Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C323
  Reference Plasmid   NC_016833.1
  Reference Plasmid Size   215774
  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
M0153045 GAAIMDDD_00206 178418 3 Gut 0.01 protein_coding missense_variant MODERATE 4718T>C Leu1573Pro
M0153046 GAAIMDDD_00208 180067 5 Gut 0.02 protein_coding missense_variant MODERATE 278T>C Leu93Pro
M0153047 GAAIMDDD_00055 49142 6 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4258C>T None
M0153048 GAAIMDDD_00055 49151 6 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4267G>A None
M0153049 GAAIMDDD_00183 152102 5 Gut 0.02 protein_coding missense_variant MODERATE 1247T>C Phe416Ser
M0153050 GAAIMDDD_00183 152177 5 Gut 0.02 protein_coding missense_variant MODERATE 1322C>T Thr441Met
M0153051 GAAIMDDD_00223 188612 3 Gut 0.01 protein_coding missense_variant MODERATE 1555T>C Ser519Pro
M0153052 GAAIMDDD_00223 188637 3 Gut 0.01 protein_coding synonymous_variant LOW 1530G>A Lys510Lys
M0153053 GAAIMDDD_00223 188653 3 Gut 0.01 protein_coding missense_variant MODERATE 1514A>T Gln505Leu
M0153054 GAAIMDDD_00119 101864 9 Gut 0.04 protein_coding synonymous_variant LOW 222A>G Ala74Ala
M0153055 GAAIMDDD_00058 47110 7 Gut 0.03 protein_coding synonymous_variant LOW 81A>G Leu27Leu
M0153056 GAAIMDDD_00181 154160 5 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4581G>A None
M0153057 GAAIMDDD_00206 173772 5 Gut 0.02 protein_coding synonymous_variant LOW 72G>T Val24Val
M0153058 GAAIMDDD_00010 11583 6 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -4201T>C None
M0153059 GAAIMDDD_00030 23488 3 Gut 0.01 protein_coding synonymous_variant LOW 552A>T Pro184Pro
M0153060 GAAIMDDD_00025 18413 3 Gut 0.01 protein_coding missense_variant MODERATE 58C>T Arg20Cys
M0153061 GAAIMDDD_00220 190657 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -3020G>A None
M0153062 GAAIMDDD_00220 190800 3 Gut 0.01 protein_coding upstream_gene_variant MODIFIER -3163T>C None
M0153063 GAAIMDDD_00213 183186 5 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -732A>G None
M0153064 GAAIMDDD_00079 68250 3 Gut 0.01 protein_coding synonymous_variant LOW 477C>T Ile159Ile
M0153065 GAAIMDDD_00079 68280 3 Gut 0.01 protein_coding synonymous_variant LOW 507A>G Glu169Glu
M0153066 GAAIMDDD_00206 178559 4 Gut 0.02 protein_coding missense_variant MODERATE 4859G>A Gly1620Asp
M0153067 GAAIMDDD_00242 209108 3 Gut 0.01 protein_coding synonymous_variant LOW 276A>G Gln92Gln
M0153068 GAAIMDDD_00242 209138 3 Gut 0.01 protein_coding synonymous_variant LOW 306C>T Phe102Phe
M0153069 GAAIMDDD_00093 79444 5 Gut 0.02 protein_coding synonymous_variant LOW 72G>A Gln24Gln
M0153070 GAAIMDDD_00136 115590 3 Gut 0.01 protein_coding missense_variant MODERATE 263G>A Ser88Asn
M0153071 GAAIMDDD_00138 117257 3 Gut 0.01 protein_coding missense_variant MODERATE 809T>G Leu270Arg
M0153072 GAAIMDDD_00213 185055 3 Gut 0.01 protein_coding upstream_gene_variant MODIFIER -2601C>T None
M0153073 GAAIMDDD_00157 127337 3 Gut 0.01 protein_coding missense_variant MODERATE 260C>T Thr87Met
M0153074 GAAIMDDD_00206 174441 3 Gut 0.01 protein_coding synonymous_variant LOW 741C>T Asp247Asp






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
GAAIMDDD_00003 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
GAAIMDDD_00010 VFG012793 TTSS secreted effectors 99.5 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
GAAIMDDD_00011 VFG012812 TTSS secreted effectors 99.2 1.9e-136 1 239 1.0 1 Effector delivery system type III secretion system effector OspF, phosphothreonine lyase experiment
GAAIMDDD_00021 VFG012788 TTSS secreted effectors 98.2 1.3e-123 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
GAAIMDDD_00024 VFG012760 TTSS secreted effectors 99.5 4.6e-104 14 201 0.9353 1 Effector delivery system type III secretion system effector IpgB2, guanine nucleotide exchange factor (GEF) experiment
GAAIMDDD_00046 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
GAAIMDDD_00050 VFG012825 TTSS secreted effectors 95.4 8.4e-42 1 87 0.9886 0.9886 Effector delivery system type III secretion system effector OspE2 experiment
GAAIMDDD_00054 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
GAAIMDDD_00056 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
GAAIMDDD_00076 VFG002041 TTSS secreted effectors 99.8 0 1 565 1.0 1 Effector delivery system type III secretion system effector ipaH7.8, E3 ubiquitin ligase experiment
