Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C733
  Reference Plasmid   NZ_CP053752.1
  Reference Plasmid Size   212834
  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
M0173798 LLHKHADL_00212 183191 6 Gut 0.04 protein_coding synonymous_variant LOW 342T>C Pro114Pro
M0173799 LLHKHADL_00023 25732 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4758C>T None
M0173800 LLHKHADL_00023 25736 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4762G>A None
M0173801 LLHKHADL_00023 25748 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4774G>C None
M0173802 LLHKHADL_00023 25750 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4776G>T None
M0173803 LLHKHADL_00023 25751 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4777G>A None
M0173804 LLHKHADL_00023 25760 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4786C>A None
M0173805 LLHKHADL_00023 25761 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4787C>A None
M0173806 LLHKHADL_00023 25772 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4798A>G None
M0173807 LLHKHADL_00023 25816 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4842T>A None
M0173808 LLHKHADL_00023 25817 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4843T>G None
M0173809 LLHKHADL_00023 25818 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4844A>T None
M0173810 LLHKHADL_00023 25828 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4854C>T None
M0173811 LLHKHADL_00023 25836 4 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4862C>T None
M0173812 LLHKHADL_00033 26381 3 Gut 0.02 protein_coding synonymous_variant LOW 474G>A Glu158Glu
M0173813 LLHKHADL_00209 185256 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4577G>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
LLHKHADL_00009 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
LLHKHADL_00017 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
LLHKHADL_00060 VFG002043 TTSS secreted effectors 100 1e-111 1 196 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase experiment
LLHKHADL_00062 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
LLHKHADL_00073 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
LLHKHADL_00085 VFG000667 IcsA (VirG) 99.4 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
LLHKHADL_00086 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
LLHKHADL_00113 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
LLHKHADL_00114 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
LLHKHADL_00115 VFG001013 TTSS 100 4.8e-42 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
LLHKHADL_00116 VFG001012 TTSS 99.5 2e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
LLHKHADL_00117 VFG001011 TTSS 99.2 5.5e-138 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
LLHKHADL_00118 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
LLHKHADL_00119 VFG001009 TTSS 100 2.4e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
LLHKHADL_00120 VFG001008 TTSS 99.8 7.5e-245 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
LLHKHADL_00121 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
LLHKHADL_00122 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
LLHKHADL_00123 VFG001005 TTSS 99.7 1.2e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
LLHKHADL_00124 VFG001004 TTSS 99.5 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
LLHKHADL_00125 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
LLHKHADL_00126 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
LLHKHADL_00127 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
LLHKHADL_00128 VFG001000 TTSS 99.6 6.3e-126 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
LLHKHADL_00129 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
LLHKHADL_00130 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
LLHKHADL_00131 VFG000997 TTSS 100 1.1e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
LLHKHADL_00132 VFG000996 TTSS 100 1.4e-41 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
LLHKHADL_00133 VFG000995 TTSS 100 4.5e-214 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
LLHKHADL_00134 VFG000994 TTSS 99.3 1.6e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
LLHKHADL_00135 VFG000993 TTSS 100 3e-66 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
LLHKHADL_00136 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
LLHKHADL_00137 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
LLHKHADL_00138 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
LLHKHADL_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
LLHKHADL_00140 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
LLHKHADL_00141 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
LLHKHADL_00142 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
LLHKHADL_00143 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
LLHKHADL_00147 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
LLHKHADL_00148 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
LLHKHADL_00162 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
LLHKHADL_00169 VFG012773 TTSS secreted effectors 99.4 7.6e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
LLHKHADL_00176 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
LLHKHADL_00177 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
LLHKHADL_00185 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
LLHKHADL_00186 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
LLHKHADL_00190 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
LLHKHADL_00193 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
LLHKHADL_00214 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
LLHKHADL_00217 VFG012788 TTSS secreted effectors 98.7 2e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 experiment
LLHKHADL_00229 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
LLHKHADL_00230 VFG012793 TTSS secreted effectors 99.6 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
LLHKHADL_00235 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
LLHKHADL_00238 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
LLHKHADL_00240 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
LLHKHADL_00008 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
LLHKHADL_00009 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
LLHKHADL_00017 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
LLHKHADL_00051 VFG013084 MsbB2 100 2e-165 1 279 1.0 0.8885 Others lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase prediction
