Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C704
  Reference Plasmid   NZ_CP049282.1
  Reference Plasmid Size   208836
  Reference Plasmid GC Content   0.46
  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
M0173092 LDEBMEDG_00176 140792 3 Gut 0.04 protein_coding synonymous_variant LOW 699T>C Pro233Pro
M0173093 LDEBMEDG_00182 145808 3 Gut 0.04 protein_coding missense_variant MODERATE 163T>C Ser55Pro






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
LDEBMEDG_00026 VFG012773 TTSS secreted effectors 99.6 1.5e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 experiment
LDEBMEDG_00037 VFG042215 TTSS secreted effectors 100 1.8e-131 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ experiment
LDEBMEDG_00039 VFG001017 IcsP (SopA) 99 1.3e-185 1 315 1.0 1 Exoenzyme outer membrane protease of the OmpP family, involved in cleavage of surface exposed IcsA experiment
LDEBMEDG_00045 VFG012802 TTSS secreted effectors 100 2.9e-168 1 288 1.0 1 Effector delivery system type III secretion system effector OspB experiment
LDEBMEDG_00060 VFG012793 TTSS secreted effectors 99.5 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 experiment
LDEBMEDG_00061 VFG012812 TTSS secreted effectors 99.5 4.8e-123 1 215 1.0 0.8996 Effector delivery system type III secretion system effector OspF, phosphothreonine lyase experiment
LDEBMEDG_00078 VFG012760 TTSS secreted effectors 99.4 1.3e-85 1 158 1.0 0.8404 Effector delivery system type III secretion system effector IpgB2, guanine nucleotide exchange factor (GEF) experiment
LDEBMEDG_00102 VFG042325 TTSS secreted effectors 100 3e-122 1 212 1.0 1 Effector delivery system type III secretion system effector OspI, glutamine deamidase experiment
LDEBMEDG_00110 VFG012833 TTSS secreted effectors 98.4 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase experiment
LDEBMEDG_00118 VFG013075 VirF 100 2.8e-141 1 261 1.0 0.9962 Regulation transcriptional activator VirF experiment
LDEBMEDG_00120 VFG012825 TTSS secreted effectors 94.3 3.2e-41 1 87 0.9886 0.9886 Effector delivery system type III secretion system effector OspE2 experiment
LDEBMEDG_00131 VFG012817 TTSS secreted effectors 99.6 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 experiment
LDEBMEDG_00132 VFG012807 TTSS secreted effectors 99.4 4.3e-270 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 experiment
LDEBMEDG_00135 VFG001827 ShET2 100 2.7e-225 1 391 1.0 1 Exotoxin enterotoxin experiment
LDEBMEDG_00146 VFG002041 TTSS secreted effectors 99.5 0 1 565 1.0 1 Effector delivery system type III secretion system effector ipaH7.8, E3 ubiquitin ligase experiment
LDEBMEDG_00147 VFG012841 TTSS secreted effectors 99.1 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase experiment
LDEBMEDG_00152 VFG012778 TTSS secreted effectors 95.5 7.9e-267 1 484 1.0 1 Effector delivery system type III secretion system effector OspC3, ADP-riboxanase experiment
LDEBMEDG_00166 VFG041905 TTSS secreted effectors 100 1.2e-115 1 201 1.0 0.7761 Effector delivery system type III secretion system effector IpaJ, cysteine protease experiment
LDEBMEDG_00167 VFG012636 TTSS 100 6.3e-169 1 309 1.0 1 Effector delivery system transcriptional activator VirB experiment
LDEBMEDG_00169 VFG000984 TTSS secreted effectors 99.4 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein experiment
LDEBMEDG_00170 VFG000985 TTSS 94.9 1.5e-171 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD experiment
LDEBMEDG_00171 VFG000986 TTSS 96.4 3e-178 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC experiment
LDEBMEDG_00172 VFG000987 TTSS 97.9 4.1e-294 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB experiment
LDEBMEDG_00173 VFG000988 TTSS 100 8.3e-85 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC experiment
