Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| HMBIOMIE_1 | 678402 | 679571 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| HMBIOMIE_1 | 456053 | 457255 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| HMBIOMIE_1 | 437658 | 438512 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| HMBIOMIE_4 | 425545 | 425862 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| HMBIOMIE_4 | 425207 | 425545 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HMBIOMIE_2 | 162838 | 163431 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| HMBIOMIE_2 | 112335 | 113774 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| HMBIOMIE_2 | 99521 | 100441 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
| HMBIOMIE_14 | 48625 | 50268 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| HMBIOMIE_6 | 27640 | 30210 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
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. |
|---|---|---|---|---|---|---|---|
| HMBIOMIE_2 | 99521 | 100441 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| HMBIOMIE_8 | 1004306 | 1005682 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| HMBIOMIE_1 | 437658 | 438512 | aadK | Streptomycin | 98.48 | 100.00 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HMBIOMIE_2 | 99521 | 100438 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| HMBIOMIE_8 | 1001786 | 1002304 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| HMBIOMIE_8 | 1004309 | 1005682 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| HMBIOMIE_14 | 48628 | 50268 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| HMBIOMIE_1 | 437658 | 438509 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| HMBIOMIE_3 | 56210 | 58804 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HMBIOMIE_8 | 519270 | 520412 | capA | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391469 |
| HMBIOMIE_8 | 520895 | 522076 | capB | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391471 |
| HMBIOMIE_8 | 520431 | 520880 | capC | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_391470 |
| HMBIOMIE_3 | 9552 | 11315 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| HMBIOMIE_8 | 109092 | 110030 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| HMBIOMIE_8 | 112928 | 113713 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| HMBIOMIE_1 | 878278 | 878919 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| HMBIOMIE_8 | 111706 | 112902 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.00 | 100.00 | NP_391079 |
| HMBIOMIE_8 | 101936 | 109072 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.98 | 100.00 | NP_391076 |
| HMBIOMIE_8 | 110058 | 111677 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.95 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| HMBIOMIE_13 | 31692 | 32828 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HMBIOMIE_5 | 4361 | 5230 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HMBIOMIE_4 | 738805 | 739581 | CodY | 7.93e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HMBIOMIE_8 | 367654 | 368223 | ClpP | 6.27e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HMBIOMIE_4 | 276396 | 276788 | spxA1 | 6.24e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HMBIOMIE_4 | 276396 | 276788 | spx | 3.72e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HMBIOMIE_12 | 20918 | 21160 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HMBIOMIE_14 | 1904 | 2101 | CspA | 3.43e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| HMBIOMIE_1 | 866314 | 866120 | CspD | 5.57e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HMBIOMIE_1 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_2 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_3 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_4 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_5 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_6 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_7 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_8 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_10 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_11 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_12 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_13 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_14 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_15 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_17 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_18 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_19 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_20 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_21 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_22 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_23 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_24 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_25 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_26 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_27 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_28 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_29 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_30 | 1.0 | 0.0 | 1.0 |
| HMBIOMIE_31 | 0.0 | 1.0 | 0.0 |
| HMBIOMIE_32 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HMBIOMIE_1 | 476805 | 507182 | 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 |
| HMBIOMIE_4 | 369260 | 395368 | 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 |
| HMBIOMIE_4 | 930237 | 932345 | False | Siphoviridae | VOG9667, VOG5353, VOG0181 |
| HMBIOMIE_4 | 945647 | 968540 | False | Siphoviridae | VOG4841, VOG4581, VOG1886, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG5910, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG4705, VOG0641, VOG4918 |
| HMBIOMIE_7 | 8277 | 34170 | False | Myoviridae | VOG7895, VOG3390, VOG7718, VOG0906, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315 |
| HMBIOMIE_7 | 45518 | 52351 | False | Siphoviridae | VOG3709, VOG11060, VOG1292, VOG1309, VOG0083, VOG1878, VOG3549 |
Phigaro v2.4.0 (Database: Jan. 2024 release)