Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 2 | 19 | 34 | 39.00 |
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. |
|---|---|---|---|---|---|---|---|
| JNLCIPBI_21 | 222388 | 223605 | mef(A) | Erythromycin, Azithromycin | 100.00 | 100.00 | U83667 |
| JNLCIPBI_21 | 223725 | 225188 | 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. |
|---|---|---|---|---|---|---|---|---|
| JNLCIPBI_21 | 222388 | 223602 | mef(A) | macrolide efflux MFS transporter Mef(A) | EXACTX | 100.00 | 100.00 | WP_000417519.1 |
| JNLCIPBI_21 | 223725 | 225185 | 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. |
|---|---|---|---|---|---|---|---|---|---|
| JNLCIPBI_12 | 159597 | 160565 | STER_RS07090 | 0.0 | Capsule | Immune modulation | 98.45 | 100.00 | WP_011681443 |
| JNLCIPBI_12 | 161533 | 162786 | STER_RS07100 | 0.0 | Capsule | Immune modulation | 96.81 | 99.52 | WP_011681445 |
| JNLCIPBI_12 | 158880 | 159595 | STER_RS07085 | 0.0 | Capsule | Immune modulation | 96.09 | 99.86 | WP_011681442 |
| JNLCIPBI_12 | 162905 | 163756 | rfbD | 0.0 | Capsule | Immune modulation | 94.72 | 100.00 | WP_014621820 |
| JNLCIPBI_21 | 147302 | 148762 | STU_RS14650 | 0.0 | Capsule | Immune modulation | 93.91 | 100.14 | WP_011226049 |
| JNLCIPBI_21 | 147302 | 148762 | STER_RS05320 | 0.0 | Capsule | Immune modulation | 93.91 | 100.00 | WP_011681177 |
| JNLCIPBI_21 | 147302 | 148762 | STR_RS05265 | 0.0 | Capsule | Immune modulation | 93.16 | 100.14 | WP_041827043 |
| JNLCIPBI_21 | 151003 | 152370 | STU_RS14630 | 0.0 | Capsule | Immune modulation | 93.13 | 100.00 | WP_011226045 |
| JNLCIPBI_12 | 157764 | 158534 | STER_RS07075 | 0.0 | Capsule | Immune modulation | 93.00 | 99.10 | WP_011681440 |
| JNLCIPBI_21 | 151003 | 152368 | STER_RS05300 | 0.0 | Capsule | Immune modulation | 92.97 | 99.85 | WP_011681173 |
| JNLCIPBI_23 | 141815 | 142408 | STR_RS05880 | 0.0 | Capsule | Immune modulation | 92.42 | 100.00 | WP_011226149 |
| JNLCIPBI_23 | 141815 | 142408 | STER_RS06030 | 0.0 | Capsule | Immune modulation | 92.26 | 100.00 | WP_011226149 |
| JNLCIPBI_23 | 141815 | 142408 | STU_RS15260 | 0.0 | Capsule | Immune modulation | 92.26 | 100.00 | WP_011226149 |
| JNLCIPBI_21 | 148763 | 149494 | STU_RS14645 | 0.0 | Capsule | Immune modulation | 91.94 | 100.00 | WP_011226048 |
| JNLCIPBI_23 | 140946 | 141815 | rfbA | 0.0 | Capsule | Immune modulation | 91.61 | 100.00 | WP_011681286 |
| JNLCIPBI_21 | 148763 | 149494 | STER_RS05315 | 0.0 | Capsule | Immune modulation | 91.53 | 100.00 | WP_011681176 |
| JNLCIPBI_21 | 148763 | 149494 | STR_RS05260 | 0.0 | Capsule | Immune modulation | 90.98 | 100.00 | WP_011227248 |
| JNLCIPBI_21 | 150205 | 150945 | STER_RS05305 | 0.0 | Capsule | Immune modulation | 90.84 | 99.87 | WP_011681174 |
| JNLCIPBI_4 | 43562 | 45216 | fbp54 | 0.0 | FBPs | Adherence | 90.52 | 99.70 | WP_011227179 |
| JNLCIPBI_21 | 150205 | 150945 | STU_RS14635 | 0.0 | Capsule | Immune modulation | 89.89 | 99.87 | WP_011226046 |
| JNLCIPBI_21 | 150205 | 150940 | STR_RS05250 | 0.0 | Capsule | Immune modulation | 89.55 | 98.00 | WP_011227246 |
| JNLCIPBI_22 | 69323 | 70228 | cbpD | 0.0 | Autolysin | Exoenzyme | 88.85 | 93.50 | WP_082302295 |
| JNLCIPBI_1 | 274530 | 275833 | eno | 0.0 | Streptococcal enolase | Exoenzyme | 88.17 | 99.54 | WP_000022832 |