LDEBMEDG_00174 VFG000989 TTSS secreted effectors 98.6 3.1e-111 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) experiment
LDEBMEDG_00175 VFG000990 TTSS 100 7.9e-73 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB experiment
LDEBMEDG_00176 VFG000991 TTSS secreted effectors 97.2 1.2e-278 1 494 1.0 1 Effector delivery system type III secretion system effector IcsB, fatty acyltransferase experiment
LDEBMEDG_00177 VFG000992 TTSS secreted effectors 94.8 1.9e-293 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase experiment
LDEBMEDG_00178 VFG000993 TTSS 96.7 2.1e-64 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD experiment
LDEBMEDG_00179 VFG000994 TTSS 96.7 5.3e-84 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF experiment
LDEBMEDG_00180 VFG000995 TTSS 95.7 2.8e-203 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG experiment
LDEBMEDG_00181 VFG000996 TTSS 91.6 7.7e-37 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH experiment
LDEBMEDG_00182 VFG000997 TTSS 99 2e-44 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI experiment
LDEBMEDG_00183 VFG000998 TTSS 99.1 1.5e-122 1 228 1.0 0.9461 Effector delivery system type III secretion system inner MS ring protein MxiJ experiment
LDEBMEDG_00184 VFG000999 TTSS 100 2.7e-100 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK experiment
LDEBMEDG_00185 VFG001000 TTSS 98.7 1.8e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN experiment
LDEBMEDG_00186 VFG001001 TTSS 99.3 3.8e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL experiment
LDEBMEDG_00187 VFG001002 TTSS 100 1.5e-77 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM experiment
LDEBMEDG_00188 VFG001003 TTSS 100 3.5e-118 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE experiment
LDEBMEDG_00189 VFG001004 TTSS 99.3 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD experiment
LDEBMEDG_00190 VFG001005 TTSS 99.2 8e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD experiment
LDEBMEDG_00191 VFG001006 TTSS 99.7 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA experiment
LDEBMEDG_00192 VFG001007 TTSS 99.2 4.2e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone experiment
LDEBMEDG_00193 VFG001008 TTSS 99.1 1.9e-243 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 experiment
LDEBMEDG_00194 VFG001009 TTSS 99.1 3.1e-57 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 experiment
LDEBMEDG_00195 VFG001010 TTSS 100 4.9e-163 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 experiment
LDEBMEDG_00196 VFG001011 TTSS 98.4 4.6e-137 46 293 0.8464 1 Effector delivery system type III secretion system C ring protein Spa33 experiment
LDEBMEDG_00197 VFG001012 TTSS 98.6 7.7e-113 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 experiment
LDEBMEDG_00198 VFG001013 TTSS 98.8 1.4e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 experiment
LDEBMEDG_00199 VFG001014 TTSS 100 9.3e-134 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 experiment
LDEBMEDG_00200 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
LDEBMEDG_00225 VFG001016 TTSS secreted effectors 99.2 4.9e-230 1 400 1.0 1 Effector delivery system type III secretion system effector VirA, GTPase-activating protein (GAP) experiment
LDEBMEDG_00226 VFG000667 IcsA (VirG) 99.2 0 18 1073 0.9842 0.9583 Motility autotransporter, actin tail assembly protein IcsA/VirG experiment
LDEBMEDG_00256 VFG002042 TTSS secreted effectors 99.3 2.19999999999998e-310 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase experiment
LDEBMEDG_00258 VFG002043 TTSS secreted effectors 98.8 2e-89 1 161 1.0 0.8214 Effector delivery system type III secretion system effector OspG, protein kinase experiment
LDEBMEDG_00026 VFG020131 TTSS secreted effectors 100 2.3e-278 1 484 1.0 1 Effector delivery system type III secretion system effector OspC2 prediction
