Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1270
  Reference Plasmid   NZ_CP146291.1
  Reference Plasmid Size   214566
  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
M0205126 GBFGEAPM_00187 154411 4 Gut 0.05 protein_coding synonymous_variant LOW 222C>T Gly74Gly
M0205127 GBFGEAPM_00187 154435 4 Gut 0.05 protein_coding synonymous_variant LOW 246G>A Ala82Ala
M0205128 GBFGEAPM_00187 154440 4 Gut 0.05 protein_coding missense_variant MODERATE 251G>T Ser84Ile
M0205129 GBFGEAPM_00187 154447 4 Gut 0.05 protein_coding missense_variant MODERATE 258T>G Asn86Lys
M0205130 GBFGEAPM_00187 154450 4 Gut 0.05 protein_coding synonymous_variant LOW 261T>C Gly87Gly
M0205131 GBFGEAPM_00187 154495 4 Gut 0.05 protein_coding synonymous_variant LOW 306T>G Arg102Arg
M0205132 GBFGEAPM_00187 154496 4 Gut 0.05 protein_coding missense_variant MODERATE 307G>A Ala103Thr
M0205133 GBFGEAPM_00187 154507 4 Gut 0.05 protein_coding synonymous_variant LOW 318A>G Glu106Glu
M0205134 GBFGEAPM_00244 210981 17 Gut 0.21 protein_coding synonymous_variant LOW 474G>A Glu158Glu
M0205135 GBFGEAPM_00246 211526 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -128C>T None
M0205136 GBFGEAPM_00246 211534 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -120C>T None
M0205137 GBFGEAPM_00246 211544 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -110A>T None
M0205138 GBFGEAPM_00246 211545 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -109T>G None
M0205139 GBFGEAPM_00246 211546 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -108T>A None
M0205140 GBFGEAPM_00246 211590 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -64A>G None
M0205141 GBFGEAPM_00246 211601 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -53C>A None
M0205142 GBFGEAPM_00246 211602 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0205143 GBFGEAPM_00246 211611 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -43G>A None
M0205144 GBFGEAPM_00246 211612 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -42G>T None
M0205145 GBFGEAPM_00246 211614 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -40G>C None
M0205146 GBFGEAPM_00246 211626 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -28G>A None
M0205147 GBFGEAPM_00246 211630 17 Gut 0.21 protein_coding upstream_gene_variant MODIFIER -24C>T None
M0205148 GBFGEAPM_00246 211475 6 Gut 0.08 protein_coding upstream_gene_variant MODIFIER -179C>T None
M0205149 GBFGEAPM_00113 99904 4 Gut 0.05 protein_coding synonymous_variant LOW 72A>G Thr24Thr
M0205150 GBFGEAPM_00113 99922 4 Gut 0.05 protein_coding synonymous_variant LOW 54G>A Thr18Thr
M0205151 GBFGEAPM_00113 99931 4 Gut 0.05 protein_coding synonymous_variant LOW 45T>C Arg15Arg
M0205152 GBFGEAPM_00114 100114 4 Gut 0.05 protein_coding missense_variant MODERATE 115G>A Ala39Thr
M0205153 GBFGEAPM_00114 100126 4 Gut 0.05 protein_coding missense_variant MODERATE 103A>G Thr35Ala
M0205154 GBFGEAPM_00196 164787 4 Gut 0.05 protein_coding missense_variant MODERATE 302T>C Val101Ala
M0205155 GBFGEAPM_00201 169666 3 Gut 0.04 protein_coding missense_variant MODERATE 122T>C Phe41Ser
M0205156 GBFGEAPM_00196 164929 3 Gut 0.04 protein_coding synonymous_variant LOW 444G>A Glu148Glu
M0205157 GBFGEAPM_00078 67577 7 Gut 0.09 protein_coding synonymous_variant LOW 762A>G Glu254Glu
M0205158 GBFGEAPM_00078 67588 7 Gut 0.09 protein_coding missense_variant MODERATE 751G>A Ala251Thr
M0205159 GBFGEAPM_00078 67589 7 Gut 0.09 protein_coding synonymous_variant LOW 750T>G Arg250Arg
M0205160 GBFGEAPM_00078 67621 8 Gut 0.10 protein_coding missense_variant MODERATE 718A>G Lys240Glu
M0205161 GBFGEAPM_00078 67634 7 Gut 0.09 protein_coding synonymous_variant LOW 705T>C Gly235Gly
M0205162 GBFGEAPM_00078 67637 7 Gut 0.09 protein_coding missense_variant MODERATE 702T>G Asn234Lys
M0205163 GBFGEAPM_00078 67644 7 Gut 0.09 protein_coding missense_variant MODERATE 695G>T Ser232Ile
M0205164 GBFGEAPM_00078 67649 7 Gut 0.09 protein_coding synonymous_variant LOW 690G>A Ala230Ala
M0205165 GBFGEAPM_00078 67673 7 Gut 0.09 protein_coding synonymous_variant LOW 666C>T Gly222Gly
M0205166 GBFGEAPM_00005 3766 3 Gut 0.04 protein_coding upstream_gene_variant MODIFIER -1187C>A None






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
GBFGEAPM_00010 VFG012833 TTSS secreted effectors 99.1 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase experiment
GBFGEAPM_00020 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
GBFGEAPM_00035 VFG042215 TTSS secreted effectors 98.7 1.3e-129 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ experiment
GBFGEAPM_00037 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
GBFGEAPM_00040 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
GBFGEAPM_00045 VFG012793 TTSS secreted effectors 99.6 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
GBFGEAPM_00046 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
GBFGEAPM_00058 VFG012788 TTSS secreted effectors 98.7 2e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
GBFGEAPM_00061 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
GBFGEAPM_00084 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
