Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 12 | 9 | 9 | 17.49 |
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. |
|---|---|---|---|---|---|---|---|---|
| NNMJCPGC_77 | 149561 | 150763 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| NNMJCPGC_77 | 131176 | 132030 | aadK | ARO:3002627 | aadK | 97.89 | 100.00 | AL009126.1 |
| NNMJCPGC_2 | 100706 | 101875 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| NNMJCPGC_7 | 64011 | 65639 | vmlR | ARO:3004476 | vmlR | 98.34 | 99.09 | NC_000964.3 |
| NNMJCPGC_20 | 52518 | 53957 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| NNMJCPGC_26 | 42267 | 42584 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| NNMJCPGC_26 | 41929 | 42267 | ykkC | ARO:3003063 | ykkC | 97.32 | 100.00 | AL009126.1 |
| NNMJCPGC_20 | 39705 | 40625 | mphK | ARO:3004541 | mphK | 98.37 | 100.00 | CP010314.1 |
| NNMJCPGC_16 | 9403 | 11973 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.65 | 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. |
|---|---|---|---|---|---|---|---|
| NNMJCPGC_4 | 77262 | 78638 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 99.27 | 100.00 | X08034 |
| NNMJCPGC_77 | 131176 | 132028 | aadK | Streptomycin | 98.59 | 99.77 | M26879 |
| NNMJCPGC_20 | 39705 | 40625 | mph(K) | Spiramycin, Telithromycin | 97.72 | 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. |
|---|---|---|---|---|---|---|---|---|
| NNMJCPGC_4 | 77265 | 78638 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_003242953.1 |
| NNMJCPGC_20 | 39705 | 40622 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.37 | 100.00 | WP_003246254.1 |
| NNMJCPGC_7 | 64014 | 65639 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.34 | 98.90 | WP_003234144.1 |
| NNMJCPGC_77 | 131176 | 132027 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.89 | 100.00 | WP_003229862.1 |
| NNMJCPGC_4 | 74763 | 75281 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| NNMJCPGC_3 | 106871 | 109468 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.71 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| NNMJCPGC_34 | 1660 | 2802 | capA | 0.0 | Capsule | Immune modulation | 99.65 | 100.00 | NP_391469 |
| NNMJCPGC_33 | 162552 | 163193 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| NNMJCPGC_55 | 103512 | 104297 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.49 | 100.00 | NP_391080 |
| NNMJCPGC_34 | 2821 | 3270 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| NNMJCPGC_3 | 57798 | 59561 | dep/capD | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_389723 |
| NNMJCPGC_55 | 100642 | 102261 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.64 | 100.00 | NP_391078 |
| NNMJCPGC_55 | 92529 | 99656 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.22 | 99.99 | NP_391076 |
| NNMJCPGC_55 | 99676 | 100614 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.08 | 100.00 | NP_391077 |
| NNMJCPGC_55 | 102290 | 103486 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.00 | 100.00 | NP_391079 |
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 |
|---|---|---|---|---|---|---|---|---|
| NNMJCPGC_19 | 28041 | 26905 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| NNMJCPGC_38 | 11246 | 10377 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| NNMJCPGC_11 | 218584 | 219360 | CodY | 2.72e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| NNMJCPGC_88 | 125112 | 125681 | ClpP | 9.30e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| NNMJCPGC_14 | 38996 | 38604 | spxA1 | 5.03e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| NNMJCPGC_14 | 38996 | 38604 | spx | 3.00e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| NNMJCPGC_23 | 34655 | 34413 | SpoVG | 7.50e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| NNMJCPGC_7 | 6739 | 6936 | CspA | 4.08e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| NNMJCPGC_25 | 24245 | 24051 | CspB | 4.48e-28 | cold shock protein | 83.08 | 98.48 | CAD00094 |
| NNMJCPGC_33 | 151319 | 151125 | CspD | 4.94e-28 | cold shock protein | 80.00 | 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 |
|---|---|---|---|
| NNMJCPGC_1 | 1.0 | 0.0 | 1.0 |
| NNMJCPGC_2 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_3 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_4 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_5 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_6 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_7 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_8 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_9 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_10 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_11 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_12 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_13 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_14 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_15 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_16 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_17 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_18 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_19 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_20 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_21 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_22 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_23 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_24 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_25 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_26 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_27 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_28 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_29 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_30 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_31 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_32 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_33 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_34 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_35 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_36 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_37 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_38 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_39 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_40 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_41 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_42 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_43 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_44 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_45 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_46 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_47 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_49 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_52 | 1.0 | 0.0 | 1.0 |
| NNMJCPGC_53 | 1.0 | 0.0 | 1.0 |
| NNMJCPGC_54 | 1.0 | 0.0 | 1.0 |
| NNMJCPGC_55 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_66 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_77 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_88 | 0.0 | 1.0 | 0.0 |
| NNMJCPGC_99 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| NNMJCPGC_24 | 38102 | 48023 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685 |
| NNMJCPGC_26 | 4661 | 11206 | False | Myoviridae | VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| NNMJCPGC_88 | 347 | 19511 | False | Siphoviridae | VOG3390, VOG4626, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841 |
| NNMJCPGC_88 | 28935 | 32563 | False | Siphoviridae | VOG6495, VOG9667, VOG1563 |
Phigaro v2.4.0 (Database: Jan. 2024 release)