Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C284
  Reference Plasmid   NC_007385.1
  Reference Plasmid Size   214396
  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
M0151213 EJEFFNOH_00077 66226 3 Gut 0.01 protein_coding missense_variant MODERATE 115G>A Ala39Thr
M0151214 EJEFFNOH_00077 66238 3 Gut 0.01 protein_coding missense_variant MODERATE 103A>G Thr35Ala
M0151215 EJEFFNOH_00220 184525 7 Gut 0.03 protein_coding upstream_gene_variant MODIFIER -559C>A None
M0151216 EJEFFNOH_00038 34019 4 Gut 0.02 protein_coding synonymous_variant LOW 759A>G Glu253Glu
M0151217 EJEFFNOH_00038 34030 4 Gut 0.02 protein_coding missense_variant MODERATE 748G>A Ala250Thr
M0151218 EJEFFNOH_00038 34031 4 Gut 0.02 protein_coding synonymous_variant LOW 747T>G Arg249Arg
M0151219 EJEFFNOH_00038 34063 5 Gut 0.02 protein_coding missense_variant MODERATE 715A>G Lys239Glu
M0151220 EJEFFNOH_00038 34076 4 Gut 0.02 protein_coding synonymous_variant LOW 702T>C Gly234Gly
M0151221 EJEFFNOH_00038 34079 4 Gut 0.02 protein_coding missense_variant MODERATE 699T>G Asn233Lys
M0151222 EJEFFNOH_00038 34086 4 Gut 0.02 protein_coding missense_variant MODERATE 692G>T Ser231Ile
M0151223 EJEFFNOH_00038 34091 4 Gut 0.02 protein_coding synonymous_variant LOW 687G>A Ala229Ala
M0151224 EJEFFNOH_00038 34115 4 Gut 0.02 protein_coding synonymous_variant LOW 663C>T Gly221Gly
M0151225 EJEFFNOH_00039 34915 3 Gut 0.01 protein_coding synonymous_variant LOW 189A>T Gly63Gly
M0151226 EJEFFNOH_00039 34993 3 Gut 0.01 protein_coding synonymous_variant LOW 111T>C Ala37Ala
M0151227 EJEFFNOH_00039 35010 3 Gut 0.01 protein_coding missense_variant MODERATE 94A>G Thr32Ala
M0151228 EJEFFNOH_00039 35017 3 Gut 0.01 protein_coding synonymous_variant LOW 87A>G Gln29Gln
M0151229 EJEFFNOH_00039 35032 3 Gut 0.01 protein_coding synonymous_variant LOW 72C>T Gly24Gly
M0151230 EJEFFNOH_00039 35033 3 Gut 0.01 protein_coding missense_variant MODERATE 71G>A Gly24Asp
M0151231 EJEFFNOH_00039 35056 3 Gut 0.01 protein_coding synonymous_variant LOW 48C>T Val16Val
M0151232 EJEFFNOH_00039 35058 3 Gut 0.01 protein_coding missense_variant MODERATE 46G>A Val16Ile
M0151233 EJEFFNOH_00039 35059 3 Gut 0.01 protein_coding synonymous_variant LOW 45A>G Ala15Ala
M0151234 EJEFFNOH_00039 35065 3 Gut 0.01 protein_coding synonymous_variant LOW 39A>G Gln13Gln
M0151235 EJEFFNOH_00208 177174 15 Gut 0.07 protein_coding synonymous_variant LOW 474G>A Glu158Glu
M0151236 EJEFFNOH_00210 177719 20 Gut 0.09 protein_coding upstream_gene_variant MODIFIER -128C>T None
M0151237 EJEFFNOH_00210 177727 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -120C>T None
M0151238 EJEFFNOH_00210 177737 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -110A>T None
M0151239 EJEFFNOH_00210 177738 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -109T>G None
M0151240 EJEFFNOH_00210 177739 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -108T>A None
M0151241 EJEFFNOH_00210 177783 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -64A>G None
M0151242 EJEFFNOH_00210 177794 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -53C>A None
M0151243 EJEFFNOH_00210 177795 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0151244 EJEFFNOH_00210 177804 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -43G>A None
M0151245 EJEFFNOH_00210 177805 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -42G>T None
M0151246 EJEFFNOH_00210 177807 24 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -40G>C None
M0151247 EJEFFNOH_00210 177819 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -28G>A None
M0151248 EJEFFNOH_00210 177823 23 Gut 0.11 protein_coding upstream_gene_variant MODIFIER -24C>T None
M0151249 EJEFFNOH_00164 140671 3 Gut 0.01 protein_coding upstream_gene_variant MODIFIER -4772C>T None
M0151250 EJEFFNOH_00164 135831 3 Gut 0.01 protein_coding synonymous_variant LOW 69C>T Ser23Ser
M0151251 EJEFFNOH_00210 177668 16 Gut 0.07 protein_coding upstream_gene_variant MODIFIER -179C>T None
M0151252 EJEFFNOH_00220 185039 3 Gut 0.01 protein_coding upstream_gene_variant MODIFIER -1073C>T None
M0151253 EJEFFNOH_00208 176978 3 Gut 0.01 protein_coding missense_variant MODERATE 278C>T Pro93Leu
M0151254 EJEFFNOH_00142 115682 4 Gut 0.02 protein_coding missense_variant MODERATE 190C>T Leu64Phe
M0151255 EJEFFNOH_00185 159592 3 Gut 0.01 protein_coding upstream_gene_variant MODIFIER -4734C>T None
M0151256 EJEFFNOH_00150 120523 3 Gut 0.01 protein_coding synonymous_variant LOW 222C>T Gly74Gly
M0151257 EJEFFNOH_00150 120547 3 Gut 0.01 protein_coding synonymous_variant LOW 246G>A Ala82Ala
M0151258 EJEFFNOH_00150 120552 3 Gut 0.01 protein_coding missense_variant MODERATE 251G>T Ser84Ile
M0151259 EJEFFNOH_00150 120559 3 Gut 0.01 protein_coding missense_variant MODERATE 258T>G Asn86Lys
M0151260 EJEFFNOH_00150 120562 3 Gut 0.01 protein_coding synonymous_variant LOW 261T>C Gly87Gly
M0151261 EJEFFNOH_00150 120607 3 Gut 0.01 protein_coding synonymous_variant LOW 306T>G Arg102Arg
M0151262 EJEFFNOH_00150 120608 3 Gut 0.01 protein_coding missense_variant MODERATE 307G>A Ala103Thr
