Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 16 | 35 | 38.54 |
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. |
|---|---|---|---|---|---|---|---|
| CMHDLHII_13 | 20069 | 21286 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| CMHDLHII_13 | 18486 | 19949 | 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. |
|---|---|---|---|---|---|---|---|---|
| CMHDLHII_13 | 20072 | 21286 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| CMHDLHII_13 | 18489 | 19949 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| CMHDLHII_9 | 50920 | 51651 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 94.54 | 100.00 | WP_011227248 |
| CMHDLHII_4 | 23798 | 24514 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 94.42 | 100.00 | WP_011681442 |
| CMHDLHII_4 | 20222 | 21073 | rfbD | 0.0 | Capsule | Immune modulation | 94.37 | 100.00 | WP_014621820 |
| CMHDLHII_9 | 50920 | 51651 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 93.85 | 100.00 | WP_011226048 |
| CMHDLHII_9 | 50920 | 51651 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 93.58 | 100.00 | WP_011681176 |
| CMHDLHII_4 | 24860 | 25630 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 92.35 | 99.23 | WP_011681440 |
| CMHDLHII_9 | 49459 | 50919 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 91.26 | 99.86 | WP_011681177 |
| CMHDLHII_5 | 134978 | 135571 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.25 | 100.00 | WP_011226149 |
| CMHDLHII_5 | 134978 | 135571 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| CMHDLHII_5 | 134978 | 135571 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| CMHDLHII_9 | 49459 | 50919 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.65 | 100.00 | WP_011226049 |
| CMHDLHII_14 | 39530 | 41187 | fbp54 | 0.0 | FBPs | Adherence | 90.30 | 99.88 | WP_011227179 |
| CMHDLHII_9 | 49459 | 50919 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| CMHDLHII_9 | 51660 | 52352 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| CMHDLHII_9 | 51660 | 52352 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| CMHDLHII_9 | 51660 | 52352 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| CMHDLHII_13 | 40960 | 42263 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| CMHDLHII_10 | 12044 | 12883 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| CMHDLHII_20 | 16125 | 17138 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| CMHDLHII_7 | 80693 | 81454 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| CMHDLHII_5 | 133662 | 134708 | rfbB | 0.0 | Capsule | Immune modulation | 83.59 | 99.90 | WP_002263087 |
| CMHDLHII_29 | 8443 | 9726 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.76 | 99.61 | WP_000107753 |
| CMHDLHII_5 | 135571 | 136440 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| CMHDLHII_9 | 52362 | 53032 | STU_RS14635 | 1.16e-149 | Capsule | Immune modulation | 81.13 | 90.28 | WP_011226046 |
| CMHDLHII_9 | 52362 | 53032 | STER_RS05305 | 5.42e-148 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011681174 |
| CMHDLHII_9 | 52362 | 53032 | STR_RS05250 | 5.50e-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 |
|---|---|---|---|---|---|---|---|---|
| CMHDLHII_7 | 84143 | 85126 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| CMHDLHII_7 | 72555 | 71482 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| CMHDLHII_1 | 87528 | 85222 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| CMHDLHII_15 | 35357 | 34389 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| CMHDLHII_2 | 96281 | 94800 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 93.12 | 100.00 | ABJ54480 |
| CMHDLHII_7 | 53495 | 51249 | metE | 0.0 | methionine biosynthesis enzymes | 92.79 | 100.00 | AAK74738 |
| CMHDLHII_19 | 5382 | 6353 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| CMHDLHII_11 | 3567 | 1837 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| CMHDLHII_4 | 5089 | 7077 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| CMHDLHII_1 | 282590 | 283741 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| CMHDLHII_18 | 37636 | 36158 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| CMHDLHII_13 | 42263 | 40962 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| CMHDLHII_18 | 22286 | 20394 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| CMHDLHII_19 | 41093 | 42184 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| CMHDLHII_7 | 48331 | 50040 | PGM | 0.0 | phosphoglucomutase | 84.59 | 99.65 | ACH87041 |
| CMHDLHII_14 | 25768 | 27129 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.89 | 99.56 | ABP90420 |
| CMHDLHII_8 | 92049 | 91039 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| CMHDLHII_13 | 56669 | 55779 | bglB | 7.98e-179 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| CMHDLHII_7 | 8362 | 9312 | SP_0676 | 1.75e-170 | transcription facot | 81.39 | 98.45 | AAK74821 |
