Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 10 | 8 | 17.55 |
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. |
|---|---|---|---|---|---|---|---|---|
| NEEBJIAM_33 | 449946 | 451148 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| NEEBJIAM_33 | 433154 | 434008 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| NEEBJIAM_1 | 428592 | 428909 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| NEEBJIAM_1 | 428254 | 428592 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NEEBJIAM_32 | 355589 | 356758 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NEEBJIAM_2 | 260481 | 263051 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.42 | 100.00 | AL009126.3 |
| NEEBJIAM_23 | 154781 | 155374 | tmrB | ARO:3003059 | tmrB | 97.97 | 100.00 | AL009126.3 |
| NEEBJIAM_23 | 104233 | 105672 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| NEEBJIAM_23 | 91420 | 92340 | mphK | ARO:3004541 | mphK | 97.06 | 100.00 | CP010314.1 |
| NEEBJIAM_30 | 29222 | 30868 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
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. |
|---|---|---|---|---|---|---|---|
| NEEBJIAM_33 | 433154 | 434008 | aadK | Streptomycin | 98.48 | 100.00 | M26879 |
| NEEBJIAM_23 | 91420 | 92340 | mph(K) | Spiramycin, Telithromycin | 97.18 | 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. |
|---|---|---|---|---|---|---|---|---|
| NEEBJIAM_30 | 29222 | 30865 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| NEEBJIAM_33 | 433154 | 434005 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NEEBJIAM_23 | 91420 | 92337 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.06 | 100.00 | WP_003246254.1 |
| NEEBJIAM_12 | 37762 | 38280 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 93.06 | 100.00 | WP_003242546.1 |
| NEEBJIAM_32 | 60455 | 63052 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NEEBJIAM_12 | 531395 | 532576 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NEEBJIAM_12 | 956486 | 957424 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.68 | 100.00 | NP_391077 |
| NEEBJIAM_32 | 158292 | 158933 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NEEBJIAM_12 | 952803 | 953588 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NEEBJIAM_12 | 957444 | 964580 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.41 | 100.00 | NP_391076 |
| NEEBJIAM_12 | 532591 | 533040 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NEEBJIAM_32 | 9724 | 11487 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
| NEEBJIAM_12 | 953614 | 954810 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.91 | 100.00 | NP_391079 |
| NEEBJIAM_12 | 533059 | 534201 | capA | 0.0 | Capsule | Immune modulation | 98.78 | 100.00 | NP_391469 |
| NEEBJIAM_12 | 954839 | 956458 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.53 | 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 |
|---|---|---|---|---|---|---|---|---|
| NEEBJIAM_31 | 31734 | 32870 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NEEBJIAM_6 | 4488 | 5357 | pdxS | 1.13e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NEEBJIAM_1 | 740228 | 741004 | CodY | 7.92e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NEEBJIAM_12 | 693675 | 693106 | ClpP | 6.41e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NEEBJIAM_1 | 277507 | 277899 | spxA1 | 6.23e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NEEBJIAM_1 | 277507 | 277899 | spx | 3.71e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NEEBJIAM_3 | 34728 | 34486 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NEEBJIAM_30 | 77299 | 77102 | CspA | 9.46e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NEEBJIAM_32 | 170166 | 170360 | CspD | 1.32e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| NEEBJIAM_32 | 170166 | 170363 | CspB | 2.74e-27 | cold shock protein | 80.30 | 100.00 | 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 |
|---|---|---|---|
| NEEBJIAM_1 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_2 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_3 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_5 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_6 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_8 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_11 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_12 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_23 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_30 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_31 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_32 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_33 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_34 | 0.0 | 1.0 | 0.0 |
| NEEBJIAM_35 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NEEBJIAM_1 | 372405 | 398422 | 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 |
| NEEBJIAM_1 | 945639 | 968587 | False | Siphoviridae | VOG4841, VOG4581, VOG4544, VOG0202, VOG4556, VOG4573, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG5910, VOG6163, VOG0801, VOG4619, VOG4626, VOG3390, VOG4705, VOG4612, VOG3390, VOG4705, VOG0641, VOG4707 |
Phigaro v2.4.0 (Database: Jan. 2024 release)