Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C262
  Reference Plasmid   LR962706.1
  Reference Plasmid Size   49132
  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
M0150052 IJJFINOL_00018 19213 5 Gut 0.42 protein_coding synonymous_variant LOW 1044T>C Phe348Phe
M0150053 IJJFINOL_00018 19859 6 Gut 0.50 protein_coding missense_variant MODERATE 1690A>G Met564Val
M0150054 IJJFINOL_00018 20143 4 Gut 0.33 protein_coding synonymous_variant LOW 1974A>G Leu658Leu
M0150055 IJJFINOL_00023 25130 5 Gut 0.42 protein_coding synonymous_variant LOW 315T>C Leu105Leu
M0150056 IJJFINOL_00023 25150 5 Gut 0.42 protein_coding missense_variant MODERATE 335A>G His112Arg
M0150057 IJJFINOL_00023 25154 5 Gut 0.42 protein_coding synonymous_variant LOW 339G>A Val113Val
M0150058 IJJFINOL_00023 25275 5 Gut 0.42 protein_coding missense_variant MODERATE 460G>A Glu154Lys
M0150059 IJJFINOL_00009 10899 3 Gut 0.25 protein_coding synonymous_variant LOW 1050T>C Asn350Asn
M0150060 IJJFINOL_00009 10926 3 Gut 0.25 protein_coding synonymous_variant LOW 1077A>G Gly359Gly
M0150061 IJJFINOL_00009 10941 3 Gut 0.25 protein_coding synonymous_variant LOW 1092T>C Tyr364Tyr
M0150062 IJJFINOL_00009 10947 3 Gut 0.25 protein_coding synonymous_variant LOW 1098A>G Gly366Gly
M0150063 IJJFINOL_00009 10950 3 Gut 0.25 protein_coding synonymous_variant LOW 1101T>C Arg367Arg
M0150064 IJJFINOL_00009 10980 3 Gut 0.25 protein_coding synonymous_variant LOW 1131A>G Glu377Glu
M0150065 IJJFINOL_00009 10998 3 Gut 0.25 protein_coding synonymous_variant LOW 1149C>T Ser383Ser
M0150066 IJJFINOL_00009 11004 3 Gut 0.25 protein_coding synonymous_variant LOW 1155T>C Ser385Ser
M0150067 IJJFINOL_00009 11007 3 Gut 0.25 protein_coding synonymous_variant LOW 1158A>T Gly386Gly
M0150068 IJJFINOL_00009 11010 3 Gut 0.25 protein_coding synonymous_variant LOW 1161G>A Thr387Thr
M0150069 IJJFINOL_00009 11011 3 Gut 0.25 protein_coding synonymous_variant LOW 1162T>C Leu388Leu
M0150070 IJJFINOL_00009 11013 3 Gut 0.25 protein_coding missense_variant MODERATE 1164A>C Leu388Phe
M0150071 IJJFINOL_00009 11031 3 Gut 0.25 protein_coding synonymous_variant LOW 1182C>T Asn394Asn
M0150072 IJJFINOL_00009 11124 3 Gut 0.25 protein_coding synonymous_variant LOW 1275T>G Gly425Gly
M0150073 IJJFINOL_00009 11166 3 Gut 0.25 protein_coding synonymous_variant LOW 1317G>A Ala439Ala
M0150074 IJJFINOL_00009 11202 3 Gut 0.25 protein_coding synonymous_variant LOW 1353T>C Gly451Gly
M0150075 IJJFINOL_00009 11230 3 Gut 0.25 protein_coding missense_variant MODERATE 1381G>A Gly461Arg
M0150076 IJJFINOL_00009 11235 3 Gut 0.25 protein_coding synonymous_variant LOW 1386C>G Ala462Ala
M0150077 IJJFINOL_00009 11242 3 Gut 0.25 protein_coding missense_variant MODERATE 1393G>A Ala465Thr
M0150078 IJJFINOL_00009 11337 3 Gut 0.25 protein_coding synonymous_variant LOW 1488A>T Gly496Gly
