Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 5 | 2 | 6 | 8.06 |
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. |
|---|---|---|---|---|---|---|---|---|
| PIBGAFCF_30 | 47727 | 48773 | clbA | ARO:3002814 | clbA | 92.77 | 99.71 | CP006845.1 |
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. |
|---|---|---|---|---|---|---|---|
| PIBGAFCF_30 | 47730 | 48773 | cfr(B) | Chloramphenicol, Florfenicol, Clindamycin, Lincomycin, Linezolid, Dalfopristin, Pristinamycin IIA, Virginiamycin M, Tiamulin | 88.90 | 99.33 | KR610408 |
| PIBGAFCF_21 | 8192 | 9568 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 87.07 | 100.00 | X08034 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| PIBGAFCF_30 | 47730 | 48773 | clbA | 23S rRNA (adenine(2503)-C(8))-methyltransferase ClbA | BLASTX | 92.24 | 99.71 | WP_012116915.1 |
| PIBGAFCF_21 | 8198 | 9568 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 86.43 | 99.78 | WP_003242953.1 |
| PIBGAFCF_30 | 50524 | 51042 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 82.66 | 100.00 | WP_003242546.1 |
| PIBGAFCF_11 | 2619 | 5216 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.06 | 100.00 | WP_087347987.1 |
| PIBGAFCF_21 | 9869 | 10297 | satA | streptothricin N-acetyltransferase SatA | PARTIALX | 80.42 | 82.66 | WP_003242546.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| PIBGAFCF_4 | 137009 | 138190 | capB | 0.0 | Capsule | Immune modulation | 81.87 | 99.66 | NP_391471 |
| PIBGAFCF_4 | 136545 | 136994 | capC | 1.10e-114 | Capsule | Immune modulation | 83.59 | 99.78 | NP_391470 |
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 |
|---|---|---|---|---|---|---|---|---|
| PIBGAFCF_15 | 31665 | 32801 | tufA | 0.0 | elongation factor Tu | 86.54 | 95.69 | AHM69299 |
| PIBGAFCF_37 | 12392 | 11523 | pdxS | 6.36e-153 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 84.83 | 98.31 | ACE61268 |
| PIBGAFCF_2 | 55153 | 54377 | CodY | 6.41e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| PIBGAFCF_2 | 515613 | 515221 | spxA1 | 1.01e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| PIBGAFCF_30 | 65274 | 65077 | CspA | 1.06e-32 | cold shock protein | 92.42 | 100.00 | CAA62903 |
| PIBGAFCF_14 | 335222 | 335028 | CspD | 1.12e-27 | cold shock protein | 80.00 | 98.48 | CAC99957 |
| PIBGAFCF_14 | 335222 | 335025 | CspB | 2.32e-27 | cold shock protein | 80.30 | 100.00 | CAD00094 |
| PIBGAFCF_30 | 65274 | 65080 | CspR | 5.25e-27 | cold shock protein | 80.00 | 98.48 | AAO82613 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| PIBGAFCF_13 | 4928 | 5092 | Col(SD853) | 165 / 194 | 86.06 | NC015392 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| PIBGAFCF_1 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_2 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_3 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_4 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_5 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_6 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_7 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_8 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_9 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_10 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_11 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_12 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_13 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_14 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_15 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_17 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_18 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_19 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_20 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_21 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_22 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_23 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_24 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_25 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_26 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_27 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_28 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_29 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_30 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_31 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_32 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_33 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_35 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_36 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_37 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_38 | 0.0 | 1.0 | 0.0 |
| PIBGAFCF_39 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_40 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_41 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_43 | 1.0 | 0.0 | 1.0 |
| PIBGAFCF_46 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| PIBGAFCF_1 | 114745 | 140175 | False | Siphoviridae | VOG10230, VOG0641, VOG7896, VOG3390, VOG4612, VOG4660, VOG4772, VOG0801, VOG5910, VOG0541, VOG4586, VOG0704, VOG0539, VOG1266, VOG0204, VOG10223, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG9029, VOG0275, VOG0198, VOG6242, VOG1137 |
| PIBGAFCF_2 | 378843 | 405644 | False | Myoviridae | VOG0753, VOG4705, VOG3390, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189 |
| PIBGAFCF_18 | 966 | 28615 | False | Siphoviridae | VOG4609, VOG0327, VOG4548, VOG0198, VOG4581, VOG4544, VOG5051, VOG4556, VOG4568, VOG4553, VOG5361, VOG0204, VOG4589, VOG0539, VOG0704, VOG4586, VOG0541, VOG6163, VOG0801, VOG4619, VOG4660, VOG4612, VOG3390, VOG7896, VOG0641, VOG4707 |
| PIBGAFCF_23 | 62930 | 86372 | False | Siphoviridae | VOG7718, VOG3390, VOG4705, VOG5008, VOG8610, VOG7930, VOG0275, VOG5250, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712, VOG4660 |
| PIBGAFCF_24 | 3147 | 10938 | False | Unknown | VOG9093, VOG1309, VOG4600, VOG4552, VOG0650, VOG11075, VOG9667, VOG8483 |
| PIBGAFCF_25 | 5926 | 31755 | False | Siphoviridae | VOG5447, VOG4972, VOG4681, VOG0796, VOG10227, VOG0720, VOG4564, VOG6778, VOG4555, VOG1329, VOG2621, VOG5872, VOG4623, VOG0816, VOG5660, VOG0724, VOG0799, VOG0725, VOG4545, VOG4605, VOG4599, VOG1125, VOG3390, VOG5535, VOG0753, VOG0136, VOG4574 |
Phigaro v2.4.0 (Database: Jan. 2024 release)