Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 4 | 22 | 28 | 35.83 |
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. |
|---|---|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 1807152 | 1807889 | ErmB | ARO:3000375 | ErmB | 97.96 | 98.79 | AF242872.1 |
| CCKGGDKK_1 | 1804126 | 1806045 | 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. |
|---|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 1807152 | 1807889 | erm(B) | Erythromycin, Lincomycin, Clindamycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 100.00 | 100.00 | U86375 |
| CCKGGDKK_1 | 293153 | 294370 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| CCKGGDKK_1 | 291570 | 293033 | msr(D) | Erythromycin, Azithromycin, Telithromycin, Quinupristin, Pristinamycin IA, Virginiamycin S | 99.93 | 100.00 | AF274302 |
| CCKGGDKK_1 | 1804126 | 1806045 | tet(M) | Doxycycline, Tetracycline, Minocycline | 99.90 | 100.00 | X75073 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 1807152 | 1807886 | erm(B) | 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(B) | EXACTX | 100.00 | 100.00 | WP_001038790.1 |
| CCKGGDKK_1 | 293156 | 294370 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| CCKGGDKK_1 | 1804126 | 1806042 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | EXACTX | 100.00 | 100.00 | WP_000691727.1 |
| CCKGGDKK_1 | 291573 | 293033 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 2240903 | 2242363 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 96.85 | 100.00 | WP_011681177 |
| CCKGGDKK_1 | 2240903 | 2242363 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 96.58 | 100.21 | WP_011226049 |
| CCKGGDKK_1 | 2240903 | 2242363 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 95.89 | 100.21 | WP_041827043 |
| CCKGGDKK_1 | 2237298 | 2238663 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 95.39 | 99.85 | WP_011681173 |
| CCKGGDKK_1 | 1558958 | 1559809 | rfbD | 0.0 | Capsule | Immune modulation | 95.19 | 100.00 | WP_014621820 |
| CCKGGDKK_1 | 2238720 | 2239460 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 95.14 | 100.00 | WP_011681174 |
| CCKGGDKK_1 | 2238720 | 2239460 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 94.74 | 100.00 | WP_011226046 |
| CCKGGDKK_1 | 2237296 | 2238663 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_011226045 |
| CCKGGDKK_1 | 2238725 | 2239460 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 94.16 | 98.13 | WP_011227246 |
| CCKGGDKK_1 | 2240171 | 2240902 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 94.13 | 100.00 | WP_011681176 |
| CCKGGDKK_1 | 818145 | 819428 | tig/ropA | 0.0 | Trigger factor | Stress survival | 94.00 | 100.00 | WP_011225339 |
| CCKGGDKK_1 | 2240171 | 2240902 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.72 | 100.00 | WP_011226048 |
| CCKGGDKK_1 | 2240171 | 2240902 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.03 | 100.00 | WP_011227248 |
| CCKGGDKK_1 | 1561997 | 1562806 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.85 | 99.88 | WP_002948020 |
| CCKGGDKK_1 | 1565075 | 1566831 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.60 | 98.43 | WP_011226325 |
| CCKGGDKK_1 | 1561057 | 1562013 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.59 | 99.90 | WP_011226328 |
| CCKGGDKK_1 | 1559912 | 1561060 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 92.26 | 99.91 | WP_041828290 |
| CCKGGDKK_1 | 1562806 | 1564011 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.12 | 100.00 | WP_011226326 |
| CCKGGDKK_1 | 143270 | 143863 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.58 | 100.00 | WP_011226149 |
| CCKGGDKK_1 | 143270 | 143863 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.41 | 100.00 | WP_011226149 |
| CCKGGDKK_1 | 143270 | 143863 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.41 | 100.00 | WP_011226149 |
| CCKGGDKK_1 | 1564032 | 1565078 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.38 | 99.43 | WP_002948022 |
| CCKGGDKK_1 | 143863 | 144732 | rfbA | 0.0 | Capsule | Immune modulation | 91.03 | 100.00 | WP_011681286 |
| CCKGGDKK_1 | 914226 | 915065 | cbpD | 0.0 | Autolysin | Exoenzyme | 90.59 | 100.00 | WP_011226733 |
| CCKGGDKK_1 | 2130109 | 2131767 | fbp54 | 0.0 | FBPs | Adherence | 90.24 | 99.94 | WP_011227179 |
| CCKGGDKK_1 | 2239470 | 2240162 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 88.76 | 99.86 | WP_011227247 |
| CCKGGDKK_1 | 2239470 | 2240162 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 88.76 | 99.86 | WP_011226047 |
| CCKGGDKK_1 | 318366 | 319669 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| CCKGGDKK_1 | 2239470 | 2240162 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 88.18 | 99.86 | WP_011681175 |
