Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 0 | 20 | 35 | 40.31 |
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. |
|---|---|---|---|---|---|---|---|
| No hit found | |||||||
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| No hit found | ||||||||
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. |
|---|---|---|---|---|---|---|---|---|---|
| LKGFLNNG_69 | 18565 | 19416 | rfbD | 0.0 | Capsule | Immune modulation | 95.31 | 100.00 | WP_014621820 |
| LKGFLNNG_26 | 1845 | 2576 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 94.67 | 100.00 | WP_011681176 |
| LKGFLNNG_26 | 1845 | 2576 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 94.40 | 100.00 | WP_011226048 |
| LKGFLNNG_26 | 1845 | 2576 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 93.99 | 100.00 | WP_011227248 |
| LKGFLNNG_69 | 24744 | 26500 | STU_RS16230 | 0.0 | Capsule | Immune modulation | 92.94 | 98.43 | WP_011226325 |
| LKGFLNNG_69 | 20738 | 21694 | STU_RS16250 | 0.0 | Capsule | Immune modulation | 92.48 | 100.00 | WP_011226328 |
| LKGFLNNG_69 | 21678 | 22487 | STU_RS16245 | 0.0 | Capsule | Immune modulation | 92.23 | 99.88 | WP_002948020 |
| LKGFLNNG_69 | 22487 | 23692 | STU_RS16240 | 0.0 | Capsule | Immune modulation | 92.21 | 100.00 | WP_011226326 |
| LKGFLNNG_69 | 19593 | 20741 | STU_RS16255 | 0.0 | Capsule | Immune modulation | 91.56 | 99.91 | WP_041828290 |
| LKGFLNNG_69 | 23713 | 24747 | STU_RS16235 | 0.0 | Capsule | Immune modulation | 91.10 | 99.15 | WP_002948022 |
| LKGFLNNG_58 | 24474 | 25067 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 91.08 | 100.00 | WP_011226149 |
| LKGFLNNG_26 | 384 | 1844 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 90.92 | 99.86 | WP_011681177 |
| LKGFLNNG_58 | 24474 | 25067 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| LKGFLNNG_58 | 24474 | 25067 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 90.91 | 100.00 | WP_011226149 |
| LKGFLNNG_26 | 384 | 1844 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 90.78 | 100.00 | WP_011226049 |
| LKGFLNNG_41 | 37534 | 39192 | fbp54 | 0.0 | FBPs | Adherence | 90.54 | 99.94 | WP_011227179 |
| LKGFLNNG_26 | 384 | 1844 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 89.97 | 100.00 | WP_041827043 |
| LKGFLNNG_26 | 2585 | 3277 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 89.90 | 100.00 | WP_011226047 |
| LKGFLNNG_26 | 2585 | 3277 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 89.61 | 100.00 | WP_011227247 |
| LKGFLNNG_26 | 2585 | 3277 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 89.47 | 100.00 | WP_011681175 |
| LKGFLNNG_80 | 33406 | 34709 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.24 | 99.54 | WP_000022832 |
| LKGFLNNG_101 | 24722 | 25561 | cbpD | 0.0 | Autolysin | Exoenzyme | 87.87 | 99.88 | WP_011226733 |
| LKGFLNNG_63 | 120 | 1133 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 85.67 | 99.90 | WP_002986042 |
| LKGFLNNG_54 | 11200 | 11961 | srtA | 0.0 | Sortase A | Exoenzyme | 83.88 | 99.87 | - |
| LKGFLNNG_58 | 25337 | 26383 | rfbB | 0.0 | Capsule | Immune modulation | 83.49 | 99.90 | WP_002263087 |
| LKGFLNNG_62 | 11970 | 13253 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.61 | 99.61 | WP_000107753 |
| LKGFLNNG_58 | 23605 | 24474 | rfbA | 0.0 | Capsule | Immune modulation | 80.28 | 99.77 | WP_002904719 |
| LKGFLNNG_26 | 3287 | 3957 | STU_RS14635 | 2.72e-148 | Capsule | Immune modulation | 80.98 | 90.28 | WP_011226046 |
| LKGFLNNG_26 | 3287 | 3957 | STER_RS05305 | 1.27e-146 | Capsule | Immune modulation | 80.83 | 90.28 | WP_011681174 |
| LKGFLNNG_26 | 3287 | 3889 | STR_RS05250 | 1.28e-136 | Capsule | Immune modulation | 81.46 | 80.13 | 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 |
|---|---|---|---|---|---|---|---|---|
| LKGFLNNG_54 | 8510 | 7527 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| LKGFLNNG_54 | 20095 | 21168 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| LKGFLNNG_79 | 2526 | 4832 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.41 | 99.22 | AAK74619 |
| LKGFLNNG_36 | 5745 | 7226 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| LKGFLNNG_131 | 71214 | 72182 | spr0084 | 0.0 | pathogenitcity related | 92.88 | 98.48 | AAK98888 |
| LKGFLNNG_41 | 170557 | 168311 | metE | 0.0 | methionine biosynthesis enzymes | 92.79 | 100.00 | AAK74738 |
| LKGFLNNG_40 | 36359 | 35388 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.67 | 100.00 | ABF36968 |
| LKGFLNNG_17 | 4152 | 10625 | PrtA | 0.0 | serine protease | 91.44 | 100.61 | ABJ55268 |
| LKGFLNNG_66 | 9588 | 11318 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 89.95 | 100.00 | AAK34199 |
| LKGFLNNG_69 | 4933 | 6921 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.74 | 100.00 | AE014259_2 |
| LKGFLNNG_20 | 44646 | 45797 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| LKGFLNNG_10 | 7291 | 8769 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| LKGFLNNG_80 | 34709 | 33408 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| LKGFLNNG_10 | 23071 | 24963 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.58 | 98.90 | ABP91129 |
| LKGFLNNG_40 | 1211 | 120 | recA | 0.0 | DNA recombination and repair | 84.91 | 95.36 | AAL00560 |
| LKGFLNNG_41 | 165393 | 167102 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| LKGFLNNG_41 | 23380 | 24741 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.89 | 99.56 | ABP90420 |
| LKGFLNNG_111 | 19528 | 20538 | pdh | 0.0 | pyruvate dehydrogenase | 82.79 | 99.70 | ABP91006 |
| LKGFLNNG_80 | 49119 | 48229 | bglB | 3.77e-178 | putative phospho--glucosidase | 87.20 | 99.66 | AAK33487 |
