Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1238
  Reference Plasmid   NZ_CP140620.1
  Reference Plasmid Size   212849
  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
M0200533 DIHILCHL_00245 209809 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -128C>T None
M0200534 DIHILCHL_00245 209817 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -120C>T None
M0200535 DIHILCHL_00245 209827 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -110A>T None
M0200536 DIHILCHL_00245 209828 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -109T>G None
M0200537 DIHILCHL_00245 209829 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -108T>A None
M0200538 DIHILCHL_00245 209873 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -64A>G None
M0200539 DIHILCHL_00245 209884 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -53C>A None
M0200540 DIHILCHL_00245 209885 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -52C>A None
M0200541 DIHILCHL_00245 209894 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -43G>A None
M0200542 DIHILCHL_00245 209895 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -42G>T None
M0200543 DIHILCHL_00245 209897 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -40G>C None
M0200544 DIHILCHL_00245 209909 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -28G>A None
M0200545 DIHILCHL_00245 209913 56 Gut 0.53 protein_coding upstream_gene_variant MODIFIER -24C>T None
M0200546 DIHILCHL_00245 209758 27 Gut 0.26 protein_coding upstream_gene_variant MODIFIER -179C>T None
M0200547 DIHILCHL_00184 152781 5 Gut 0.05 protein_coding synonymous_variant LOW 222C>T Gly74Gly
M0200548 DIHILCHL_00184 152805 5 Gut 0.05 protein_coding synonymous_variant LOW 246G>A Ala82Ala
M0200549 DIHILCHL_00184 152810 5 Gut 0.05 protein_coding missense_variant MODERATE 251G>T Ser84Ile
M0200550 DIHILCHL_00184 152817 5 Gut 0.05 protein_coding missense_variant MODERATE 258T>G Asn86Lys
M0200551 DIHILCHL_00184 152820 5 Gut 0.05 protein_coding synonymous_variant LOW 261T>C Gly87Gly
M0200552 DIHILCHL_00184 152865 5 Gut 0.05 protein_coding synonymous_variant LOW 306T>G Arg102Arg
M0200553 DIHILCHL_00184 152866 5 Gut 0.05 protein_coding missense_variant MODERATE 307G>A Ala103Thr
M0200554 DIHILCHL_00184 152877 5 Gut 0.05 protein_coding synonymous_variant LOW 318A>G Glu106Glu
M0200555 DIHILCHL_00101 90477 27 Gut 0.26 protein_coding synonymous_variant LOW 663C>T Gly221Gly
M0200556 DIHILCHL_00101 90501 27 Gut 0.26 protein_coding synonymous_variant LOW 687G>A Ala229Ala
M0200557 DIHILCHL_00101 90506 27 Gut 0.26 protein_coding missense_variant MODERATE 692G>T Ser231Ile
M0200558 DIHILCHL_00101 90513 27 Gut 0.26 protein_coding missense_variant MODERATE 699T>G Asn233Lys
M0200559 DIHILCHL_00101 90516 27 Gut 0.26 protein_coding synonymous_variant LOW 702T>C Gly234Gly
M0200560 DIHILCHL_00101 90561 26 Gut 0.25 protein_coding synonymous_variant LOW 747T>G Arg249Arg
M0200561 DIHILCHL_00101 90562 26 Gut 0.25 protein_coding missense_variant MODERATE 748G>A Ala250Thr
M0200562 DIHILCHL_00101 90573 26 Gut 0.25 protein_coding synonymous_variant LOW 759A>G Glu253Glu
M0200563 DIHILCHL_00168 144617 13 Gut 0.12 protein_coding synonymous_variant LOW 1560C>T Tyr520Tyr






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
DIHILCHL_00009 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
DIHILCHL_00017 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
DIHILCHL_00032 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
DIHILCHL_00034 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
DIHILCHL_00037 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
DIHILCHL_00042 VFG012793 TTSS secreted effectors 99.6 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
DIHILCHL_00043 VFG012812 TTSS secreted effectors 99.1 2.4e-122 1 215 1.0 0.8996 Effector delivery system type III secretion system effector OspF, phosphothreonine lyase experiment
DIHILCHL_00056 VFG012788 TTSS secreted effectors 98.7 2e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
DIHILCHL_00059 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
DIHILCHL_00081 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
DIHILCHL_00084 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
DIHILCHL_00088 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
DIHILCHL_00090 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
DIHILCHL_00098 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
DIHILCHL_00099 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
DIHILCHL_00107 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
DIHILCHL_00114 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
DIHILCHL_00128 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
DIHILCHL_00129 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
DIHILCHL_00131 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
DIHILCHL_00132 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
DIHILCHL_00133 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
DIHILCHL_00134 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
DIHILCHL_00135 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
DIHILCHL_00136 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
DIHILCHL_00137 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
DIHILCHL_00138 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
DIHILCHL_00139 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
DIHILCHL_00140 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
DIHILCHL_00141 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
DIHILCHL_00142 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
DIHILCHL_00143 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
DIHILCHL_00144 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
DIHILCHL_00145 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
DIHILCHL_00146 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
DIHILCHL_00147 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
DIHILCHL_00148 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
DIHILCHL_00149 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
DIHILCHL_00150 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
DIHILCHL_00151 VFG001004 TTSS 99.5 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
DIHILCHL_00152 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
DIHILCHL_00153 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
DIHILCHL_00154 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
DIHILCHL_00155 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
DIHILCHL_00156 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
DIHILCHL_00157 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
DIHILCHL_00158 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
