Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 17 | 34 | 38.07 |
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. |
|---|---|---|---|---|---|---|---|
| HCKODEND_6 | 126170 | 127387 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| HCKODEND_6 | 124587 | 126050 | 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. |
|---|---|---|---|---|---|---|---|---|
| HCKODEND_6 | 126173 | 127387 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| HCKODEND_6 | 124590 | 126050 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| HCKODEND_7 | 51148 | 51864 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 96.79 | 100.00 | WP_011681442 |
| HCKODEND_1 | 223799 | 225259 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 96.58 | 100.00 | WP_011681177 |
| HCKODEND_1 | 223799 | 225259 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 96.23 | 100.21 | WP_011226049 |
| HCKODEND_1 | 223799 | 225259 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 95.69 | 100.21 | WP_041827043 |
| HCKODEND_1 | 220194 | 221559 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.17 | 99.85 | WP_011681173 |
| HCKODEND_1 | 220192 | 221559 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_011226045 |
| HCKODEND_1 | 221616 | 222356 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 94.06 | 100.00 | WP_011681174 |
| HCKODEND_7 | 46152 | 47003 | rfbD | 0.0 | Capsule | Immune modulation | 93.90 | 100.00 | WP_014621820 |
| HCKODEND_1 | 223067 | 223798 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011681176 |
| HCKODEND_1 | 223067 | 223798 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| HCKODEND_1 | 221616 | 222356 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 93.12 | 100.00 | WP_011226046 |
| HCKODEND_1 | 223067 | 223798 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.03 | 100.00 | WP_011227248 |
| HCKODEND_7 | 52210 | 52980 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.88 | 99.10 | WP_011681440 |
| HCKODEND_1 | 221621 | 222356 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 92.80 | 98.13 | WP_011227246 |
| HCKODEND_13 | 24504 | 25097 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.58 | 100.00 | WP_011226149 |
| HCKODEND_13 | 24504 | 25097 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.41 | 100.00 | WP_011226149 |
| HCKODEND_13 | 24504 | 25097 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.41 | 100.00 | WP_011226149 |
| HCKODEND_13 | 23635 | 24504 | rfbA | 0.0 | Capsule | Immune modulation | 90.69 | 100.00 | WP_011681286 |
| HCKODEND_1 | 114795 | 116453 | fbp54 | 0.0 | FBPs | Adherence | 90.48 | 99.94 | WP_011227179 |
| HCKODEND_15 | 19244 | 20083 | cbpD | 0.0 | Autolysin | Exoenzyme | 89.76 | 100.00 | WP_011226733 |
| HCKODEND_1 | 222366 | 223058 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.62 | 99.86 | WP_011227247 |
| HCKODEND_1 | 222366 | 223058 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.62 | 99.86 | WP_011226047 |
| HCKODEND_2 | 14433 | 15443 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 88.55 | 99.80 | WP_002986042 |
| HCKODEND_4 | 208455 | 209758 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.32 | 99.54 | WP_000022832 |
| HCKODEND_1 | 222366 | 223058 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 87.75 | 99.86 | WP_011681175 |
| HCKODEND_13 | 25483 | 26529 | rfbB | 0.0 | Capsule | Immune modulation | 84.45 | 99.90 | WP_002263087 |
| HCKODEND_3 | 27128 | 27889 | srtA | 0.0 | Sortase A | Exoenzyme | 83.75 | 99.87 | - |
| HCKODEND_5 | 1891 | 3174 | tig/ropA | 0.0 | Trigger factor | Stress survival | 81.08 | 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 |
|---|---|---|---|---|---|---|---|---|
| HCKODEND_3 | 30579 | 31553 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.61 | 99.09 | AAK75326 |
| HCKODEND_3 | 18994 | 17921 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| HCKODEND_2 | 135843 | 133537 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.28 | 99.22 | AAK74619 |
