Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 7 | 17.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| HAEIICFG_11 | 1776128 | 1776466 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| HAEIICFG_11 | 1775811 | 1776128 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| HAEIICFG_11 | 626256 | 627425 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| HAEIICFG_11 | 456148 | 457350 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| HAEIICFG_11 | 437752 | 438606 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| HAEIICFG_25 | 378448 | 379368 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| HAEIICFG_25 | 365122 | 366561 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| HAEIICFG_25 | 29062 | 30705 | vmlR | ARO:3004476 | vmlR | 98.54 | 100.00 | NC_000964.3 |
| HAEIICFG_26 | 27451 | 30021 | 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. |
|---|---|---|---|---|---|---|---|
| HAEIICFG_22 | 1025823 | 1027199 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.20 | 100.00 | D12567 |
| HAEIICFG_25 | 378448 | 379368 | mph(K) | Spiramycin, Telithromycin | 99.13 | 100.00 | NC_000964 |
| HAEIICFG_11 | 437752 | 438604 | aadK | Streptomycin | 98.59 | 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. |
|---|---|---|---|---|---|---|---|---|
| HAEIICFG_22 | 1025826 | 1027199 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 99.13 | 100.00 | WP_063856081.1 |
| HAEIICFG_25 | 29062 | 30702 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.54 | 100.00 | WP_003234144.1 |
| HAEIICFG_25 | 378451 | 379368 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| HAEIICFG_11 | 437752 | 438603 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| HAEIICFG_22 | 1023328 | 1023846 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.64 | 100.00 | WP_003242546.1 |
| HAEIICFG_11 | 1053949 | 1056546 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HAEIICFG_11 | 826106 | 826747 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| HAEIICFG_22 | 109186 | 110124 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| HAEIICFG_22 | 536307 | 537488 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| HAEIICFG_22 | 102030 | 109166 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391076 |
| HAEIICFG_22 | 111800 | 112996 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.42 | 100.00 | NP_391079 |
| HAEIICFG_22 | 534682 | 535824 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| HAEIICFG_11 | 1106637 | 1108400 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| HAEIICFG_22 | 535843 | 536292 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| HAEIICFG_22 | 113022 | 113807 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.11 | 100.00 | NP_391080 |
| HAEIICFG_22 | 110152 | 111771 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 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 |
|---|---|---|---|---|---|---|---|---|
| HAEIICFG_27 | 28137 | 27001 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| HAEIICFG_29 | 11278 | 10409 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| HAEIICFG_11 | 1466130 | 1465354 | CodY | 1.79e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| HAEIICFG_22 | 377770 | 378339 | ClpP | 6.44e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| HAEIICFG_11 | 1931747 | 1931355 | spxA1 | 1.41e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| HAEIICFG_11 | 1931747 | 1931355 | spx | 8.41e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| HAEIICFG_28 | 34705 | 34463 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| HAEIICFG_25 | 105024 | 104827 | CspA | 2.02e-31 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HAEIICFG_11 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_22 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_25 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_26 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_27 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_28 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_29 | 0.0 | 1.0 | 0.0 |
| HAEIICFG_30 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HAEIICFG_11 | 855645 | 874953 | False | Unknown | VOG8440, VOG5070, VOG9712, VOG5042, VOG3389, VOG4910, VOG9312, VOG9667 |
| HAEIICFG_11 | 1239498 | 1262708 | False | Siphoviridae | VOG0136, VOG5221, VOG4705, VOG3390, VOG4612, VOG4705, VOG3390, VOG4626, VOG4619, VOG0801, VOG6163, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG5361, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841 |
| HAEIICFG_11 | 1272496 | 1274114 | False | Unknown | VOG4552, VOG6495 |
| HAEIICFG_11 | 1805956 | 1833552 | 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)