Probiotic potential risk score
| ARGs | VFs | PGs | PPRS |
|---|---|---|---|
| 13 | 10 | 9 | 18.71 |
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. |
|---|---|---|---|---|---|---|---|---|
| CKPAKIGA_90 | 538512 | 539366 | aadK | ARO:3002627 | aadK | 97.54 | 100.00 | AL009126.1 |
| CKPAKIGA_90 | 519320 | 520522 | blt | ARO:3003006 | blt | 99.75 | 100.00 | L32599.1 |
| CKPAKIGA_109 | 417043 | 418686 | vmlR | ARO:3004476 | vmlR | 98.90 | 100.00 | NC_000964.3 |
| CKPAKIGA_90 | 289814 | 290983 | bmr | ARO:3003007 | bmr | 99.23 | 100.00 | M33768.1 |
| CKPAKIGA_131 | 256635 | 259205 | Bacillus subtilis mprF | ARO:3003324 | Bsub_mprF | 99.30 | 100.00 | AL009126.3 |
| CKPAKIGA_109 | 161730 | 162323 | tmrB | ARO:3003059 | tmrB | 98.48 | 100.00 | AL009126.3 |
| CKPAKIGA_109 | 111169 | 112602 | lmrB | ARO:3002813 | lmrB | 99.37 | 100.00 | JYFL01000006.1 |
| CKPAKIGA_109 | 98354 | 99274 | mphK | ARO:3004541 | mphK | 98.69 | 100.00 | CP010314.1 |
| CKPAKIGA_100 | 42278 | 42595 | ykkD | ARO:3003064 | ykkD | 99.05 | 100.00 | AL009126.1 |
| CKPAKIGA_100 | 41940 | 42278 | ykkC | ARO:3003063 | ykkC | 100.00 | 100.00 | AL009126.1 |
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. |
|---|---|---|---|---|---|---|---|
| CKPAKIGA_109 | 98354 | 99274 | mph(K) | Spiramycin, Telithromycin | 99.02 | 100.00 | NC_000964 |
| CKPAKIGA_79 | 1008710 | 1010086 | tet(L) | Doxycycline, Tetracycline, Doxycycline, Tetracycline, Minocycline, Tigecycline | 98.77 | 100.00 | D12567 |
| CKPAKIGA_90 | 538514 | 539366 | aadK | Streptomycin | 98.12 | 99.77 | M26879 |
ResFinder v4.6.0 (Database: resfinder_db, Aug. 2024 release)
AMRFinderPlus
| Query ID | Begin | End | Gene symbol | Sequence name | Method | Identity | Coverage | Accession no. |
|---|---|---|---|---|---|---|---|---|
| CKPAKIGA_109 | 417046 | 418686 | vmlR | ABC-F type ribosomal protection protein VmlR | BLASTX | 98.90 | 100.00 | WP_003234144.1 |
| CKPAKIGA_109 | 98354 | 99271 | mphK | macrolide 2'-phosphotransferase MphK | BLASTX | 98.69 | 100.00 | WP_003246254.1 |
| CKPAKIGA_79 | 1008713 | 1010086 | tet(L) | tetracycline efflux MFS transporter Tet(L) | BLASTX | 98.69 | 100.00 | WP_063856081.1 |
| CKPAKIGA_90 | 538515 | 539366 | aadK | aminoglycoside 6-adenylyltransferase AadK | BLASTX | 97.54 | 100.00 | WP_003229862.1 |
| CKPAKIGA_79 | 1006189 | 1006707 | satA | streptothricin N-acetyltransferase SatA | BLASTX | 90.17 | 100.00 | WP_003242546.1 |
| CKPAKIGA_142 | 178621 | 181218 | rphC | rifamycin-inactivating phosphotransferase RphC | BLASTX | 81.40 | 100.00 | WP_087347987.1 |
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. |
|---|---|---|---|---|---|---|---|---|---|
| CKPAKIGA_79 | 527296 | 528477 | capB | 0.0 | Capsule | Immune modulation | 99.75 | 100.00 | NP_391471 |
| CKPAKIGA_79 | 101948 | 109084 | dhbF | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.62 | 100.00 | NP_391076 |
| CKPAKIGA_90 | 90679 | 91320 | hlyIII | 0.0 | Hemolysin III | Exotoxin | 99.53 | 100.00 | NP_390062 |
| CKPAKIGA_79 | 525671 | 526813 | capA | 0.0 | Capsule | Immune modulation | 99.39 | 100.00 | NP_391469 |
| CKPAKIGA_79 | 112940 | 113725 | dhbA | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.36 | 100.00 | NP_391080 |
| CKPAKIGA_79 | 526832 | 527281 | capC | 0.0 | Capsule | Immune modulation | 99.33 | 100.00 | NP_391470 |
| CKPAKIGA_79 | 109104 | 110042 | dhbB | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.25 | 100.00 | NP_391077 |
| CKPAKIGA_79 | 111718 | 112914 | dhbC | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.17 | 100.00 | NP_391079 |
