Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 15 | 10 | 7 | 19.34 |
PPRS is classified as low-risk (≤4), medium-risk (4-6), and high-risk (≥6).
Antibiotic resistance genes
Comprehensive Antibiotic Resistance Database (CARD)
| Query ID | Begin | End | ARO name | ARO accession | CARD name | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| BPFGHMIA_7 | 678015 | 679184 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| BPFGHMIA_7 | 455664 | 456866 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| BPFGHMIA_7 | 437303 | 438157 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| BPFGHMIA_6 | 425677 | 425994 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| BPFGHMIA_6 | 425339 | 425677 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| BPFGHMIA_3 | 276545 | 279115 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| BPFGHMIA_4 | 218101 | 219021 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| BPFGHMIA_4 | 204767 | 206206 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| BPFGHMIA_4 | 155110 | 155703 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| BPFGHMIA_5 | 110183 | 111826 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| BPFGHMIA_2 | 2512 | 3162 | Streptococcus suis chloramphenicol acetyltransferase | ARO:3004455 | Ssui_ACT_CHL | 94.91 | 100.00 | AB080798.1 |
| BPFGHMIA_2 | 1216 | 1986 | ANT(4')-Ia | ARO:3002623 | ANT(4')-Ia | 99.21 | 101.19 | K02551.1 |
RGI v6.0.3 (Database: CARD Variants v4.0.2, Nov. 2023 release)
ResFinder
| Query ID | Begin | End | Resistance gene | Phenotype | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|
| BPFGHMIA_2 | 1225 | 1986 | aadD | Amikacin, Tobramycin | 100.00 | 100.00 | M19465 |
| BPFGHMIA_7 | 437303 | 438157 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| BPFGHMIA_2 | 2512 | 3162 | cat(pC194) | Chloramphenicol | 100.00 | 100.00 | NC_002013 |
| BPFGHMIA_4 | 218101 | 219021 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| BPFGHMIA_1 | 36293 | 37669 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| BPFGHMIA_2 | 1216 | 1983 | aadD1 | aminoglycoside O-nucleotidyltransferase ANT(4')-Ia | EXACTX | 100.00 | 100.00 | WP_001795128.1 |
| BPFGHMIA_7 | 437303 | 438154 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| BPFGHMIA_2 | 2512 | 3159 | catA | type A-9 chloramphenicol O-acetyltransferase | EXACTX | 100.00 | 100.00 | WP_001010387.1 |
| BPFGHMIA_4 | 218104 | 219021 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| BPFGHMIA_1 | 39669 | 40187 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| BPFGHMIA_1 | 36293 | 37666 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| BPFGHMIA_5 | 110186 | 111826 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| BPFGHMIA_7 | 1119910 | 1122504 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | WP_087347987.1 |
AMRFinderPlus v4.0.3 (Database: Oct. 2024 release)
Virulence factors
Virulence Factor Database (VFDB)
| Query ID | qstart | qend | Gene name | e-value | VF name | VF category | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| BPFGHMIA_1 | 526388 | 527530 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| BPFGHMIA_1 | 524724 | 525905 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| BPFGHMIA_1 | 525920 | 526369 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| BPFGHMIA_17 | 8766 | 10529 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| BPFGHMIA_1 | 933055 | 933840 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| BPFGHMIA_1 | 936738 | 937676 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| BPFGHMIA_1 | 933866 | 935062 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| BPFGHMIA_1 | 935091 | 936710 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| BPFGHMIA_1 | 937696 | 944832 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| BPFGHMIA_7 | 877895 | 878536 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
BLASTN v2.16.0 (Database: VFDB, Dec. 2024 release)
VirulenceFinder
| Query ID | Begin | End | Database | Virulence factor | Protein function | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
VirulenceFinder v2.0. 4 (Database: virulencefinder_db, Feb . 2024 release)
Pathogenic genes
PHI-base
| Query ID | qstart | qend | Gene name | e-value | Function | Identity | Coverage | Gene ID |
|---|---|---|---|---|---|---|---|---|
| BPFGHMIA_9 | 31753 | 32889 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| BPFGHMIA_11 | 11314 | 10445 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| BPFGHMIA_6 | 738942 | 739718 | CodY | 8.08e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| BPFGHMIA_1 | 679117 | 678548 | ClpP | 6.30e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| BPFGHMIA_6 | 276516 | 276908 | spxA1 | 2.39e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| BPFGHMIA_8 | 20784 | 21026 | SpoVG | 2.74e-38 | RNA-binding protein | 80.25 | 79.41 | AAT02994 |
| BPFGHMIA_5 | 64711 | 64908 | CspA | 6.09e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| BPFGHMIA_2 | 52 | 1056 | rep22 | 1005 / 1005 | 100.00 | AF503772 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| BPFGHMIA_1 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_2 | 1.0 | 0.0 | 1.0 |
| BPFGHMIA_3 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_4 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_5 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_6 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_7 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_8 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_9 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_11 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_13 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_15 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_16 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_17 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_18 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_19 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_20 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_21 | 0.0 | 1.0 | 0.0 |
| BPFGHMIA_23 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| BPFGHMIA_6 | 369392 | 395500 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG4705 |
| BPFGHMIA_7 | 476417 | 506794 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)