LDEBMEDG_00037 VFG042215 TTSS secreted effectors 100 1.3e-130 1 230 1.0 1 Effector delivery system type III secretion system effector cysteine methyltransferase OspZ prediction
LDEBMEDG_00039 VFG012928 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
LDEBMEDG_00045 VFG012802 TTSS secreted effectors 100 2.2e-167 1 288 1.0 1 Effector delivery system type III secretion system effector OspB prediction
LDEBMEDG_00060 VFG020134 TTSS secreted effectors 100 0 1 569 1.0 1 Effector delivery system type III secretion system effector OspD2 prediction
LDEBMEDG_00061 VFG012813 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
LDEBMEDG_00078 VFG012762 TTSS secreted effectors 100 1.2e-85 1 158 1.0 0.8404 Effector delivery system type III secretion system effector IpgB2, guanine nucleotide exchange factor (GEF) prediction
LDEBMEDG_00102 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
LDEBMEDG_00110 VFG020143 TTSS secreted effectors 100 0 1 575 1.0 1 Effector delivery system type III secretion system effector ipaH1.4, E3 ubiquitin ligase prediction
LDEBMEDG_00118 VFG013075 VirF 100 2.1e-140 1 261 1.0 0.9962 Regulation transcriptional activator VirF prediction
LDEBMEDG_00120 VFG012826 TTSS secreted effectors 100 6.1e-44 1 88 1.0 1 Effector delivery system type III secretion system effector OspE2 prediction
LDEBMEDG_00131 VFG012820 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector OspD3 prediction
LDEBMEDG_00132 VFG012809 TTSS secreted effectors 100 7.7e-271 1 470 1.0 1 Effector delivery system type III secretion system effector OspC1 prediction
LDEBMEDG_00135 VFG001827 ShET2 100 2e-224 1 391 1.0 1 Exotoxin enterotoxin prediction
LDEBMEDG_00146 VFG020145 TTSS secreted effectors 100 0 1 565 1.0 1 Effector delivery system type III secretion system effector ipaH7.8, E3 ubiquitin ligase prediction
LDEBMEDG_00147 VFG020144 TTSS secreted effectors 100 0 1 574 1.0 1 Effector delivery system type III secretion system effector ipaH4.5, E3 ubiquitin ligase prediction
LDEBMEDG_00152 VFG020132 TTSS secreted effectors 100 4.7e-279 1 484 1.0 1 Effector delivery system type III secretion system effector OspC3, ADP-riboxanase prediction
LDEBMEDG_00166 VFG041905 TTSS secreted effectors 100 8.8e-115 1 201 1.0 0.7761 Effector delivery system type III secretion system effector IpaJ, cysteine protease prediction
LDEBMEDG_00167 VFG012636 TTSS 100 4.7e-168 1 309 1.0 1 Effector delivery system transcriptional activator VirB prediction
LDEBMEDG_00169 VFG020123 TTSS secreted effectors 100 0 1 633 1.0 1 Effector delivery system type III secretion system effector IpaA, vinculin binding protein prediction
LDEBMEDG_00170 VFG020124 TTSS secreted effectors 100 6.8e-181 1 332 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, needle tip protein IpaD prediction
LDEBMEDG_00171 VFG020125 TTSS secreted effectors 100 3.6e-183 1 363 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaC prediction
LDEBMEDG_00172 VFG020126 TTSS secreted effectors 99.8 2.2e-299 1 580 1.0 1 Effector delivery system type III secretion system hydrophilic translocator, pore protein IpaB prediction
LDEBMEDG_00173 VFG000988 TTSS 100 6.2e-84 1 155 1.0 1 Effector delivery system type III secretion system chaperone for IpaB and IpaC prediction
LDEBMEDG_00174 VFG020127 TTSS secreted effectors 100 5.5e-112 1 208 1.0 1 Effector delivery system type III secretion system effector IpgB1, guanine nucleotide exchange factor (GEF) prediction
LDEBMEDG_00175 VFG000990 TTSS 100 5.9e-72 1 129 1.0 1 Effector delivery system type III secretion system chaperone for IcsB prediction
LDEBMEDG_00176 VFG020130 TTSS secreted effectors 99.8 3.8e-284 1 494 1.0 1 Effector delivery system type III secretion system effector IcsB, fatty acyltransferase prediction
