Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 16 | 28 | 32.31 |
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. |
|---|---|---|---|---|---|---|---|
| HPCIBOKB_1 | 1490355 | 1491572 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| HPCIBOKB_1 | 1488707 | 1490170 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 99.25 | 100.00 | AF274302 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HPCIBOKB_1 | 1490358 | 1491572 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| HPCIBOKB_1 | 1488710 | 1490170 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | BLASTX | 98.97 | 100.00 | WP_000420313.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| HPCIBOKB_1 | 526442 | 527293 | rfbD | 0.0 | Capsule | Immune modulation | 94.48 | 100.00 | WP_014621820 |
| HPCIBOKB_1 | 1155374 | 1156834 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.98 | 100.00 | WP_011681177 |
| HPCIBOKB_1 | 1151768 | 1153135 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 93.93 | 100.00 | WP_011226045 |
| HPCIBOKB_1 | 1155374 | 1156834 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.84 | 100.14 | WP_011226049 |
| HPCIBOKB_1 | 1151770 | 1153135 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 93.78 | 99.85 | WP_011681173 |
| HPCIBOKB_1 | 1153191 | 1153931 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 93.52 | 100.00 | WP_011681174 |
| HPCIBOKB_1 | 1333166 | 1333759 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 93.27 | 100.00 | WP_011226149 |
| HPCIBOKB_1 | 1155374 | 1156834 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| HPCIBOKB_1 | 1333166 | 1333759 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 93.10 | 100.00 | WP_011226149 |
| HPCIBOKB_1 | 1333166 | 1333759 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 93.10 | 100.00 | WP_011226149 |
| HPCIBOKB_1 | 1153191 | 1153931 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 92.98 | 100.00 | WP_011226046 |
| HPCIBOKB_1 | 1153196 | 1153931 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 92.53 | 98.13 | WP_011227246 |
| HPCIBOKB_1 | 1154642 | 1155373 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.35 | 100.00 | WP_011226048 |
| HPCIBOKB_1 | 1154642 | 1155373 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011681176 |
| HPCIBOKB_1 | 1333759 | 1334628 | rfbA | 0.0 | Capsule | Immune modulation | 91.49 | 100.00 | WP_011681286 |
| HPCIBOKB_1 | 1154642 | 1155373 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.39 | 100.00 | WP_011227248 |
| HPCIBOKB_1 | 2124942 | 2125781 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.95 | 100.00 | WP_011226733 |
| HPCIBOKB_1 | 1041147 | 1042805 | fbp54 | 0.0 | FBPs | Adherence | 89.76 | 99.94 | WP_011227179 |
| HPCIBOKB_1 | 205431 | 206441 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.75 | 99.80 | WP_002986042 |
| HPCIBOKB_1 | 1153941 | 1154633 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.62 | 99.86 | WP_011227247 |
| HPCIBOKB_1 | 1153941 | 1154633 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.62 | 99.86 | WP_011226047 |
| HPCIBOKB_1 | 1519555 | 1520858 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| HPCIBOKB_1 | 1153941 | 1154633 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 86.89 | 99.86 | WP_011681175 |
| HPCIBOKB_1 | 901092 | 901812 | srtA | 0.0 | Sortase A | Exoenzyme | 84.49 | 94.49 | - |
| HPCIBOKB_1 | 2026354 | 2027637 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.61 | 99.61 | WP_000107753 |
| HPCIBOKB_1 | 1331917 | 1332963 | rfbB | 0.0 | Capsule | Immune modulation | 80.36 | 99.90 | WP_009659423 |
| HPCIBOKB_1 | 1142026 | 1142609 | SPD_RS01775 | 1.26e-156 | Capsule | Immune modulation | 84.10 | 96.20 | WP_001819836 |
| HPCIBOKB_1 | 531438 | 531907 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 95.32 | 65.41 | WP_011681442 |
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 |
|---|---|---|---|---|---|---|---|---|
| HPCIBOKB_1 | 896922 | 895948 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.31 | 99.09 | AAK75326 |
| HPCIBOKB_1 | 909948 | 911021 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| HPCIBOKB_1 | 333215 | 330909 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.28 | 99.22 | AAK74619 |
| HPCIBOKB_1 | 764586 | 763105 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.52 | 100.00 | ABJ54480 |
| HPCIBOKB_1 | 1612558 | 1611590 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| HPCIBOKB_1 | 929488 | 931734 | metE | 0.0 | methionine biosynthesis enzymes | 92.79 | 100.00 | AAK74738 |
| HPCIBOKB_1 | 2140203 | 2139232 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| HPCIBOKB_1 | 1360005 | 1358275 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| HPCIBOKB_1 | 485768 | 486916 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.82 | 99.48 | AAL00050 |
| HPCIBOKB_1 | 13626 | 15104 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| HPCIBOKB_1 | 1520858 | 1519557 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| HPCIBOKB_1 | 28977 | 30869 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| HPCIBOKB_1 | 934652 | 932943 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| HPCIBOKB_1 | 2103778 | 2102687 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| HPCIBOKB_1 | 151610 | 150600 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| HPCIBOKB_1 | 1058361 | 1057000 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| HPCIBOKB_1 | 1535265 | 1534375 | bglB | 2.69e-177 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| HPCIBOKB_1 | 931921 | 932778 | metF | 2.84e-170 | methionine biosynthesis enzymes | 88.46 | 99.31 | AAK74739 |
| HPCIBOKB_1 | 975443 | 974493 | SP_0676 | 3.45e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| HPCIBOKB_1 | 829774 | 830448 | rr01 | 1.08e-126 | response regulator | 84.89 | 100.00 | CAB54566 |
| HPCIBOKB_1 | 1201610 | 1200906 | covR | 9.65e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| HPCIBOKB_1 | 938618 | 939289 | ciaR | 2.07e-124 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| HPCIBOKB_1 | 938618 | 939286 | CiaR | 3.83e-124 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| HPCIBOKB_1 | 1201610 | 1200906 | walR | 2.19e-119 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| HPCIBOKB_1 | 1871436 | 1870750 | CovR | 4.73e-119 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| HPCIBOKB_1 | 2102513 | 2102118 | SpxA2 | 2.13e-74 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| HPCIBOKB_1 | 1069830 | 1070231 | SpxA1 | 6.22e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| HPCIBOKB_1 | 2043130 | 2042717 | GrpE | 3.99e-66 | protein grpE | 81.16 | 80.59 | ABP89267 |
| HPCIBOKB_1 | 2026187 | 2025696 | RopE (M5005_Spy_1611) | 1.05e-71 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| HPCIBOKB_1 | 333215 | 330915 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.97 | 98.08 | MYN69560 |
| HPCIBOKB_1 | 114895 | 115914 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 97.35 | 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 |
|---|---|---|---|
| HPCIBOKB_1 | 0.0 | 1.0 | 0.0 |
| HPCIBOKB_2 | 1.0 | 0.0 | 1.0 |
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)