Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 16 | 34 | 37.63 |
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. |
|---|---|---|---|---|---|---|---|
| EMDINGLP_23 | 523925 | 525388 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 99.93 | 100.00 | AF274302 |
| EMDINGLP_23 | 525508 | 526725 | mef(A) | Erythromycin, Azithromycin | 99.92 | 100.00 | U83667 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| EMDINGLP_23 | 525511 | 526725 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| EMDINGLP_23 | 523928 | 525388 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | BLASTX | 99.79 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| EMDINGLP_23 | 149944 | 151309 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.46 | 99.85 | WP_011681173 |
| EMDINGLP_23 | 149942 | 151309 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.96 | 100.00 | WP_011226045 |
| EMDINGLP_48 | 25836 | 26687 | rfbD | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_014621820 |
| EMDINGLP_23 | 153549 | 155009 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.25 | 100.14 | WP_011226049 |
| EMDINGLP_23 | 151366 | 152106 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.20 | 100.00 | WP_011681174 |
| EMDINGLP_23 | 366115 | 367161 | rfbB | 0.0 | Capsule | Immune modulation | 94.17 | 100.00 | WP_002947383 |
| EMDINGLP_23 | 153549 | 155009 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.11 | 100.00 | WP_011681177 |
| EMDINGLP_23 | 153549 | 155009 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.36 | 100.14 | WP_041827043 |
| EMDINGLP_23 | 151366 | 152106 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.12 | 100.00 | WP_011226046 |
| EMDINGLP_23 | 151371 | 152106 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 92.94 | 98.13 | WP_011227246 |
| EMDINGLP_23 | 367364 | 367957 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 92.59 | 100.00 | WP_011226149 |
| EMDINGLP_23 | 367364 | 367957 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| EMDINGLP_23 | 367364 | 367957 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| EMDINGLP_23 | 152817 | 153548 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011226048 |
| EMDINGLP_23 | 152817 | 153548 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.26 | 100.00 | WP_011681176 |
| EMDINGLP_23 | 367957 | 368826 | rfbA | 0.0 | Capsule | Immune modulation | 91.15 | 100.00 | WP_011681286 |
| EMDINGLP_23 | 47339 | 48996 | fbp54 | 0.0 | FBPs | Adherence | 90.90 | 99.88 | WP_011227179 |
| EMDINGLP_23 | 152817 | 153548 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.57 | 100.00 | WP_011227248 |
| EMDINGLP_54 | 21497 | 22507 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.65 | 99.80 | WP_002986042 |
| EMDINGLP_23 | 550703 | 552006 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| EMDINGLP_14 | 125 | 964 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.99 | 99.88 | WP_011226733 |
| EMDINGLP_23 | 152116 | 152808 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 87.90 | 99.86 | WP_011227247 |
| EMDINGLP_23 | 152116 | 152808 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 87.90 | 99.86 | WP_011226047 |
| EMDINGLP_23 | 152116 | 152808 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.61 | 99.86 | WP_011681175 |
| EMDINGLP_8 | 86167 | 86928 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| EMDINGLP_15 | 218300 | 219583 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.93 | 99.53 | WP_000107753 |
| EMDINGLP_23 | 141143 | 141726 | SPD_RS01775 | 3.34e-157 | Capsule | Immune modulation | 84.10 | 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 |
|---|---|---|---|---|---|---|---|---|
| EMDINGLP_8 | 78039 | 76966 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| EMDINGLP_8 | 89617 | 90591 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.00 | 99.09 | AAK75326 |
| EMDINGLP_61 | 47029 | 49335 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| EMDINGLP_29 | 83236 | 84717 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| EMDINGLP_8 | 58987 | 56741 | metE | 0.0 | methionine biosynthesis enzymes | 93.19 | 100.00 | AAK74738 |
| EMDINGLP_38 | 9366 | 10334 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| EMDINGLP_19 | 15427 | 14456 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| EMDINGLP_29 | 7049 | 486 | PrtA | 0.0 | serine protease | 90.14 | 101.96 | ABJ55268 |
| EMDINGLP_23 | 395693 | 393963 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.78 | 100.00 | AAK34199 |
| EMDINGLP_44 | 95324 | 96475 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| EMDINGLP_48 | 11945 | 13933 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.29 | 100.00 | AE014259_2 |
