Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 15 | 38 | 40.90 |
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. |
|---|---|---|---|---|---|---|---|
| KMMCNEJI_4 | 114523 | 115740 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| KMMCNEJI_4 | 115860 | 117323 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|
| KMMCNEJI_4 | 114523 | 115737 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| KMMCNEJI_4 | 115860 | 117320 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | EXACTX | 100.00 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| KMMCNEJI_4 | 47466 | 48831 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.24 | 99.85 | WP_011681173 |
| KMMCNEJI_4 | 47466 | 48833 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.30 | 100.00 | WP_011226045 |
| KMMCNEJI_4 | 43766 | 45226 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.18 | 100.14 | WP_011226049 |
| KMMCNEJI_6 | 77862 | 78908 | rfbB | 0.0 | Capsule | Immune modulation | 94.17 | 100.00 | WP_002947383 |
| KMMCNEJI_4 | 43766 | 45226 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.05 | 100.00 | WP_011681177 |
| KMMCNEJI_4 | 46669 | 47409 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 93.79 | 100.00 | WP_011681174 |
| KMMCNEJI_4 | 43766 | 45226 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.29 | 100.14 | WP_041827043 |
| KMMCNEJI_4 | 46669 | 47409 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.12 | 100.00 | WP_011226046 |
| KMMCNEJI_4 | 45227 | 45958 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.62 | 100.00 | WP_011226048 |
| KMMCNEJI_6 | 77066 | 77659 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 92.59 | 100.00 | WP_011226149 |
| KMMCNEJI_4 | 46669 | 47404 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 92.53 | 98.13 | WP_011227246 |
| KMMCNEJI_4 | 45227 | 45958 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 92.49 | 100.00 | WP_011681176 |
| KMMCNEJI_6 | 77066 | 77659 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| KMMCNEJI_6 | 77066 | 77659 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| KMMCNEJI_25 | 86304 | 87154 | rfbD | 0.0 | Capsule | Immune modulation | 92.01 | 99.88 | WP_014621820 |
| KMMCNEJI_4 | 45227 | 45958 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011227248 |
| KMMCNEJI_6 | 76197 | 77066 | rfbA | 0.0 | Capsule | Immune modulation | 91.15 | 100.00 | WP_011681286 |
| KMMCNEJI_26 | 73844 | 75502 | fbp54 | 0.0 | FBPs | Adherence | 91.08 | 99.94 | WP_011227179 |
| KMMCNEJI_4 | 45967 | 46659 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.92 | 99.71 | WP_011227247 |
| KMMCNEJI_4 | 45967 | 46659 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.92 | 99.71 | WP_011226047 |
| KMMCNEJI_23 | 14247 | 15257 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.65 | 99.80 | WP_002986042 |
| KMMCNEJI_33 | 90517 | 91820 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.40 | 99.54 | WP_000022832 |
| KMMCNEJI_2 | 5363 | 6268 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.30 | 93.50 | WP_082302295 |
| KMMCNEJI_4 | 45967 | 46659 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.05 | 99.71 | WP_011681175 |
| KMMCNEJI_5 | 53435 | 54196 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| KMMCNEJI_43 | 2155 | 3438 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.93 | 99.53 | WP_000107753 |
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 |
|---|---|---|---|---|---|---|---|---|
| KMMCNEJI_5 | 62327 | 63400 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| KMMCNEJI_5 | 50747 | 49773 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.00 | 99.09 | AAK75326 |
| KMMCNEJI_19 | 36920 | 39226 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| KMMCNEJI_15 | 74946 | 76427 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| KMMCNEJI_14 | 74514 | 75482 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| KMMCNEJI_5 | 81871 | 84117 | metE | 0.0 | methionine biosynthesis enzymes | 92.39 | 100.00 | AAK74738 |
| KMMCNEJI_35 | 15376 | 14405 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| KMMCNEJI_15 | 6998 | 435 | PrtA | 0.0 | serine protease | 90.05 | 101.96 | ABJ55268 |
| KMMCNEJI_6 | 49330 | 51060 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.78 | 100.00 | AAK34199 |
| KMMCNEJI_24 | 63396 | 64547 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| KMMCNEJI_24 | 92142 | 94130 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.29 | 100.00 | AE014259_2 |
| KMMCNEJI_17 | 29704 | 28226 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.63 | 100.00 | ADE32434 |