| CKPAKIGA_142 | 128540 | 130303 | dep/capD | 0.0 | Capsule | Immune modulation | 99.15 | 100.00 | NP_389723 |
| CKPAKIGA_79 | 110070 | 111689 | dhbE | 0.0 | Bacillibactin | Nutritional/Metabolic factor | 99.07 | 100.00 | NP_391078 |
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 |
|---|---|---|---|---|---|---|---|---|
| CKPAKIGA_11 | 27996 | 26860 | tufA | 0.0 | elongation factor Tu | 84.96 | 95.69 | AHM69299 |
| CKPAKIGA_32 | 11198 | 10329 | pdxS | 1.11e-151 | encodes the putative pyridoxal 5'-phosphate synthase subunit PdxS | 83.79 | 98.31 | ACE61268 |
| CKPAKIGA_100 | 352090 | 352866 | CodY | 4.53e-125 | nutrient-responsive regulator | 81.08 | 100.00 | ACJ80679 |
| CKPAKIGA_79 | 365940 | 366509 | ClpP | 6.31e-99 | part of proteolytic complex | 81.05 | 97.44 | BAB94595 |
| CKPAKIGA_120 | 276387 | 276779 | spxA1 | 9.29e-70 | redox-responsive transcription factor | 83.21 | 100.00 | AAF21893 |
| CKPAKIGA_21 | 34708 | 34466 | SpoVG | 7.51e-39 | RNA-binding protein | 81.48 | 79.41 | AAT02994 |
| CKPAKIGA_109 | 362578 | 362775 | CspA | 1.93e-31 | cold shock protein | 90.91 | 100.00 | CAA62903 |
| CKPAKIGA_90 | 103245 | 103439 | CspD | 6.06e-28 | cold shock protein | 81.54 | 98.48 | CAC99957 |
| CKPAKIGA_120 | 33191 | 32997 | CspB | 3.55e-27 | cold shock protein | 83.08 | 98.48 | CAD00094 |
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 |
|---|---|---|---|
| CKPAKIGA_11 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_21 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_32 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_63 | 1.0 | 0.0 | 1.0 |
| CKPAKIGA_79 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_90 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_100 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_109 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_120 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_131 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_142 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_153 | 0.0 | 1.0 | 0.0 |
| CKPAKIGA_164 | 1.0 | 0.0 | 1.0 |
PlasmidHunter v 1.4.5 (Database: May. 2024 release)
Prophage
Phigaro
| Query ID | Begin | End | Transposable | Taxonomy | pVOGs |
|---|---|---|---|---|---|
| CKPAKIGA_90 | 20386 | 26467 | False | Siphoviridae | VOG10940, VOG7134, VOG9867, VOG6036, VOG5495, VOG9219, VOG9713 |
| CKPAKIGA_90 | 31030 | 48020 | False | Siphoviridae | VOG0275, VOG4662, VOG9312, VOG4910, VOG3389, VOG5042, VOG9712 |
| CKPAKIGA_90 | 467992 | 486304 | False | Myoviridae | VOG7718, VOG4862, VOG4691, VOG4550, VOG3894, VOG4885, VOG4865, VOG6163, VOG3892, VOG3891, VOG3890, VOG10055, VOG4870, VOG4589, VOG0749 |
| CKPAKIGA_100 | 4706 | 12456 | False | Myoviridae | VOG4885, VOG3894, VOG4550, VOG4691, VOG4862, VOG7718, VOG3390, VOG4705 |
| CKPAKIGA_120 | 371218 | 381138 | False | Siphoviridae | VOG4602, VOG9667, VOG3490, VOG0189, VOG4861, VOG5447, VOG0796, VOG10227, VOG4773, VOG4685 |
| CKPAKIGA_153 | 106048 | 114396 | False | Siphoviridae | VOG0918, VOG4551, VOG0025, VOG7476, VOG0322, VOG6211 |
| CKPAKIGA_164 | 4155 | 28646 | False | Siphoviridae | VOG1024, VOG10944, VOG9244, VOG4599, VOG4605, VOG6163, VOG5852, VOG4586, VOG0704, VOG0539, VOG4589, VOG0204, VOG4553, VOG4568, VOG4556, VOG1886, VOG5819, VOG4581, VOG0221 |
| CKPAKIGA_164 | 50570 | 68682 | False | Siphoviridae | VOG0025, VOG4551, VOG0918, VOG1574, VOG5292, VOG4549, VOG2725, VOG3851, VOG2352, VOG4714, VOG4561, VOG1198, VOG0397, VOG2352 |
Phigaro v2.4.0 (Database: Jan. 2024 release)