| JNLCIPBI_11 | 14419 | 15429 | plr/gapA | 0.0 | Streptococcal plasmin receptor/GAPDH | Adherence | 87.36 | 99.80 | WP_002986042 |
| JNLCIPBI_21 | 149503 | 150195 | STU_RS14640 | 0.0 | Capsule | Immune modulation | 85.45 | 99.86 | WP_011226047 |
| JNLCIPBI_21 | 149503 | 150195 | STR_RS05255 | 0.0 | Capsule | Immune modulation | 85.16 | 99.86 | WP_011227247 |
| JNLCIPBI_21 | 149503 | 150195 | STER_RS05310 | 0.0 | Capsule | Immune modulation | 84.87 | 99.86 | WP_011681175 |
| JNLCIPBI_23 | 142611 | 143657 | rfbB | 0.0 | Capsule | Immune modulation | 84.54 | 99.90 | WP_002263087 |
| JNLCIPBI_2 | 33270 | 34031 | srtA | 0.0 | Sortase A | Exoenzyme | 84.40 | 99.87 | - |
| JNLCIPBI_8 | 1941 | 3224 | tig/ropA | 0.0 | Trigger factor | Stress survival | 80.68 | 99.61 | 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 |
|---|---|---|---|---|---|---|---|---|
| JNLCIPBI_2 | 30581 | 29598 | ldh(Sp_1220) | 0.0 | L-lactate dehydrogenase | 96.95 | 100.00 | AAK75326 |
| JNLCIPBI_2 | 42169 | 43242 | MntE | 0.0 | manganese homeostasis | 96.09 | 99.72 | ABF32167 |
| JNLCIPBI_25 | 48194 | 45888 | pfl2(Sp_0459) | 0.0 | formate acetyltransferase | 94.54 | 99.22 | AAK74619 |
| JNLCIPBI_2 | 61226 | 63472 | metE | 0.0 | methionine biosynthesis enzymes | 93.19 | 100.00 | AAK74738 |
| JNLCIPBI_1 | 184064 | 185032 | spr0084 | 0.0 | pathogenitcity related | 93.19 | 98.48 | AAK98888 |
| JNLCIPBI_26 | 61627 | 63108 | SPD_0310 | 0.0 | UPF0371 protein SPD_0310 | 92.92 | 100.00 | ABJ54480 |
| JNLCIPBI_27 | 82402 | 83373 | prsA2 | 0.0 | ribose-phosphate pyrophosphokinase | 91.36 | 100.00 | ABF36968 |
| JNLCIPBI_6 | 19051 | 12503 | PrtA | 0.0 | serine protease | 90.35 | 101.73 | ABJ55268 |
| JNLCIPBI_23 | 109839 | 111569 | ptsI | 0.0 | phosphoenolpyruvate-protein phosphotransferase | 90.12 | 100.00 | AAK34199 |
| JNLCIPBI_12 | 177665 | 175677 | uvrB | 0.0 | excinuclease ABC, B subunit | 89.59 | 100.00 | AE014259_2 |
| JNLCIPBI_12 | 206070 | 204919 | potA | 0.0 | ABC transporter ATP-binding protein-spermidine/putrescine transport | 89.58 | 99.74 | AAL00050 |
| JNLCIPBI_27 | 46892 | 45414 | IMPDH | 0.0 | inosine-5'-monophosphate dehydrogenase | 87.83 | 100.00 | ADE32434 |
| JNLCIPBI_1 | 274530 | 275831 | Eno | 0.0 | enolase | 86.44 | 99.77 | ABP90468 |
| JNLCIPBI_27 | 31570 | 29678 | gidA | 0.0 | tRNA uridine 5-carboxymethylaminomethyl modification enzyme | 85.26 | 98.90 | ABP91129 |
| JNLCIPBI_2 | 66394 | 64685 | PGM | 0.0 | phosphoglucomutase | 84.76 | 99.65 | ACH87041 |
| JNLCIPBI_27 | 121796 | 122887 | recA | 0.0 | DNA recombination and repair | 84.64 | 95.36 | AAL00560 |
| JNLCIPBI_3 | 84503 | 83493 | pdh | 0.0 | pyruvate dehydrogenase | 83.09 | 99.70 | ABP91006 |
| JNLCIPBI_4 | 27713 | 29074 | mnmE | 0.0 | central tRNA-modifying GTPase | 82.67 | 99.56 | ABP90420 |
| JNLCIPBI_1 | 260122 | 261012 | bglB | 4.23e-178 | putative phospho--glucosidase | 87.88 | 99.66 | AAK33487 |
| JNLCIPBI_2 | 63662 | 64519 | metF | 1.73e-170 | methionine biosynthesis enzymes | 88.11 | 99.31 | AAK74739 |
| JNLCIPBI_2 | 106364 | 105402 | SP_0676 | 3.28e-170 | transcription facot | 80.69 | 99.69 | AAK74821 |
| JNLCIPBI_6 | 56233 | 55562 | rr01 | 1.43e-127 | response regulator | 84.82 | 99.56 | CAB54566 |
| JNLCIPBI_21 | 102364 | 103068 | covR | 1.05e-126 | responder protein | 85.53 | 100.00 | AAK71319 |
