Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 17 | 34 | 38.07 |
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. |
|---|---|---|---|---|---|---|---|---|
| CMBEKOCF_33 | 43048 | 44967 | tet(M) | ARO:3000186 | tet(M) | 91.39 | 100.00 | AB039845.1 |
| CMBEKOCF_33 | 41386 | 42123 | ErmB | ARO:3000375 | ErmB | 97.96 | 98.79 | AF242872.1 |
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. |
|---|---|---|---|---|---|---|---|
| CMBEKOCF_33 | 41386 | 42123 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | U86375 |
| CMBEKOCF_33 | 43048 | 44967 | tet(M) | Doxycycline, Tetracycline, Minocycline | 94.90 | 99.95 | X04388 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CMBEKOCF_33 | 41389 | 42123 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_001038790.1 |
| CMBEKOCF_33 | 43051 | 44967 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | BLASTX | 97.81 | 100.00 | WP_011860841.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CMBEKOCF_13 | 20050 | 20901 | rfbD | 0.0 | Capsule | Immune modulation | 95.07 | 100.00 | WP_014621820 |
| CMBEKOCF_12 | 1756 | 2487 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 94.81 | 100.00 | WP_011681176 |
| CMBEKOCF_12 | 1756 | 2487 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 94.54 | 100.00 | WP_011226048 |
| CMBEKOCF_13 | 23325 | 24040 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 94.41 | 99.86 | WP_011681442 |
| CMBEKOCF_12 | 1756 | 2487 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.13 | 100.00 | WP_011227248 |
| CMBEKOCF_13 | 24386 | 25156 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.48 | 99.23 | WP_011681440 |
| CMBEKOCF_13 | 21020 | 22278 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 92.22 | 99.92 | WP_011681445 |
| CMBEKOCF_35 | 92483 | 93076 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| CMBEKOCF_12 | 295 | 1755 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 90.92 | 99.86 | WP_011681177 |
| CMBEKOCF_35 | 92483 | 93076 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| CMBEKOCF_35 | 92483 | 93076 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| CMBEKOCF_12 | 295 | 1755 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| CMBEKOCF_12 | 112797 | 114454 | fbp54 | 0.0 | FBPs | Adherence | 90.36 | 99.88 | WP_011227179 |
| CMBEKOCF_12 | 295 | 1755 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| CMBEKOCF_12 | 2496 | 3188 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| CMBEKOCF_12 | 2496 | 3188 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| CMBEKOCF_12 | 2496 | 3188 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| CMBEKOCF_36 | 80059 | 81362 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| CMBEKOCF_33 | 57267 | 58106 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| CMBEKOCF_1 | 31595 | 32356 | srtA | 0.0 | Sortase A | Exoenzyme | 86.65 | 99.74 | - |
| CMBEKOCF_18 | 123 | 1136 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| CMBEKOCF_35 | 91167 | 92213 | rfbB | 0.0 | Capsule | Immune modulation | 83.49 | 99.90 | WP_002263087 |
| CMBEKOCF_17 | 1821 | 3104 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.68 | 99.61 | WP_000107753 |
| CMBEKOCF_35 | 93076 | 93945 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| CMBEKOCF_12 | 3198 | 3868 | STU_RS14635 | 1.43e-147 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011226046 |
| CMBEKOCF_12 | 3198 | 3868 | STER_RS05305 | 6.64e-146 | Capsule | Immune modulation | 80.83 | 90.28 | WP_011681174 |
| CMBEKOCF_12 | 3198 | 3800 | STR_RS05250 | 6.73e-136 | Capsule | Immune modulation | 81.46 | 80.13 | WP_011227246 |
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 |
|---|---|---|---|---|---|---|---|---|
| CMBEKOCF_1 | 35045 | 36019 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.31 | 99.09 | AAK75326 |
| CMBEKOCF_1 | 23463 | 22390 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| CMBEKOCF_23 | 81196 | 83502 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| CMBEKOCF_1 | 169679 | 171160 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| CMBEKOCF_38 | 82101 | 83069 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| CMBEKOCF_1 | 3922 | 1676 | metE | 0.0 | methionine biosynthesis enzymes | 92.92 | 100.00 | AAK74738 |
| CMBEKOCF_6 | 36856 | 35885 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| CMBEKOCF_1 | 87985 | 81512 | PrtA | 0.0 | serine protease | 91.44 | 100.61 | ABJ55268 |
| CMBEKOCF_21 | 9593 | 11323 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| CMBEKOCF_13 | 4918 | 6906 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| CMBEKOCF_5 | 11036 | 9885 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| CMBEKOCF_2 | 7293 | 8771 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| CMBEKOCF_36 | 80059 | 81360 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| CMBEKOCF_2 | 23261 | 25153 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| CMBEKOCF_6 | 1213 | 122 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| CMBEKOCF_12 | 239496 | 241205 | PGM | 0.0 | phosphoglucomutase | 84.59 | 99.65 | ACH87041 |