DIHILCHL_00159 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
DIHILCHL_00160 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
DIHILCHL_00161 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
DIHILCHL_00162 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
DIHILCHL_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
DIHILCHL_00193 VFG000667 IcsA (VirG) 99.4 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
DIHILCHL_00204 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
DIHILCHL_00215 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
DIHILCHL_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
DIHILCHL_00009 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
DIHILCHL_00017 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
DIHILCHL_00018 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
DIHILCHL_00032 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
DIHILCHL_00034 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
DIHILCHL_00037 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
DIHILCHL_00042 VFG012795 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
DIHILCHL_00043 VFG012815 TTSS secreted effectors 100 4.2e-123 1 215 1.0 0.8996 Effector delivery system type III secretion system effector OspF, phosphothreonine lyase prediction
DIHILCHL_00056 VFG012791 TTSS secreted effectors 100 1.4e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
DIHILCHL_00059 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
DIHILCHL_00081 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
DIHILCHL_00084 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
DIHILCHL_00088 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
DIHILCHL_00090 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
DIHILCHL_00098 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
DIHILCHL_00099 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
DIHILCHL_00107 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
DIHILCHL_00114 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
DIHILCHL_00128 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
DIHILCHL_00129 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
DIHILCHL_00131 VFG012742 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
DIHILCHL_00132 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
DIHILCHL_00133 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
DIHILCHL_00134 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
DIHILCHL_00135 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
DIHILCHL_00136 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
DIHILCHL_00137 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
DIHILCHL_00138 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
DIHILCHL_00139 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
DIHILCHL_00140 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
DIHILCHL_00141 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
DIHILCHL_00142 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
DIHILCHL_00143 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
DIHILCHL_00144 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
DIHILCHL_00145 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
DIHILCHL_00146 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
DIHILCHL_00147 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
DIHILCHL_00148 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
DIHILCHL_00149 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
DIHILCHL_00150 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
DIHILCHL_00151 VFG012678 TTSS 99.8 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
DIHILCHL_00152 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
DIHILCHL_00153 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
DIHILCHL_00154 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
DIHILCHL_00155 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
DIHILCHL_00156 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
DIHILCHL_00157 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
DIHILCHL_00158 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
DIHILCHL_00159 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
DIHILCHL_00160 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
DIHILCHL_00161 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
DIHILCHL_00162 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
DIHILCHL_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
DIHILCHL_00193 VFG013074 IcsA (VirG) 100 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
DIHILCHL_00204 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
DIHILCHL_00215 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
DIHILCHL_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
DIHILCHL_00225 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
DIHILCHL_00226 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
DIHILCHL_00034 PHI:6577 IcsP 98.7 2.2e-184 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence
DIHILCHL_00059 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
DIHILCHL_00128 PHI:9253 ipaJ 100 1.3e-139 1 242 1.0000 0.9344 primates shigellosis effector protein effector (plant avirulence determinant)
DIHILCHL_00132 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
DIHILCHL_00136 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
DIHILCHL_00138 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
DIHILCHL_00143 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
DIHILCHL_00155 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
DIHILCHL_00158 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
DIHILCHL_00192 PHI:9252 virA 99 4.9e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
DIHILCHL_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
DIHILCHL_00224 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
DIHILCHL_00023 QSE36316.1|GT2 100 2.33e-233 1 328 1 1
DIHILCHL_00141 QKF39747.1|GH23 100 4.93e-109 1 152 1 1
DIHILCHL_00224 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
DIHILCHL_00134 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
DIHILCHL_00154 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
DIHILCHL_00155 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
DIHILCHL_00156 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
DIHILCHL_00157 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
DIHILCHL_00158 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
DIHILCHL_00159 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
DIHILCHL_00161 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
DIHILCHL_00162 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
DIHILCHL_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