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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 APIS068
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844
gene_page: 339 39942.6 6.5697 0.5
Phage property
Phage Assembly id
IMGVR_UViG_3300035698_004593
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_20113
Host taxa
Gene Location Start: 7825;  End: 8844;  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_3300035698_004593 10147 10668 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_10147_10668 173 19905.28 -13.0 4.4384 plasmid maintenance system antidote protein VapI
IMGVR_UViG_3300035698_004593 10737 11141 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_10737_11141 134 16157.20 -0.5 5.9448 hypothetical protein
IMGVR_UViG_3300035698_004593 11306 11425 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_11306_11425 39 4379.27 2.0 8.5513 hypothetical protein
IMGVR_UViG_3300035698_004593 5052 5615 - IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_5052_5615 187 21645.44 -2.5 5.4476 cell division protein FtsB
IMGVR_UViG_3300035698_004593 5578 5751 - IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_5578_5751 57 6673.55 -1.5 5.0343 hypothetical protein
IMGVR_UViG_3300035698_004593 5798 6040 - IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_5798_6040 80 9287.54 -8.0 4.2626 hypothetical protein
IMGVR_UViG_3300035698_004593 6097 6432 - IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_6097_6432 111 12117.71 -10.0 4.1642 hypothetical protein
IMGVR_UViG_3300035698_004593 6893 7756 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_6893_7756 287 31365.55 3.0 7.5745 DNA (cytosine-5)-methyltransferase 1 phrog_116 ; phrog_5999 ; phrog_32758 ; phrog_29583 ; phrog_363 PF00145.20
IMGVR_UViG_3300035698_004593 7825 8844 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844 339 39942.60 0.5 6.5697 hypothetical protein phrog_20113
IMGVR_UViG_3300035698_004593 9020 9619 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_9020_9619 199 22558.83 1.5 7.2424 hypothetical protein
IMGVR_UViG_3300035698_004593 9693 10061 + IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_9693_10061 122 14687.55 -7.0 4.5316 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.67 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
APIS068 IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844 5 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
APIS046 2.60E-115 1 329 4 325 IMGVR_UViG_3300009034_000088|3300009034|Ga0115863_100105265
APIS005 8.21E-82 2 329 10 302 Gabija APD21271.1
APIS083 1.95E-75 1 329 24 341 CP067347_00056
APIS071 1.16E-64 1 329 6 336 IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751
APIS065 1.42E-64 1 329 7 340 KJ018209_00009
APIS088 2.12E-41 2 329 8 302 uvig_218805_40
APIS057 6.24E-39 1 329 1 319 IMGVR_UViG_3300021167_000128|3300021167|Ga0216365_13592277
APIS053 4.95E-31 6 328 86 373 IMGVR_UViG_3300014203_000236|3300014203|Ga0172378_100030802

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
IMGVR_UViG_3300007533_000212|3300007533|Ga0102944_100109613 40.909 2.46e-75 244 96% IMGVR phrog_20113
IMGVR_UViG_3300012931_000043|3300012931|Ga0153915_1000043910 38.788 8.98e-70 229 96% IMGVR phrog_20113
IMGVR_UViG_3300026184_000080|3300026184|Ga0209918_100067512 40.909 2.39e-75 244 96% IMGVR phrog_20113
IMGVR_UViG_3300026487_000004|3300026487|Ga0256408_100019828 43.202 1.34e-81 259 97% IMGVR phrog_20113
IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844 100.000 0.0 710 100% IMGVR phrog_20113