Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1087
  Reference Plasmid   NZ_CP109776.1
  Reference Plasmid Size   214749
  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
M0195801 BJPHGMHJ_00175 146327 7 Gut 0.07 protein_coding synonymous_variant LOW 1560C>T Tyr520Tyr
M0195802 BJPHGMHJ_00190 154491 3 Gut 0.03 protein_coding synonymous_variant LOW 222C>T Gly74Gly
M0195803 BJPHGMHJ_00190 154515 3 Gut 0.03 protein_coding synonymous_variant LOW 246G>A Ala82Ala
M0195804 BJPHGMHJ_00190 154520 3 Gut 0.03 protein_coding missense_variant MODERATE 251G>T Ser84Ile
M0195805 BJPHGMHJ_00190 154527 3 Gut 0.03 protein_coding missense_variant MODERATE 258T>G Asn86Lys
M0195806 BJPHGMHJ_00190 154530 3 Gut 0.03 protein_coding synonymous_variant LOW 261T>C Gly87Gly
M0195807 BJPHGMHJ_00190 154575 3 Gut 0.03 protein_coding synonymous_variant LOW 306T>G Arg102Arg
M0195808 BJPHGMHJ_00190 154576 3 Gut 0.03 protein_coding missense_variant MODERATE 307G>A Ala103Thr
M0195809 BJPHGMHJ_00190 154587 3 Gut 0.03 protein_coding synonymous_variant LOW 318A>G Glu106Glu
M0195810 BJPHGMHJ_00251 211658 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -179C>T None
M0195811 BJPHGMHJ_00251 211709 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -128C>T None
M0195812 BJPHGMHJ_00251 211717 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -120C>T None
M0195813 BJPHGMHJ_00251 211727 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -110A>T None
M0195814 BJPHGMHJ_00251 211728 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -109T>G None
M0195815 BJPHGMHJ_00251 211729 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -108T>A None
M0195816 BJPHGMHJ_00251 211773 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -64A>G None
M0195817 BJPHGMHJ_00251 211784 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -53C>A None
M0195818 BJPHGMHJ_00251 211785 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0195819 BJPHGMHJ_00251 211794 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -43G>A None
M0195820 BJPHGMHJ_00251 211795 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -42G>T None
M0195821 BJPHGMHJ_00251 211797 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -40G>C None
M0195822 BJPHGMHJ_00251 211809 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -28G>A None
M0195823 BJPHGMHJ_00251 211813 3 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -24C>T None
M0195824 BJPHGMHJ_00116 99984 3 Gut 0.03 protein_coding synonymous_variant LOW 72A>G Thr24Thr
M0195825 BJPHGMHJ_00116 100002 3 Gut 0.03 protein_coding synonymous_variant LOW 54G>A Thr18Thr
M0195826 BJPHGMHJ_00116 100011 3 Gut 0.03 protein_coding synonymous_variant LOW 45T>C Arg15Arg
M0195827 BJPHGMHJ_00117 100194 5 Gut 0.05 protein_coding missense_variant MODERATE 115G>A Ala39Thr
M0195828 BJPHGMHJ_00117 100206 5 Gut 0.05 protein_coding missense_variant MODERATE 103A>G Thr35Ala
M0195829 BJPHGMHJ_00173 143647 3 Gut 0.03 protein_coding synonymous_variant LOW 525C>T Ser175Ser
M0195830 BJPHGMHJ_00173 143675 3 Gut 0.03 protein_coding missense_variant MODERATE 497A>G His166Arg






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
BJPHGMHJ_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
BJPHGMHJ_00021 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
BJPHGMHJ_00036 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
BJPHGMHJ_00038 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
BJPHGMHJ_00041 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
BJPHGMHJ_00046 VFG012793 TTSS secreted effectors 99.6 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
BJPHGMHJ_00047 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
BJPHGMHJ_00059 VFG012788 TTSS secreted effectors 98.7 2e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
BJPHGMHJ_00062 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
BJPHGMHJ_00085 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
BJPHGMHJ_00089 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
BJPHGMHJ_00094 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
BJPHGMHJ_00095 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
BJPHGMHJ_00103 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
BJPHGMHJ_00104 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
BJPHGMHJ_00113 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
BJPHGMHJ_00120 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
BJPHGMHJ_00134 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
BJPHGMHJ_00135 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
BJPHGMHJ_00137 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
BJPHGMHJ_00138 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
BJPHGMHJ_00139 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
BJPHGMHJ_00140 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
BJPHGMHJ_00141 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
BJPHGMHJ_00142 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
BJPHGMHJ_00143 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
BJPHGMHJ_00144 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
BJPHGMHJ_00145 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
BJPHGMHJ_00146 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
BJPHGMHJ_00147 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
BJPHGMHJ_00148 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
BJPHGMHJ_00149 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
BJPHGMHJ_00150 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
BJPHGMHJ_00151 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
BJPHGMHJ_00152 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
BJPHGMHJ_00153 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
BJPHGMHJ_00154 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
BJPHGMHJ_00155 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
BJPHGMHJ_00157 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
BJPHGMHJ_00158 VFG001004 TTSS 99.5 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
BJPHGMHJ_00159 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
BJPHGMHJ_00160 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
BJPHGMHJ_00161 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
BJPHGMHJ_00162 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
BJPHGMHJ_00163 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
BJPHGMHJ_00164 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
BJPHGMHJ_00165 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
BJPHGMHJ_00166 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
BJPHGMHJ_00167 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