GBFGEAPM_00087 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
GBFGEAPM_00091 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
GBFGEAPM_00092 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
GBFGEAPM_00101 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
GBFGEAPM_00102 VFG012841 TTSS secreted effectors 99.5 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase experiment
GBFGEAPM_00110 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
GBFGEAPM_00117 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
GBFGEAPM_00131 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
GBFGEAPM_00132 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
GBFGEAPM_00134 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
GBFGEAPM_00135 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
GBFGEAPM_00136 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
GBFGEAPM_00137 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
GBFGEAPM_00138 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
GBFGEAPM_00139 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
GBFGEAPM_00140 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
GBFGEAPM_00141 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
GBFGEAPM_00142 VFG000992 TTSS secreted effectors 98.9 3e-307 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase experiment
GBFGEAPM_00143 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
GBFGEAPM_00144 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
GBFGEAPM_00145 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
GBFGEAPM_00146 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
GBFGEAPM_00147 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
GBFGEAPM_00148 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
GBFGEAPM_00149 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
GBFGEAPM_00150 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
GBFGEAPM_00151 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
GBFGEAPM_00152 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
GBFGEAPM_00153 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
GBFGEAPM_00154 VFG001004 TTSS 99.5 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
GBFGEAPM_00155 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
GBFGEAPM_00156 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
GBFGEAPM_00157 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
GBFGEAPM_00158 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
GBFGEAPM_00159 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
GBFGEAPM_00160 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
GBFGEAPM_00161 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
GBFGEAPM_00162 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
GBFGEAPM_00163 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
GBFGEAPM_00164 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
GBFGEAPM_00165 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
GBFGEAPM_00192 VFG001016 TTSS secreted effectors 99 1.9e-229 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) experiment
GBFGEAPM_00193 VFG000667 IcsA (VirG) 99.4 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
GBFGEAPM_00205 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
GBFGEAPM_00216 VFG002042 TTSS secreted effectors 99.4 2.19999999999998e-310 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase experiment
GBFGEAPM_00218 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
GBFGEAPM_00010 VFG012836 TTSS secreted effectors 100 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase prediction
GBFGEAPM_00020 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
GBFGEAPM_00021 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
GBFGEAPM_00035 VFG042215 TTSS secreted effectors 98.7 9.4e-129 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ prediction
GBFGEAPM_00037 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
GBFGEAPM_00040 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
GBFGEAPM_00045 VFG012795 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
GBFGEAPM_00046 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
GBFGEAPM_00058 VFG012791 TTSS secreted effectors 100 1.4e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
GBFGEAPM_00061 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
GBFGEAPM_00084 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
GBFGEAPM_00087 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
GBFGEAPM_00091 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
GBFGEAPM_00092 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
GBFGEAPM_00101 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
GBFGEAPM_00102 VFG012844 TTSS secreted effectors 99.8 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase prediction
GBFGEAPM_00110 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
GBFGEAPM_00117 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
GBFGEAPM_00131 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
GBFGEAPM_00132 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
