| APIS family ID | APIS038 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Inhibited defense system | ||||||||||||||
| CLAN ID | CLAN003 | |||||||||||||
| Seed protein property |
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| Phage property |
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| PMID/References | ||||||||||||||
| PDB structures | ; | |||||||||||||
| Pfam domains | PF03230.16 | |||||||||||||
| Phrog | phrog_10132 | |||||||||||||
| Host taxa | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Caballeronia;s__Caballeronia jiangsuensis | |||||||||||||
| Gene Location | Start: 22792; End: 23244; Strand: - | |||||||||||||
| Description | ||||||||||||||
| Note | This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS007,ArdB which has seed protein. | |||||||||||||
| Genome accession | Start | End | Strand | Protein ID | Length | Molecular weight | Charge | Isoelectric point | Function | Phrog | PFAM |
|---|---|---|---|---|---|---|---|---|---|---|---|
| IMGVR_UViG_2576861805_000002 | 18260 | 18541 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667879 | 93 | 10331.61 | -3.5 | 4.5535 | hypothetical protein | ||
| IMGVR_UViG_2576861805_000002 | 19264 | 20364 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667880 | 366 | 41459.11 | -21.0 | 4.4712 | hypothetical protein | phrog_3927 | |
| IMGVR_UViG_2576861805_000002 | 20389 | 21837 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667881 | 482 | 55957.70 | 8.0 | 8.2125 | phage terminase large subunit | phrog_3717 ; phrog_2472 ; phrog_2 | PF04466.16 |
| IMGVR_UViG_2576861805_000002 | 21888 | 22157 | + | IMGVR_UViG_2576861805_000002|2576861805|2579667882 | 89 | 10600.20 | -6.5 | 4.2094 | hypothetical protein | ||
| IMGVR_UViG_2576861805_000002 | 22402 | 22719 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667883 | 105 | 11764.29 | 2.0 | 7.7374 | hypothetical protein | ||
| IMGVR_UViG_2576861805_000002 | 22792 | 23244 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667884 | 150 | 16845.49 | -3.5 | 4.9444 | Antirestriction protein | phrog_10132 | PF03230.16 |
| IMGVR_UViG_2576861805_000002 | 23276 | 23548 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667885 | 90 | 10170.52 | -6.5 | 4.3365 | hypothetical protein | phrog_17391 | |
| IMGVR_UViG_2576861805_000002 | 23620 | 23841 | + | IMGVR_UViG_2576861805_000002|2576861805|2579667886 | 73 | 8001.04 | -6.0 | 3.8103 | hypothetical protein | ||
| IMGVR_UViG_2576861805_000002 | 23838 | 24161 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667887 | 107 | 12483.74 | -11.5 | 4.1111 | hypothetical protein | ||
| IMGVR_UViG_2576861805_000002 | 24158 | 24823 | - | IMGVR_UViG_2576861805_000002|2576861805|2579667888 | 221 | 24828.01 | 7.0 | 7.9562 | HNH endonuclease | phrog_826 ; phrog_6254 ; phrog_3593 ; phrog_4842 ; phrog_1872 ; phrog_99 ; phrog_1492 ; phrog_59 | PF13392.9 |
| IMGVR_UViG_2576861805_000002 | 25155 | 25532 | + | IMGVR_UViG_2576861805_000002|2576861805|2579667889 | 125 | 14128.12 | -4.0 | 4.8211 | hypothetical protein |
