Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C536
  Reference Plasmid   NZ_CP027028.1
  Reference Plasmid Size   149179
  Reference Plasmid GC Content   0.45
  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
M0168074 CONKDFJN_00108 85094 6 Gut 0.32 protein_coding missense_variant MODERATE 562C>A His188Asn
M0168075 CONKDFJN_00108 85215 6 Gut 0.32 protein_coding missense_variant MODERATE 683A>G Tyr228Cys
M0168076 CONKDFJN_00108 85380 6 Gut 0.32 protein_coding missense_variant MODERATE 848G>T Gly283Val
M0168077 CONKDFJN_00108 85472 6 Gut 0.32 protein_coding missense_variant MODERATE 940C>A Arg314Ser
M0168078 CONKDFJN_00108 85549 6 Gut 0.32 protein_coding synonymous_variant LOW 1017A>G Gly339Gly






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
CONKDFJN_00001 VFG001013 TTSS 98.8 1.4e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
CONKDFJN_00002 VFG001012 TTSS 98.6 7.7e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
CONKDFJN_00003 VFG001011 TTSS 98 3e-136 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
CONKDFJN_00004 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
CONKDFJN_00005 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
CONKDFJN_00006 VFG001008 TTSS 99.3 2.9e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
CONKDFJN_00007 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
CONKDFJN_00008 VFG001006 TTSS 99.7 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
CONKDFJN_00009 VFG001005 TTSS 99.2 8e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
CONKDFJN_00010 VFG001004 TTSS 99.3 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
CONKDFJN_00011 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
CONKDFJN_00012 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
CONKDFJN_00013 VFG001001 TTSS 98.5 8.6e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
CONKDFJN_00017 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
CONKDFJN_00018 VFG000998 TTSS 99.2 2.2e-129 1 241 1.0 1 Effector delivery system type III secretion system inner MS ring protein MxiJ experiment
CONKDFJN_00019 VFG000997 TTSS 99 1.8e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
CONKDFJN_00020 VFG000996 TTSS 95.2 1.1e-38 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
CONKDFJN_00021 VFG000995 TTSS 95.7 4.3e-204 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
CONKDFJN_00022 VFG000994 TTSS 97.4 3.1e-84 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
CONKDFJN_00023 VFG000993 TTSS 96.7 2.1e-64 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
CONKDFJN_00024 VFG000992 TTSS secreted effectors 94.8 3.8e-294 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase experiment
CONKDFJN_00025 VFG000991 TTSS secreted effectors 97.6 6.4e-280 1 494 1.0 1 Effector delivery system type III secretion system effector IcsB, fatty acyltransferase experiment
CONKDFJN_00026 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
CONKDFJN_00027 VFG000989 TTSS secreted effectors 97.1 1.1e-108 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) experiment
CONKDFJN_00028 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
CONKDFJN_00029 VFG000987 TTSS 99.1 2.6e-296 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB experiment
CONKDFJN_00030 VFG000986 TTSS 98.3 2.2e-181 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC experiment
CONKDFJN_00031 VFG000985 TTSS 92.5 5.4e-166 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD experiment
CONKDFJN_00035 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
CONKDFJN_00036 VFG041905 TTSS secreted effectors 100 3.8e-131 1 227 1.0 0.8764 Effector delivery system type III secretion system effector IpaJ, cysteine protease experiment
CONKDFJN_00045 VFG012778 TTSS secreted effectors 95.9 7.1e-268 1 484 1.0 1 Effector delivery system type III secretion system effector OspC3, ADP-riboxanase experiment
CONKDFJN_00065 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
CONKDFJN_00069 VFG001017 IcsP (SopA) 98.7 8.4e-185 1 315 1.0 1 Exoenzyme outer membrane protease of the OmpP family, involved in cleavage of surface exposed IcsA experiment
CONKDFJN_00071 VFG042215 TTSS secreted effectors 99.1 3.4e-124 1 218 1.0 0.9478 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ experiment
CONKDFJN_00088 VFG012773 TTSS secreted effectors 99.2 6.4e-277 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
CONKDFJN_00116 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
CONKDFJN_00118 VFG002042 TTSS secreted effectors 99.3 8.5e-310 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase experiment
CONKDFJN_00136 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
CONKDFJN_00165 VFG000667 IcsA (VirG) 99.5 0 1 1103 1.0 1.0009 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
CONKDFJN_00166 VFG001016 TTSS secreted effectors 99.5 4.4e-231 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) experiment
CONKDFJN_00187 VFG001015 TTSS 99.4 4.2e-182 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 experiment
CONKDFJN_00188 VFG001014 TTSS 99 4.7e-107 1 210 1.0 0.8203 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
CONKDFJN_00001 VFG012711 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
CONKDFJN_00002 VFG012707 TTSS 100 1.5e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
CONKDFJN_00003 VFG012705 TTSS 99 1.7e-162 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
CONKDFJN_00004 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
CONKDFJN_00005 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
CONKDFJN_00006 VFG020111 TTSS 99.8 1.6e-243 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
CONKDFJN_00007 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
CONKDFJN_00008 VFG001006 TTSS 99.7 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
CONKDFJN_00009 VFG020108 TTSS 100 1.4e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
CONKDFJN_00010 VFG020107 TTSS 99.6 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
CONKDFJN_00011 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
CONKDFJN_00012 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
