG002164 AS 96.9 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 experiment
GILNKEGI_00022 VFG032519 BSH 73.9 2.4e-106 5 242 0.9835 0.7323 Stress survival bile salt hydrolase prediction
GILNKEGI_00057 VFG002164 AS 96.9 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 prediction
GILNKEGI_00094 VFG019385 BSH 74.4 3.3e-148 1 324 1.0 0.9969 Stress survival bile salt hydrolase prediction
GILNKEGI_00128 VFG002164 AS 96.9 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 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






        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
GILNKEGI_00034 3.A.7.19.1 83.1 6.2e-198 1 414 0.9696 0.7380 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
GILNKEGI_00038 3.A.7.19.1 98.6 0 1 719 1.0000 1.2816 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
GILNKEGI_00039 3.A.7.19.1 99.2 0 1 590 1.0000 1.0517 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
GILNKEGI_00109 3.A.7.19.1 98.1 1.2e-253 5 471 0.9915 0.8324 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family
GILNKEGI_00112 3.A.7.19.1 99.2 0 1 609 1.0000 1.0856 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.7 The Type IV (Conjugal DNA-Protein Transfer or VirB) Secretory Pathway (IVSP) Family