Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 8 | 18.25 |
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. |
|---|---|---|---|---|---|---|---|---|
| CMNDCLCM_1 | 228710 | 229879 | bmr | ARO:3003007 | bmr | 99.49 | 100.00 | M33768.1 |
| CMNDCLCM_10 | 125403 | 125720 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CMNDCLCM_10 | 125065 | 125403 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
| CMNDCLCM_31 | 110632 | 111225 | tmrB | ARO:3003059 | tmrB | 100.00 | 100.00 | AL009126.3 |
| CMNDCLCM_28 | 79666 | 82236 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.88 | 100.00 | AL009126.3 |
| CMNDCLCM_2 | 76648 | 78276 | vmlR | ARO:3004476 | vmlR | 99.08 | 99.09 | NC_000964.3 |
| CMNDCLCM_31 | 60107 | 61546 | lmrB | ARO:3002813 | lmrB | 99.16 | 100.42 | JYFL01000006.1 |
| CMNDCLCM_31 | 47292 | 48158 | mphK | ARO:3004541 | mphK | 98.61 | 94.12 | CP010314.1 |
| CMNDCLCM_54 | 10028 | 10882 | aadK | ARO:3002627 | aadK | 98.94 | 100.00 | AL009126.1 |
| CMNDCLCM_1 | 6937 | 8139 | blt | ARO:3003006 | blt | 99.25 | 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. |
|---|---|---|---|---|---|---|---|
| CMNDCLCM_54 | 10028 | 10880 | aadK | Streptomycin | 98.94 | 99.77 | M26879 |
| CMNDCLCM_11 | 155821 | 157197 | tet(L) | Doxycycline, Tetracycline, Minocycline, Tigecycline, Doxycycline, Tetracycline | 98.91 | 100.00 | D12567 |
| CMNDCLCM_31 | 47292 | 48212 | 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. |
|---|---|---|---|---|---|---|---|---|
| CMNDCLCM_2 | 76651 | 78276 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 99.08 | 98.90 | WP_003234144.1 |
| CMNDCLCM_54 | 10028 | 10879 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 98.94 | 100.00 | WP_003229862.1 |
| CMNDCLCM_11 | 155824 | 157197 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.91 | 100.00 | WP_063856081.1 |
| CMNDCLCM_31 | 47292 | 48209 | mphK | macrolide 2'-phosphotransferase MphK | INTERNAL_STOP | 98.04 | 100.00 | WP_003246254.1 |
| CMNDCLCM_11 | 153350 | 153868 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CMNDCLCM_30 | 23517 | 26105 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 80.37 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CMNDCLCM_22 | 15963 | 16748 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 100.00 | 100.00 | NP_391080 |
| CMNDCLCM_22 | 20604 | 27740 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.99 | 100.00 | NP_391076 |
| CMNDCLCM_22 | 19646 | 20584 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.89 | 100.00 | NP_391077 |
| CMNDCLCM_4 | 37109 | 38290 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CMNDCLCM_22 | 17999 | 19618 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.57 | 100.00 | NP_391078 |
| CMNDCLCM_4 | 36645 | 37094 | capC | 0.0 | Capsule | Immune modulation | 99.56 | 100.00 | NP_391470 |
| CMNDCLCM_22 | 16774 | 17970 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.50 | 100.00 | NP_391079 |
| CMNDCLCM_42 | 60811 | 61452 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.22 | 100.00 | NP_390062 |
| CMNDCLCM_4 | 35484 | 36626 | capA | 0.0 | Capsule | Immune modulation | 99.21 | 100.00 | NP_391469 |
| CMNDCLCM_25 | 6561 | 8324 | dep/capD | 0.0 | Capsule | Immune modulation | 98.92 | 100.00 | NP_389723 |
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 |
|---|---|---|---|---|---|---|---|---|
| CMNDCLCM_16 | 31659 | 32795 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CMNDCLCM_60 | 4251 | 5120 | pdxS | 1.10e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CMNDCLCM_6 | 249434 | 248658 | CodY | 2.94e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CMNDCLCM_17 | 174055 | 174624 | ClpP | 1.75e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CMNDCLCM_26 | 21682 | 21290 | spxA1 | 3.92e-71 | redox-responsive transcription factor | 83.97 | 100.00 | AAF21893 |
| CMNDCLCM_26 | 21682 | 21290 | spx | 2.34e-69 | essential gene which is a thiol/oxidative stress sensor | 80.15 | 100.00 | BAB57159 |
| CMNDCLCM_24 | 34595 | 34353 | SpoVG | 7.48e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CMNDCLCM_2 | 23726 | 23923 | CspA | 4.64e-32 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CMNDCLCM_12 | 38020 | 38214 | CspB | 5.64e-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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CMNDCLCM_1 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_2 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_4 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_5 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_6 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_7 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_10 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_11 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_12 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_13 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_14 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_15 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_16 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_17 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_18 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_19 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_20 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_21 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_22 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_23 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_24 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_25 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_26 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_27 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_28 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_29 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_30 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_31 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_32 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_33 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_34 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_35 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_36 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_37 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_38 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_39 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_40 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_41 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_42 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_43 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_44 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_45 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_46 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_47 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_48 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_49 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_50 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_51 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_52 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_53 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_54 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_56 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_57 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_58 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_59 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_60 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_62 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_63 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_64 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_65 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_66 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_67 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_68 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_70 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_71 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_74 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_75 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_76 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_79 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_80 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_85 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_87 | 1.0 | 0.0 | 1.0 |
| CMNDCLCM_89 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_90 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_92 | 0.0 | 1.0 | 0.0 |
| CMNDCLCM_95 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CMNDCLCM_1 | 25959 | 55094 | False | Myoviridae | VOG1309, VOG11060, VOG0189, VOG4693, VOG9587, VOG4673, VOG0796, VOG10227, VOG4773, VOG4688, VOG4685, VOG0749, VOG4589, VOG4870, VOG10055, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4691, VOG4862, VOG7718 |
| CMNDCLCM_10 | 69096 | 95578 | False | Myoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685, VOG0749, VOG3890, VOG3891, VOG3892, VOG6163, VOG4865, VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG4612, VOG4705 |
Phigaro v2.4.0 (Database: Jan. 2024 release)