Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 7 | 17.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| ECHAFICC_2 | 679754 | 680923 | bmr | ARO:3003007 | bmr | 99.74 | 100.00 | M33768.1 |
| ECHAFICC_4 | 591887 | 592225 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| ECHAFICC_4 | 591570 | 591887 | ykkD | ARO:3003064 | ykkD | 100.00 | 100.00 | AL009126.1 |
| ECHAFICC_2 | 457403 | 458605 | blt | ARO:3003006 | blt | 100.00 | 100.00 | L32599.1 |
| ECHAFICC_2 | 439042 | 439896 | aadK | ARO:3002627 | aadK | 100.00 | 100.00 | AL009126.1 |
| ECHAFICC_1 | 428525 | 430168 | vmlR | ARO:3004476 | vmlR | 100.00 | 100.00 | NC_000964.3 |
| ECHAFICC_3 | 276696 | 279266 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 100.00 | 100.00 | AL009126.3 |
| ECHAFICC_1 | 162945 | 163538 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| ECHAFICC_1 | 112442 | 113881 | lmrB | ARO:3002813 | lmrB | 99.79 | 100.42 | JYFL01000006.1 |
| ECHAFICC_1 | 99627 | 100547 | mphK | ARO:3004541 | mphK | 100.00 | 100.00 | CP010314.1 |
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. |
|---|---|---|---|---|---|---|---|
| ECHAFICC_2 | 439042 | 439896 | aadK | Streptomycin | 100.00 | 100.00 | M26879 |
| ECHAFICC_1 | 99627 | 100547 | mph(K) | Spiramycin, Telithromycin | 100.00 | 100.00 | NC_000964 |
| ECHAFICC_6 | 1009219 | 1010595 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| ECHAFICC_2 | 439042 | 439893 | aadK | aminoglycoside 6-adenylyltransferase AadK | EXACTX | 100.00 | 100.00 | WP_003229862.1 |
| ECHAFICC_1 | 99627 | 100544 | mphK | macrolide 2'-phosphotransferase MphK | EXACTX | 100.00 | 100.00 | WP_003246254.1 |
| ECHAFICC_6 | 1006701 | 1007219 | satA | streptothricin N-acetyltransferase SatA | EXACTX | 100.00 | 100.00 | WP_003242546.1 |
| ECHAFICC_6 | 1009222 | 1010595 | tet(L) | tetracycline efflux MFS transporter Tet(L) | EXACTX | 100.00 | 100.00 | WP_003242953.1 |
| ECHAFICC_1 | 428528 | 430168 | vmlR | ABC-F type ribosomal protection protein VmlR | EXACTX | 100.00 | 100.00 | WP_003234144.1 |
| ECHAFICC_2 | 987249 | 989843 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.15 | 99.88 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| ECHAFICC_2 | 1034738 | 1036501 | dep/capD | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | NP_389723 |
| ECHAFICC_6 | 113048 | 113833 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| ECHAFICC_6 | 109212 | 110150 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391077 |
| ECHAFICC_6 | 111826 | 113022 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391079 |
| ECHAFICC_6 | 110178 | 111797 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391078 |
| ECHAFICC_6 | 102056 | 109192 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391076 |
| ECHAFICC_2 | 879637 | 880278 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 100.00 | 100.00 | NP_390062 |
| ECHAFICC_6 | 519358 | 520500 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| ECHAFICC_6 | 520519 | 520968 | capC | 0.0 | Capsule | Immune modulation | 98.22 | 100.00 | NP_391470 |
| ECHAFICC_6 | 520983 | 522164 | capB | 0.0 | Capsule | Immune modulation | 96.78 | 100.00 | NP_391471 |
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 |
|---|---|---|---|---|---|---|---|---|
| ECHAFICC_5 | 28139 | 27003 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| ECHAFICC_8 | 4270 | 5139 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| ECHAFICC_4 | 278624 | 277848 | CodY | 8.25e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| ECHAFICC_6 | 367771 | 368340 | ClpP | 6.29e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| ECHAFICC_4 | 741048 | 740656 | spxA1 | 2.45e-69 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| ECHAFICC_9 | 20895 | 21137 | SpoVG | 2.74e-38 | RNA-binding protein | 80.25 | 79.41 | AAT02994 |
| ECHAFICC_1 | 383053 | 383250 | CspA | 1.98e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
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 |
|---|---|---|---|
| ECHAFICC_1 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_2 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_3 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_4 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_5 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_6 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_8 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_9 | 0.0 | 1.0 | 0.0 |
| ECHAFICC_11 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| ECHAFICC_2 | 478156 | 508533 | False | Myoviridae | VOG4600, VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718 |
| ECHAFICC_4 | 622064 | 648172 | False | Myoviridae | VOG4705, VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG0749, VOG4685, VOG4773, VOG10227, VOG0796, VOG5447, VOG4861, VOG0189, VOG3490, VOG9667 |
Phigaro v2.4.0 (Database: Jan. 2024 release)