LDEBMEDG_00177 VFG020129 TTSS secreted effectors 100 2.4e-308 1 538 1.0 1 Effector delivery system type III secretion system effector IpgD, phosphoinositide 4-phosphatase prediction
LDEBMEDG_00178 VFG012731 TTSS 100 2.2e-65 1 120 1.0 1 Effector delivery system type III secretion system chaperone for IpgD prediction
LDEBMEDG_00179 VFG020122 TTSS 100 8.5e-86 1 152 1.0 1 Effector delivery system type III secretion system protein IpgF prediction
LDEBMEDG_00180 VFG020098 TTSS 100 1.4e-211 1 371 1.0 1 Effector delivery system type III secretion system outer MS ring protein MixG prediction
LDEBMEDG_00181 VFG020099 TTSS 100 3.8e-40 1 83 1.0 1 Effector delivery system type III secretion system needle filament protein MxiH prediction
LDEBMEDG_00182 VFG000997 TTSS 99 1.5e-43 1 97 1.0 1 Effector delivery system type III secretion system inner rod protein MxiI prediction
LDEBMEDG_00183 VFG020101 TTSS 100 3.8e-122 1 228 1.0 0.9461 Effector delivery system type III secretion system inner MS ring protein MxiJ prediction
LDEBMEDG_00184 VFG000999 TTSS 100 2e-99 1 175 1.0 1 Effector delivery system type III secretion system accessory cytosolic protein MxiK prediction
LDEBMEDG_00185 VFG020103 TTSS 100 1.2e-125 1 226 1.0 0.9784 Effector delivery system type III secretion system stator MxiN prediction
LDEBMEDG_00186 VFG012665 TTSS 100 4.4e-70 1 135 1.0 1 Effector delivery system type III secretion system protein MxiL prediction
LDEBMEDG_00187 VFG001002 TTSS 100 1.1e-76 1 142 1.0 1 Effector delivery system type III secretion system pilotin MxiM prediction
LDEBMEDG_00188 VFG001003 TTSS 100 2.6e-117 1 210 1.0 1 Effector delivery system type III secretion system regulatory protein MxiE prediction
LDEBMEDG_00189 VFG020107 TTSS 100 0 1 566 1.0 1 Effector delivery system type III secretion system secretin MxiD prediction
LDEBMEDG_00190 VFG020108 TTSS 100 1.4e-192 1 355 1.0 1 Effector delivery system type III secretion system gatekeeper MxiD prediction
LDEBMEDG_00191 VFG020109 TTSS 100 0 1 686 1.0 1 Effector delivery system type III secretion system major export apparatus protein MxiA prediction
LDEBMEDG_00192 VFG012690 TTSS 100 4.8e-69 1 133 1.0 1 Effector delivery system type III secretion system chaparone prediction
LDEBMEDG_00193 VFG020111 TTSS 100 7.4e-244 1 430 1.0 1 Effector delivery system type III secretion system ATPase spa47 prediction
LDEBMEDG_00194 VFG020112 TTSS 100 1.8e-56 1 112 1.0 1 Effector delivery system type III secretion system stalk protein Spa13 prediction
LDEBMEDG_00195 VFG001010 TTSS 100 3.7e-162 1 292 1.0 1 Effector delivery system type III secretion system needle length regulator Spa32 prediction
LDEBMEDG_00196 VFG020114 TTSS 100 3e-164 1 293 1.0 1 Effector delivery system type III secretion system C ring protein Spa33 prediction
LDEBMEDG_00197 VFG012707 TTSS 100 1.5e-112 1 216 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa24 prediction
LDEBMEDG_00198 VFG012711 TTSS 100 3.6e-41 1 86 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa9 prediction
LDEBMEDG_00199 VFG001014 TTSS 100 7e-133 1 256 1.0 1 Effector delivery system type III secretion system minor export apparatus protein Spa29 prediction
LDEBMEDG_00200 VFG012719 TTSS 100 7.5e-183 1 342 1.0 1 Effector delivery system type III secretion system export apparatus switch protein Spa40 prediction
LDEBMEDG_00225 VFG020135 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
LDEBMEDG_00226 VFG020184 IcsA (VirG) 99.8 0 18 1073 0.9842 0.9583 Motility autotransporter, actin tail assembly protein IcsA/VirG prediction
LDEBMEDG_00256 VFG020146 TTSS secreted effectors 100 3.59999999999843e-312 1 545 1.0 1 Effector delivery system type III secretion system effector ipaH9.8, E3 ubiquitin ligase prediction