| JNLCIPBI_2 | 71061 | 71732 | ciaR | 1.51e-124 | two component system response regulator | 85.71 | 99.12 | AIK75708 |
| JNLCIPBI_2 | 71061 | 71729 | CiaR | 4.26e-124 | two-component response regulator | 86.55 | 99.55 | AAK74935 |
| JNLCIPBI_21 | 102364 | 103068 | walR | 2.38e-120 | DNA-binding response regulator | 82.13 | 100.00 | ANC99504 |
| JNLCIPBI_24 | 100830 | 101516 | CovR | 3.41e-120 | serves to repress GAS virulence factor-encoding genes | 81.66 | 100.00 | ACE75886 |
| JNLCIPBI_27 | 123061 | 123456 | SpxA2 | 1.22e-75 | transcriptional regulator | 91.67 | 100.00 | ERL21461 |
| JNLCIPBI_4 | 16239 | 15838 | SpxA1 | 1.49e-70 | transcriptional regulator | 82.84 | 100.00 | ERL19273 |
| JNLCIPBI_7 | 6152 | 5739 | GrpE | 4.27e-68 | protein grpE | 81.88 | 80.59 | ABP89267 |
| JNLCIPBI_24 | 124048 | 124335 | spr0479 | 3.31e-48 | essential gene | 85.42 | 98.97 | AAK99283 |
| JNLCIPBI_1 | 147450 | 147704 | spr1327 | 1.55e-44 | essential gene | 92.94 | 100.00 | AAL00131 |
| JNLCIPBI_10 | 6987 | 7250 | spr0175 | 1.43e-43 | pathogenitcity related | 85.23 | 100.00 | AAK98979 |
| JNLCIPBI_10 | 7813 | 8079 | spr0177 | 2.00e-42 | essential gene | 83.15 | 88.12 | AAK98981 |
| JNLCIPBI_8 | 3391 | 3882 | RopE (M5005_Spy_1611) | 2.35e-73 | probable DNA-directed RNA polymerase subunit delta | 82.93 | 85.86 | AAK34603 |
| JNLCIPBI_25 | 48194 | 45894 | PFL (B9H01_RS01125) | 0.0 | formate C-acetyltransferase | 83.22 | 98.08 | MYN69560 |
| JNLCIPBI_3 | 47813 | 48832 | 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 |
|---|---|---|---|
| JNLCIPBI_1 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_2 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_3 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_4 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_5 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_6 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_7 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_8 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_9 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_10 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_11 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_12 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_13 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_14 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_15 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_16 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_21 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_22 | 1.0 | 0.0 | 1.0 |
| JNLCIPBI_23 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_24 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_25 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_26 | 0.0 | 1.0 | 0.0 |
| JNLCIPBI_27 | 0.0 | 1.0 | 0.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| JNLCIPBI_1 | 278107 | 314081 | False | Siphoviridae | VOG4602, VOG4373, VOG8520, VOG2338, VOG4552, VOG3478, VOG4908, VOG0651, VOG0283, VOG0685, VOG0226, VOG4693, VOG0655, VOG0656, VOG0152, VOG0657, VOG5439, VOG0044, VOG5562, VOG0658, VOG0198, VOG0796, VOG10227, VOG0720, VOG4564, VOG5041, VOG4553, VOG3649, VOG4713, VOG0723, VOG9583, VOG0724, VOG0799, VOG0725, VOG0800, VOG9762, VOG0727, VOG4763, VOG0429, VOG4684, VOG0641, VOG0054, VOG5034, VOG7557, VOG3631 |
Phigaro v2.4.0 (Database: Jan. 2024 release)