Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 22 | 29 | 36.62 |
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. |
|---|---|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 790137 | 790874 | ErmB | ARO:3000375 | ErmB | 97.96 | 98.79 | AF242872.1 |
| NHKNCPHF_1 | 787111 | 789030 | tet(M) | ARO:3000186 | tet(M) | 99.37 | 100.00 | AB039845.1 |
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. |
|---|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 790137 | 790874 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | U86375 |
| NHKNCPHF_1 | 1504935 | 1506152 | mef(A) | Erythromycin, Azithromycin | 99.92 | 100.00 | HG423652 |
| NHKNCPHF_1 | 787111 | 789030 | tet(M) | Doxycycline, Tetracycline, Minocycline | 99.74 | 100.00 | X75073 |
| NHKNCPHF_1 | 1503346 | 1504809 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 98.50 | 100.00 | AF227520 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 790137 | 790871 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_001038790.1 |
| NHKNCPHF_1 | 787111 | 789027 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | EXACTX | 100.00 | 100.00 | WP_000691727.1 |
| NHKNCPHF_1 | 1504938 | 1506152 | mef(A) | macrolide efflux MFS transporter Mef(A) | BLASTX | 98.02 | 100.00 | WP_063853563.1 |
| NHKNCPHF_1 | 1503349 | 1504809 | msr(D) | ABC-F type ribosomal protection protein Msr(D) | BLASTX | 97.74 | 100.00 | WP_000420317.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 1178190 | 1178930 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.87 | 100.00 | WP_011681174 |
| NHKNCPHF_1 | 1176768 | 1178133 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 94.58 | 99.85 | WP_011681173 |
| NHKNCPHF_1 | 533845 | 534696 | rfbD | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_014621820 |
| NHKNCPHF_1 | 1180373 | 1181833 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 94.18 | 100.14 | WP_011226049 |
| NHKNCPHF_1 | 1180373 | 1181833 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 94.05 | 100.00 | WP_011681177 |
| NHKNCPHF_1 | 1176766 | 1178133 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.01 | 100.00 | WP_011226045 |
| NHKNCPHF_1 | 1178190 | 1178930 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.79 | 100.00 | WP_011226046 |
| NHKNCPHF_1 | 535797 | 537068 | STU_RS16265 | 0.0 | Capsule | Immune modulation | 93.63 | 99.76 | WP_011226331 |
| NHKNCPHF_1 | 1178195 | 1178930 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 93.61 | 98.13 | WP_011227246 |
| NHKNCPHF_1 | 1180373 | 1181833 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.29 | 100.14 | WP_041827043 |
| NHKNCPHF_1 | 542643 | 543848 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 93.28 | 100.00 | WP_011226326 |
| NHKNCPHF_1 | 544899 | 546683 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.83 | 99.94 | WP_011226325 |
| NHKNCPHF_1 | 540894 | 541850 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.37 | 100.00 | WP_011226328 |
| NHKNCPHF_1 | 541834 | 542643 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.35 | 100.00 | WP_002948020 |
| NHKNCPHF_1 | 1179641 | 1180372 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 92.08 | 100.00 | WP_011226048 |
| NHKNCPHF_1 | 1179641 | 1180372 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.67 | 100.00 | WP_011681176 |
| NHKNCPHF_1 | 539749 | 540897 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.56 | 99.91 | WP_041828290 |
| NHKNCPHF_1 | 1352374 | 1352967 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.41 | 100.00 | WP_011226149 |
| NHKNCPHF_1 | 543868 | 544902 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.30 | 99.05 | WP_002948022 |
| NHKNCPHF_1 | 1352374 | 1352967 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.25 | 100.00 | WP_011226149 |
| NHKNCPHF_1 | 1352374 | 1352967 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.25 | 100.00 | WP_011226149 |
| NHKNCPHF_1 | 1179641 | 1180372 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 91.12 | 100.00 | WP_011227248 |
| NHKNCPHF_1 | 1068888 | 1070546 | fbp54 | 0.0 | FBPs | Adherence | 90.90 | 99.94 | WP_011227179 |
| NHKNCPHF_1 | 1352967 | 1353836 | rfbA | 0.0 | Capsule | Immune modulation | 90.69 | 100.00 | WP_011681286 |
| NHKNCPHF_1 | 2110626 | 2111459 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.65 | 99.29 | WP_011226733 |