M0150079 IJJFINOL_00009 11367 3 Gut 0.25 protein_coding synonymous_variant LOW 1518G>T Gly506Gly
M0150080 IJJFINOL_00009 11406 3 Gut 0.25 protein_coding synonymous_variant LOW 1557T>C Ala519Ala
M0150081 IJJFINOL_00009 11412 3 Gut 0.25 protein_coding synonymous_variant LOW 1563A>G Gly521Gly
M0150082 IJJFINOL_00009 11574 3 Gut 0.25 protein_coding synonymous_variant LOW 1725C>T Phe575Phe
M0150083 IJJFINOL_00009 11578 3 Gut 0.25 protein_coding missense_variant MODERATE 1729C>G Arg577Gly
M0150084 IJJFINOL_00009 11616 3 Gut 0.25 protein_coding synonymous_variant LOW 1767C>T Asn589Asn
M0150085 IJJFINOL_00009 11673 3 Gut 0.25 protein_coding synonymous_variant LOW 1824C>T Asp608Asp
M0150086 IJJFINOL_00009 11739 3 Gut 0.25 protein_coding synonymous_variant LOW 1890C>A Thr630Thr
M0150087 IJJFINOL_00009 11802 3 Gut 0.25 protein_coding synonymous_variant LOW 1953G>A Lys651Lys
M0150088 IJJFINOL_00009 11877 3 Gut 0.25 protein_coding synonymous_variant LOW 2028T>C Ala676Ala
M0150089 IJJFINOL_00009 11901 3 Gut 0.25 protein_coding synonymous_variant LOW 2052C>T Asp684Asp
M0150090 IJJFINOL_00009 11913 3 Gut 0.25 protein_coding synonymous_variant LOW 2064C>T Asp688Asp
M0150091 IJJFINOL_00009 11925 3 Gut 0.25 protein_coding synonymous_variant LOW 2076T>C Val692Val
M0150092 IJJFINOL_00009 11955 3 Gut 0.25 protein_coding synonymous_variant LOW 2106C>T Gly702Gly
M0150093 IJJFINOL_00009 12048 3 Gut 0.25 protein_coding synonymous_variant LOW 2199G>A Gln733Gln
M0150094 IJJFINOL_00009 12049 3 Gut 0.25 protein_coding missense_variant MODERATE 2200C>G Leu734Val
M0150095 IJJFINOL_00009 12057 3 Gut 0.25 protein_coding synonymous_variant LOW 2208T>C Asn736Asn
M0150096 IJJFINOL_00009 12063 3 Gut 0.25 protein_coding synonymous_variant LOW 2214C>T Gly738Gly
M0150097 IJJFINOL_00009 12126 3 Gut 0.25 protein_coding synonymous_variant LOW 2277G>A Lys759Lys
M0150098 IJJFINOL_00009 12168 3 Gut 0.25 protein_coding synonymous_variant LOW 2319T>C Asp773Asp
M0150099 IJJFINOL_00009 12186 3 Gut 0.25 protein_coding synonymous_variant LOW 2337A>G Gln779Gln
M0150100 IJJFINOL_00009 12510 3 Gut 0.25 protein_coding synonymous_variant LOW 2661C>T Ile887Ile
M0150101 IJJFINOL_00009 12522 3 Gut 0.25 protein_coding synonymous_variant LOW 2673T>C Asp891Asp
M0150102 IJJFINOL_00009 12585 3 Gut 0.25 protein_coding synonymous_variant LOW 2736A>G Thr912Thr
M0150103 IJJFINOL_00009 12588 3 Gut 0.25 protein_coding synonymous_variant LOW 2739C>T His913His
M0150104 IJJFINOL_00009 12611 3 Gut 0.25 protein_coding missense_variant MODERATE 2762T>C Ile921Thr
M0150105 IJJFINOL_00009 12680 3 Gut 0.25 protein_coding missense_variant MODERATE 2831T>C Phe944Ser
M0150106 IJJFINOL_00009 12693 3 Gut 0.25 protein_coding synonymous_variant LOW 2844C>T Thr948Thr
