Seed protein information help

APIS family ID APIS115
Inhibited defense system
CLAN ID CLAN049
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
MN047793_00257
gene_page: 367 41914.66 5.9068 -3.0
Phage property
Phage Assembly id
MN047793
PMID/References
PDB structures ;
Pfam domains PF00293.33,PF01467.31,PF00293.33,PF01467.31
Phrog phrog_1185,phrog_1185
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Lysobacterales;f__Lysobacteraceae;g__Xanthomonas;s__unclassified Xanthomonas species
Gene Location Start: 122606;  End: 123709;  Strand: -
Description
Note This family does not have seed protein, but we infer its function is defending NAD+ reconstitution pathway (NARP) because it belongs to the same clan as family APIS170 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
MN047793 120313 121452 - MN047793_00252 379 43401.17 -2.5 5.6866 hypothetical protein phrog_4182
MN047793 121449 121613 - MN047793_00253 54 6179.06 -1.0 5.6013 hypothetical protein
MN047793 121610 122011 - MN047793_00254 133 14964.64 -3.0 4.7920 hypothetical protein
MN047793 122004 122282 - MN047793_00255 92 10655.00 -6.5 4.3296 hypothetical protein
MN047793 122350 122598 - MN047793_00256 82 9945.13 -0.5 5.8075 hypothetical protein
MN047793 122606 123709 - MN047793_00257 367 41914.66 -3.0 5.9068 Bifunctional NMN adenylyltransferase/Nudix hydrolase phrog_1185 ; phrog_1185 PF00293.33 ;PF01467.31 ;PF00293.33 ;PF01467.31
MN047793 123799 124134 + MN047793_00258 111 12501.43 1.5 7.3201 hypothetical protein
MN047793 124086 124301 - MN047793_00259 71 7584.84 -1.0 4.8532 hypothetical protein PF04324.20
MN047793 124365 125498 - MN047793_00260 377 42253.62 -19.0 4.5953 hypothetical protein
MN047793 125509 125844 - MN047793_00261 111 12923.02 4.5 9.9083 hypothetical protein
MN047793 125841 126230 - MN047793_00262 129 14525.76 1.0 7.9404 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.88 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

Structure homologs against by afdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
AF-Q58361-F1-model_v4 9 366 48 338 0.5165 0.4947

Structure homologs against by esmdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000400551823.pdb 6 367 1 340 0.9709 0.9304
MGYP001592028481.pdb 7 367 1 341 0.967 0.9272
MGYP001111241452.pdb 9 367 1 344 0.9618 0.927
MGYP003574359643.pdb 5 367 7 351 0.9518 0.9264
MGYP000138452357.pdb 6 366 1 344 0.9598 0.9242
MGYP001390947301.pdb 6 366 1 350 0.9475 0.9202
MGYP001822565791.pdb 1 367 1 350 0.948 0.9198
MGYP002652398978.pdb 2 367 4 348 0.9487 0.9183
MGYP003652350255.pdb 8 366 1 342 0.9554 0.9165
MGYP001371600575.pdb 6 366 1 351 0.9414 0.9155

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS115 MN047793_00257 6 HMM model Member alignment

Host Taxa distribution

Length distribution

Length Distribution Bar chart

Homology to other families       help

Clan ID: CLAN049

APIS115 has no similar APIS family.