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. |
|---|---|---|---|---|---|---|---|---|
| NNCNLKPB_21 | 555111 | 556280 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NNCNLKPB_19 | 425205 | 425522 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NNCNLKPB_19 | 424867 | 425205 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| NNCNLKPB_18 | 400863 | 402509 | vmlR | ARO:3004476 | vmlR | 98.72 | 100.18 | NC_000964.3 |
| NNCNLKPB_12 | 307611 | 310181 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 100.00 | AL009126.3 |
| NNCNLKPB_18 | 148665 | 149258 | tmrB | ARO:3003059 | tmrB | 96.45 | 100.00 | AL009126.3 |
| NNCNLKPB_18 | 98108 | 99547 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.42 | JYFL01000006.1 |
| NNCNLKPB_18 | 85315 | 86235 | mphK | ARO:3004541 | mphK | 97.71 | 100.00 | CP010314.1 |
| NNCNLKPB_20 | 42805 | 43659 | aadK | ARO:3002627 | aadK | 98.59 | 100.00 | AL009126.1 |
| NNCNLKPB_20 | 25681 | 26883 | blt | ARO:3003006 | blt | 99.50 | 100.00 | L32599.1 |
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. |
|---|---|---|---|---|---|---|---|
| NNCNLKPB_20 | 42805 | 43659 | aadK | Streptomycin | 98.83 | 100.00 | M26879 |
| NNCNLKPB_18 | 85315 | 86235 | mph(K) | Spiramycin, Telithromycin | 98.05 | 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. |
|---|---|---|---|---|---|---|---|---|
| NNCNLKPB_18 | 400866 | 402509 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.72 | 100.00 | WP_003234144.1 |
| NNCNLKPB_20 | 42808 | 43659 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.59 | 100.00 | WP_003229862.1 |
| NNCNLKPB_18 | 85315 | 86232 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 97.71 | 100.00 | WP_003246254.1 |
| NNCNLKPB_25 | 384999 | 385517 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NNCNLKPB_21 | 230199 | 232796 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.60 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NNCNLKPB_21 | 357606 | 358247 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.84 | 100.00 | NP_390062 |
| NNCNLKPB_1 | 540618 | 541799 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| NNCNLKPB_1 | 105920 | 106705 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.75 | 100.00 | NP_391080 |
| NNCNLKPB_21 | 184534 | 186297 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| NNCNLKPB_1 | 102084 | 103022 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.15 | 100.00 | NP_391077 |
| NNCNLKPB_1 | 540154 | 540603 | capC | 0.0 | Capsule | Immune modulation | 99.11 | 100.00 | NP_391470 |
| NNCNLKPB_1 | 538993 | 540135 | capA | 0.0 | Capsule | Immune modulation | 98.86 | 100.00 | NP_391469 |
| NNCNLKPB_1 | 104698 | 105894 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.66 | 100.00 | NP_391079 |
| NNCNLKPB_1 | 94928 | 102064 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.40 | 100.00 | NP_391076 |
| NNCNLKPB_1 | 103050 | 104669 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 96.67 | 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 |
|---|---|---|---|---|---|---|---|---|
| NNCNLKPB_9 | 32392 | 33528 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| NNCNLKPB_4 | 11872 | 11003 | pdxS | 1.21e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NNCNLKPB_2 | 180024 | 179248 | CodY | 1.61e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NNCNLKPB_1 | 380986 | 381555 | ClpP | 4.04e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NNCNLKPB_19 | 277845 | 278237 | spxA1 | 4.56e-70 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NNCNLKPB_19 | 277845 | 278237 | spx | 2.72e-68 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NNCNLKPB_24 | 21202 | 21444 | SpoVG | 7.64e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NNCNLKPB_18 | 354467 | 354664 | CspA | 1.87e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NNCNLKPB_21 | 369477 | 369671 | CspD | 1.85e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| NNCNLKPB_21 | 369477 | 369674 | CspB | 3.84e-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. |
|---|---|---|---|---|---|---|
| NNCNLKPB_14 | 2501 | 2664 | Col(SD853) | 164 / 194 | 87.20 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NNCNLKPB_1 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_2 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_3 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_4 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_9 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_12 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_14 | 1.0 | 0.0 | 1.0 |
| NNCNLKPB_17 | 1.0 | 0.0 | 1.0 |
| NNCNLKPB_18 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_19 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_20 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_21 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_22 | 1.0 | 0.0 | 1.0 |
| NNCNLKPB_24 | 0.0 | 1.0 | 0.0 |
| NNCNLKPB_25 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NNCNLKPB_12 | 12577 | 20985 | False | Siphoviridae | VOG0275, VOG4602, VOG4662, VOG9667, VOG9667, VOG0650, VOG4552, VOG4600, VOG1309 |
| NNCNLKPB_12 | 23826 | 45622 | False | Siphoviridae | VOG0198, VOG7983, VOG0796, VOG10227, VOG0691, VOG0692, VOG9317, VOG4572, VOG2621, VOG0695, VOG0696, VOG0697, VOG0698, VOG10044, VOG0701, VOG9745, VOG4605, VOG4599, VOG5535, VOG10940 |
| NNCNLKPB_19 | 370293 | 395594 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705, VOG0753 |
Phigaro v2.4.0 (Database: Jan. 2024 release)