| EMDINGLP_67 | 108533 | 107055 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| EMDINGLP_23 | 552006 | 550705 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| EMDINGLP_67 | 92749 | 90857 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| EMDINGLP_8 | 53819 | 55528 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| EMDINGLP_14 | 20320 | 21411 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| EMDINGLP_16 | 28689 | 29699 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| EMDINGLP_23 | 62777 | 61416 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| EMDINGLP_23 | 566416 | 565526 | bglB | 8.01e-177 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| EMDINGLP_8 | 13817 | 14767 | SP_0676 | 2.57e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| EMDINGLP_8 | 56551 | 55694 | metF | 3.91e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| EMDINGLP_29 | 25155 | 24484 | rr01 | 2.51e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| EMDINGLP_8 | 49085 | 48414 | ciaR | 8.67e-126 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| EMDINGLP_23 | 198026 | 197322 | covR | 9.09e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| EMDINGLP_8 | 49085 | 48417 | CiaR | 1.60e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| EMDINGLP_15 | 53637 | 52951 | CovR | 4.85e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| EMDINGLP_23 | 198026 | 197322 | walR | 1.67e-119 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| EMDINGLP_14 | 21584 | 21979 | SpxA2 | 2.19e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| EMDINGLP_23 | 74235 | 74636 | SpxA1 | 1.18e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| EMDINGLP_35 | 11906 | 12319 | GrpE | 3.29e-68 | protein grpE | 81.16 | 80.59 | ABP89267 |
| EMDINGLP_15 | 30423 | 30136 | spr0479 | 4.69e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| EMDINGLP_20 | 31793 | 32047 | spr1327 | 1.45e-44 | essential gene | 90.59 | 100.00 | AAL00131 |
| EMDINGLP_67 | 30734 | 30997 | spr0175 | 6.94e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| EMDINGLP_67 | 31558 | 31824 | spr0177 | 1.54e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| EMDINGLP_15 | 218133 | 217642 | RopE (M5005_Spy_1611) | 1.07e-72 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| EMDINGLP_61 | 47029 | 49329 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| EMDINGLP_16 | 65378 | 64359 | 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 |
|---|---|---|---|
| EMDINGLP_2 | 1.0 | 0.0 | 1.0 |
| EMDINGLP_5 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_8 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_9 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_11 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_14 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_15 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_16 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_19 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_20 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_21 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_22 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_23 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_24 | 1.0 | 0.0 | 1.0 |
| EMDINGLP_26 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_28 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_29 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_35 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_36 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_37 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_38 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_44 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_45 | 1.0 | 0.0 | 1.0 |
| EMDINGLP_46 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_47 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_48 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_49 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_50 | 1.0 | 0.0 | 1.0 |
| EMDINGLP_54 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_56 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_60 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_61 | 0.0 | 1.0 | 0.0 |
| EMDINGLP_67 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| EMDINGLP_23 | 224184 | 266101 | False | Siphoviridae | VOG10230, VOG5221, VOG7557, VOG5034, VOG0054, VOG0641, VOG0648, VOG0647, VOG4599, VOG4605, VOG4545, VOG0209, VOG4586, VOG0207, VOG0205, VOG0204, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG0198, VOG0658, VOG0044, VOG6495, VOG0152, VOG7484, VOG8749, VOG6140, VOG0656, VOG0655, VOG4693, VOG0226, VOG0186, VOG1309, VOG3430, VOG0189, VOG4566, VOG0651, VOG0650, VOG7236, VOG1563, VOG8337, VOG9667, VOG11003, VOG6450 |
Phigaro v2.4.0 (Database: Jan. 2024 release)