Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 11 | 7 | 17.72 |
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. |
|---|---|---|---|---|---|---|---|---|
| PJPJCEAH_80 | 1632737 | 1633075 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| PJPJCEAH_80 | 1632420 | 1632737 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| PJPJCEAH_80 | 637080 | 638249 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| PJPJCEAH_80 | 465136 | 466338 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| PJPJCEAH_80 | 446306 | 447160 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| PJPJCEAH_102 | 415605 | 417248 | vmlR | ARO:3004476 | vmlR | 98.35 | 100.00 | NC_000964.3 |
| PJPJCEAH_102 | 111017 | 112450 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| PJPJCEAH_102 | 98201 | 99121 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| PJPJCEAH_113 | 27419 | 29989 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 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. |
|---|---|---|---|---|---|---|---|
| PJPJCEAH_91 | 34746 | 36122 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 100.00 | 100.00 | X08034 |
| PJPJCEAH_80 | 446306 | 447158 | aadK | Streptomycin | 98.48 | 99.77 | M26879 |
| PJPJCEAH_102 | 98201 | 99121 | mph(K) | Spiramycin, Telithromycin | 97.50 | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| PJPJCEAH_91 | 34746 | 36119 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| PJPJCEAH_102 | 415608 | 417248 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.35 | 100.00 | WP_003234144.1 |
| PJPJCEAH_102 | 98201 | 99118 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| PJPJCEAH_80 | 446306 | 447157 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| PJPJCEAH_91 | 38121 | 38639 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 89.60 | 100.00 | WP_003242546.1 |
| PJPJCEAH_80 | 939369 | 941966 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| PJPJCEAH_80 | 836771 | 837412 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| PJPJCEAH_91 | 528305 | 529486 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| PJPJCEAH_91 | 529969 | 531111 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| PJPJCEAH_91 | 943216 | 944001 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| PJPJCEAH_91 | 946899 | 947837 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391077 |
| PJPJCEAH_91 | 529501 | 529950 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| PJPJCEAH_91 | 944027 | 945223 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| PJPJCEAH_80 | 986787 | 988550 | dep/capD | 0.0 | Capsule | Immune modulation | 99.09 | 100.00 | NP_389723 |
| PJPJCEAH_91 | 947857 | 954993 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.09 | 100.00 | NP_391076 |
| PJPJCEAH_91 | 945252 | 946871 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.52 | 100.00 | NP_391078 |
| PJPJCEAH_153 | 1 | 451 | gspG | 0.0 | Gsp | Effector delivery system | 92.26 | 99.34 | WP_004196811 |
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 |
|---|---|---|---|---|---|---|---|---|
| PJPJCEAH_135 | 28139 | 27003 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| PJPJCEAH_168 | 11296 | 10427 | pdxS | 1.12e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| PJPJCEAH_80 | 1322836 | 1322060 | CodY | 1.67e-124 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PJPJCEAH_91 | 690844 | 690275 | ClpP | 6.36e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| PJPJCEAH_80 | 1785217 | 1784825 | spxA1 | 1.31e-69 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| PJPJCEAH_80 | 1785217 | 1784825 | spx | 7.84e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| PJPJCEAH_146 | 34758 | 34516 | SpoVG | 7.52e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| PJPJCEAH_102 | 364863 | 365060 | CspA | 1.93e-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 |
|---|---|---|---|
| PJPJCEAH_80 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_91 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_102 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_113 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_124 | 1.0 | 0.0 | 1.0 |
| PJPJCEAH_135 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_146 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_157 | 0.0 | 1.0 | 0.0 |
| PJPJCEAH_168 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PJPJCEAH_80 | 1662885 | 1690386 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| PJPJCEAH_124 | 35785 | 58883 | False | Siphoviridae | VOG0221, VOG4581, VOG5819, VOG1886, VOG4556, VOG4568, VOG4553, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5852, VOG6163, VOG4605, VOG4599, VOG9244, VOG10944, VOG1024 |
| PJPJCEAH_157 | 19668 | 38292 | False | Myoviridae | VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
Phigaro v2.4.0 (Database: Jan. 2024 release)