Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 1 | 20 | 35 | 40.32 |
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. |
|---|---|---|---|---|---|---|---|---|
| HLKJGPCH_3 | 148133 | 150052 | tet(M) | ARO:3000186 | tet(M) | 90.77 | 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. |
|---|---|---|---|---|---|---|---|
| HLKJGPCH_3 | 148133 | 150051 | tet(M) | Doxycycline, Tetracycline, Minocycline | 95.15 | 99.95 | JN846696 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| HLKJGPCH_3 | 148133 | 150049 | tet(M) | tetracycline resistance ribosomal protection protein Tet(M) | BLASTX | 98.28 | 100.00 | WP_011860841.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| HLKJGPCH_5 | 91647 | 92498 | rfbD | 0.0 | Capsule | Immune modulation | 95.31 | 100.00 | WP_014621820 |
| HLKJGPCH_15 | 24306 | 25037 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.99 | 100.00 | WP_011227248 |
| HLKJGPCH_15 | 24306 | 25037 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011681176 |
| HLKJGPCH_15 | 24306 | 25037 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.31 | 100.00 | WP_011226048 |
| HLKJGPCH_5 | 84563 | 86319 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.60 | 98.43 | WP_011226325 |
| HLKJGPCH_5 | 89369 | 90325 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.48 | 100.00 | WP_011226328 |
| HLKJGPCH_5 | 88576 | 89385 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.23 | 99.88 | WP_002948020 |
| HLKJGPCH_5 | 87371 | 88576 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.21 | 100.00 | WP_011226326 |
| HLKJGPCH_5 | 90322 | 91470 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.56 | 99.91 | WP_041828290 |
| HLKJGPCH_6 | 35700 | 36293 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.25 | 100.00 | WP_011226149 |
| HLKJGPCH_15 | 25038 | 26498 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.19 | 99.86 | WP_011681177 |
| HLKJGPCH_5 | 86316 | 87350 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.10 | 99.15 | WP_002948022 |
| HLKJGPCH_6 | 35700 | 36293 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| HLKJGPCH_6 | 35700 | 36293 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| HLKJGPCH_2 | 143179 | 144837 | fbp54 | 0.0 | FBPs | Adherence | 91.08 | 99.94 | WP_011227179 |
| HLKJGPCH_15 | 25038 | 26498 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| HLKJGPCH_15 | 25038 | 26498 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 90.10 | 100.00 | WP_041827043 |
| HLKJGPCH_15 | 23605 | 24297 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 90.04 | 100.00 | WP_011226047 |
| HLKJGPCH_15 | 23605 | 24297 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.75 | 100.00 | WP_011227247 |
| HLKJGPCH_15 | 23605 | 24297 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011681175 |
| HLKJGPCH_17 | 16278 | 17117 | cbpD | 0.0 | Autolysin | Exoenzyme | 89.06 | 99.88 | WP_011226733 |
| HLKJGPCH_14 | 1 | 1302 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.23 | 99.39 | WP_000022832 |
| HLKJGPCH_1 | 403344 | 404357 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| HLKJGPCH_19 | 17594 | 18355 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| HLKJGPCH_6 | 36563 | 37609 | rfbB | 0.0 | Capsule | Immune modulation | 83.40 | 99.90 | WP_002263087 |
| HLKJGPCH_4 | 187825 | 189108 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.84 | 99.61 | WP_000107753 |
| HLKJGPCH_6 | 34831 | 35700 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| HLKJGPCH_15 | 22925 | 23595 | STU_RS14635 | 7.36e-147 | Capsule | Immune modulation | 80.83 | 90.28 | WP_011226046 |
| HLKJGPCH_15 | 22925 | 23595 | STER_RS05305 | 3.42e-145 | Capsule | Immune modulation | 80.68 | 90.28 | WP_011681174 |
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 |
|---|---|---|---|---|---|---|---|---|
| HLKJGPCH_19 | 21044 | 22027 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| HLKJGPCH_19 | 9458 | 8385 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| HLKJGPCH_1 | 275018 | 277324 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.15 | 99.22 | AAK74619 |
| HLKJGPCH_1 | 54729 | 53761 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| HLKJGPCH_2 | 10077 | 12323 | metE | 0.0 | methionine biosynthesis enzymes | 93.06 | 100.00 | AAK74738 |
| HLKJGPCH_3 | 106850 | 108331 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.51 | 100.00 | ABJ54480 |
| HLKJGPCH_38 | 3823 | 4794 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| HLKJGPCH_3 | 17282 | 10809 | PrtA | 0.0 | serine protease | 91.35 | 100.61 | ABJ55268 |
| HLKJGPCH_6 | 9454 | 11184 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 90.12 | 100.00 | AAK34199 |
| HLKJGPCH_1 | 129381 | 128230 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| HLKJGPCH_5 | 104685 | 102697 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.44 | 100.00 | AE014259_2 |
| HLKJGPCH_10 | 42934 | 41456 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| HLKJGPCH_14 | 1302 | 1 | Eno | 0.0 | enolase | 86.21 | 99.77 | ABP90468 |