| HCKODEND_1 | 324 | 2570 | metE | 0.0 | methionine biosynthesis enzymes | 93.32 | 100.00 | AAK74738 |
| HCKODEND_3 | 186920 | 188401 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| HCKODEND_4 | 118014 | 118982 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| HCKODEND_15 | 4820 | 5791 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| HCKODEND_3 | 80297 | 73734 | PrtA | 0.0 | serine protease | 90.10 | 101.96 | ABJ55268 |
| HCKODEND_6 | 1892 | 162 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| HCKODEND_7 | 3815 | 4966 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| HCKODEND_7 | 32422 | 34410 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| HCKODEND_11 | 49416 | 47938 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.42 | 100.00 | ADE32434 |
| HCKODEND_4 | 208455 | 209756 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| HCKODEND_11 | 34088 | 32196 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| HCKODEND_1 | 5492 | 3783 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| HCKODEND_16 | 2725 | 1634 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| HCKODEND_8 | 86856 | 85846 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| HCKODEND_1 | 130384 | 129023 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| HCKODEND_4 | 194049 | 194939 | bglB | 2.66e-177 | putative phospho--glucosidase | 87.54 | 99.66 | AAK33487 |
| HCKODEND_1 | 47799 | 46849 | SP_0676 | 4.94e-169 | transcription facot | 81.07 | 98.45 | AAK74821 |
| HCKODEND_1 | 2760 | 3617 | metF | 1.54e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| HCKODEND_3 | 112370 | 111699 | rr01 | 1.04e-126 | response regulator | 84.38 | 99.56 | CAB54566 |
| HCKODEND_1 | 271027 | 270323 | covR | 5.64e-126 | responder protein | 85.11 | 100.00 | AAK71319 |
| HCKODEND_1 | 9460 | 10131 | ciaR | 3.41e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| HCKODEND_1 | 9460 | 10128 | CiaR | 6.31e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| HCKODEND_5 | 149710 | 150396 | CovR | 3.54e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| HCKODEND_1 | 271027 | 270323 | walR | 1.04e-119 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| HCKODEND_16 | 694 | 299 | SpxA2 | 1.50e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| HCKODEND_1 | 141850 | 142251 | SpxA1 | 4.19e-68 | transcriptional regulator | 81.34 | 100.00 | ERL19273 |
| HCKODEND_10 | 83481 | 83894 | GrpE | 1.65e-67 | protein grpE | 81.16 | 80.59 | ABP89267 |
| HCKODEND_14 | 11312 | 11599 | spr0479 | 1.25e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| HCKODEND_4 | 71393 | 71647 | spr1327 | 9.56e-45 | essential gene | 92.94 | 100.00 | AAL00131 |
| HCKODEND_11 | 2861 | 3124 | spr0175 | 3.89e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| HCKODEND_11 | 3687 | 3953 | spr0177 | 5.42e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| HCKODEND_5 | 3341 | 3832 | RopE (M5005_Spy_1611) | 7.84e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| HCKODEND_2 | 135843 | 133543 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.97 | 98.08 | MYN69560 |
| HCKODEND_8 | 50166 | 51185 | 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 |
|---|---|---|---|
| HCKODEND_1 | 0.0 | 1.0 | 0.0 |
| HCKODEND_2 | 0.0 | 1.0 | 0.0 |
| HCKODEND_3 | 0.0 | 1.0 | 0.0 |
| HCKODEND_4 | 0.0 | 1.0 | 0.0 |
| HCKODEND_5 | 0.0 | 1.0 | 0.0 |
| HCKODEND_6 | 0.0 | 1.0 | 0.0 |
| HCKODEND_7 | 0.0 | 1.0 | 0.0 |
| HCKODEND_8 | 0.0 | 1.0 | 0.0 |
| HCKODEND_9 | 0.0 | 1.0 | 0.0 |
| HCKODEND_10 | 0.0 | 1.0 | 0.0 |
| HCKODEND_11 | 0.0 | 1.0 | 0.0 |
| HCKODEND_12 | 0.0 | 1.0 | 0.0 |
| HCKODEND_13 | 0.0 | 1.0 | 0.0 |
| HCKODEND_14 | 0.0 | 1.0 | 0.0 |
| HCKODEND_15 | 0.0 | 1.0 | 0.0 |
| HCKODEND_16 | 0.0 | 1.0 | 0.0 |
| HCKODEND_18 | 1.0 | 0.0 | 1.0 |
| HCKODEND_19 | 0.0 | 1.0 | 0.0 |
| HCKODEND_20 | 0.0 | 1.0 | 0.0 |
| HCKODEND_21 | 1.0 | 0.0 | 1.0 |
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)