M0150107 IJJFINOL_00009 12774 3 Gut 0.25 protein_coding synonymous_variant LOW 2925T>C Tyr975Tyr
M0150108 IJJFINOL_00009 12777 3 Gut 0.25 protein_coding synonymous_variant LOW 2928C>T Asp976Asp
M0150109 IJJFINOL_00009 12790 3 Gut 0.25 protein_coding missense_variant MODERATE 2941T>A Ser981Thr
M0150110 IJJFINOL_00009 12798 3 Gut 0.25 protein_coding synonymous_variant LOW 2949C>T Ile983Ile
M0150111 IJJFINOL_00009 13020 3 Gut 0.25 protein_coding synonymous_variant LOW 3171T>C Gly1057Gly
M0150112 IJJFINOL_00009 13041 3 Gut 0.25 protein_coding synonymous_variant LOW 3192C>T Thr1064Thr
M0150113 IJJFINOL_00009 13068 3 Gut 0.25 protein_coding synonymous_variant LOW 3219C>T Asn1073Asn
M0150114 IJJFINOL_00009 13077 3 Gut 0.25 protein_coding synonymous_variant LOW 3228A>G Lys1076Lys
M0150115 IJJFINOL_00009 13080 3 Gut 0.25 protein_coding synonymous_variant LOW 3231C>T Asp1077Asp
M0150116 IJJFINOL_00009 13083 3 Gut 0.25 protein_coding synonymous_variant LOW 3234A>G Val1078Val
M0150117 IJJFINOL_00009 13086 3 Gut 0.25 protein_coding synonymous_variant LOW 3237T>C Val1079Val
M0150118 IJJFINOL_00009 13095 3 Gut 0.25 protein_coding synonymous_variant LOW 3246C>T Val1082Val
M0150119 IJJFINOL_00009 13119 3 Gut 0.25 protein_coding synonymous_variant LOW 3270C>T Gly1090Gly
M0150120 IJJFINOL_00009 13122 3 Gut 0.25 protein_coding synonymous_variant LOW 3273T>C Ala1091Ala
M0150121 IJJFINOL_00009 13143 3 Gut 0.25 protein_coding synonymous_variant LOW 3294A>G Lys1098Lys
M0150122 IJJFINOL_00009 13191 3 Gut 0.25 protein_coding synonymous_variant LOW 3342T>A Gly1114Gly
M0150123 IJJFINOL_00009 13210 3 Gut 0.25 protein_coding missense_variant MODERATE 3361C>A Leu1121Ile
M0150124 IJJFINOL_00009 13215 3 Gut 0.25 protein_coding synonymous_variant LOW 3366T>C Ser1122Ser
M0150125 IJJFINOL_00009 13218 3 Gut 0.25 protein_coding synonymous_variant LOW 3369C>T Asp1123Asp
M0150126 IJJFINOL_00009 13251 3 Gut 0.25 protein_coding synonymous_variant LOW 3402C>A Gly1134Gly
M0150127 IJJFINOL_00009 13276 3 Gut 0.25 protein_coding missense_variant MODERATE 3427G>A Ala1143Thr
M0150128 IJJFINOL_00009 13277 3 Gut 0.25 protein_coding missense_variant MODERATE 3428C>A Ala1143Glu
M0150129 IJJFINOL_00009 13278 3 Gut 0.25 protein_coding synonymous_variant LOW 3429G>T Ala1143Ala
M0150130 IJJFINOL_00009 13284 3 Gut 0.25 protein_coding synonymous_variant LOW 3435C>T Val1145Val
M0150131 IJJFINOL_00009 13293 3 Gut 0.25 protein_coding synonymous_variant LOW 3444C>T Asp1148Asp
M0150132 IJJFINOL_00009 13317 3 Gut 0.25 protein_coding synonymous_variant LOW 3468T>C Asp1156Asp
M0150133 IJJFINOL_00009 13350 3 Gut 0.25 protein_coding missense_variant MODERATE 3501A>C Glu1167Asp
M0150134 IJJFINOL_00009 13351 3 Gut 0.25 protein_coding missense_variant MODERATE 3502C>A Gln1168Lys
