Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 24 | 27 | 36.12 |
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. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
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. |
|---|---|---|---|---|---|---|---|
| No hit found | |||||||
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
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. |
|---|---|---|---|---|---|---|---|---|---|
| CODMFHAM_1 | 44156 | 44995 | cbpD | 0.0 | Autolysin | Exoenzyme | 100.00 | 100.00 | WP_011226733 |
| CODMFHAM_1 | 1040576 | 1041169 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 100.00 | 100.00 | WP_011226149 |
| CODMFHAM_1 | 1249472 | 1250281 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 99.88 | 100.00 | WP_002948020 |
| CODMFHAM_1 | 1040576 | 1041169 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | WP_011226149 |
| CODMFHAM_1 | 1040576 | 1041169 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 99.83 | 100.00 | WP_011226149 |
| CODMFHAM_1 | 1250265 | 1251221 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 99.48 | 100.00 | WP_011226328 |
| CODMFHAM_1 | 817371 | 819029 | fbp54 | 0.0 | FBPs | Adherence | 99.46 | 100.00 | WP_011227179 |
| CODMFHAM_1 | 1245412 | 1247196 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 99.44 | 100.00 | WP_011226325 |
| CODMFHAM_1 | 1041169 | 1042038 | rfbA | 0.0 | Capsule | Immune modulation | 99.42 | 100.00 | WP_011681286 |
| CODMFHAM_1 | 1248267 | 1249472 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 99.25 | 100.00 | WP_011226326 |
| CODMFHAM_1 | 1247193 | 1248248 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | WP_002948022 |
| CODMFHAM_1 | 1257765 | 1258616 | rfbD | 0.0 | Capsule | Immune modulation | 98.94 | 100.00 | WP_014621820 |
| CODMFHAM_1 | 921033 | 921764 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 98.91 | 100.00 | WP_011681176 |
| CODMFHAM_1 | 1075938 | 1076699 | srtA | 0.0 | Sortase A | Exoenzyme | 98.82 | 100.00 | - |
| CODMFHAM_1 | 1254426 | 1255388 | STU_RS16260 | 0.0 | Capsule | Immune modulation | 98.75 | 95.25 | WP_011226330 |
| CODMFHAM_1 | 921033 | 921764 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 98.63 | 100.00 | WP_011226048 |
| CODMFHAM_1 | 1251218 | 1252366 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 98.52 | 100.00 | WP_041828290 |
| CODMFHAM_1 | 921033 | 921764 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 98.50 | 100.00 | WP_011227248 |
| CODMFHAM_1 | 1181739 | 1182879 | STER_RS05250 | 0.0 | Capsule | Immune modulation | 98.07 | 80.58 | WP_011681165 |
| CODMFHAM_1 | 921765 | 923225 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 97.95 | 100.00 | WP_011681177 |
| CODMFHAM_1 | 1255391 | 1256662 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 97.72 | 99.76 | WP_011226331 |
| CODMFHAM_1 | 919584 | 920322 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 97.43 | 99.73 | WP_011681174 |
| CODMFHAM_1 | 920332 | 921024 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 97.40 | 100.00 | WP_011227247 |
| CODMFHAM_1 | 920332 | 921024 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 97.40 | 100.00 | WP_011226047 |
| CODMFHAM_1 | 921765 | 923225 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 97.19 | 100.21 | WP_011226049 |
| CODMFHAM_1 | 919584 | 920322 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 97.02 | 99.73 | WP_011226046 |
| CODMFHAM_1 | 919587 | 920322 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 96.88 | 98.13 | WP_011227246 |
| CODMFHAM_1 | 921765 | 923225 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 96.23 | 100.21 | WP_041827043 |
| CODMFHAM_1 | 918157 | 919524 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.81 | 100.00 | WP_011226045 |
| CODMFHAM_1 | 918159 | 919524 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 94.22 | 99.85 | WP_011681173 |
| CODMFHAM_1 | 920332 | 921024 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.77 | 99.86 | WP_011681175 |