| LKGFLNNG_41 | 168121 | 167264 | metF | 5.98e-170 | methionine biosynthesis enzymes | 87.76 | 99.31 | AAK74739 |
| LKGFLNNG_41 | 123855 | 124793 | SP_0676 | 1.24e-168 | transcription facot | 81.47 | 97.20 | AAK74821 |
| LKGFLNNG_91 | 74693 | 73836 | mtsA | 1.24e-151 | substrate-binding lipoprotein of manganese transporter | 80.14 | 92.86 | AIK76191 |
| LKGFLNNG_55 | 2301 | 3005 | covR | 1.06e-127 | responder protein | 85.53 | 100.00 | AAK71319 |
| LKGFLNNG_8 | 9487 | 8816 | rr01 | 1.64e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| LKGFLNNG_41 | 160728 | 160057 | ciaR | 1.73e-125 | two component system response regulator | 86.16 | 99.12 | AIK75708 |
| LKGFLNNG_41 | 160728 | 160060 | CiaR | 3.20e-125 | two-component response regulator | 87.44 | 99.55 | AAK74935 |
| LKGFLNNG_55 | 2301 | 3005 | walR | 2.40e-121 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| LKGFLNNG_22 | 10780 | 11466 | CovR | 3.93e-121 | serves to repress GAS virulence factor-encoding genes | 82.10 | 100.00 | ACE75886 |
| LKGFLNNG_93 | 726 | 331 | SpxA2 | 1.17e-84 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| LKGFLNNG_41 | 11922 | 11521 | SpxA1 | 1.15e-69 | transcriptional regulator | 82.09 | 100.00 | ERL19273 |
| LKGFLNNG_43 | 33256 | 33669 | GrpE | 3.10e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| LKGFLNNG_22 | 33985 | 34272 | spr0479 | 1.25e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| LKGFLNNG_131 | 37553 | 37807 | spr1327 | 2.67e-46 | essential gene | 94.12 | 100.00 | AAL00131 |
| LKGFLNNG_10 | 54250 | 53987 | spr0175 | 3.45e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| LKGFLNNG_10 | 53425 | 53159 | spr0177 | 7.65e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| LKGFLNNG_62 | 11803 | 11312 | RopE (M5005_Spy_1611) | 7.13e-74 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| LKGFLNNG_79 | 2526 | 4826 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| LKGFLNNG_111 | 55658 | 54639 | 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. |
|---|---|---|---|---|---|---|
| No hit found | ||||||
PlasmidFinder v 2.1.6 (Database: plasmidfinder_db v 2.2.0 , Nov. 2024 release)
PlasmidHunter
| Query ID | Prediction | Chromosome | Plasmid |
|---|---|---|---|
| LKGFLNNG_8 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_10 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_13 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_17 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_20 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_22 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_26 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_31 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_36 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_40 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_41 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_43 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_49 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_50 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_51 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_52 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_53 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_54 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_55 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_56 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_57 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_58 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_59 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_60 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_61 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_62 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_63 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_64 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_65 | 1.0 | 0.0 | 1.0 |
| LKGFLNNG_66 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_67 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_68 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_69 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_70 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_71 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_72 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_73 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_75 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_77 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_79 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_80 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_81 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_86 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_87 | 1.0 | 0.0 | 1.0 |
| LKGFLNNG_88 | 1.0 | 0.0 | 1.0 |
| LKGFLNNG_90 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_91 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_101 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_111 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_121 | 0.0 | 1.0 | 0.0 |
| LKGFLNNG_131 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| LKGFLNNG_58 | 102042 | 142713 | False | Siphoviridae | VOG9667, VOG8230, VOG4552, VOG3478, VOG3938, VOG4555, VOG0651, VOG5996, VOG4566, VOG0189, VOG3430, VOG1309, VOG0685, VOG0226, VOG4693, VOG0655, VOG6414, VOG0656, VOG0152, VOG4567, VOG0657, VOG5439, VOG0044, VOG5562, VOG0658, VOG0198, VOG0796, VOG4544, VOG5047, VOG0720, VOG4564, VOG3434, VOG1887, VOG3435, VOG4713, VOG0723, VOG5660, VOG0724, VOG0799, VOG0725, VOG0800, VOG3636, VOG4605, VOG4599, VOG0647, VOG0648, VOG0641, VOG0054, VOG4649, VOG3299, VOG8184, VOG3300 |
Phigaro v2.4.0 (Database: Jan. 2024 release)