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. |
|---|---|---|---|---|---|---|---|---|
| KNDAHMHA_4 | 435887 | 436204 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| KNDAHMHA_4 | 435549 | 435887 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| KNDAHMHA_6 | 263998 | 264852 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| KNDAHMHA_6 | 245372 | 246574 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| KNDAHMHA_3 | 185734 | 187380 | vmlR | ARO:3004476 | vmlR | 97.99 | 100.18 | NC_000964.3 |
| KNDAHMHA_1 | 109032 | 109952 | mphK | ARO:3004541 | mphK | 99.35 | 100.00 | CP010314.1 |
| KNDAHMHA_1 | 95696 | 97135 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| KNDAHMHA_1 | 45986 | 46579 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| KNDAHMHA_10 | 27509 | 30079 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 100.00 | AL009126.3 |
| KNDAHMHA_6 | 20386 | 21555 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
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. |
|---|---|---|---|---|---|---|---|
| KNDAHMHA_1 | 109032 | 109952 | mph(K) | Spiramycin, Telithromycin | 99.24 | 100.00 | NC_000964 |
| KNDAHMHA_5 | 1100531 | 1101907 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.06 | 100.00 | D12567 |
| KNDAHMHA_6 | 264000 | 264852 | aadK | Streptomycin | 98.83 | 99.77 | 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. |
|---|---|---|---|---|---|---|---|---|
| KNDAHMHA_1 | 109035 | 109952 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 99.35 | 100.00 | WP_003246254.1 |
| KNDAHMHA_6 | 264001 | 264852 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| KNDAHMHA_5 | 1100534 | 1101907 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| KNDAHMHA_3 | 185737 | 187380 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 97.99 | 100.00 | WP_003234144.1 |
| KNDAHMHA_5 | 1098045 | 1098563 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| KNDAHMHA_9 | 154585 | 157182 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KNDAHMHA_5 | 152582 | 153520 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| KNDAHMHA_5 | 153548 | 155167 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| KNDAHMHA_9 | 264434 | 265075 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| KNDAHMHA_5 | 155196 | 156392 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.67 | 100.00 | NP_391079 |
| KNDAHMHA_5 | 603424 | 604605 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| KNDAHMHA_5 | 601799 | 602941 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| KNDAHMHA_5 | 156418 | 157203 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| KNDAHMHA_5 | 602960 | 603409 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| KNDAHMHA_9 | 104495 | 106258 | dep/capD | 0.0 | Capsule | Immune modulation | 99.26 | 100.00 | NP_389723 |
| KNDAHMHA_5 | 145426 | 152562 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.92 | 100.00 | NP_391076 |
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 |
|---|---|---|---|---|---|---|---|---|
| KNDAHMHA_13 | 31732 | 32868 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| KNDAHMHA_17 | 4382 | 5251 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| KNDAHMHA_4 | 745671 | 746447 | CodY | 7.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| KNDAHMHA_5 | 448955 | 449524 | ClpP | 6.85e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| KNDAHMHA_4 | 276470 | 276862 | spxA1 | 5.98e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| KNDAHMHA_4 | 276470 | 276862 | spx | 3.57e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| KNDAHMHA_8 | 34891 | 34649 | SpoVG | 7.54e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| KNDAHMHA_3 | 137690 | 137887 | CspA | 9.35e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| KNDAHMHA_9 | 277037 | 277231 | CspD | 2.80e-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 |
|---|---|---|---|
| KNDAHMHA_1 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_2 | 1.0 | 0.0 | 1.0 |
| KNDAHMHA_3 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_4 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_5 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_6 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_8 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_9 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_10 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_12 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_13 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_14 | 1.0 | 0.0 | 1.0 |
| KNDAHMHA_16 | 1.0 | 0.0 | 1.0 |
| KNDAHMHA_17 | 0.0 | 1.0 | 0.0 |
| KNDAHMHA_18 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| KNDAHMHA_4 | 379574 | 406058 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
| KNDAHMHA_5 | 18479 | 39532 | False | Siphoviridae | VOG0136, VOG0753, VOG5535, VOG4599, VOG4605, VOG4545, VOG1323, VOG0725, VOG0799, VOG0724, VOG5660, VOG0816, VOG4623, VOG3480, VOG1329, VOG4555, VOG1183, VOG4564, VOG0720, VOG0796 |
| KNDAHMHA_5 | 49308 | 55401 | False | Siphoviridae | VOG0189, VOG4566, VOG1309, VOG4600, VOG4603, VOG4552 |
| KNDAHMHA_5 | 228462 | 260436 | False | Siphoviridae | VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4660, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG1886, VOG4581, VOG4841, VOG0198, VOG1884, VOG0025, VOG9600, VOG11060, VOG4552, VOG1638, VOG5651, VOG0550, VOG0549, VOG0181, VOG5353, VOG9667 |
| KNDAHMHA_6 | 198563 | 228412 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749, VOG4685, VOG4688, VOG4773, VOG9315, VOG0796, VOG4673, VOG4693, VOG0189, VOG11060, VOG1309 |
Phigaro v2.4.0 (Database: Jan. 2024 release)