| CCKGGDKK_1 | 1235674 | 1236684 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 87.36 | 99.80 | WP_002986042 |
| CCKGGDKK_1 | 141953 | 142999 | rfbB | 0.0 | Capsule | Immune modulation | 84.06 | 99.90 | WP_002263087 |
| CCKGGDKK_1 | 1974498 | 1975259 | srtA | 0.0 | Sortase A | Exoenzyme | 83.90 | 99.74 | - |
| CCKGGDKK_1 | 2228600 | 2229183 | SPD_RS01775 | 1.31e-156 | 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 |
|---|---|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 1983389 | 1984462 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| CCKGGDKK_1 | 1971810 | 1970836 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.00 | 99.09 | AAK75326 |
| CCKGGDKK_1 | 1357302 | 1354996 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| CCKGGDKK_1 | 1840341 | 1838860 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| CCKGGDKK_1 | 416944 | 415976 | spr0084 | 0.0 | pathogenitcity related | 92.57 | 98.48 | AAK98888 |
| CCKGGDKK_1 | 2002450 | 2004696 | metE | 0.0 | methionine biosynthesis enzymes | 92.39 | 100.00 | AAK74738 |
| CCKGGDKK_1 | 929489 | 928518 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| CCKGGDKK_1 | 170117 | 168387 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| CCKGGDKK_1 | 1518614 | 1519765 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| CCKGGDKK_1 | 1547021 | 1549009 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| CCKGGDKK_1 | 965039 | 966517 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.42 | 100.00 | ADE32434 |
| CCKGGDKK_1 | 319669 | 318368 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| CCKGGDKK_1 | 2007615 | 2005906 | PGM | 0.0 | phosphoglucomutase | 84.94 | 99.65 | ACH87041 |
| CCKGGDKK_1 | 894508 | 893417 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| CCKGGDKK_1 | 1180436 | 1179426 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| CCKGGDKK_1 | 2147329 | 2145968 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.46 | 99.56 | ABP90420 |
| CCKGGDKK_1 | 334075 | 333185 | bglB | 2.81e-177 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| CCKGGDKK_1 | 2004883 | 2005740 | metF | 1.02e-168 | methionine biosynthesis enzymes | 88.11 | 99.31 | AAK74739 |
| CCKGGDKK_1 | 2046956 | 2045994 | SP_0676 | 1.85e-168 | transcription facot | 80.69 | 99.69 | AAK74821 |
| CCKGGDKK_1 | 1895759 | 1896430 | rr01 | 4.85e-126 | response regulator | 84.82 | 99.56 | CAB54566 |
| CCKGGDKK_1 | 29326 | 28622 | covR | 1.01e-125 | responder protein | 85.53 | 100.00 | AAK71319 |
| CCKGGDKK_1 | 2011583 | 2012254 | ciaR | 1.01e-123 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| CCKGGDKK_1 | 2011583 | 2012251 | CiaR | 1.25e-123 | two-component response regulator | 87.00 | 99.55 | AAK74935 |
| CCKGGDKK_1 | 29326 | 28622 | walR | 2.29e-119 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| CCKGGDKK_1 | 662742 | 662056 | CovR | 4.94e-119 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| CCKGGDKK_1 | 893242 | 892868 | SpxA2 | 6.80e-70 | transcriptional regulator | 92.00 | 94.70 | ERL21461 |
| CCKGGDKK_1 | 2158797 | 2159198 | SpxA1 | 4.29e-69 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| CCKGGDKK_1 | 833527 | 833114 | GrpE | 4.16e-66 | protein grpE | 81.16 | 80.59 | ABP89267 |
| CCKGGDKK_1 | 817978 | 817487 | RopE (M5005_Spy_1611) | 1.09e-71 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| CCKGGDKK_1 | 1357302 | 1355002 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.09 | 98.08 | MYN69560 |
| CCKGGDKK_1 | 1069551 | 1070570 | 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. |
|---|---|---|---|---|---|---|
| CCKGGDKK_1 | 1794647 | 1795852 | repUS43 | 1206 / 1206 | 99.83 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| CCKGGDKK_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 |
|---|---|---|---|---|---|
| CCKGGDKK_1 | 1083869 | 1159865 | False | Siphoviridae | VOG0221, VOG4757, VOG4602, VOG0743, VOG6495, VOG7236, VOG7526, VOG4908, VOG0651, VOG5996, VOG8355, VOG1309, VOG0685, VOG0226, VOG4693, VOG0655, VOG3468, VOG0656, VOG0152, VOG0657, VOG0658, VOG0198, VOG0796, VOG4544, VOG0691, VOG0692, VOG4555, VOG4572, VOG0695, VOG0697, VOG8357, VOG0701, VOG3636, VOG3636, VOG4633, VOG4828, VOG5008, VOG0641, VOG0054, VOG5034, VOG7557, VOG7235, VOG10230, VOG0221, VOG4757, VOG4602, VOG0743, VOG6495, VOG7236, VOG7526, VOG4908, VOG0651, VOG5996, VOG8355, VOG1309, VOG0685, VOG0226, VOG4693, VOG0655, VOG3468, VOG0656, VOG0152, VOG0657, VOG0658, VOG0198, VOG0796, VOG4544, VOG0691, VOG0691, VOG0692, VOG0692, VOG4555, VOG4572, VOG0695, VOG0696, VOG0697, VOG0698, VOG8357, VOG0701, VOG3636, VOG4633, VOG4828, VOG5008, VOG0641, VOG0054, VOG5034, VOG7557, VOG7235, VOG10230, VOG3946 |
Phigaro v2.4.0 (Database: Jan. 2024 release)