LDEBMEDG_00258 VFG020142 TTSS secreted effectors 99.4 3e-89 1 161 1.0 1 Effector delivery system type III secretion system effector OspG, protein kinase prediction
LDEBMEDG_00264 VFG020186 VirK 100 2.2e-189 1 316 1.0 1 Others virulence factor VirK prediction
LDEBMEDG_00265 VFG020187 MsbB2 100 1e-186 1 314 1.0 1 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
LDEBMEDG_00039 PHI:6577 IcsP 99 3.4e-185 1 315 1.0000 1.0000 rodents shigellosis outer membrane protease reduced virulence
LDEBMEDG_00078 PHI:4512 ipgB2 99.4 3.4e-85 1 158 1.0000 0.8404 rodents shigellosis type III effector effector (plant avirulence determinant)
LDEBMEDG_00135 PHI:10795 senB 99.7 2.1e-224 1 391 1.0000 1.0000 primates neonatal meningitis enterotoxin increased virulence (hypervirulence)
LDEBMEDG_00136 PHI:10794 cjrC 98.9 0 1 753 1.0000 1.0000 primates neonatal meningitis TonB-dependent colicin J protein increased virulence (hypervirulence)
LDEBMEDG_00137 PHI:10793 cjrB 98.8 7e-136 1 258 1.0000 1.0000 primates neonatal meningitis colicin Js sensitivity protein increased virulence (hypervirulence)
LDEBMEDG_00138 PHI:10792 cjrA 97.9 6.8e-164 1 291 1.0000 1.0000 primates neonatal meningitis iron-regulated protein increased virulence (hypervirulence)
LDEBMEDG_00166 PHI:9253 ipaJ 100 3.1e-115 1 201 1.0000 0.7761 primates shigellosis effector protein effector (plant avirulence determinant)
LDEBMEDG_00170 PHI:7721 IpaD 94.9 3e-171 1 332 1.0000 1.0000 primates shigellosis type three secretion system tip protein reduced virulence
LDEBMEDG_00174 PHI:4511 ipgB1 100 1.9e-112 1 208 1.0000 1.0000 rodents shigellosis type III effector effector (plant avirulence determinant)
LDEBMEDG_00176 PHI:11423 icsB 96.8 4.6e-277 1 494 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
LDEBMEDG_00193 PHI:12182 spa47 99.1 4.9e-243 1 430 1.0000 1.0000 primates shigellosis protein-secreting ATPase unaffected pathogenicity
LDEBMEDG_00196 PHI:9889 Spa33 98.6 9.9e-163 1 293 1.0000 1.0000 primates shigellosis surface presentation of antigens protein reduced virulence
LDEBMEDG_00225 PHI:9252 virA 99.2 1.3e-229 1 400 1.0000 1.0000 primates shigellosis effector protein effector (plant avirulence determinant)
LDEBMEDG_00226 PHI:4647 IcsA 99.2 0 18 1073 0.9842 0.9583 rodents shigellosis adhesin regulated by the type III secretion system reduced virulence
LDEBMEDG_00263 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
LDEBMEDG_00179 QIV77460.1|GH23 100 4.93e-109 1 152 1 1
LDEBMEDG_00263 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
LDEBMEDG_00136 1.B.14.7.1 98.9 0 1 753 1.0000 1.0000 1 Channels/Pores 1.B β-Barrel Porins 1.B.14 The Outer Membrane Receptor (OMR) Family
LDEBMEDG_00137 2.C.1.1.3 98.8 1.6e-135 1 258 1.0000 1.0000 2 Electrochemical Potential-driven Transporters 2.C Ion-gradient-driven energizers 2.C.1 The TonB-ExbB-ExbD/TolA-TolQ-TolR Outer Membrane Receptor Energizers and Stabilizers (TonB/TolA) Family
LDEBMEDG_00172 1.C.36.3.1 97.8 2.7e-292 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
LDEBMEDG_00192 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
LDEBMEDG_00193 3.A.6.1.2 99.1 1.1e-242 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
LDEBMEDG_00194 3.A.6.1.2 99.1 1.8e-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
LDEBMEDG_00195 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
LDEBMEDG_00196 3.A.6.1.2 98.6 2.2e-162 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
LDEBMEDG_00197 3.A.6.1.2 98.6 4.5e-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
LDEBMEDG_00199 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
LDEBMEDG_00200 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
LDEBMEDG_00226 1.B.12.1.2 99.2 0 18 1073 0.9842 0.9583 1 Channels/Pores 1.B β-Barrel Porins 1.B.12 The Autotransporter-1 (AT-1) Family