LLHKHADL_00052 VFG013079 VirK 100 5.5e-188 1 316 1.0 1 Others virulence factor VirK prediction
LLHKHADL_00060 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
LLHKHADL_00062 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
LLHKHADL_00073 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
LLHKHADL_00085 VFG013074 IcsA (VirG) 100 0 1 1102 1.0 1 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
LLHKHADL_00086 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
LLHKHADL_00113 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
LLHKHADL_00114 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
LLHKHADL_00115 VFG001013 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
LLHKHADL_00116 VFG012710 TTSS 100 1.2e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
LLHKHADL_00117 VFG012705 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
LLHKHADL_00118 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
LLHKHADL_00119 VFG001009 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
LLHKHADL_00120 VFG012694 TTSS 100 1.5e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
LLHKHADL_00121 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
LLHKHADL_00122 VFG001006 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
LLHKHADL_00123 VFG012682 TTSS 100 1.9e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
LLHKHADL_00124 VFG012678 TTSS 99.8 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
LLHKHADL_00125 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
LLHKHADL_00126 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
LLHKHADL_00127 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
LLHKHADL_00128 VFG012662 TTSS 100 1.6e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
LLHKHADL_00129 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
LLHKHADL_00130 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
LLHKHADL_00131 VFG000997 TTSS 100 7.9e-45 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
LLHKHADL_00132 VFG000996 TTSS 100 1e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
LLHKHADL_00133 VFG000995 TTSS 100 3.4e-213 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
LLHKHADL_00134 VFG012738 TTSS 100 1.4e-85 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
LLHKHADL_00135 VFG000993 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
LLHKHADL_00136 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
LLHKHADL_00137 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
LLHKHADL_00138 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
LLHKHADL_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
LLHKHADL_00140 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
LLHKHADL_00141 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
LLHKHADL_00142 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
LLHKHADL_00143 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
LLHKHADL_00147 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
LLHKHADL_00148 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
LLHKHADL_00162 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
LLHKHADL_00169 VFG012776 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
LLHKHADL_00176 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
LLHKHADL_00177 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
LLHKHADL_00185 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
LLHKHADL_00186 VFG012810 TTSS secreted effectors 100 1e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
LLHKHADL_00190 VFG012827 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
LLHKHADL_00193 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
LLHKHADL_00214 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
LLHKHADL_00217 VFG012791 TTSS secreted effectors 100 1.4e-124 1 225 1.0 1 Effector delivery system type III secretion system effector OspD1 prediction
LLHKHADL_00229 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
LLHKHADL_00230 VFG012795 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
LLHKHADL_00235 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
LLHKHADL_00238 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
LLHKHADL_00240 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
LLHKHADL_00246 VFG023800 O-antigen 74 1.7e-201 1 461 0.9957 0.7226 Immune modulation polysaccharide biosynthesis protein 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
LLHKHADL_00053 PHI:10400 Sfgtr4 (ORF186) 99.7 9.6e-216 1 362 1.0000 1.0000 primates shigellosis putative lipopolysaccharides (LPS) glycosyltransferase (Gtr) reduced virulence
LLHKHADL_00085 PHI:4647 IcsA 99.4 0 1 1102 1.0000 1.0000 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
LLHKHADL_00086 PHI:9252 virA 99 4.9e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
LLHKHADL_00117 PHI:9889 Spa33 100 1.1e-164 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
LLHKHADL_00120 PHI:12182 spa47 99.8 2e-244 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
LLHKHADL_00132 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
LLHKHADL_00137 PHI:11423 icsB 97.2 2.4e-278 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
LLHKHADL_00139 PHI:4511 ipgB1 98.1 6.9e-110 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
LLHKHADL_00143 PHI:7721 IpaD 97.3 2.3e-176 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
LLHKHADL_00148 PHI:9253 ipaJ 100 1.3e-139 1 242 1.0000 0.9344 primates shigellosis effector protein effector (plant avirulence determinant)
LLHKHADL_00214 PHI:4512 ipgB2 99.5 1.2e-103 14 201 0.9353 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
LLHKHADL_00238 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
LLHKHADL_00003 QSE36316.1|GT2 100 2.33e-233 1 328 1 1
LLHKHADL_00053 ACD06066.1|GT4 100 1.09e-271 1 362 1 1
LLHKHADL_00134 QKF39747.1|GH23 100 4.93e-109 1 152 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
LLHKHADL_00085 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
LLHKHADL_00113 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
LLHKHADL_00114 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
LLHKHADL_00116 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
LLHKHADL_00117 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
LLHKHADL_00118 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
LLHKHADL_00119 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
LLHKHADL_00120 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
LLHKHADL_00121 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
LLHKHADL_00141 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