M0151263 EJEFFNOH_00150 120619 3 Gut 0.01 protein_coding synonymous_variant LOW 318A>G Glu106Glu






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
EJEFFNOH_00002 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
EJEFFNOH_00007 VFG012793 TTSS secreted effectors 99.6 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
EJEFFNOH_00008 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
EJEFFNOH_00020 VFG012788 TTSS secreted effectors 98.7 2e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
EJEFFNOH_00023 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
EJEFFNOH_00044 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
EJEFFNOH_00047 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
EJEFFNOH_00051 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
EJEFFNOH_00053 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
EJEFFNOH_00062 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
EJEFFNOH_00063 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
EJEFFNOH_00072 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
EJEFFNOH_00080 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
EJEFFNOH_00094 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
EJEFFNOH_00095 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
EJEFFNOH_00097 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
EJEFFNOH_00098 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
EJEFFNOH_00099 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
EJEFFNOH_00100 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
EJEFFNOH_00101 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
EJEFFNOH_00102 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
EJEFFNOH_00103 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
EJEFFNOH_00104 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
EJEFFNOH_00105 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
EJEFFNOH_00106 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
EJEFFNOH_00107 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
EJEFFNOH_00108 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
EJEFFNOH_00109 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
EJEFFNOH_00110 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
EJEFFNOH_00111 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
EJEFFNOH_00112 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
EJEFFNOH_00113 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
EJEFFNOH_00114 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
EJEFFNOH_00115 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
EJEFFNOH_00116 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
EJEFFNOH_00117 VFG001004 TTSS 99.6 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
EJEFFNOH_00118 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
EJEFFNOH_00119 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
EJEFFNOH_00120 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
EJEFFNOH_00121 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
EJEFFNOH_00122 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
EJEFFNOH_00123 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
EJEFFNOH_00124 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
EJEFFNOH_00125 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
EJEFFNOH_00126 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
EJEFFNOH_00127 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
EJEFFNOH_00128 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
EJEFFNOH_00155 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
EJEFFNOH_00156 VFG000667 IcsA (VirG) 99.4 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
EJEFFNOH_00168 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
EJEFFNOH_00180 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
EJEFFNOH_00182 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
EJEFFNOH_00224 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
EJEFFNOH_00234 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
EJEFFNOH_00249 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
EJEFFNOH_00251 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
EJEFFNOH_00002 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
EJEFFNOH_00007 VFG012795 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
EJEFFNOH_00008 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
EJEFFNOH_00020 VFG012791 TTSS secreted effectors 100 1.4e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
EJEFFNOH_00023 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
EJEFFNOH_00044 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
EJEFFNOH_00047 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
EJEFFNOH_00051 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
EJEFFNOH_00053 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
EJEFFNOH_00062 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
EJEFFNOH_00063 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
EJEFFNOH_00072 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
EJEFFNOH_00080 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
EJEFFNOH_00094 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
