Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C1084
  Reference Plasmid   NZ_CP104765.1
  Reference Plasmid Size   1144253
  Reference Plasmid GC Content   0.40
  Reference Plasmid Mobility Type   non-mobilizable





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
M0195760 GAJCFAHA_01018 1046112 6 Gut 0.03 protein_coding missense_variant MODERATE 818T>C Val273Ala
M0195761 GAJCFAHA_01105 1136122 3 Gut 0.02 protein_coding missense_variant MODERATE 821C>A Ser274Tyr
M0195762 GAJCFAHA_01079 1105864 4 Gut 0.02 protein_coding synonymous_variant LOW 1203G>C Pro401Pro
M0195763 GAJCFAHA_01059 1085219 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4960C>T None
M0195764 GAJCFAHA_01067 1088896 4 Gut 0.02 protein_coding missense_variant MODERATE 778G>A Glu260Lys
M0195765 GAJCFAHA_00303 316410 4 Gut 0.02 protein_coding missense_variant MODERATE 581A>G Asp194Gly
M0195766 GAJCFAHA_00106 104063 3 Gut 0.02 protein_coding synonymous_variant LOW 252A>G Leu84Leu
M0195767 GAJCFAHA_00116 115141 4 Gut 0.02 protein_coding stop_lost&splice_region_variant HIGH 178T>C Ter60Glnext*?
M0195768 GAJCFAHA_00412 434879 3 Gut 0.02 protein_coding stop_lost&splice_region_variant HIGH 295T>C Ter99Glnext*?
M0195769 GAJCFAHA_00444 470974 3 Gut 0.02 protein_coding missense_variant MODERATE 929C>T Pro310Leu
M0195770 GAJCFAHA_00447 473309 5 Gut 0.03 protein_coding missense_variant MODERATE 713T>A Leu238Gln
M0195771 GAJCFAHA_00375 394759 3 Gut 0.02 protein_coding synonymous_variant LOW 75T>C Phe25Phe
M0195772 GAJCFAHA_00468 497391 6 Gut 0.03 protein_coding synonymous_variant LOW 1692T>C Ile564Ile
M0195773 GAJCFAHA_00851 889292 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4987C>T None
M0195774 GAJCFAHA_00877 908619 3 Gut 0.02 protein_coding upstream_gene_variant MODIFIER -4587G>A None
M0195775 GAJCFAHA_00122 124222 4 Gut 0.02 protein_coding missense_variant MODERATE 35T>C Val12Ala






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
GAJCFAHA_00812 VFG002162 BSH 78.1 3.5e-154 1 324 1.0 0.9969 Stress survival bile salt hydrolase experiment
GAJCFAHA_00812 VFG006815 BSH 78.4 4.1e-154 1 324 1.0 0.9969 Stress survival bile salt hydrolase 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
GAJCFAHA_00195 Arsenic (As) 80 3.2e-57 1 130 0.9701 0.9701 prediction






        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
GAJCFAHA_00075 PHI:7637 CspA 81.5 2e-26 1 65 0.9848 0.9848 bony fishes listeriosis cold shock protein reduced virulence
GAJCFAHA_00150 PHI:124066 prdB 85.5 1.4e-34 1 83 1.0000 0.9668 rodents nosocomial diarrhea proline reductase reduced virulence
GAJCFAHA_00151 PHI:124066 prdB 74 2.5e-61 1 150 1.0000 0.9668 rodents nosocomial diarrhea proline reductase reduced virulence
GAJCFAHA_01002 PHI:8586 mntH1 76.2 7.3e-217 3 516 0.9828 0.9699 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity
GAJCFAHA_01011 PHI:8586 mntH1 87.5 9.7e-249 15 524 0.9497 0.9699 moths nosocomial infection divalent metal cation transporter unaffected pathogenicity






