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. |
|---|---|---|---|---|---|---|---|---|
| MHCIJHAF_15 | 603819 | 604673 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| MHCIJHAF_15 | 585446 | 586648 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
| MHCIJHAF_22 | 454479 | 454817 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| MHCIJHAF_22 | 454162 | 454479 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| MHCIJHAF_15 | 366298 | 367467 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| MHCIJHAF_13 | 272937 | 275507 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| MHCIJHAF_17 | 109709 | 110629 | mphK | ARO:3004541 | mphK | 98.02 | 100.00 | CP010314.1 |
| MHCIJHAF_17 | 96375 | 97814 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| MHCIJHAF_4 | 50630 | 52273 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| MHCIJHAF_17 | 46658 | 47251 | tmrB | ARO:3003059 | tmrB | 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. |
|---|---|---|---|---|---|---|---|
| MHCIJHAF_15 | 603821 | 604673 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| MHCIJHAF_6 | 39565 | 40941 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.91 | 100.00 | D12567 |
| MHCIJHAF_17 | 109709 | 110629 | mph(K) | Spiramycin, Telithromycin | 97.61 | 99.89 | NC_000964 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| MHCIJHAF_15 | 603822 | 604673 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| MHCIJHAF_6 | 39565 | 40938 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| MHCIJHAF_4 | 50633 | 52273 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| MHCIJHAF_17 | 109721 | 110629 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.02 | 99.02 | WP_003246254.1 |
| MHCIJHAF_6 | 42894 | 43412 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| MHCIJHAF_15 | 58479 | 61076 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.83 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| MHCIJHAF_15 | 9176 | 10939 | dep/capD | 0.0 | Capsule | Immune modulation | 99.94 | 100.00 | NP_389723 |
| MHCIJHAF_6 | 940134 | 941072 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| MHCIJHAF_6 | 941092 | 948228 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.78 | 100.00 | NP_391076 |
| MHCIJHAF_6 | 522144 | 523325 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| MHCIJHAF_6 | 523340 | 523789 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| MHCIJHAF_6 | 936451 | 937236 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| MHCIJHAF_6 | 523808 | 524950 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| MHCIJHAF_15 | 166334 | 166975 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| MHCIJHAF_6 | 937262 | 938458 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| MHCIJHAF_6 | 938487 | 940106 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 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 |
|---|---|---|---|---|---|---|---|---|
| MHCIJHAF_9 | 32210 | 33346 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| MHCIJHAF_10 | 4803 | 5672 | pdxS | 2.21e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.45 | 98.31 | ACE61268 |
| MHCIJHAF_22 | 141190 | 140414 | CodY | 4.59e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| MHCIJHAF_6 | 682525 | 681956 | ClpP | 6.32e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| MHCIJHAF_11 | 276718 | 277110 | spxA1 | 2.04e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| MHCIJHAF_11 | 276718 | 277110 | spx | 1.22e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| MHCIJHAF_5 | 34919 | 34677 | SpoVG | 7.60e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| MHCIJHAF_4 | 2704 | 2901 | CspA | 3.52e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| MHCIJHAF_11 | 33485 | 33291 | CspB | 2.95e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| MHCIJHAF_4 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_5 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_6 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_9 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_10 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_11 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_12 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_13 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_14 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_15 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_16 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_17 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_18 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_19 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_21 | 0.0 | 1.0 | 0.0 |
| MHCIJHAF_22 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| MHCIJHAF_12 | 11521 | 15292 | False | Siphoviridae | VOG4552, VOG0650, VOG4603, VOG9667, VOG9607 |
| MHCIJHAF_13 | 2236 | 27952 | False | Siphoviridae | VOG10227, VOG0720, VOG4564, VOG4555, VOG4553, VOG1125, VOG0815, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG5535, VOG0753, VOG0136, VOG4707, VOG1993, VOG2703, VOG9953, VOG3477, VOG3490 |
| MHCIJHAF_15 | 538882 | 568785 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG10227, VOG0796, VOG4673, VOG9587, VOG4693, VOG0189, VOG11060, VOG1309, VOG4600 |
| MHCIJHAF_21 | 123770 | 126982 | False | Unknown | VOG4551, VOG0025 |
| MHCIJHAF_22 | 484305 | 512036 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)