EJEFFNOH_00095 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
EJEFFNOH_00097 VFG012742 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
EJEFFNOH_00098 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
EJEFFNOH_00099 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
EJEFFNOH_00100 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
EJEFFNOH_00101 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
EJEFFNOH_00102 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
EJEFFNOH_00103 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
EJEFFNOH_00104 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
EJEFFNOH_00105 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
EJEFFNOH_00106 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
EJEFFNOH_00107 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
EJEFFNOH_00108 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
EJEFFNOH_00109 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
EJEFFNOH_00110 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
EJEFFNOH_00111 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
EJEFFNOH_00112 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
EJEFFNOH_00113 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
EJEFFNOH_00114 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
EJEFFNOH_00115 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
EJEFFNOH_00116 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
EJEFFNOH_00117 VFG012678 TTSS 100 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
EJEFFNOH_00118 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
EJEFFNOH_00119 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
EJEFFNOH_00120 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
EJEFFNOH_00121 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
EJEFFNOH_00122 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
EJEFFNOH_00123 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
EJEFFNOH_00124 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
EJEFFNOH_00125 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
EJEFFNOH_00126 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
EJEFFNOH_00127 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
EJEFFNOH_00128 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
EJEFFNOH_00155 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
EJEFFNOH_00156 VFG013074 IcsA (VirG) 100 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
EJEFFNOH_00168 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
EJEFFNOH_00180 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
EJEFFNOH_00182 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
EJEFFNOH_00190 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
EJEFFNOH_00191 VFG013084 MsbB2 100 2e-165 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
EJEFFNOH_00224 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
EJEFFNOH_00234 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
EJEFFNOH_00235 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
EJEFFNOH_00249 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
EJEFFNOH_00251 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
EJEFFNOH_00023 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
EJEFFNOH_00094 PHI:9253 ipaJ 100 1.3e-139 1 242 1.0000 0.9344 primates shigellosis effector protein effector (plant avirulence determinant)
EJEFFNOH_00098 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
EJEFFNOH_00102 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
EJEFFNOH_00104 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
EJEFFNOH_00109 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
EJEFFNOH_00121 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
EJEFFNOH_00124 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
EJEFFNOH_00155 PHI:9252 virA 99 4.9e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
EJEFFNOH_00156 PHI:4647 IcsA 99.4 0 1 1102 1.0000 1.0000 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
EJEFFNOH_00189 PHI:10400 Sfgtr4 (ORF186) 99.7 9.6e-216 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
EJEFFNOH_00251 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
EJEFFNOH_00107 QKF39747.1|GH23 100 4.93e-109 1 152 1 1
EJEFFNOH_00189 ACD06066.1|GT4 100 1.09e-271 1 362 1 1
EJEFFNOH_00240 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
EJEFFNOH_00100 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
EJEFFNOH_00120 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
EJEFFNOH_00121 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
EJEFFNOH_00122 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
EJEFFNOH_00123 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
EJEFFNOH_00124 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
EJEFFNOH_00125 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
EJEFFNOH_00127 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
EJEFFNOH_00128 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
EJEFFNOH_00156 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