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. |
|---|---|---|---|---|---|---|---|---|
| IGHDCBEA_34 | 94912 | 96831 | tet(M) | ARO:3000186 | tet(M) | 99.37 | 100.00 | AB039845.1 |
| IGHDCBEA_34 | 93066 | 93803 | 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. |
|---|---|---|---|---|---|---|---|
| IGHDCBEA_34 | 93066 | 93803 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | U86375 |
| IGHDCBEA_34 | 94912 | 96831 | tet(M) | Doxycycline, Tetracycline, Minocycline | 99.74 | 100.00 | X75073 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| IGHDCBEA_34 | 93069 | 93803 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_001038790.1 |
| IGHDCBEA_34 | 94915 | 96831 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | EXACTX | 100.00 | 100.00 | WP_000691727.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| IGHDCBEA_48 | 86455 | 87306 | rfbD | 0.0 | Capsule | Immune modulation | 95.42 | 100.00 | WP_014621820 |
| IGHDCBEA_16 | 1718 | 2449 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.40 | 100.00 | WP_011227248 |
| IGHDCBEA_16 | 1718 | 2449 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.99 | 100.00 | WP_011681176 |
| IGHDCBEA_16 | 1718 | 2449 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| IGHDCBEA_48 | 83317 | 84032 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 93.72 | 99.86 | WP_011681442 |
| IGHDCBEA_48 | 82201 | 82971 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.61 | 99.23 | WP_011681440 |
| IGHDCBEA_48 | 85078 | 86336 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 92.54 | 99.92 | WP_011681445 |
| IGHDCBEA_16 | 257 | 1717 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.33 | 99.86 | WP_011681177 |
| IGHDCBEA_45 | 45382 | 45975 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.25 | 100.00 | WP_011226149 |
| IGHDCBEA_45 | 45382 | 45975 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| IGHDCBEA_45 | 45382 | 45975 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| IGHDCBEA_23 | 108041 | 109699 | fbp54 | 0.0 | FBPs | Adherence | 91.02 | 99.94 | WP_011227179 |
| IGHDCBEA_16 | 257 | 1717 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.72 | 100.00 | WP_011226049 |
| IGHDCBEA_4 | 34446 | 35351 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.07 | 93.50 | WP_082302295 |
| IGHDCBEA_16 | 2458 | 3150 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 90.04 | 100.00 | WP_011226047 |
| IGHDCBEA_16 | 257 | 1717 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 90.03 | 100.00 | WP_041827043 |
| IGHDCBEA_16 | 2458 | 3150 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.75 | 100.00 | WP_011227247 |
| IGHDCBEA_16 | 2458 | 3150 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011681175 |
| IGHDCBEA_1 | 31860 | 33163 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.17 | 99.54 | WP_000022832 |
| IGHDCBEA_1 | 477115 | 478128 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| IGHDCBEA_2 | 27516 | 28277 | srtA | 0.0 | Sortase A | Exoenzyme | 84.14 | 99.87 | - |
| IGHDCBEA_25 | 5881 | 7164 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.53 | 99.61 | WP_000107753 |
| IGHDCBEA_45 | 46245 | 47291 | rfbB | 0.0 | Capsule | Immune modulation | 80.52 | 100.00 | WP_009659423 |
| IGHDCBEA_45 | 44513 | 45382 | rfbA | 0.0 | Capsule | Immune modulation | 80.16 | 99.77 | WP_002904719 |
| IGHDCBEA_16 | 3160 | 3830 | STU_RS14635 | 4.98e-147 | Capsule | Immune modulation | 80.83 | 90.28 | WP_011226046 |
| IGHDCBEA_16 | 3160 | 3830 | STER_RS05305 | 2.32e-145 | Capsule | Immune modulation | 80.68 | 90.28 | WP_011681174 |
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 |
|---|---|---|---|---|---|---|---|---|
| IGHDCBEA_2 | 30967 | 31950 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| IGHDCBEA_2 | 19377 | 18304 | MntE | 0.0 | manganese homeostasis | 95.81 | 99.72 | ABF32167 |
| IGHDCBEA_1 | 352541 | 354847 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| IGHDCBEA_34 | 83438 | 84919 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| IGHDCBEA_30 | 223 | 2469 | metE | 0.0 | methionine biosynthesis enzymes | 92.92 | 100.00 | AAK74738 |
| IGHDCBEA_1 | 124702 | 123734 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| IGHDCBEA_29 | 1028 | 57 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| IGHDCBEA_45 | 10895 | 12625 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| IGHDCBEA_48 | 102675 | 100687 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| IGHDCBEA_1 | 214024 | 212873 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| IGHDCBEA_49 | 25678 | 27156 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| IGHDCBEA_1 | 33163 | 31862 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| IGHDCBEA_49 | 41019 | 42911 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| IGHDCBEA_18 | 11759 | 12850 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| IGHDCBEA_26 | 1824 | 115 | PGM | 0.0 | phosphoglucomutase | 84.59 | 99.65 | ACH87041 |