GAAIMDDD_00077 VFG012841 TTSS secreted effectors 99.7 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase experiment
GAAIMDDD_00085 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
GAAIMDDD_00092 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
GAAIMDDD_00098 VFG041905 TTSS secreted effectors 100 4.8e-140 1 242 1.0 0.9344 Effector delivery system type III secretion system effector IpaJ, cysteine protease experiment
GAAIMDDD_00099 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
GAAIMDDD_00101 VFG000984 TTSS secreted effectors 99.2 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein experiment
GAAIMDDD_00102 VFG000985 TTSS 97 3.4e-176 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD experiment
GAAIMDDD_00103 VFG000986 TTSS 98.6 1.3e-181 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC experiment
GAAIMDDD_00104 VFG000987 TTSS 99.1 4.4e-296 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB experiment
GAAIMDDD_00105 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
GAAIMDDD_00106 VFG000989 TTSS secreted effectors 97.1 3.8e-109 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) experiment
GAAIMDDD_00107 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
GAAIMDDD_00108 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
GAAIMDDD_00109 VFG000992 TTSS secreted effectors 99.1 1.3e-307 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase experiment
GAAIMDDD_00110 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
GAAIMDDD_00111 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
GAAIMDDD_00112 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
GAAIMDDD_00113 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
GAAIMDDD_00114 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
GAAIMDDD_00115 VFG000998 TTSS 99.6 5.1e-123 1 228 1.0 0.9461 Effector delivery system type III secretion system inner MS ring protein MxiJ experiment
GAAIMDDD_00116 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
GAAIMDDD_00117 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
GAAIMDDD_00118 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
GAAIMDDD_00119 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
GAAIMDDD_00120 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
GAAIMDDD_00121 VFG001004 TTSS 99.6 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
GAAIMDDD_00122 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
GAAIMDDD_00123 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
GAAIMDDD_00124 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
GAAIMDDD_00125 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
GAAIMDDD_00126 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
GAAIMDDD_00127 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
GAAIMDDD_00128 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
GAAIMDDD_00129 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
GAAIMDDD_00130 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
GAAIMDDD_00131 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
GAAIMDDD_00132 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
GAAIMDDD_00160 VFG001016 TTSS secreted effectors 98.8 2.1e-228 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) experiment
GAAIMDDD_00161 VFG000667 IcsA (VirG) 99.5 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
GAAIMDDD_00173 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
GAAIMDDD_00183 VFG002042 TTSS secreted effectors 99.1 1.4e-309 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase experiment
GAAIMDDD_00186 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
GAAIMDDD_00223 VFG012833 TTSS secreted effectors 99.3 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase experiment
GAAIMDDD_00231 VFG037897 Capsule 72.2 2.7e-181 20 437 0.9565 0.9858 Immune modulation Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB experiment
GAAIMDDD_00246 VFG042215 TTSS secreted effectors 99.1 2.5e-130 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ experiment
GAAIMDDD_00248 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
GAAIMDDD_00003 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
GAAIMDDD_00010 VFG012795 TTSS secreted effectors 99.8 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
