Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 20 | 35 | 40.36 |
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. |
|---|---|---|---|---|---|---|---|
| CPNEBNBK_11 | 199657 | 201120 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | AF274302 |
| CPNEBNBK_11 | 201240 | 202457 | mef(A) | Erythromycin, Azithromycin | 99.84 | 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. |
|---|---|---|---|---|---|---|---|---|
| CPNEBNBK_11 | 199660 | 201120 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | EXACTX | 100.00 | 100.00 | WP_000420313.1 |
| CPNEBNBK_11 | 201243 | 202457 | mef(A) | macrolide efflux MFS transporter Mef(A) | BLASTX | 99.75 | 100.00 | WP_000417519.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CPNEBNBK_1 | 155825 | 156676 | rfbD | 0.0 | Capsule | Immune modulation | 95.31 | 100.00 | WP_014621820 |
| CPNEBNBK_31 | 67296 | 68027 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.26 | 100.00 | WP_011227248 |
| CPNEBNBK_31 | 67296 | 68027 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.58 | 100.00 | WP_011226048 |
| CPNEBNBK_31 | 67296 | 68027 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.31 | 100.00 | WP_011681176 |
| CPNEBNBK_1 | 162004 | 163760 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.60 | 98.43 | WP_011226325 |
| CPNEBNBK_1 | 157998 | 158954 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.48 | 100.00 | WP_011226328 |
| CPNEBNBK_1 | 158938 | 159747 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.23 | 99.88 | WP_002948020 |
| CPNEBNBK_1 | 159747 | 160952 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.21 | 100.00 | WP_011226326 |
| CPNEBNBK_1 | 156853 | 158001 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.56 | 99.91 | WP_041828290 |
| CPNEBNBK_31 | 68028 | 69488 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.40 | 99.86 | WP_011681177 |
| CPNEBNBK_13 | 24425 | 25018 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| CPNEBNBK_1 | 160973 | 162007 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.00 | 99.15 | WP_002948022 |
| CPNEBNBK_13 | 24425 | 25018 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| CPNEBNBK_13 | 24425 | 25018 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| CPNEBNBK_31 | 68028 | 69488 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| CPNEBNBK_11 | 143123 | 144781 | fbp54 | 0.0 | FBPs | Adherence | 90.43 | 99.88 | WP_011227179 |
| CPNEBNBK_31 | 68028 | 69488 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 90.10 | 100.00 | WP_041827043 |
| CPNEBNBK_31 | 66595 | 67287 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| CPNEBNBK_1 | 95585 | 96490 | cbpD | 0.0 | Autolysin | Exoenzyme | 89.84 | 93.50 | WP_082302295 |
| CPNEBNBK_31 | 66595 | 67287 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| CPNEBNBK_31 | 66595 | 67287 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| CPNEBNBK_17 | 51723 | 53026 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.17 | 99.54 | WP_000022832 |
| CPNEBNBK_15 | 14214 | 15227 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| CPNEBNBK_34 | 17141 | 17902 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| CPNEBNBK_13 | 25288 | 26334 | rfbB | 0.0 | Capsule | Immune modulation | 83.59 | 99.90 | WP_002263087 |
| CPNEBNBK_5 | 41344 | 42627 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | WP_000107753 |
| CPNEBNBK_13 | 23556 | 24425 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| CPNEBNBK_31 | 65915 | 66585 | STU_RS14635 | 1.27e-149 | Capsule | Immune modulation | 81.13 | 90.28 | WP_011226046 |
| CPNEBNBK_31 | 65915 | 66585 | STER_RS05305 | 5.89e-148 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011681174 |
| CPNEBNBK_31 | 65915 | 66585 | STR_RS05250 | 5.97e-138 | Capsule | Immune modulation | 80.09 | 89.20 | WP_011227246 |
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 |
|---|---|---|---|---|---|---|---|---|
| CPNEBNBK_34 | 20591 | 21574 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| CPNEBNBK_34 | 9004 | 7931 | MntE | 0.0 | manganese homeostasis | 95.81 | 99.72 | ABF32167 |
| CPNEBNBK_32 | 149302 | 146996 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| CPNEBNBK_33 | 98731 | 100212 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.32 | 100.00 | ABJ54480 |
| CPNEBNBK_11 | 10105 | 12351 | metE | 0.0 | methionine biosynthesis enzymes | 92.79 | 100.00 | AAK74738 |
| CPNEBNBK_7 | 41444 | 40476 | spr0084 | 0.0 | pathogenitcity related | 92.26 | 98.48 | AAK98888 |
| CPNEBNBK_9 | 3855 | 4826 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| CPNEBNBK_33 | 13585 | 7022 | PrtA | 0.0 | serine protease | 90.10 | 101.96 | ABJ55268 |
| CPNEBNBK_3 | 99092 | 100822 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| CPNEBNBK_1 | 143649 | 145637 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| CPNEBNBK_20 | 44074 | 45225 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.32 | 99.74 | AAL00050 |
