Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 22 | 33 | 39.66 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| HDCEGNDM_26 | 73897 | 74706 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 95.68 | 100.00 | WP_002948020 |
| HDCEGNDM_13 | 49228 | 50593 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.61 | 99.85 | WP_011681173 |
| HDCEGNDM_13 | 49226 | 50593 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 95.10 | 100.00 | WP_011226045 |
| HDCEGNDM_26 | 78052 | 78903 | rfbD | 0.0 | Capsule | Immune modulation | 94.48 | 100.00 | WP_014621820 |
| HDCEGNDM_13 | 50650 | 51390 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.20 | 100.00 | WP_011681174 |
| HDCEGNDM_13 | 52833 | 54293 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.98 | 100.00 | WP_011681177 |
| HDCEGNDM_13 | 52833 | 54293 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.84 | 100.14 | WP_011226049 |
| HDCEGNDM_13 | 50650 | 51390 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.66 | 100.00 | WP_011226046 |
| HDCEGNDM_13 | 52833 | 54293 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.22 | 100.14 | WP_041827043 |
| HDCEGNDM_13 | 50655 | 51390 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.21 | 98.13 | WP_011227246 |
| HDCEGNDM_26 | 69856 | 71640 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.94 | 100.00 | WP_011226325 |
| HDCEGNDM_13 | 52101 | 52832 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.35 | 100.00 | WP_011226048 |
| HDCEGNDM_26 | 72692 | 73897 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.21 | 100.00 | WP_011226326 |
| HDCEGNDM_13 | 223545 | 224138 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.92 | 100.00 | WP_011226149 |
| HDCEGNDM_26 | 75643 | 76791 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.91 | 100.00 | WP_041828290 |
| HDCEGNDM_13 | 223545 | 224138 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| HDCEGNDM_13 | 223545 | 224138 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.75 | 100.00 | WP_011226149 |
| HDCEGNDM_13 | 52101 | 52832 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011681176 |
| HDCEGNDM_26 | 71637 | 72671 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.67 | 99.05 | WP_002948022 |
| HDCEGNDM_26 | 74690 | 75646 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 91.64 | 100.00 | WP_011226328 |
| HDCEGNDM_13 | 224138 | 225007 | rfbA | 0.0 | Capsule | Immune modulation | 91.49 | 100.00 | WP_011681286 |
| HDCEGNDM_13 | 52101 | 52832 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.39 | 100.00 | WP_011227248 |
| HDCEGNDM_20 | 66521 | 68179 | fbp54 | 0.0 | FBPs | Adherence | 91.08 | 99.94 | WP_011227179 |
| HDCEGNDM_13 | 602413 | 603318 | cbpD | 0.0 | Autolysin | Exoenzyme | 89.51 | 93.50 | WP_082302295 |
| HDCEGNDM_13 | 51400 | 52092 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.91 | 99.86 | WP_011227247 |
| HDCEGNDM_13 | 51400 | 52092 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.91 | 99.86 | WP_011226047 |
| HDCEGNDM_21 | 13966 | 14976 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.65 | 99.80 | WP_002986042 |
| HDCEGNDM_13 | 409169 | 410472 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| HDCEGNDM_13 | 51400 | 52092 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.18 | 99.86 | WP_011681175 |
| HDCEGNDM_13 | 222297 | 223343 | rfbB | 0.0 | Capsule | Immune modulation | 84.06 | 99.90 | WP_002263087 |
| HDCEGNDM_20 | 210930 | 211691 | srtA | 0.0 | Sortase A | Exoenzyme | 83.77 | 99.74 | - |
| HDCEGNDM_7 | 31140 | 32423 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 99.61 | WP_000107753 |
| HDCEGNDM_13 | 37813 | 38396 | SPD_RS01775 | 1.84e-150 | Capsule | Immune modulation | 83.42 | 96.20 | WP_001819836 |
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 |
|---|---|---|---|---|---|---|---|---|
| HDCEGNDM_20 | 214378 | 215361 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| HDCEGNDM_20 | 202800 | 201727 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| HDCEGNDM_21 | 143550 | 141244 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| HDCEGNDM_20 | 320663 | 322144 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| HDCEGNDM_20 | 183744 | 181498 | metE | 0.0 | methionine biosynthesis enzymes | 92.66 | 100.00 | AAK74738 |