CONKDFJN_00013 VFG012665 TTSS 99.3 9.9e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
CONKDFJN_00017 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
CONKDFJN_00018 VFG020101 TTSS 100 5.8e-129 1 241 1.0 1 Effector delivery system type III secretion system inner MS ring protein MxiJ prediction
CONKDFJN_00019 VFG000997 TTSS 99 1.3e-44 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
CONKDFJN_00020 VFG000996 TTSS 95.2 8e-38 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
CONKDFJN_00021 VFG020098 TTSS 98.9 2.3e-209 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
CONKDFJN_00022 VFG012735 TTSS 98.7 7.9e-84 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
CONKDFJN_00023 VFG012731 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
CONKDFJN_00024 VFG012764 TTSS secreted effectors 99.1 5.5e-305 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase prediction
CONKDFJN_00025 VFG012771 TTSS secreted effectors 100 7.6e-285 1 494 1.0 1 Effector delivery system type III secretion system effector IcsB, fatty acyltransferase prediction
CONKDFJN_00026 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
CONKDFJN_00027 VFG012758 TTSS secreted effectors 99 4e-110 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) prediction
CONKDFJN_00028 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
CONKDFJN_00029 VFG012754 TTSS secreted effectors 99.7 4.5e-297 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB prediction
CONKDFJN_00030 VFG012750 TTSS secreted effectors 99.2 6.8e-182 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC prediction
CONKDFJN_00031 VFG020124 TTSS secreted effectors 92.5 8.1e-166 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD prediction
CONKDFJN_00035 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
CONKDFJN_00036 VFG041905 TTSS secreted effectors 100 2.9e-130 1 227 1.0 0.8764 Effector delivery system type III secretion system effector IpaJ, cysteine protease prediction
CONKDFJN_00045 VFG012777 TTSS secreted effectors 99.6 5.1e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC3, ADP-riboxanase prediction
CONKDFJN_00065 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
CONKDFJN_00069 VFG012929 IcsP (SopA) 100 1.4e-186 1 315 1.0 1 Exoenzyme outer membrane protease of the OmpP family, involved in cleavage of surface exposed IcsA prediction
CONKDFJN_00071 VFG042215 TTSS secreted effectors 99.1 2.5e-123 1 218 1.0 0.9478 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ prediction
CONKDFJN_00088 VFG012776 TTSS secreted effectors 99.8 2e-277 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
CONKDFJN_00109 VFG013084 MsbB2 100 2.5e-163 15 290 0.9517 0.879 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
CONKDFJN_00110 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
CONKDFJN_00116 VFG002043 TTSS secreted effectors 100 7.5e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase prediction
CONKDFJN_00118 VFG012854 TTSS secreted effectors 99.8 8.90000000000018e-311 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase prediction
CONKDFJN_00136 VFG042325 TTSS secreted effectors 100 2.3e-121 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase prediction
CONKDFJN_00165 VFG000667 IcsA (VirG) 99.5 0 1 1103 1.0 1.0009 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
CONKDFJN_00166 VFG001016 TTSS secreted effectors 99.5 3.3e-230 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) prediction
CONKDFJN_00187 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
CONKDFJN_00188 VFG001014 TTSS 99 3.5e-106 1 210 1.0 0.8203 Effector delivery system type III secretion system minor export apparatus protein Spa29 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
CONKDFJN_00003 PHI:9889 Spa33 99 5.8e-163 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
CONKDFJN_00006 PHI:12182 spa47 99.3 7.5e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
CONKDFJN_00025 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
CONKDFJN_00027 PHI:4511 ipgB1 98.1 2e-109 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
CONKDFJN_00031 PHI:7721 IpaD 92.5 8.3e-166 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
CONKDFJN_00036 PHI:9253 ipaJ 100 1e-130 1 227 1.0000 0.8764 primates shigellosis effector protein effector (plant avirulence determinant)
CONKDFJN_00069 PHI:6577 IcsP 98.7 2.2e-184 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence
CONKDFJN_00111 PHI:10400 Sfgtr4 (ORF186) 99.2 4e-214 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
CONKDFJN_00165 PHI:4647 IcsA 99.5 0 1 1103 1.0000 1.0000 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
CONKDFJN_00166 PHI:9252 virA 99.5 1.2e-230 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)






        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
CONKDFJN_00022 AKH27418.1|GH23 99.3 2.85e-108 1 152 1 1
CONKDFJN_00111 ACD06066.1|GT4 99.4 1.48e-269 1 362 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
CONKDFJN_00002 3.A.6.1.2 98.6 4.5e-112 1 216 1.0000 1.6241 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00003 3.A.6.1.2 99 1.3e-162 1 293 1.0000 2.2030 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00004 3.A.6.1.2 100 2.9e-162 1 292 1.0000 2.1955 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00005 3.A.6.1.2 100 1.4e-56 1 112 1.0000 0.8421 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00006 3.A.6.1.2 99.3 1.7e-243 1 430 1.0000 3.2331 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00007 3.A.6.1.2 99.2 2.5e-68 1 133 1.0000 1.0000 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00029 1.C.36.3.1 99.7 6.1e-297 1 580 1.0000 1.0000 1 Channels/Pores 1.C Pore-Forming Toxins (Proteins and Peptides) 1.C.36 The Bacterial Type III-Target Cell Pore (IIITCP) Family
CONKDFJN_00165 1.B.12.1.2 99.5 0 1 1103 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family
CONKDFJN_00187 3.A.6.1.2 99.4 2.5e-181 1 342 1.0000 2.5714 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
CONKDFJN_00188 3.A.6.1.2 98.6 3.6e-106 1 210 1.0000 1.5789 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family