Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 16 | 35 | 38.54 |
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. |
|---|---|---|---|---|---|---|---|---|
| EBGPAMNA_11 | 317530 | 319449 | tet(M) | ARO:3000186 | tet(M) | 99.37 | 100.00 | AB039845.1 |
| EBGPAMNA_11 | 306878 | 307615 | ErmB | ARO:3000375 | ErmB | 99.18 | 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. |
|---|---|---|---|---|---|---|---|
| EBGPAMNA_11 | 306878 | 307615 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | X72021 |
| EBGPAMNA_11 | 317530 | 319449 | tet(M) | Doxycycline, Tetracycline, Minocycline | 99.90 | 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. |
|---|---|---|---|---|---|---|---|---|
| EBGPAMNA_11 | 306878 | 307612 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_001038795.1 |
| EBGPAMNA_11 | 317530 | 319446 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| EBGPAMNA_22 | 188774 | 189505 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 94.81 | 100.00 | WP_011681176 |
| EBGPAMNA_22 | 188774 | 189505 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 94.54 | 100.00 | WP_011226048 |
| EBGPAMNA_11 | 63366 | 64217 | rfbD | 0.0 | Capsule | Immune modulation | 94.48 | 100.00 | WP_014621820 |
| EBGPAMNA_11 | 66942 | 67658 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 94.42 | 100.00 | WP_011681442 |
| EBGPAMNA_22 | 188774 | 189505 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.13 | 100.00 | WP_011227248 |
| EBGPAMNA_11 | 68004 | 68774 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.35 | 99.23 | WP_011681440 |
| EBGPAMNA_32 | 138779 | 139372 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| EBGPAMNA_22 | 189506 | 190966 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 90.92 | 99.86 | WP_011681177 |
| EBGPAMNA_32 | 138779 | 139372 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| EBGPAMNA_32 | 138779 | 139372 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| EBGPAMNA_22 | 189506 | 190966 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| EBGPAMNA_11 | 4542 | 5447 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.07 | 93.50 | WP_082302295 |
| EBGPAMNA_22 | 189506 | 190966 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| EBGPAMNA_22 | 81691 | 83349 | fbp54 | 0.0 | FBPs | Adherence | 89.94 | 99.94 | WP_011227179 |
| EBGPAMNA_22 | 188073 | 188765 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| EBGPAMNA_22 | 188073 | 188765 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| EBGPAMNA_22 | 188073 | 188765 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| EBGPAMNA_1 | 41079 | 42382 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| EBGPAMNA_21 | 123 | 1136 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| EBGPAMNA_20 | 3154 | 3915 | srtA | 0.0 | Sortase A | Exoenzyme | 84.27 | 99.87 | - |
| EBGPAMNA_32 | 137463 | 138509 | rfbB | 0.0 | Capsule | Immune modulation | 83.49 | 99.90 | WP_002263087 |
| EBGPAMNA_19 | 11972 | 13255 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 99.61 | WP_000107753 |
| EBGPAMNA_32 | 139372 | 140241 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| EBGPAMNA_22 | 187393 | 188063 | STU_RS14635 | 1.13e-147 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011226046 |
| EBGPAMNA_22 | 187393 | 188063 | STER_RS05305 | 5.26e-146 | Capsule | Immune modulation | 80.83 | 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 |
|---|---|---|---|---|---|---|---|---|
| EBGPAMNA_20 | 6605 | 7588 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| EBGPAMNA_2 | 5227 | 6300 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| EBGPAMNA_51 | 95871 | 98177 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.28 | 99.22 | AAK74619 |
| EBGPAMNA_11 | 325649 | 324168 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.52 | 100.00 | ABJ54480 |
| EBGPAMNA_2 | 24286 | 26532 | metE | 0.0 | methionine biosynthesis enzymes | 92.92 | 100.00 | AAK74738 |
| EBGPAMNA_3 | 12300 | 13268 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| EBGPAMNA_7 | 36361 | 35390 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| EBGPAMNA_11 | 409461 | 415934 | PrtA | 0.0 | serine protease | 91.35 | 100.61 | ABJ55268 |
| EBGPAMNA_50 | 1936 | 206 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| EBGPAMNA_11 | 48880 | 50868 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| EBGPAMNA_5 | 38079 | 39230 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| EBGPAMNA_10 | 7293 | 8771 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| EBGPAMNA_1 | 42382 | 41081 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| EBGPAMNA_10 | 23073 | 24965 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.42 | 98.90 | ABP91129 |