GAAIMDDD_00011 VFG012815 TTSS secreted effectors 100 3.3e-137 1 239 1.0 1 Effector delivery system type III secretion system effector OspF, phosphothreonine lyase prediction
GAAIMDDD_00021 VFG012791 TTSS secreted effectors 99.6 8.9e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
GAAIMDDD_00024 VFG012763 TTSS secreted effectors 100 1.2e-103 14 201 0.9353 1 Effector delivery system type III secretion system effector IpgB2, guanine nucleotide exchange factor (GEF) prediction
GAAIMDDD_00046 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
GAAIMDDD_00050 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
GAAIMDDD_00054 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
GAAIMDDD_00056 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
GAAIMDDD_00062 VFG042533 CS31A capsule-like antigen 81.6 6.5e-77 11 180 0.9444 0.9444 Adherence ClpC prediction
GAAIMDDD_00063 VFG042494 Adhesive fimbriae 92.1 0 15 812 0.9828 0.9975 Adherence cshB porin (usher) prediction
GAAIMDDD_00064 VFG043643 CS31A capsule-like antigen 93.8 9e-136 1 259 0.9962 0.9848 Adherence unknown protein prediction
GAAIMDDD_00065 VFG043645 CS31A capsule-like antigen 90.2 6.5e-76 1 163 1.0 1 Adherence unknown protein prediction
GAAIMDDD_00067 VFG043647 CS31A capsule-like antigen 84.9 2.8e-129 1 265 1.0 0.9962 Adherence fimbrial protein prediction
GAAIMDDD_00068 VFG043644 CS31A capsule-like antigen 85.8 3.8e-123 1 250 1.0 0.9843 Adherence CS31A minor subunit prediction
GAAIMDDD_00076 VFG012849 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector ipaH7.8, E3 ubiquitin ligase prediction
GAAIMDDD_00077 VFG012844 TTSS secreted effectors 100 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase prediction
GAAIMDDD_00085 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
GAAIMDDD_00092 VFG012781 TTSS secreted effectors 100 1.4e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC3, ADP-riboxanase prediction
GAAIMDDD_00098 VFG041905 TTSS secreted effectors 100 3.6e-139 1 242 1.0 0.9344 Effector delivery system type III secretion system effector IpaJ, cysteine protease prediction
GAAIMDDD_00099 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
GAAIMDDD_00101 VFG012742 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
GAAIMDDD_00102 VFG012746 TTSS secreted effectors 100 2e-180 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD prediction
GAAIMDDD_00103 VFG012750 TTSS secreted effectors 100 2.1e-183 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC prediction
GAAIMDDD_00104 VFG012754 TTSS secreted effectors 100 1.6e-297 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB prediction
GAAIMDDD_00105 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
GAAIMDDD_00106 VFG012758 TTSS secreted effectors 100 9.4e-112 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) prediction
GAAIMDDD_00107 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
GAAIMDDD_00108 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
GAAIMDDD_00109 VFG012767 TTSS secreted effectors 100 9.69999999999999e-310 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase prediction
GAAIMDDD_00110 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
GAAIMDDD_00111 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
GAAIMDDD_00112 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
GAAIMDDD_00113 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
GAAIMDDD_00114 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
GAAIMDDD_00115 VFG012654 TTSS 100 2.9e-122 1 228 1.0 0.9461 Effector delivery system type III secretion system inner MS ring protein MxiJ prediction
GAAIMDDD_00116 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
GAAIMDDD_00117 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
GAAIMDDD_00118 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
GAAIMDDD_00119 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
GAAIMDDD_00120 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
GAAIMDDD_00121 VFG012678 TTSS 100 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
GAAIMDDD_00122 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
GAAIMDDD_00123 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
GAAIMDDD_00124 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
GAAIMDDD_00125 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
GAAIMDDD_00126 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