| NHKNCPHF_1 | 1178940 | 1179632 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.63 | 99.71 | WP_011227247 |
| NHKNCPHF_1 | 1178940 | 1179632 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.63 | 99.71 | WP_011226047 |
| NHKNCPHF_1 | 224794 | 225804 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.45 | 99.80 | WP_002986042 |
| NHKNCPHF_1 | 1526218 | 1527521 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| NHKNCPHF_1 | 1178940 | 1179632 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 86.91 | 99.71 | WP_011681175 |
| NHKNCPHF_1 | 934615 | 935376 | srtA | 0.0 | Sortase A | Exoenzyme | 84.67 | 99.87 | - |
| NHKNCPHF_1 | 1351125 | 1352171 | rfbB | 0.0 | Capsule | Immune modulation | 84.35 | 99.90 | WP_002263087 |
| NHKNCPHF_1 | 2017603 | 2018886 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | 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 |
|---|---|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 931926 | 930943 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.04 | 100.00 | AAK75326 |
| NHKNCPHF_1 | 943511 | 944584 | MntE | 0.0 | manganese homeostasis | 95.53 | 99.72 | ABF32167 |
| NHKNCPHF_1 | 351952 | 349646 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| NHKNCPHF_1 | 800501 | 799020 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| NHKNCPHF_1 | 1618138 | 1617170 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| NHKNCPHF_1 | 962569 | 964815 | metE | 0.0 | methionine biosynthesis enzymes | 92.12 | 100.00 | AAK74738 |
| NHKNCPHF_1 | 2125886 | 2124915 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| NHKNCPHF_1 | 1379225 | 1377495 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| NHKNCPHF_1 | 493309 | 494460 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| NHKNCPHF_1 | 521908 | 523896 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.29 | 100.00 | AE014259_2 |
| NHKNCPHF_1 | 13636 | 15114 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| NHKNCPHF_1 | 1527521 | 1526220 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| NHKNCPHF_1 | 28995 | 30887 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| NHKNCPHF_1 | 967734 | 966025 | PGM | 0.0 | phosphoglucomutase | 85.11 | 99.65 | ACH87041 |
| NHKNCPHF_1 | 2090486 | 2089395 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| NHKNCPHF_1 | 170954 | 169944 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| NHKNCPHF_1 | 1086102 | 1084741 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.24 | 99.56 | ABP90420 |
| NHKNCPHF_1 | 1541940 | 1541050 | bglB | 1.23e-176 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| NHKNCPHF_1 | 1007038 | 1006088 | SP_0676 | 2.66e-169 | transcription facot | 81.39 | 98.45 | AAK74821 |
| NHKNCPHF_1 | 965002 | 965859 | metF | 5.42e-168 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| NHKNCPHF_1 | 855528 | 856199 | rr01 | 4.52e-126 | response regulator | 84.82 | 99.56 | CAB54566 |
| NHKNCPHF_1 | 1226622 | 1225918 | covR | 9.58e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| NHKNCPHF_1 | 971702 | 972373 | ciaR | 2.06e-124 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| NHKNCPHF_1 | 971702 | 972370 | CiaR | 3.81e-124 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| NHKNCPHF_1 | 1226622 | 1225918 | walR | 2.18e-119 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| NHKNCPHF_1 | 1859716 | 1859030 | CovR | 4.70e-119 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| NHKNCPHF_1 | 2089221 | 2088826 | SpxA2 | 2.12e-74 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| NHKNCPHF_1 | 1097568 | 1097969 | SpxA1 | 4.40e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| NHKNCPHF_1 | 2032504 | 2032091 | GrpE | 1.67e-66 | protein grpE | 81.88 | 80.59 | ABP89267 |
| NHKNCPHF_1 | 2017436 | 2016945 | RopE (M5005_Spy_1611) | 1.04e-71 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| NHKNCPHF_1 | 351952 | 349652 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| NHKNCPHF_1 | 134536 | 135555 | 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. |
|---|---|---|---|---|---|---|
| NHKNCPHF_1 | 777632 | 778837 | repUS43 | 1206 / 1206 | 100.00 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| NHKNCPHF_1 | 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)