| IGHDCBEA_3 | 35589 | 34579 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| IGHDCBEA_23 | 123457 | 122096 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| IGHDCBEA_30 | 2658 | 3515 | metF | 2.03e-179 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| IGHDCBEA_1 | 47577 | 46687 | bglB | 5.34e-177 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| IGHDCBEA_23 | 34713 | 33763 | SP_0676 | 4.70e-171 | transcription facot | 81.39 | 98.45 | AAK74821 |
| IGHDCBEA_6 | 11656 | 10799 | mtsA | 1.10e-152 | substrate-binding lipoprotein of manganese transporter | 80.49 | 92.86 | AIK76191 |
| IGHDCBEA_20 | 303 | 1007 | covR | 4.89e-128 | responder protein | 85.53 | 100.00 | AAK71319 |
| IGHDCBEA_34 | 23470 | 22799 | rr01 | 3.04e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| IGHDCBEA_26 | 6489 | 7160 | ciaR | 7.90e-127 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| IGHDCBEA_26 | 6489 | 7157 | CiaR | 1.46e-126 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| IGHDCBEA_20 | 303 | 1007 | walR | 1.11e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| IGHDCBEA_12 | 152594 | 153280 | CovR | 1.64e-120 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| IGHDCBEA_43 | 156 | 551 | SpxA2 | 9.27e-86 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| IGHDCBEA_23 | 134922 | 135323 | SpxA1 | 1.08e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| IGHDCBEA_51 | 72515 | 72928 | GrpE | 6.13e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| IGHDCBEA_12 | 175784 | 176071 | spr0479 | 5.19e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| IGHDCBEA_1 | 171715 | 171461 | spr1327 | 2.26e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| IGHDCBEA_49 | 81728 | 81465 | spr0175 | 4.91e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| IGHDCBEA_49 | 80904 | 80638 | spr0177 | 1.09e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| IGHDCBEA_25 | 5714 | 5223 | RopE (M5005_Spy_1611) | 4.14e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| IGHDCBEA_1 | 352541 | 354841 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| IGHDCBEA_10 | 1580 | 561 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| IGHDCBEA_23 | 95057 | 95596 | pnuC | 9.55e-93 | 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. |
|---|---|---|---|---|---|---|
| IGHDCBEA_34 | 105105 | 106310 | repUS43 | 1206 / 1206 | 100.00 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| IGHDCBEA_1 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_2 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_3 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_4 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_5 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_6 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_7 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_8 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_9 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_10 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_11 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_12 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_13 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_14 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_15 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_16 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_17 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_18 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_19 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_20 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_21 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_22 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_23 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_24 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_25 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_26 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_27 | 1.0 | 0.0 | 1.0 |
| IGHDCBEA_29 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_30 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_32 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_34 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_35 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_36 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_37 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_38 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_39 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_45 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_48 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_49 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_50 | 0.0 | 1.0 | 0.0 |
| IGHDCBEA_51 | 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)