Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 11 | 10 | 9 | 17.38 |
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. |
|---|---|---|---|---|---|---|---|---|
| GAMLCGEA_39 | 50078 | 51517 | lmrB | ARO:3002813 | lmrB | 98.74 | 100.42 | JYFL01000006.1 |
| GAMLCGEA_13 | 41905 | 42243 | ykkC | ARO:3003063 | ykkC | 98.21 | 100.00 | AL009126.1 |
| GAMLCGEA_13 | 41588 | 41905 | ykkD | ARO:3003064 | ykkD | 98.10 | 100.00 | AL009126.1 |
| GAMLCGEA_39 | 37274 | 38194 | mphK | ARO:3004541 | mphK | 98.68 | 100.00 | CP010314.1 |
| GAMLCGEA_79 | 35004 | 36650 | vmlR | ARO:3004476 | vmlR | 98.36 | 100.18 | NC_000964.3 |
| GAMLCGEA_40 | 15302 | 16156 | aadK | ARO:3002627 | aadK | 98.24 | 100.00 | AL009126.1 |
| GAMLCGEA_94 | 7045 | 8247 | blt | ARO:3003006 | blt | 99.25 | 100.00 | L32599.1 |
| GAMLCGEA_72 | 1011 | 1604 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| GAMLCGEA_7 | 205 | 2775 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.77 | 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. |
|---|---|---|---|---|---|---|---|
| GAMLCGEA_40 | 15302 | 16156 | aadK | Streptomycin | 98.71 | 100.00 | M26879 |
| GAMLCGEA_39 | 37274 | 38194 | 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. |
|---|---|---|---|---|---|---|---|---|
| GAMLCGEA_39 | 37274 | 38182 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.68 | 99.02 | WP_003246254.1 |
| GAMLCGEA_79 | 35007 | 36650 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.36 | 100.00 | WP_003234144.1 |
| GAMLCGEA_40 | 15305 | 16156 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.24 | 100.00 | WP_003229862.1 |
| GAMLCGEA_63 | 51093 | 51611 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.75 | 100.00 | WP_003242546.1 |
| GAMLCGEA_15 | 73151 | 75748 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.48 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| GAMLCGEA_6 | 35057 | 36238 | capB | 0.0 | Capsule | Immune modulation | 99.66 | 100.00 | NP_391471 |
| GAMLCGEA_21 | 2654 | 3439 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| GAMLCGEA_6 | 33432 | 34574 | capA | 0.0 | Capsule | Immune modulation | 99.30 | 100.00 | NP_391469 |
| GAMLCGEA_15 | 20210 | 21973 | dep/capD | 0.0 | Capsule | Immune modulation | 98.98 | 100.00 | NP_389723 |
| GAMLCGEA_21 | 6326 | 7264 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.94 | 100.00 | NP_391077 |
| GAMLCGEA_35 | 91481 | 92122 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 98.91 | 100.00 | NP_390062 |
| GAMLCGEA_6 | 34593 | 35042 | capC | 0.0 | Capsule | Immune modulation | 98.89 | 100.00 | NP_391470 |
| GAMLCGEA_21 | 3465 | 4661 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.75 | 100.00 | NP_391079 |
| GAMLCGEA_21 | 7284 | 14420 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 98.57 | 100.00 | NP_391076 |
| GAMLCGEA_21 | 4679 | 6298 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 97.28 | 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 |
|---|---|---|---|---|---|---|---|---|
| GAMLCGEA_47 | 27991 | 26855 | tufA | 0.0 | elongation factor Tu | 85.75 | 95.69 | AHM69299 |
| GAMLCGEA_69 | 11645 | 10776 | pdxS | 1.14e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| GAMLCGEA_8 | 150249 | 151025 | CodY | 2.29e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| GAMLCGEA_18 | 121533 | 122102 | ClpP | 9.44e-100 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| GAMLCGEA_20 | 28885 | 28493 | spxA1 | 3.33e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| GAMLCGEA_20 | 28885 | 28493 | spx | 1.99e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| GAMLCGEA_73 | 11291 | 11533 | SpoVG | 6.26e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| GAMLCGEA_98 | 2091 | 1894 | CspA | 3.12e-33 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| GAMLCGEA_35 | 103351 | 103545 | CspD | 1.16e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| GAMLCGEA_64 | 11947 | 12141 | CspB | 3.40e-28 | cold shock protein | 83.08 | 98.48 | 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. |
|---|---|---|---|---|---|---|
| GAMLCGEA_103 | 1512 | 2006 | rep21 | 495 / 717 | 90.51 | FR821780 |
| GAMLCGEA_103 | 3638 | 3802 | 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 |
|---|---|---|---|
| GAMLCGEA_1 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_2 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_3 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_4 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_5 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_6 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_7 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_8 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_9 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_10 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_11 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_12 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_13 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_14 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_15 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_16 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_17 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_18 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_19 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_20 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_21 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_22 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_23 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_24 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_25 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_26 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_27 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_28 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_29 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_30 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_32 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_33 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_34 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_35 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_36 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_37 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_38 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_39 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_40 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_41 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_42 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_43 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_44 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_45 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_46 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_47 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_48 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_49 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_50 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_51 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_52 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_53 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_54 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_55 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_56 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_57 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_58 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_59 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_60 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_62 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_63 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_64 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_65 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_67 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_68 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_69 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_70 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_71 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_72 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_73 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_74 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_75 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_76 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_77 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_78 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_79 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_80 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_81 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_82 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_84 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_85 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_86 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_88 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_90 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_91 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_92 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_93 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_94 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_95 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_96 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_97 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_98 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_99 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_100 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_101 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_102 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_103 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_104 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_105 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_107 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_108 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_109 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_110 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_112 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_114 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_115 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_116 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_117 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_118 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_119 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_121 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_122 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_123 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_124 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_126 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_127 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_130 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_131 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_133 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_134 | 0.0 | 1.0 | 0.0 |
| GAMLCGEA_135 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_136 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_137 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_141 | 1.0 | 0.0 | 1.0 |
| GAMLCGEA_145 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| GAMLCGEA_8 | 265759 | 273475 | False | Siphoviridae | VOG4552, VOG0650, VOG0535, VOG1936, VOG1227, VOG4606 |
| GAMLCGEA_13 | 71707 | 99151 | False | Myoviridae | VOG0753, VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
| GAMLCGEA_18 | 1913 | 19171 | False | Siphoviridae | VOG0801, VOG0083, VOG5910, VOG0541, VOG4586, VOG0704, VOG9583, VOG0204, VOG5361, VOG4553, VOG4568, VOG4556, VOG3607, VOG1886, VOG4581, VOG0713, VOG4841, VOG0275 |
| GAMLCGEA_18 | 25991 | 33725 | True | Siphoviridae | VOG7581, VOG9667, VOG9667, VOG1563, VOG0275, VOG0275 |
| GAMLCGEA_22 | 41555 | 51592 | False | Unknown | VOG7438, VOG1047, VOG0021, VOG1565, VOG0026, VOG4609, VOG0327, VOG4548 |
Phigaro v2.4.0 (Database: Jan. 2024 release)