| KMMCNEJI_33 | 91820 | 90519 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| KMMCNEJI_17 | 13928 | 12036 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| KMMCNEJI_5 | 87039 | 85330 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| KMMCNEJI_32 | 2075 | 984 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| KMMCNEJI_10 | 24064 | 23054 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| KMMCNEJI_26 | 89277 | 87916 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| KMMCNEJI_33 | 106230 | 105340 | bglB | 1.58e-177 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| KMMCNEJI_26 | 12858 | 11908 | SP_0676 | 3.33e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| KMMCNEJI_5 | 84307 | 85164 | metF | 4.92e-169 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| KMMCNEJI_25 | 87154 | 86315 | GacA | 6.49e-151 | dTDP-4-dehydrorhamnose reductas | 80.00 | 98.59 | AAZ51220 |
| KMMCNEJI_11 | 114545 | 115225 | NisR | 1.57e-131 | two-component signal-transduction systems | 93.83 | 100.00 | ABP89873 |
| KMMCNEJI_11 | 115213 | 115917 | NisK | 8.06e-131 | two-component signal-transduction systems | 90.64 | 100.00 | ABP89872 |
| KMMCNEJI_15 | 25107 | 24436 | rr01 | 3.74e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| KMMCNEJI_4 | 1764 | 2468 | covR | 2.07e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| KMMCNEJI_5 | 91777 | 92448 | ciaR | 1.09e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| KMMCNEJI_5 | 91777 | 92445 | CiaR | 2.01e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| KMMCNEJI_4 | 1764 | 2468 | walR | 3.79e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| KMMCNEJI_1 | 147314 | 148000 | CovR | 4.39e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| KMMCNEJI_32 | 811 | 416 | SpxA2 | 2.18e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| KMMCNEJI_26 | 100744 | 101145 | SpxA1 | 1.30e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| KMMCNEJI_34 | 26058 | 26471 | GrpE | 5.90e-68 | protein grpE | 81.16 | 80.59 | ABP89267 |
| KMMCNEJI_1 | 170483 | 170770 | spr0479 | 4.25e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| KMMCNEJI_14 | 31742 | 31996 | spr1327 | 3.22e-44 | essential gene | 90.59 | 100.00 | AAL00131 |
| KMMCNEJI_7 | 38263 | 38000 | spr0175 | 3.56e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| KMMCNEJI_7 | 37439 | 37173 | spr0177 | 7.90e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| KMMCNEJI_11 | 24045 | 24182 | srtA | 2.25e-17 | sortase | 82.61 | 100.00 | AAK33966 |
| KMMCNEJI_43 | 3605 | 4096 | RopE (M5005_Spy_1611) | 4.21e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| KMMCNEJI_19 | 36920 | 39220 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| KMMCNEJI_40 | 22080 | 23099 | 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 |
|---|---|---|---|
| KMMCNEJI_1 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_2 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_4 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_5 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_6 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_7 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_8 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_9 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_10 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_11 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_12 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_13 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_14 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_15 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_17 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_19 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_21 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_22 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_23 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_24 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_25 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_26 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_27 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_29 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_30 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_31 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_32 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_33 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_34 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_35 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_36 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_38 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_40 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_41 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_42 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_43 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_44 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_45 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_47 | 0.0 | 1.0 | 0.0 |
| KMMCNEJI_48 | 1.0 | 0.0 | 1.0 |
| KMMCNEJI_49 | 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)