| CMBEKOCF_12 | 99036 | 100397 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.89 | 99.56 | ABP90420 |
| CMBEKOCF_33 | 165277 | 166287 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| CMBEKOCF_36 | 65645 | 66535 | bglB | 1.24e-177 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| CMBEKOCF_1 | 1486 | 629 | metF | 1.05e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| CMBEKOCF_12 | 197956 | 198894 | SP_0676 | 1.65e-168 | transcription facot | 81.47 | 97.20 | AAK74821 |
| CMBEKOCF_10 | 32221 | 31517 | covR | 2.71e-128 | responder protein | 85.96 | 100.00 | AAK71319 |
| CMBEKOCF_1 | 105965 | 105294 | rr01 | 5.18e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| CMBEKOCF_12 | 234830 | 234159 | ciaR | 2.31e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| CMBEKOCF_12 | 234830 | 234162 | CiaR | 4.27e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| CMBEKOCF_4 | 17587 | 18273 | CovR | 4.51e-121 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| CMBEKOCF_10 | 32221 | 31517 | walR | 1.63e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| CMBEKOCF_31 | 610 | 215 | SpxA2 | 2.98e-85 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| CMBEKOCF_12 | 87578 | 87177 | SpxA1 | 1.54e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| CMBEKOCF_7 | 33439 | 33852 | GrpE | 3.09e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| CMBEKOCF_4 | 40789 | 41076 | spr0479 | 1.43e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| CMBEKOCF_38 | 31684 | 31938 | spr1327 | 2.91e-46 | essential gene | 94.12 | 100.00 | AAL00131 |
| CMBEKOCF_2 | 54440 | 54177 | spr0175 | 3.45e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| CMBEKOCF_2 | 53615 | 53349 | spr0177 | 7.67e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| CMBEKOCF_17 | 3271 | 3762 | RopE (M5005_Spy_1611) | 7.13e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| CMBEKOCF_23 | 81196 | 83496 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| CMBEKOCF_33 | 201692 | 200673 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| CMBEKOCF_12 | 133712 | 133173 | pnuC | 1.36e-92 | NAD salvage pathway importer | 82.78 | 66.91 | AAK75931 |
BLASTX v2.16.0 (Database: PHI base v4.16, May. 2024 release)
Plasmid
PlasmidFinder
| Query ID | Begin | End | Plasmid | Query / Template | Identity | Accession no. |
|---|---|---|---|---|---|---|
| CMBEKOCF_33 | 53166 | 54370 | repUS43 | 1206 / 1206 | 90.13 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CMBEKOCF_1 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_2 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_3 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_4 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_5 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_6 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_7 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_8 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_9 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_10 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_11 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_12 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_13 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_14 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_15 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_16 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_17 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_18 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_19 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_20 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_21 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_22 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_23 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_24 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_25 | 1.0 | 0.0 | 1.0 |
| CMBEKOCF_26 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_27 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_28 | 1.0 | 0.0 | 1.0 |
| CMBEKOCF_29 | 1.0 | 0.0 | 1.0 |
| CMBEKOCF_30 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_33 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_34 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_35 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_36 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_37 | 0.0 | 1.0 | 0.0 |
| CMBEKOCF_38 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| No hit found | |||||
Phigaro v2.4.0 (Database: Jan. 2024 release)