GAAIMDDD_00127 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
GAAIMDDD_00128 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
GAAIMDDD_00129 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
GAAIMDDD_00130 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
GAAIMDDD_00131 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
GAAIMDDD_00132 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
GAAIMDDD_00160 VFG012800 TTSS secreted effectors 99.8 7.4e-230 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) prediction
GAAIMDDD_00161 VFG013074 IcsA (VirG) 99.9 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
GAAIMDDD_00173 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
GAAIMDDD_00183 VFG012850 TTSS secreted effectors 99.4 4.40000000000002e-310 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase prediction
GAAIMDDD_00186 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
GAAIMDDD_00193 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
GAAIMDDD_00194 VFG013084 MsbB2 100 2.7e-187 1 314 1.0 1 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
GAAIMDDD_00223 VFG012836 TTSS secreted effectors 99.8 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase prediction
GAAIMDDD_00231 VFG037903 Capsule 73.9 4.5e-188 20 437 0.9565 0.9858 Immune modulation Vi polysaccharide biosynthesis UDP-N-acetylglucosamine C-6 dehydrogenase TviB prediction
GAAIMDDD_00232 VFG038016 Capsule 73.6 2e-143 1 339 0.9941 0.9971 Immune modulation Vi polysaccharide biosynthesis UDP-N-acetylglucosaminuronic acid C-4 epimerase TviC prediction
GAAIMDDD_00246 VFG042215 TTSS secreted effectors 99.1 1.9e-129 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ prediction
GAAIMDDD_00248 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







        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
GAAIMDDD_00024 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
GAAIMDDD_00098 PHI:9253 ipaJ 100 1.3e-139 1 242 1.0000 0.9344 primates shigellosis effector protein effector (plant avirulence determinant)
GAAIMDDD_00102 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
GAAIMDDD_00106 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
GAAIMDDD_00108 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
GAAIMDDD_00113 PHI:10094 STM14_RS15405 (prgI) 70.8 8.2e-22 12 83 0.8675 0.9000 eudicots infection type III secretion system needle complex protein unaffected pathogenicity
GAAIMDDD_00125 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
GAAIMDDD_00128 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
GAAIMDDD_00160 PHI:9252 virA 98.8 5.4e-228 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
GAAIMDDD_00161 PHI:4647 IcsA 99.5 0 1 1102 1.0000 1.0000 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
GAAIMDDD_00192 PHI:10400 Sfgtr4 (ORF186) 99.7 9.6e-216 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
GAAIMDDD_00248 PHI:6577 IcsP 98.7 2.2e-184 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence






        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
GAAIMDDD_00111 QKF39747.1|GH23 100 4.93e-109 1 152 1 1
GAAIMDDD_00192 ACD06066.1|GT4 100 1.09e-271 1 362 1 1
GAAIMDDD_00237 QSE36316.1|GT2 100 2.33e-233 1 328 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
GAAIMDDD_00063 1.B.11.1.1 92.2 0 21 812 0.9754 0.9754 1 Channels/Pores 1.B β-Barrel Porins 1.B.11 The Outer Membrane Fimbrial Usher Porin (FUP) Family
GAAIMDDD_00104 1.C.36.3.1 99.3 8.8e-296 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
GAAIMDDD_00124 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
GAAIMDDD_00125 3.A.6.1.2 99.8 4.4e-244 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
GAAIMDDD_00126 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
GAAIMDDD_00127 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
GAAIMDDD_00128 3.A.6.1.2 100 2.4e-164 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
GAAIMDDD_00129 3.A.6.1.2 99.5 1.2e-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
GAAIMDDD_00131 3.A.6.1.2 99.6 7.2e-133 1 256 1.0000 1.9248 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.6 The Type III (Virulence-related) Secretory Pathway (IIISP) Family
GAAIMDDD_00132 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
GAAIMDDD_00161 1.B.12.1.2 99.5 0 1 1102 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family