M0150135 IJJFINOL_00009 13389 3 Gut 0.25 protein_coding synonymous_variant LOW 3540A>G Leu1180Leu
M0150136 IJJFINOL_00009 13417 3 Gut 0.25 protein_coding missense_variant MODERATE 3568C>A His1190Asn
M0150137 IJJFINOL_00009 13521 3 Gut 0.25 protein_coding synonymous_variant LOW 3672T>G Thr1224Thr
M0150138 IJJFINOL_00009 13560 3 Gut 0.25 protein_coding synonymous_variant LOW 3711G>A Thr1237Thr
M0150139 IJJFINOL_00019 21672 3 Gut 0.25 protein_coding synonymous_variant LOW 1101G>A Glu367Glu
M0150140 IJJFINOL_00019 21687 3 Gut 0.25 protein_coding synonymous_variant LOW 1116G>A Ser372Ser
M0150141 IJJFINOL_00019 22492 3 Gut 0.25 protein_coding synonymous_variant LOW 1921C>T Leu641Leu
M0150142 IJJFINOL_00019 22604 4 Gut 0.33 protein_coding missense_variant MODERATE 2033T>C Val678Ala
M0150143 IJJFINOL_00019 22881 4 Gut 0.33 protein_coding synonymous_variant LOW 2310A>G Val770Val
M0150144 IJJFINOL_00019 22959 4 Gut 0.33 protein_coding missense_variant MODERATE 2388T>A Ser796Arg
M0150145 IJJFINOL_00019 23012 3 Gut 0.25 protein_coding missense_variant MODERATE 2441T>C Ile814Thr
M0150146 IJJFINOL_00019 23019 3 Gut 0.25 protein_coding synonymous_variant LOW 2448A>T Thr816Thr
M0150147 IJJFINOL_00019 23081 3 Gut 0.25 protein_coding missense_variant MODERATE 2510C>T Ser837Phe
M0150148 IJJFINOL_00019 23088 4 Gut 0.33 protein_coding synonymous_variant LOW 2517T>A Gly839Gly
M0150149 IJJFINOL_00019 23130 4 Gut 0.33 protein_coding synonymous_variant LOW 2559T>C Ser853Ser
M0150150 IJJFINOL_00020 23231 3 Gut 0.25 protein_coding synonymous_variant LOW 12A>G Leu4Leu
M0150151 IJJFINOL_00020 23251 4 Gut 0.33 protein_coding missense_variant MODERATE 32C>G Ala11Gly
M0150152 IJJFINOL_00020 23256 4 Gut 0.33 protein_coding missense_variant MODERATE 37G>A Val13Ile
M0150153 IJJFINOL_00020 23354 4 Gut 0.33 protein_coding synonymous_variant LOW 135T>C Val45Val
M0150154 IJJFINOL_00020 23369 4 Gut 0.33 protein_coding synonymous_variant LOW 150G>A Glu50Glu
M0150155 IJJFINOL_00020 23815 4 Gut 0.33 protein_coding missense_variant MODERATE 596G>A Ser199Asn
M0150156 IJJFINOL_00021 23841 4 Gut 0.33 protein_coding synonymous_variant LOW 27G>A Val9Val
M0150157 IJJFINOL_00021 23862 4 Gut 0.33 protein_coding synonymous_variant LOW 48A>G Lys16Lys
M0150158 IJJFINOL_00022 24130 4 Gut 0.33 protein_coding synonymous_variant LOW 90A>T Ser30Ser
M0150159 IJJFINOL_00022 24152 4 Gut 0.33 protein_coding missense_variant MODERATE 112G>A Val38Met
M0150160 IJJFINOL_00022 24154 4 Gut 0.33 protein_coding synonymous_variant LOW 114G>C Val38Val
M0150161 IJJFINOL_00022 24196 4 Gut 0.33 protein_coding synonymous_variant LOW 156A>G Gly52Gly
M0150162 IJJFINOL_00022 24299 4 Gut 0.33 protein_coding missense_variant MODERATE 259G>A Asp87Asn
M0150163 IJJFINOL_00022 24362 4 Gut 0.33 protein_coding missense_variant MODERATE 322A>G Ile108Val
