Seed proteins |
Seed genomic context | Seed protein 3D structures |
Structural homologs |
Family infomation |
Homology to other families |
Family members, sources, and their hosts
Seed protein information help
| APIS family ID | APIS071 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Inhibited defense system | ||||||||||||||
| CLAN ID | CLAN004 | |||||||||||||
| Seed protein property |
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| Phage property |
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| PMID/References | ||||||||||||||
| PDB structures | ; | |||||||||||||
| Pfam domains | ||||||||||||||
| Phrog | phrog_20113 | |||||||||||||
| Host taxa | ||||||||||||||
| Gene Location | Start: 90720; End: 91751; Strand: + | |||||||||||||
| Description | ||||||||||||||
| Note | This family does not have seed protein, but we infer its function is defending Gabija because it belongs to the same clan as family APIS005 which has seed protein. | |||||||||||||
Seed genomic context Download table help
| Genome accession | Start | End | Strand | Protein ID | Length | Molecular weight | Charge | Isoelectric point | Function | Phrog | PFAM |
|---|---|---|---|---|---|---|---|---|---|---|---|
| IMGVR_UViG_3300037628_000643 | 86259 | 87203 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_86259_87203 | 314 | 35358.84 | -5.5 | 5.0064 | ribonucleoside-diphosphate reductase alpha chain | phrog_84 ; phrog_3987 | PF00317.24 |
| IMGVR_UViG_3300037628_000643 | 86259 | 87203 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_86259_87203 | 314 | 35358.84 | -5.5 | 5.0064 | ribonucleoside-diphosphate reductase alpha chain | phrog_84 ; phrog_3987 | PF02867.18 |
| IMGVR_UViG_3300037628_000643 | 87398 | 89005 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_87398_89005 | 535 | 60398.50 | -8.0 | 5.3682 | ribonucleoside-diphosphate reductase alpha chain | phrog_3844 ; phrog_84 ; phrog_3987 ; phrog_367 | PF02867.18 |
| IMGVR_UViG_3300037628_000643 | 89040 | 89414 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89040_89414 | 124 | 14731.86 | -7.5 | 4.5097 | hypothetical protein | ||
| IMGVR_UViG_3300037628_000643 | 89488 | 90135 | - | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89488_90135 | 215 | 24550.85 | 15.0 | 9.9016 | group I intron endonuclease | phrog_655 ; phrog_314 ; phrog_19446 | PF07460.14 |
| IMGVR_UViG_3300037628_000643 | 89488 | 90135 | - | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89488_90135 | 215 | 24550.85 | 15.0 | 9.9016 | group I intron endonuclease | phrog_655 ; phrog_314 ; phrog_19446 | PF07460.14 |
| IMGVR_UViG_3300037628_000643 | 90308 | 90727 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90308_90727 | 139 | 16143.93 | -9.5 | 4.3326 | hypothetical protein | phrog_98 ; phrog_21205 | PF09643.13 |
| IMGVR_UViG_3300037628_000643 | 90720 | 91751 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 | 343 | 39700.05 | 3.5 | 7.1914 | hypothetical protein | phrog_20113 | |
| IMGVR_UViG_3300037628_000643 | 91748 | 92182 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_91748_92182 | 144 | 16265.24 | -9.0 | 4.4963 | hypothetical protein | ||
| IMGVR_UViG_3300037628_000643 | 92193 | 92393 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92193_92393 | 66 | 7334.27 | -4.5 | 4.3297 | hypothetical protein | ||
| IMGVR_UViG_3300037628_000643 | 92390 | 92827 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92390_92827 | 145 | 16210.75 | -2.5 | 4.8947 | hypothetical protein | phrog_30914 ; phrog_335 | |
| IMGVR_UViG_3300037628_000643 | 92824 | 93186 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92824_93186 | 120 | 14217.32 | 5.5 | 9.4221 | hypothetical protein | ||
| IMGVR_UViG_3300037628_000643 | 93173 | 93331 | + | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_93173_93331 | 52 | 5814.65 | -5.0 | 4.2829 | hypothetical protein |
Seed genomic context- JBrowse
Predicted 3D structure by alphafold2 with pTM = 0.7 Download help
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 .
Residues were colored according to plddt ( blue-> high quality; red-> low quality ).
Full Sequence
90 < plddt <=100 ;
70 < plddt <= 90 ;
50 < plddt <= 70 ;
0 <= plddt <= 50 ;
Download
help
Structural homologs
No homologs found in AlphaFold database
No homologs found in esmfold database
Family information Download help
| Fam ID | Seed protein | Member count | Model | Alignment | APIS071 | IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 | 8 | HMM model | Member alignment |
|---|
Host Taxa distribution
Length distribution
Homology to other families download full data without filtering help
Clan ID: CLAN004
| Hit APIS family | E-Value | Query Start | Query End | Hit Start | Hit End | Immune system | Seed protein |
|---|---|---|---|---|---|---|---|
| APIS065 | 4.85E-117 | 1 | 343 | 4 | 350 | - | KJ018209_00009 |
| APIS046 | 3.01E-81 | 1 | 341 | 1 | 333 | - | IMGVR_UViG_3300009034_000088|3300009034|Ga0115863_100105265 |
| APIS068 | 1.95E-63 | 1 | 333 | 1 | 330 | - | IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844 |
| APIS083 | 8.42E-62 | 2 | 334 | 22 | 342 | - | CP067347_00056 |
| APIS057 | 1.03E-55 | 4 | 336 | 1 | 322 | - | IMGVR_UViG_3300021167_000128|3300021167|Ga0216365_13592277 |
| APIS005 | 1.80E-50 | 2 | 334 | 7 | 303 | Gabija | APD21271.1 |
| APIS088 | 5.23E-35 | 2 | 335 | 5 | 304 | - | uvig_218805_40 |
| APIS053 | 4.40E-29 | 5 | 333 | 81 | 374 | - | IMGVR_UViG_3300014203_000236|3300014203|Ga0172378_100030802 |
Family members, sources, and their hosts help
| Member | pident | evalue | bitscore | qcovs | phage | host | SourceDB | Pfam | Phrog |
|---|---|---|---|---|---|---|---|---|---|
| IMGVR_UViG_3300006192_000111|3300006192|Ga0075011_100015277 | 41.593 | 5.39e-82 | 261 | 97% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300007988_000001|3300007988|Ga0100402_100016990 | 43.636 | 1.52e-76 | 247 | 95% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300008005_000001|3300008005|Ga0100385_1000211103 | 43.333 | 2.04e-75 | 244 | 95% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300020047_003347|3300020047|Ga0206650_100312810 | 41.813 | 3.94e-87 | 274 | 99% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300022690_003208|3300022690|Ga0247388_100048132 | 43.917 | 2.67e-94 | 292 | 97% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300025018_000005|3300025018|Ga0210043_100013681 | 43.636 | 1.04e-76 | 247 | 95% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300037587_000320|3300037587|Ga0310923_0000225_16300_17337 | 37.982 | 8.07e-70 | 230 | 95% | IMGVR | phrog_20113 | |||
| IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 | 100.000 | 0.0 | 705 | 100% | IMGVR | phrog_20113 |