BJPHGMHJ_00168 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
BJPHGMHJ_00169 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
BJPHGMHJ_00196 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
BJPHGMHJ_00197 VFG000667 IcsA (VirG) 99.4 0 1 1092 1.0 0.9909 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
BJPHGMHJ_00209 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
BJPHGMHJ_00221 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
BJPHGMHJ_00223 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
BJPHGMHJ_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
BJPHGMHJ_00021 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
BJPHGMHJ_00022 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
BJPHGMHJ_00036 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
BJPHGMHJ_00038 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
BJPHGMHJ_00041 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
BJPHGMHJ_00046 VFG012795 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
BJPHGMHJ_00047 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
BJPHGMHJ_00059 VFG012791 TTSS secreted effectors 100 1.4e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
BJPHGMHJ_00062 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
BJPHGMHJ_00085 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
BJPHGMHJ_00089 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
BJPHGMHJ_00094 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
BJPHGMHJ_00095 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
BJPHGMHJ_00103 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
BJPHGMHJ_00104 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
BJPHGMHJ_00113 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
BJPHGMHJ_00120 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
BJPHGMHJ_00134 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
BJPHGMHJ_00135 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
BJPHGMHJ_00137 VFG012742 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
BJPHGMHJ_00138 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
BJPHGMHJ_00139 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
BJPHGMHJ_00140 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
BJPHGMHJ_00141 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
BJPHGMHJ_00142 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
BJPHGMHJ_00143 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
BJPHGMHJ_00144 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
BJPHGMHJ_00145 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
BJPHGMHJ_00146 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
BJPHGMHJ_00147 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
BJPHGMHJ_00148 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
BJPHGMHJ_00149 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
BJPHGMHJ_00150 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
BJPHGMHJ_00151 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
BJPHGMHJ_00152 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
BJPHGMHJ_00153 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
BJPHGMHJ_00154 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
BJPHGMHJ_00155 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
BJPHGMHJ_00157 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
BJPHGMHJ_00158 VFG012678 TTSS 99.8 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
BJPHGMHJ_00159 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
BJPHGMHJ_00160 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
BJPHGMHJ_00161 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
BJPHGMHJ_00162 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
BJPHGMHJ_00163 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
BJPHGMHJ_00164 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
BJPHGMHJ_00165 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
BJPHGMHJ_00166 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
BJPHGMHJ_00167 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
BJPHGMHJ_00168 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
BJPHGMHJ_00169 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
BJPHGMHJ_00196 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
BJPHGMHJ_00197 VFG013074 IcsA (VirG) 100 0 1 1092 1.0 0.9909 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
BJPHGMHJ_00209 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
BJPHGMHJ_00221 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
BJPHGMHJ_00223 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
BJPHGMHJ_00231 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
BJPHGMHJ_00232 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
BJPHGMHJ_00038 PHI:6577 IcsP 98.7 2.2e-184 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence
BJPHGMHJ_00062 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
BJPHGMHJ_00134 PHI:9253 ipaJ 100 1e-130 1 227 1.0000 0.8764 primates shigellosis effector protein effector (plant avirulence determinant)
BJPHGMHJ_00138 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
BJPHGMHJ_00142 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
BJPHGMHJ_00144 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
BJPHGMHJ_00149 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
BJPHGMHJ_00162 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
BJPHGMHJ_00165 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
BJPHGMHJ_00196 PHI:9252 virA 99 4.9e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
BJPHGMHJ_00197 PHI:4647 IcsA 99.4 0 1 1092 1.0000 0.9909 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
BJPHGMHJ_00230 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
BJPHGMHJ_00027 QSE36316.1|GT2 100 2.33e-233 1 328 1 1
BJPHGMHJ_00147 QKF39747.1|GH23 100 4.93e-109 1 152 1 1
BJPHGMHJ_00230 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
BJPHGMHJ_00140 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
BJPHGMHJ_00161 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
BJPHGMHJ_00162 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
BJPHGMHJ_00163 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
BJPHGMHJ_00164 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
BJPHGMHJ_00165 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
BJPHGMHJ_00166 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
BJPHGMHJ_00168 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
BJPHGMHJ_00169 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
BJPHGMHJ_00197 1.B.12.1.2 99.4 0 1 1092 1.0000 0.9909 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family