M0150164 IJJFINOL_00022 24393 4 Gut 0.33 protein_coding missense_variant MODERATE 353A>T Asn118Ile
M0150165 IJJFINOL_00022 24450 4 Gut 0.33 protein_coding missense_variant MODERATE 410A>C Asn137Thr
M0150166 IJJFINOL_00022 24466 4 Gut 0.33 protein_coding synonymous_variant LOW 426A>C Thr142Thr
M0150167 IJJFINOL_00022 24491 4 Gut 0.33 protein_coding missense_variant MODERATE 451A>G Lys151Glu
M0150168 IJJFINOL_00022 24589 4 Gut 0.33 protein_coding synonymous_variant LOW 549G>A Lys183Lys
M0150169 IJJFINOL_00023 24813 4 Gut 0.33 protein_coding upstream_gene_variant MODIFIER -3T>A None
M0150170 IJJFINOL_00023 24924 4 Gut 0.33 protein_coding synonymous_variant LOW 109T>C Leu37Leu
M0150171 IJJFINOL_00023 25198 4 Gut 0.33 protein_coding missense_variant MODERATE 383C>T Pro128Leu
M0150172 IJJFINOL_00023 25211 4 Gut 0.33 protein_coding synonymous_variant LOW 396T>C Thr132Thr
M0150173 IJJFINOL_00023 25265 4 Gut 0.33 protein_coding synonymous_variant LOW 450T>C Ile150Ile
M0150174 IJJFINOL_00023 25278 4 Gut 0.33 protein_coding missense_variant MODERATE 463A>G Thr155Ala
M0150175 IJJFINOL_00023 25303 4 Gut 0.33 protein_coding splice_region_variant&stop_retained_variant LOW 488A>G Ter163Ter
M0150176 IJJFINOL_00024 25349 4 Gut 0.33 protein_coding missense_variant MODERATE 46G>A Val16Ile
M0150177 IJJFINOL_00024 25756 4 Gut 0.33 protein_coding synonymous_variant LOW 453T>C Asp151Asp
M0150178 IJJFINOL_00024 25879 4 Gut 0.33 protein_coding synonymous_variant LOW 576C>A Gly192Gly
M0150179 IJJFINOL_00024 25910 4 Gut 0.33 protein_coding missense_variant MODERATE 607A>G Thr203Ala
M0150180 IJJFINOL_00024 26023 3 Gut 0.25 protein_coding synonymous_variant LOW 720C>T Thr240Thr
M0150181 IJJFINOL_00024 26098 4 Gut 0.33 protein_coding synonymous_variant LOW 795C>T Arg265Arg
M0150182 IJJFINOL_00024 26184 4 Gut 0.33 protein_coding missense_variant MODERATE 881C>T Ala294Val
M0150183 IJJFINOL_00024 26530 4 Gut 0.33 protein_coding synonymous_variant LOW 1227A>C Gly409Gly
M0150184 IJJFINOL_00024 26551 4 Gut 0.33 protein_coding synonymous_variant LOW 1248T>C Arg416Arg
M0150185 IJJFINOL_00024 26815 4 Gut 0.33 protein_coding synonymous_variant LOW 1512T>C Asn504Asn






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
IJJFINOL_00009 VFG002164 AS 98.5 0 1 1305 1.0 1 Adherence aggregation substance PrgB/Asc10 experiment
IJJFINOL_00009 VFG002164 AS 98.5 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
IJJFINOL_00024 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
IJJFINOL_00025 3.A.7.19.1 99 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
IJJFINOL_00028 3.A.7.19.1 99.6 0 1 561 1.0000 1.0000 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
IJJFINOL_00030 3.A.7.19.1 93.5 2.4e-245 3 447 0.9955 0.7932 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