| CMHDLHII_7 | 51059 | 50202 | metF | 1.35e-168 | methionine biosynthesis enzymes | 86.71 | 99.31 | AAK74739 |
| CMHDLHII_11 | 41180 | 42037 | mtsA | 2.22e-152 | substrate-binding lipoprotein of manganese transporter | 80.49 | 92.86 | AIK76191 |
| CMHDLHII_4 | 20222 | 21043 | GacA | 2.94e-147 | dTDP-4-dehydrorhamnose reductas | 80.29 | 96.48 | AAZ51220 |
| CMHDLHII_2 | 167041 | 167712 | rr01 | 4.27e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| CMHDLHII_9 | 17152 | 17856 | covR | 5.76e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| CMHDLHII_7 | 43666 | 42995 | ciaR | 1.14e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| CMHDLHII_7 | 43666 | 42998 | CiaR | 2.11e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| CMHDLHII_3 | 134605 | 135291 | CovR | 1.58e-120 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| CMHDLHII_9 | 17152 | 17856 | walR | 5.12e-120 | DNA-binding response regulator | 81.70 | 100.00 | ANC99504 |
| CMHDLHII_19 | 42357 | 42752 | SpxA2 | 4.22e-76 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| CMHDLHII_14 | 14311 | 13910 | SpxA1 | 4.06e-70 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| CMHDLHII_12 | 67813 | 68226 | GrpE | 5.78e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| CMHDLHII_3 | 157811 | 158098 | spr0479 | 1.03e-47 | essential gene | 85.42 | 98.97 | AAK99283 |
| CMHDLHII_23 | 17021 | 17275 | spr1327 | 8.18e-45 | essential gene | 90.59 | 100.00 | AAL00131 |
| CMHDLHII_8 | 1266 | 1003 | spr0175 | 5.76e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| CMHDLHII_8 | 441 | 175 | spr0177 | 1.28e-41 | essential gene | 83.15 | 88.12 | AAK98981 |
| CMHDLHII_29 | 8276 | 7785 | RopE (M5005_Spy_1611) | 5.08e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| CMHDLHII_1 | 87528 | 85228 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| CMHDLHII_8 | 55910 | 56929 | ilvC (SPD_0406) | 0.0 | ketol-acid reductoisomerase (NADP(+)) | 85.88 | 100.00 | ABJ55451 |
| CMHDLHII_14 | 54173 | 53634 | pnuC | 1.47e-98 | NAD salvage pathway importer | 88.33 | 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 |
|---|---|---|---|
| CMHDLHII_1 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_2 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_3 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_4 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_5 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_6 | 1.0 | 0.0 | 1.0 |
| CMHDLHII_7 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_8 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_9 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_10 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_11 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_12 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_13 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_14 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_15 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_16 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_17 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_18 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_19 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_20 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_21 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_22 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_23 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_24 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_25 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_26 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_27 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_28 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_29 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_30 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_33 | 0.0 | 1.0 | 0.0 |
| CMHDLHII_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 |
|---|---|---|---|---|---|
| CMHDLHII_1 | 193742 | 250633 | True | Siphoviridae | VOG1279, VOG10085, VOG0221, VOG1297, VOG3594, VOG9403, VOG9404, VOG6396, VOG9405, VOG9667, VOG3801, VOG4567, VOG8715, VOG8301, VOG0026, VOG4162, VOG0021, VOG1047, VOG7438, VOG9408, VOG4606, VOG0327, VOG4548, VOG9197, VOG8302, VOG8303, VOG8304, VOG4571, VOG4567, VOG7439, VOG4581, VOG4544, VOG4556, VOG4573, VOG4553, VOG0204, VOG4589, VOG1900, VOG0704, VOG4586, VOG1049, VOG3474, VOG4545, VOG4633, VOG4763, VOG0647, VOG0641, VOG4941, VOG9409, VOG0221, VOG0221 |
| CMHDLHII_5 | 21810 | 58248 | False | Siphoviridae | VOG4649, VOG0054, VOG7888, VOG0648, VOG0647, VOG4599, VOG4605, VOG6163, VOG0209, VOG4586, VOG0207, VOG0205, VOG0204, VOG4553, VOG4573, VOG4556, VOG0202, VOG1886, VOG4581, VOG4841, VOG0198, VOG0658, VOG0044, VOG5439, VOG0657, VOG4567, VOG9667, VOG0152, VOG6414, VOG0655, VOG4693, VOG0226, VOG0685, VOG0283, VOG5996, VOG0651, VOG4908, VOG3478, VOG9469, VOG1564 |
Phigaro v2.4.0 (Database: Jan. 2024 release)