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 | APIS079 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Inhibited defense system | ||||||||||||||
| CLAN ID | CLAN001 | |||||||||||||
| Seed protein property |
|
|||||||||||||
| Phage property |
|
|||||||||||||
| PMID/References | ||||||||||||||
| PDB structures | ; | |||||||||||||
| Pfam domains | PF11195.11 | |||||||||||||
| Phrog | phrog_2709,phrog_30130,phrog_872,phrog_32732,phrog_9467,phrog_1048 | |||||||||||||
| Host taxa | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas; | |||||||||||||
| Gene Location | Start: 4858; End: 5352; Strand: + | |||||||||||||
| Description | ||||||||||||||
| Note | This family does not have seed protein, but we infer its function is defending Thoeris because it belongs to the same clan as family APIS024,APIS029,APIS211,APIS245,APIS283,APIS315,APIS356,APIS372,APIS373,APIS378 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|
| MF042361 | 1415 | 2983 | + | MF042361_00003 | 522 | 60145.17 | 60145.17 | 6.9336 | hypothetical protein | phrog_26724 ; phrog_2472 ; phrog_38407 | |
| MF042361 | 2980 | 3450 | + | MF042361_00004 | 156 | 16610.59 | 16610.59 | 4.0302 | hypothetical protein | phrog_17424 | |
| MF042361 | 3456 | 3701 | + | MF042361_00005 | 81 | 8783.17 | 8783.17 | 4.5878 | hypothetical protein | ||
| MF042361 | 3698 | 4513 | + | MF042361_00006 | 271 | 28666.30 | 28666.30 | 4.1973 | hypothetical protein | ||
| MF042361 | 4559 | 4861 | + | MF042361_00007 | 100 | 11277.66 | 11277.66 | 4.2972 | hypothetical protein | ||
| MF042361 | 4858 | 5352 | + | MF042361_00008 | 164 | 17982.27 | 17982.27 | 4.9286 | hypothetical protein | phrog_1048 ; phrog_32732 ; phrog_30130 ; phrog_872 ; phrog_2709 ; phrog_18865 ; phrog_9467 | PF11195.11 |
| MF042361 | 5349 | 5768 | + | MF042361_00009 | 139 | 15556.63 | 15556.63 | 4.9130 | DNA methyltransferase | phrog_10057 | |
| MF042361 | 5761 | 8127 | + | MF042361_00010 | 788 | 88929.29 | 88929.29 | 4.3944 | portal protein | phrog_18470 ; phrog_27974 ; phrog_156 ; phrog_24564 ; phrog_25797 | |
| MF042361 | 8139 | 9095 | + | MF042361_00011 | 318 | 34012.92 | 34012.92 | 3.9565 | hypothetical protein | phrog_8246 | |
| MF042361 | 9108 | 9293 | + | MF042361_00012 | 61 | 6484.84 | 6484.84 | 9.2532 | CsrA-like regulator | phrog_8397 | PF02599.19 |
| MF042361 | 9400 | 10494 | + | MF042361_00013 | 364 | 40384.66 | 40384.66 | 7.9320 | major head protein | phrog_13784 ; phrog_334 ; phrog_31117 | PF13252.9 |
Seed genomic context- JBrowse
Predicted 3D structure by alphafold2 with pTM = 0.55 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
Structure homologs against by esmdb (html) ; download full result table
| Hit | Query start | Query end | Hit start | Hit end | TMscore(ali) | TMscore(avg) |
|---|---|---|---|---|---|---|
| MGYP000632396215.pdb | 6 | 160 | 6 | 152 | 0.7472 | 0.7042 |
| MGYP003620421190.pdb | 5 | 161 | 6 | 142 | 0.7595 | 0.6766 |
| MGYP001070471033.pdb | 72 | 160 | 1 | 89 | 0.8799 | 0.6706 |
| MGYP001121567902.pdb | 76 | 160 | 1 | 86 | 0.8666 | 0.6511 |
| MGYP002732175134.pdb | 6 | 159 | 6 | 147 | 0.721 | 0.6504 |
| MGYP002731914620.pdb | 72 | 160 | 1 | 85 | 0.8676 | 0.6487 |
| MGYP002777370215.pdb | 10 | 161 | 2 | 84 | 0.8649 | 0.646 |
| MGYP000498482146.pdb | 5 | 160 | 6 | 172 | 0.6995 | 0.646 |
| MGYP003665317257.pdb | 5 | 160 | 9 | 167 | 0.694 | 0.643 |
| MGYP003586902511.pdb | 74 | 159 | 1 | 85 | 0.8568 | 0.642 |
Family information Download help
| Fam ID | Seed protein | Member count | Model | Alignment | APIS079 | MF042361_00008 | 47 | HMM model | Member alignment |
|---|
Host Taxa distribution
Length distribution
Homology to other families download full data without filtering help
Clan ID: CLAN001
| Hit APIS family | E-Value | Query Start | Query End | Hit Start | Hit End | Immune system | Seed protein |
|---|---|---|---|---|---|---|---|
| APIS052 | 1.08E-66 | 1 | 160 | 3 | 163 | - | IMGVR_UViG_3300012991_000489|3300012991|Ga0157148_10003866 |
| APIS029 | 7.84E-47 | 72 | 161 | 14 | 103 | Thoeris | YP_002300464.1 |
| APIS043 | 4.05E-36 | 73 | 160 | 119 | 209 | - | MH238467_00052 |
| APIS045 | 3.48E-25 | 74 | 159 | 21 | 115 | - | IMGVR_UViG_3300005805_000580|3300005805|Ga0079957_100145420 |
| APIS070 | 1.71E-23 | 1 | 75 | 12 | 76 | - | IMGVR_UViG_3300037297_000240|3300037297|Ga0394146_0000041_21955_22497 |