| HLKJGPCH_10 | 27591 | 25699 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.74 | 98.90 | ABP91129 |
| HLKJGPCH_29 | 11943 | 13034 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| HLKJGPCH_2 | 15245 | 13536 | PGM | 0.0 | phosphoglucomutase | 84.59 | 99.65 | ACH87041 |
| HLKJGPCH_7 | 7420 | 8430 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| HLKJGPCH_2 | 158766 | 157405 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| HLKJGPCH_14 | 15712 | 14822 | bglB | 4.28e-179 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| HLKJGPCH_2 | 55243 | 54293 | SP_0676 | 2.58e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| HLKJGPCH_2 | 12513 | 13370 | metF | 1.69e-168 | methionine biosynthesis enzymes | 87.06 | 99.31 | AAK74739 |
| HLKJGPCH_11 | 10934 | 11791 | mtsA | 5.96e-152 | substrate-binding lipoprotein of manganese transporter | 80.14 | 92.86 | AIK76191 |
| HLKJGPCH_20 | 4932 | 5636 | covR | 1.35e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| HLKJGPCH_3 | 35136 | 34465 | rr01 | 1.39e-126 | response regulator | 84.38 | 99.56 | CAB54566 |
| HLKJGPCH_2 | 19910 | 20581 | ciaR | 2.24e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| HLKJGPCH_2 | 19910 | 20578 | CiaR | 4.14e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| HLKJGPCH_20 | 4932 | 5636 | walR | 1.20e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| HLKJGPCH_4 | 38221 | 37535 | CovR | 1.60e-120 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| HLKJGPCH_47 | 128 | 523 | SpxA2 | 6.63e-86 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| HLKJGPCH_2 | 170234 | 170635 | SpxA1 | 1.49e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| HLKJGPCH_12 | 33364 | 33777 | GrpE | 3.11e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| HLKJGPCH_4 | 15015 | 14728 | spr0479 | 5.05e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| HLKJGPCH_1 | 86215 | 85961 | spr1327 | 1.32e-45 | essential gene | 94.12 | 100.00 | AAL00131 |
| HLKJGPCH_7 | 97194 | 97457 | spr0175 | 5.08e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| HLKJGPCH_7 | 98019 | 98285 | spr0177 | 1.13e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| HLKJGPCH_4 | 187667 | 187167 | RopE (M5005_Spy_1611) | 2.16e-74 | probable DNA-directed RNA polymerase subunit delta | 82.64 | 87.43 | AAK34603 |
| HLKJGPCH_1 | 275018 | 277318 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 82.97 | 98.08 | MYN69560 |
| HLKJGPCH_7 | 44068 | 43049 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 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. |
|---|---|---|---|---|---|---|
| HLKJGPCH_3 | 138730 | 139934 | repUS43 | 1206 / 1206 | 90.05 | CP003584 |
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| HLKJGPCH_1 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_2 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_3 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_4 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_5 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_6 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_7 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_8 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_9 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_10 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_11 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_12 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_13 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_14 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_15 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_16 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_17 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_18 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_19 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_20 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_21 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_22 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_23 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_24 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_25 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_26 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_27 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_28 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_29 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_30 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_31 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_32 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_33 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_36 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_37 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_38 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_40 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_41 | 1.0 | 0.0 | 1.0 |
| HLKJGPCH_42 | 0.0 | 1.0 | 0.0 |
| HLKJGPCH_43 | 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)