| EBGPAMNA_7 | 1213 | 122 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| EBGPAMNA_2 | 29450 | 27741 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| EBGPAMNA_52 | 60100 | 59090 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| EBGPAMNA_22 | 97275 | 95914 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| EBGPAMNA_1 | 56792 | 55902 | bglB | 8.50e-178 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| EBGPAMNA_2 | 26722 | 27579 | metF | 2.19e-170 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| EBGPAMNA_23 | 3051 | 2113 | SP_0676 | 7.33e-170 | transcription facot | 81.47 | 97.20 | AAK74821 |
| EBGPAMNA_11 | 63366 | 64187 | GacA | 2.93e-146 | dTDP-4-dehydrorhamnose reductas | 80.29 | 96.48 | AAZ51220 |
| EBGPAMNA_6 | 13868 | 14572 | covR | 2.04e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| EBGPAMNA_11 | 391593 | 392264 | rr01 | 7.64e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| EBGPAMNA_2 | 34115 | 34786 | ciaR | 8.32e-126 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| EBGPAMNA_2 | 34115 | 34783 | CiaR | 1.52e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| EBGPAMNA_6 | 13868 | 14572 | walR | 4.63e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| EBGPAMNA_48 | 106192 | 106878 | CovR | 1.20e-120 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| EBGPAMNA_36 | 622 | 227 | SpxA2 | 5.08e-85 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| EBGPAMNA_22 | 108743 | 109144 | SpxA1 | 1.22e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| EBGPAMNA_8 | 33437 | 33850 | GrpE | 3.11e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| EBGPAMNA_48 | 129394 | 129681 | spr0479 | 3.78e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| EBGPAMNA_4 | 30547 | 30801 | spr1327 | 1.77e-46 | essential gene | 94.12 | 100.00 | AAL00131 |
| EBGPAMNA_13 | 13080 | 12817 | spr0175 | 1.29e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| EBGPAMNA_13 | 12255 | 11989 | spr0177 | 2.87e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| EBGPAMNA_19 | 11805 | 11314 | RopE (M5005_Spy_1611) | 7.17e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| EBGPAMNA_51 | 95871 | 98171 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.97 | 98.08 | MYN69560 |
| EBGPAMNA_52 | 23680 | 24699 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 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. |
|---|---|---|---|---|---|---|
| EBGPAMNA_11 | 305244 | 306446 | repUS43 | 1203 / 1206 | 99.83 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| EBGPAMNA_1 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_2 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_3 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_4 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_5 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_6 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_7 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_8 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_9 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_10 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_11 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_12 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_13 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_14 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_15 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_16 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_17 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_18 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_19 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_20 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_21 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_22 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_23 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_24 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_25 | 1.0 | 0.0 | 1.0 |
| EBGPAMNA_27 | 1.0 | 0.0 | 1.0 |
| EBGPAMNA_28 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_29 | 1.0 | 0.0 | 1.0 |
| EBGPAMNA_30 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_31 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_32 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_33 | 1.0 | 0.0 | 1.0 |
| EBGPAMNA_34 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_43 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_48 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_49 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_50 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_51 | 0.0 | 1.0 | 0.0 |
| EBGPAMNA_52 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| EBGPAMNA_32 | 21885 | 66443 | False | Siphoviridae | VOG3303, VOG3300, VOG8184, VOG3299, VOG4649, VOG0054, VOG7888, VOG0648, VOG0647, VOG4599, VOG4605, VOG3636, VOG0800, VOG0725, VOG0799, VOG0724, VOG5660, VOG0723, VOG4713, VOG3435, VOG1887, VOG3434, VOG4564, VOG0720, VOG4544, VOG0796, VOG0198, VOG0658, VOG5562, VOG0044, VOG5821, VOG0657, VOG4567, VOG6495, VOG10904, VOG0152, VOG7484, VOG0656, VOG0655, VOG4693, VOG0226, VOG0186, VOG1309, VOG3430, VOG0189, VOG4566, VOG5996, VOG4555, VOG3478, VOG4552, VOG1563, VOG8337, VOG9667, VOG0743, VOG6422, VOG4602 |
Phigaro v2.4.0 (Database: Jan. 2024 release)