        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
GAJCFAHA_00008 QXJ61047.1|GT2 100 2.47e-220 1 312 1 1
GAJCFAHA_00078 QXJ60979.1|GH4 100 0 1 445 1 1
GAJCFAHA_00098 UXJ97945.1|GH2 100 0 1 797 1 1
GAJCFAHA_00101 UXJ97948.1|GH3 100 0 1 561 1 1
GAJCFAHA_00102 UXJ97949.1|GH78 100 0 1 941 1 1
GAJCFAHA_00104 UXJ97951.1|CBM91|GH43_12 100 0 1 514 1 1
GAJCFAHA_00106 UXJ97953.1|GH1 100 0 1 456 1 1
GAJCFAHA_00108 UXJ97955.1|GH38 100 0 1 873 1 1
GAJCFAHA_00217 UXJ98058.1|GH92 100 0 1 713 1 1
GAJCFAHA_00219 UXJ98060.1|GH125 100 0 1 429 1 1
GAJCFAHA_00220 UXJ98061.1|GH38 100 0 1 890 1 1
GAJCFAHA_00222 UXJ98063.1|GH20 100 0 1 437 1 1
GAJCFAHA_00247 UXJ98087.1|GH1 100 0 1 487 1 1
GAJCFAHA_00250 UXJ98090.1|GH1 100 0 1 484 1 1
GAJCFAHA_00277 UXJ98116.1|GH1 100 0 1 466 1 1
GAJCFAHA_00298 QXJ60755.1|GT4 100 1.24e-253 1 346 1 1
GAJCFAHA_00302 QXJ60751.1|GT26 100 1.45e-172 1 241 1 1
GAJCFAHA_00303 UXJ98144.1|GT4 100 3.6e-302 1 416 1 1
GAJCFAHA_00347 QXJ61739.1|GH4 100 0 1 442 1 1
GAJCFAHA_00383 QXJ61708.1|CBM50 100 9.54e-150 1 286 1 1
GAJCFAHA_00424 QXJ61672.1|GH2 100 0 1 1018 1 1
GAJCFAHA_00438 QXJ61660.1|GH1 100 0 1 489 1 1
GAJCFAHA_00462 UXJ98293.1|GH1 100 0 1 469 1 1
GAJCFAHA_00491 UXJ98322.1|AA10 100 2.48e-142 1 192 1 1
GAJCFAHA_00536 QZO10835.1|GH172 100 1.58e-285 1 372 1 1
GAJCFAHA_00540 UXC28087.1|GH1 100 0 1 477 1 1
GAJCFAHA_00543 UXJ98367.1|GH39 100 0 1 809 1 1
GAJCFAHA_00571 UXK06547.1|GH1 100 0 1 483 1 1
GAJCFAHA_00584 UXJ97357.1|GH13_31 100 0 1 571 1 1
GAJCFAHA_00608 UXJ97378.1|GH1 100 0 1 466 1 1
GAJCFAHA_00642 QZO10744.1|GH43_26 100 3.95e-252 1 323 1 1
GAJCFAHA_00645 UXC27990.1|GH1 100 0 1 474 1 1
GAJCFAHA_00698 QZO10695.1|GH32 100 0 1 499 1 1
GAJCFAHA_00700 UXJ97466.1|GH13_31 100 0 1 541 1 1
GAJCFAHA_00701 UXJ97467.1|GH36 100 0 1 723 1 1
GAJCFAHA_00746 UXC27891.1|GH36 100 0 1 734 1 1
GAJCFAHA_00797 UXK06336.1|GH73 100 0 1 656 1 1
GAJCFAHA_00823 UXJ97578.1|GH0 100 0 1 1546 1 1
GAJCFAHA_00960 UXJ97710.1|GH1 100 0 1 464 1 1
GAJCFAHA_00981 UXJ97729.1|CBM50|GH73 100 8.17999998985288e-316 1 531 1 1
GAJCFAHA_01035 QXJ61128.1|GH1 100 0 1 478 1 1
GAJCFAHA_01037 QXJ61126.1|GH36 100 0 1 744 1 1
GAJCFAHA_01053 QXJ61794.1|GT8 100 1.89e-218 2 296 0.9966 1
GAJCFAHA_01054 QXJ61111.1|GT8 100 9.27e-211 1 284 1 1
GAJCFAHA_01067 UXJ97804.1|GT51 100 0 1 855 1 1
GAJCFAHA_01069 QXJ61097.1|GH1 100 0 1 464 1 1
GAJCFAHA_01071 QXJ61095.1|GH3 100 0 1 765 1 1
GAJCFAHA_01095 QXJ61071.1|CBM34|GH13_20 100 0 1 582 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
GAJCFAHA_00115 3.A.1.2.32 72.2 8.3e-120 2 296 0.9736 0.7248 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
GAJCFAHA_00354 4.A.5.1.2 75.4 2.3e-184 8 422 0.9811 0.9811 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.5 The PTS Galactitol (Gat) Family
GAJCFAHA_00505 1.S.1.1.1 74.2 5.5e-30 1 89 0.9468 0.9468 1 Channels/Pores 1.S Bacterial Micro/NanoCompartment Shell Protein Pores 1.S.1 The Bacterial Microcompartment Shell/Pore-forming Protein-1 (BMC-SP1) Family
GAJCFAHA_00524 1.S.1.1.1 74.2 1.4e-30 1 89 0.9570 0.9468 1 Channels/Pores 1.S Bacterial Micro/NanoCompartment Shell Protein Pores 1.S.1 The Bacterial Microcompartment Shell/Pore-forming Protein-1 (BMC-SP1) Family
GAJCFAHA_00678 4.A.6.1.19 70.5 3.7e-92 2 262 0.9962 0.9317 4 Group Translocators 4.A Phosphotransfer-driven Group Translocators (PTS) 4.A.6 The PTS Mannose-Fructose-Sorbose (Man) Family
GAJCFAHA_01075 2.A.3.7.7 73.1 1.7e-191 1 446 0.9429 0.9571 2 Electrochemical Potential-driven Transporters 2.A Porters (uniporters, symporters, antiporters) 2.A.3 The Amino Acid-Polyamine-Organocation (APC) Family