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) |
|---|---|---|---|---|---|---|
| AF-A0A0H3GW18-F1-model_v4 | 4 | 150 | 1 | 141 | 0.9317 | 0.8898 |
| AF-Q93GQ0-F1-model_v4 | 11 | 150 | 7 | 144 | 0.9182 | 0.8694 |
| AF-P52139-F1-model_v4 | 1 | 150 | 6 | 152 | 0.8785 | 0.8537 |
| AF-A0A077ZNG7-F1-model_v4 | 14 | 150 | 7 | 141 | 0.9086 | 0.8512 |
| AF-P75676-F1-model_v4 | 1 | 150 | 6 | 152 | 0.8701 | 0.8449 |
| AF-A0A0H3GVF3-F1-model_v4 | 10 | 150 | 1 | 132 | 0.8868 | 0.8149 |
| AF-Q327Q6-F1-model_v4 | 8 | 150 | 17 | 157 | 0.8527 | 0.808 |
| AF-Q32HM6-F1-model_v4 | 8 | 150 | 41 | 181 | 0.8515 | 0.7574 |
| AF-A0A0H3GZ47-F1-model_v4 | 12 | 150 | 87 | 221 | 0.9045 | 0.7051 |
| Hit | Query start | Query end | Hit start | Hit end | TMscore(ali) | TMscore(avg) |
|---|---|---|---|---|---|---|
| MGYP001119568936.pdb | 3 | 150 | 1 | 143 | 0.9641 | 0.9332 |
| MGYP001592595604.pdb | 5 | 150 | 1 | 144 | 0.9615 | 0.9321 |
| MGYP001571109578.pdb | 4 | 150 | 1 | 143 | 0.9642 | 0.9312 |
| MGYP003692230177.pdb | 4 | 150 | 1 | 142 | 0.9647 | 0.9294 |
| MGYP003595251015.pdb | 1 | 150 | 1 | 148 | 0.9407 | 0.9239 |
| MGYP000949801973.pdb | 8 | 150 | 1 | 139 | 0.9681 | 0.9231 |
| MGYP001809940848.pdb | 8 | 150 | 1 | 140 | 0.9646 | 0.9219 |
| MGYP001374579218.pdb | 3 | 150 | 1 | 144 | 0.9523 | 0.921 |
| MGYP001546251433.pdb | 3 | 150 | 1 | 143 | 0.951 | 0.9186 |
| MGYP001590055218.pdb | 1 | 150 | 2 | 150 | 0.9304 | 0.9167 |
| Fam ID | Seed protein | Member count | Model | Alignment | APIS038 | IMGVR_UViG_2576861805_000002|2576861805|2579667884 | 5 | HMM model | Member alignment |
|---|
| Hit APIS family | E-Value | Query Start | Query End | Hit Start | Hit End | Immune system | Seed protein |
|---|---|---|---|---|---|---|---|
| APIS007 | 1.52E-54 | 5 | 150 | 13 | 151 | restriction-modification (RM) | BAF33451.1 |
| APIS069 | 4.57E-41 | 10 | 150 | 6 | 144 | IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774 | |
| APIS055 | 2.75E-29 | 9 | 150 | 5 | 142 | OL763419_00042 | |
| APIS039 | 4.15E-24 | 6 | 150 | 39 | 179 | IMGVR_UViG_2751185776_000007|2751185776|2753238834 | |
| APIS037 | 8.82E-21 | 15 | 150 | 8 | 141 | IMGVR_UViG_2541047688_000003|2541047688|2543982737 |
| Member | pident | evalue | bitscore | qcovs | phage | host | SourceDB | Pfam | Phrog |
|---|---|---|---|---|---|---|---|---|---|
| IMGVR_UViG_2576861805_000002|2576861805|2579667884 | 100.000 | 1.36e-108 | 313 | 100% | Caballeronia jiangsuensis | IMGVR | PF03230 | phrog_10132 | |
| IMGVR_UViG_2713896995_000002|2713896995|2715157188 | 78.417 | 3.02e-80 | 241 | 99% | Caballeronia temeraria | IMGVR | PF03230 | phrog_10132 | |
| IMGVR_UViG_2823919643_000001|2823919643|2823923275 | 63.043 | 1.24e-59 | 189 | 99% | Paraburkholderia graminis | IMGVR | PF03230 | phrog_10132 | |
| IMGVR_UViG_3300028024_000018|3300028024|Ga0255336_10072623 | 60.993 | 4.10e-59 | 188 | 94% | IMGVR | PF03230 | phrog_10132 | ||
| IMGVR_UViG_3300045049_000121|3300045049|Ga0466959_0000327_18050_18475 | 63.309 | 1.17e-55 | 179 | 92% | IMGVR | PF03230 | phrog_10132 |