| CPNEBNBK_12 | 25768 | 27246 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| CPNEBNBK_17 | 51723 | 53024 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| CPNEBNBK_4 | 14079 | 12187 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| CPNEBNBK_24 | 12549 | 13640 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| CPNEBNBK_11 | 15269 | 13560 | PGM | 0.0 | phosphoglucomutase | 84.59 | 99.65 | ACH87041 |
| CPNEBNBK_28 | 22037 | 23047 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| CPNEBNBK_11 | 158550 | 157189 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| CPNEBNBK_17 | 37317 | 38207 | bglB | 8.90e-179 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| CPNEBNBK_11 | 55230 | 54280 | SP_0676 | 3.04e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| CPNEBNBK_11 | 12541 | 13398 | metF | 2.35e-168 | methionine biosynthesis enzymes | 86.71 | 99.31 | AAK74739 |
| CPNEBNBK_3 | 62225 | 61368 | mtsA | 2.88e-152 | substrate-binding lipoprotein of manganese transporter | 80.49 | 92.86 | AIK76191 |
| CPNEBNBK_25 | 3852 | 3148 | covR | 1.21e-128 | responder protein | 85.53 | 100.00 | AAK71319 |
| CPNEBNBK_33 | 37467 | 36796 | rr01 | 3.16e-127 | response regulator | 85.27 | 99.56 | CAB54566 |
| CPNEBNBK_11 | 19934 | 20605 | ciaR | 9.21e-125 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| CPNEBNBK_11 | 19934 | 20602 | CiaR | 1.14e-124 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| CPNEBNBK_25 | 3852 | 3148 | walR | 3.66e-122 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| CPNEBNBK_22 | 55154 | 54468 | CovR | 9.93e-121 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| CPNEBNBK_24 | 13814 | 14209 | SpxA2 | 1.40e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| CPNEBNBK_11 | 170019 | 170420 | SpxA1 | 1.31e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| CPNEBNBK_6 | 13923 | 14336 | GrpE | 1.57e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| CPNEBNBK_22 | 31946 | 31659 | spr0479 | 6.49e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| CPNEBNBK_10 | 32876 | 33130 | spr1327 | 1.85e-46 | essential gene | 94.12 | 100.00 | AAL00131 |
| CPNEBNBK_18 | 35372 | 35635 | spr0175 | 3.03e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| CPNEBNBK_18 | 36197 | 36463 | spr0177 | 6.73e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| CPNEBNBK_5 | 41177 | 40686 | RopE (M5005_Spy_1611) | 2.13e-73 | probable DNA-directed RNA polymerase subunit delta | 83.54 | 85.86 | AAK34603 |
| CPNEBNBK_32 | 149302 | 147002 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.36 | 98.08 | MYN69560 |
| CPNEBNBK_28 | 58169 | 57150 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| CPNEBNBK_11 | 121669 | 122208 | pnuC | 3.82e-99 | NAD salvage pathway importer | 88.89 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CPNEBNBK_1 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_2 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_3 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_4 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_5 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_6 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_7 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_8 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_9 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_10 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_11 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_12 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_13 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_15 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_16 | 1.0 | 0.0 | 1.0 |
| CPNEBNBK_17 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_18 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_19 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_20 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_21 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_22 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_23 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_24 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_25 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_26 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_27 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_28 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_29 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_30 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_31 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_32 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_33 | 0.0 | 1.0 | 0.0 |
| CPNEBNBK_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 |
|---|---|---|---|---|---|
| No hit found | |||||
Phigaro v2.4.0 (Database: Jan. 2024 release)