| APIS family ID | APIS084 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Inhibited defense system | ||||||||||||||
| CLAN ID | CLAN023 | |||||||||||||
| Seed protein property |
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| Phage property |
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| PMID/References | ||||||||||||||
| PDB structures | ; | |||||||||||||
| Pfam domains | PF17574.5 | |||||||||||||
| Phrog | phrog_2254 | |||||||||||||
| Host taxa | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium; | |||||||||||||
| Gene Location | Start: 14218; End: 14529; Strand: + | |||||||||||||
| Description | ||||||||||||||
| Note | This family does not have seed protein, but we infer its function is defending toxin-antitoxin (TA) because it belongs to the same clan as family APIS011 which has seed protein. | |||||||||||||
| Genome accession | Start | End | Strand | Protein ID | Length | Molecular weight | Charge | Isoelectric point | Function | Phrog | PFAM |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MW001769 | 11092 | 11541 | + | MW001769_00018 | 149 | 17401.21 | 17401.21 | 9.8032 | endonuclease | phrog_945 ; phrog_35520 ; phrog_5453 ; phrog_22215 ; phrog_1450 ; phrog_27028 | PF05367.14 |
| MW001769 | 11559 | 12014 | + | MW001769_00019 | 151 | 17101.49 | 17101.49 | 9.5140 | amidase | phrog_822 ; phrog_19273 ; phrog_35436 ; phrog_1493 | PF01510.28 |
| MW001769 | 12019 | 12117 | + | MW001769_00020 | 32 | 3621.33 | 3621.33 | 4.1441 | hypothetical protein | ||
| MW001769 | 12134 | 13855 | + | MW001769_00021 | 573 | 63159.95 | 63159.95 | 4.9802 | DNA primase/helicase | phrog_239 ; phrog_47 ; phrog_19 | PF03796.18 |
| MW001769 | 12134 | 13855 | + | MW001769_00021 | 573 | 63159.95 | 63159.95 | 4.9802 | DNA primase/helicase | phrog_239 ; phrog_47 ; phrog_19 | PF13155.9 |
| MW001769 | 13986 | 14198 | + | MW001769_00022 | 70 | 7707.15 | 7707.15 | 10.9862 | hypothetical protein | phrog_1950 | PF17565.5 |
| MW001769 | 14218 | 14529 | + | MW001769_00023 | 103 | 11566.16 | 11566.16 | 10.9590 | hypothetical protein | phrog_2254 | PF17574.5 |
| MW001769 | 14597 | 15100 | + | MW001769_00024 | 167 | 19112.82 | 19112.82 | 6.0930 | nucleotidyltransferase | phrog_1614 | |
| MW001769 | 15100 | 17214 | + | MW001769_00025 | 704 | 79974.78 | 79974.78 | 7.2028 | DNA polymerase I | phrog_16667 ; phrog_17 ; phrog_38876 ; phrog_403 ; phrog_15971 ; phrog_6375 | PF00476.23 |
| MW001769 | 17419 | 17709 | + | MW001769_00026 | 96 | 10952.54 | 10952.54 | 8.0232 | Gp5.5-like host HNS inhibition | phrog_17900 ; phrog_1452 | |
| MW001769 | 17709 | 17918 | + | MW001769_00027 | 69 | 7222.21 | 7222.21 | 8.5243 | hypothetical protein | phrog_1334 ; phrog_17900 | |
| MW001769 | 17918 | 18133 | + | MW001769_00028 | 71 | 7732.81 | 7732.81 | 8.4213 | hypothetical protein | phrog_2251 |
pTM is for the estimate of the TM-score, which is obtained from a pairwise error prediction. The higher pTM score indicates better model quality.
pLDDT is for per-residue accuracy of the structure, which representes the quality of the residue. A higher value indicates better prediction accuracy. More detail please see AlphaFold .
| Hit | Query start | Query end | Hit start | Hit end | TMscore(ali) | TMscore(avg) |
|---|---|---|---|---|---|---|
| MGYP003595835577.pdb | 8 | 96 | 2 | 89 | 0.7703 | 0.6793 |
| Fam ID | Seed protein | Member count | Model | Alignment | APIS084 | MW001769_00023 | 3 | HMM model | Member alignment |
|---|
| Hit APIS family | E-Value | Query Start | Query End | Hit Start | Hit End | Immune system | Seed protein |
|---|---|---|---|---|---|---|---|
| APIS011 | 2.74E-29 | 6 | 81 | 22 | 97 | toxin-antitoxin (TA) | NP_041980.1 |
| APIS080 | 6.26E-26 | 6 | 83 | 6 | 83 | ON602753_00020 | |
| APIS078 | 6.11E-20 | 8 | 76 | 3 | 71 | KX078568_00026 |
| Member | pident | evalue | bitscore | qcovs | phage | host | SourceDB | Pfam | Phrog |
|---|---|---|---|---|---|---|---|---|---|
| MF979561_00023 | 99.029 | 1.82e-69 | 211 | 100% | Pectobacterium phage DU_PP_II | Pectobacterium | INPHARED | PF17574 | phrog_2254 |
| MW001769_00023 | 100.000 | 4.36e-70 | 212 | 100% | Pectobacterium phage phiPccP-1 | Pectobacterium | INPHARED | PF17574 | phrog_2254 |
| ON995367_00021 | 97.087 | 5.90e-68 | 207 | 100% | Pectobacterium phage vB_PcaP_P15_PC2B6 | Pectobacterium | INPHARED | PF17574 | phrog_2254 |
| APIS | Contig | Range |
|---|---|---|
| APIS084 | MW001769 | 11092 - 18133 |