| HDCEGNDM_13 | 516832 | 515864 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| HDCEGNDM_6 | 4386 | 5357 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| HDCEGNDM_13 | 250389 | 248659 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| HDCEGNDM_26 | 92339 | 90351 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| HDCEGNDM_26 | 128372 | 127221 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| HDCEGNDM_32 | 45394 | 43916 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| HDCEGNDM_13 | 410472 | 409171 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| HDCEGNDM_32 | 30073 | 28181 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.10 | 98.90 | ABP91129 |
| HDCEGNDM_20 | 178577 | 180286 | PGM | 0.0 | phosphoglucomutase | 84.94 | 99.65 | ACH87041 |
| HDCEGNDM_31 | 2888 | 3979 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| HDCEGNDM_28 | 90282 | 89272 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| HDCEGNDM_20 | 41198 | 42559 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| HDCEGNDM_13 | 424882 | 423992 | bglB | 6.90e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| HDCEGNDM_20 | 137678 | 138628 | SP_0676 | 6.75e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| HDCEGNDM_20 | 181308 | 180451 | metF | 3.35e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| HDCEGNDM_13 | 97351 | 96647 | covR | 1.72e-131 | responder protein | 85.53 | 100.00 | AAK71319 |
| HDCEGNDM_20 | 277267 | 276596 | rr01 | 2.88e-127 | response regulator | 85.27 | 99.56 | CAB54566 |
| HDCEGNDM_20 | 174609 | 173938 | ciaR | 4.06e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| HDCEGNDM_20 | 174609 | 173941 | CiaR | 7.51e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| HDCEGNDM_13 | 97351 | 96647 | walR | 9.12e-122 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| HDCEGNDM_33 | 54028 | 53342 | CovR | 1.35e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| HDCEGNDM_31 | 4155 | 4550 | SpxA2 | 4.56e-77 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| HDCEGNDM_20 | 29729 | 29328 | SpxA1 | 4.69e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| HDCEGNDM_5 | 6678 | 6265 | GrpE | 9.75e-68 | protein grpE | 81.16 | 80.59 | ABP89267 |
| HDCEGNDM_33 | 30816 | 30529 | spr0479 | 1.64e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| HDCEGNDM_13 | 550934 | 550680 | spr1327 | 3.44e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| HDCEGNDM_28 | 1893 | 1630 | spr0175 | 5.71e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| HDCEGNDM_28 | 1067 | 801 | spr0177 | 7.96e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| HDCEGNDM_7 | 30973 | 30482 | RopE (M5005_Spy_1611) | 2.19e-72 | probable DNA-directed RNA polymerase subunit delta | 82.32 | 85.86 | AAK34603 |
| HDCEGNDM_21 | 143550 | 141250 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| HDCEGNDM_28 | 55162 | 56181 | 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 |
|---|---|---|---|
| HDCEGNDM_1 | 1.0 | 0.0 | 1.0 |
| HDCEGNDM_2 | 1.0 | 0.0 | 1.0 |
| HDCEGNDM_3 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_5 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_6 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_7 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_8 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_9 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_10 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_11 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_12 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_13 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_15 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_17 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_20 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_21 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_22 | 1.0 | 0.0 | 1.0 |
| HDCEGNDM_24 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_25 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_26 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_27 | 1.0 | 0.0 | 1.0 |
| HDCEGNDM_28 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_30 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_31 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_32 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_33 | 0.0 | 1.0 | 0.0 |
| HDCEGNDM_34 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| HDCEGNDM_13 | 430934 | 434631 | False | Siphoviridae | VOG2978, VOG8353, VOG8336, VOG4566, VOG0189, VOG0198 |
Phigaro v2.4.0 (Database: Jan. 2024 release)