GBFGEAPM_00134 VFG012742 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
GBFGEAPM_00135 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
GBFGEAPM_00136 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
GBFGEAPM_00137 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
GBFGEAPM_00138 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
GBFGEAPM_00139 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
GBFGEAPM_00140 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
GBFGEAPM_00141 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
GBFGEAPM_00142 VFG012767 TTSS secreted effectors 99.8 2.2e-309 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase prediction
GBFGEAPM_00143 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
GBFGEAPM_00144 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
GBFGEAPM_00145 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
GBFGEAPM_00146 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
GBFGEAPM_00147 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
GBFGEAPM_00148 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
GBFGEAPM_00149 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
GBFGEAPM_00150 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
GBFGEAPM_00151 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
GBFGEAPM_00152 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
GBFGEAPM_00153 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
GBFGEAPM_00154 VFG012678 TTSS 99.8 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
GBFGEAPM_00155 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
GBFGEAPM_00156 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
GBFGEAPM_00157 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
GBFGEAPM_00158 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
GBFGEAPM_00159 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
GBFGEAPM_00160 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
GBFGEAPM_00161 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
GBFGEAPM_00162 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
GBFGEAPM_00163 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
GBFGEAPM_00164 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
GBFGEAPM_00165 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
GBFGEAPM_00192 VFG012800 TTSS secreted effectors 100 6.6e-231 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) prediction
GBFGEAPM_00193 VFG013074 IcsA (VirG) 100 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
GBFGEAPM_00205 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
GBFGEAPM_00216 VFG012854 TTSS secreted effectors 100 2.29999999999993e-311 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase prediction
GBFGEAPM_00218 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
GBFGEAPM_00226 VFG013079 VirK 99.7 1.4e-186 1 316 1.0 1 Others virulence factor VirK prediction
GBFGEAPM_00227 VFG013084 MsbB2 100 2e-165 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase 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
GBFGEAPM_00037 PHI:6577 IcsP 98.7 2.2e-184 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence
GBFGEAPM_00061 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
GBFGEAPM_00131 PHI:9253 ipaJ 100 1.3e-139 1 242 1.0000 0.9344 primates shigellosis effector protein effector (plant avirulence determinant)
GBFGEAPM_00135 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
GBFGEAPM_00139 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
GBFGEAPM_00141 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
GBFGEAPM_00146 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
GBFGEAPM_00158 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
GBFGEAPM_00161 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
GBFGEAPM_00192 PHI:9252 virA 99 4.9e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
GBFGEAPM_00193 PHI:4647 IcsA 99.4 0 1 1102 1.0000 1.0000 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
GBFGEAPM_00225 PHI:10400 Sfgtr4 (ORF186) 99.7 9.6e-216 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) 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
GBFGEAPM_00026 QSE36316.1|GT2 100 2.33e-233 1 328 1 1
GBFGEAPM_00144 QKF39747.1|GH23 100 4.93e-109 1 152 1 1
GBFGEAPM_00225 ACD06066.1|GT4 100 1.09e-271 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
GBFGEAPM_00137 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
GBFGEAPM_00157 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
GBFGEAPM_00158 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
GBFGEAPM_00159 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
GBFGEAPM_00160 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
GBFGEAPM_00161 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
GBFGEAPM_00162 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
GBFGEAPM_00164 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
GBFGEAPM_00165 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
GBFGEAPM_00193 1.B.12.1.2 99.4 0 1 1102 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family