| CODMFHAM_1 | 581465 | 582768 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.02 | 99.54 | WP_000022832 |
| CODMFHAM_1 | 1550040 | 1551050 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 86.92 | 99.51 | WP_002986042 |
| CODMFHAM_1 | 128092 | 129375 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.65 | 99.77 | WP_000107753 |
| CODMFHAM_1 | 1039100 | 1040146 | rfbB | 0.0 | Capsule | Immune modulation | 80.23 | 100.00 | WP_009659423 |
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 |
|---|---|---|---|---|---|---|---|---|
| CODMFHAM_1 | 685691 | 686764 | MntE | 0.0 | manganese homeostasis | 94.97 | 99.72 | ABF32167 |
| CODMFHAM_1 | 1079386 | 1080369 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 94.82 | 100.00 | AAK75326 |
| CODMFHAM_1 | 498122 | 499090 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| CODMFHAM_1 | 1427363 | 1429666 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 93.10 | 99.22 | AAK74619 |
| CODMFHAM_1 | 724965 | 727211 | metE | 0.0 | methionine biosynthesis enzymes | 91.72 | 100.00 | AAK74738 |
| CODMFHAM_1 | 1168121 | 1169602 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 91.70 | 100.00 | ABJ54480 |
| CODMFHAM_1 | 63785 | 64783 | recA | 0.0 | DNA recombination and repair | 91.29 | 85.82 | AAL00560 |
| CODMFHAM_1 | 27348 | 28319 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 90.12 | 100.00 | ABF36968 |
| CODMFHAM_1 | 1312317 | 1311166 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| CODMFHAM_1 | 1272472 | 1270484 | uvrB | 0.0 | excinuclease ABC, B subunit | 88.99 | 100.00 | AE014259_2 |
| CODMFHAM_1 | 1063187 | 1061457 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 87.69 | 100.00 | AAK34199 |
| CODMFHAM_1 | 1725545 | 1724067 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.42 | 100.00 | ADE32434 |
| CODMFHAM_1 | 581465 | 582766 | Eno | 0.0 | enolase | 86.21 | 99.77 | ABP90468 |
| CODMFHAM_1 | 1710348 | 1708456 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 86.05 | 98.90 | ABP91129 |
| CODMFHAM_1 | 730136 | 728427 | PGM | 0.0 | phosphoglucomutase | 83.89 | 99.65 | ACH87041 |
| CODMFHAM_1 | 1587309 | 1588319 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| CODMFHAM_1 | 843918 | 842557 | mnmE | 0.0 | central tRNA-modifying GTPase | 81.80 | 99.56 | ABP90420 |
| CODMFHAM_1 | 567025 | 567915 | bglB | 1.25e-178 | putative phospho--glucosidase | 88.89 | 99.66 | AAK33487 |
| CODMFHAM_1 | 782634 | 781696 | SP_0676 | 1.56e-166 | transcription facot | 81.15 | 97.20 | AAK74821 |
| CODMFHAM_1 | 727403 | 728260 | metF | 1.52e-163 | methionine biosynthesis enzymes | 86.01 | 99.31 | AAK74739 |
| CODMFHAM_1 | 961072 | 960368 | covR | 4.14e-130 | responder protein | 85.11 | 100.00 | AAK71319 |
| CODMFHAM_1 | 1126869 | 1126198 | rr01 | 3.91e-125 | response regulator | 84.38 | 99.56 | CAB54566 |
| CODMFHAM_1 | 734474 | 735142 | CiaR | 2.61e-123 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| CODMFHAM_1 | 734474 | 735145 | ciaR | 2.55e-121 | two component system response regulator | 84.82 | 99.12 | AIK75708 |
| CODMFHAM_1 | 961072 | 960368 | walR | 2.72e-120 | DNA-binding response regulator | 80.85 | 100.00 | ANC99504 |
| CODMFHAM_1 | 280258 | 280944 | CovR | 9.43e-118 | serves to repress GAS virulence factor-encoding genes | 80.79 | 100.00 | ACE75886 |
| CODMFHAM_1 | 65059 | 65454 | SpxA2 | 3.47e-74 | transcriptional regulator | 90.91 | 100.00 | ERL21461 |
| CODMFHAM_1 | 129533 | 130033 | RopE (M5005_Spy_1611) | 4.61e-75 | probable DNA-directed RNA polymerase subunit delta | 81.44 | 87.43 | AAK34603 |
| CODMFHAM_1 | 1427363 | 1429660 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.07 | 98.08 | MYN69560 |
| CODMFHAM_1 | 1623170 | 1622151 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 96.47 | 100.00 | ABJ55451 |
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 |
|---|---|---|---|
| CODMFHAM_1 | 0.0 | 1.0 | 0.0 |
| CODMFHAM_5 | 1.0 | 0.0 | 1.0 |
| CODMFHAM_7 | 1.0 | 0.0 | 1.0 |
| CODMFHAM_9 | 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)