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Seed proteins  | 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 APIS139
Inhibited defense system
CLAN ID CLAN039
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300031785_000173|3300031785|Ga0310343_1000130817
gene_page: 720 80060.38 6.0114 -4.0
Phage property
Phage Assembly id
IMGVR_UViG_3300031785_000173
PMID/References
PDB structures ;
Pfam domains PF07728.19,PF00004.34
Phrog phrog_249
Host taxa ;;;;;;
Gene Location Start: ;  End: ;  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 APIS166 which has seed protein.

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)
MGYP003686209621.pdb 177 714 1 345 0.9416 0.695
MGYP001588267429.pdb 34 713 1 378 0.8782 0.6679
MGYP003147730546.pdb 2 719 7 376 0.8479 0.6434
MGYP002641684555.pdb 79 714 46 415 0.7852 0.6181
MGYP000049587256.pdb 6 705 11 409 0.7874 0.6155
MGYP003328800530.pdb 208 720 3 423 0.7511 0.5969

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS139 IMGVR_UViG_3300031785_000173|3300031785|Ga0310343_1000130817 6 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN039

APIS139 has no similar APIS family.

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_3300031785_000173|3300031785|Ga0310343_1000130817 100.000 0.000E+00 1428 1.000% IMGVR PF07728 PF00004 phrog_249
IMGVR_UViG_3300020380_000200|3300020380|Ga0211498_1000016425 90.600 0.000E+00 1362 1.000% IMGVR PF07728 PF00004 phrog_249
IMGVR_UViG_2785511441_000001|2785511441|2786499700 88.900 0.000E+00 1334 1.000% IMGVR PF07728 PF00004 phrog_249
IMGVR_UViG_3300030118_002436|3300030118|Ga0183723_10000274 90.400 0.000E+00 1359 1.000% IMGVR PF07728 PF00004 phrog_249
IMGVR_UViG_3300020400_000065|3300020400|Ga0211636_1000089921 90.200 0.000E+00 1356 1.000% IMGVR PF07728 PF00004 phrog_249
IMGVR_UViG_3300020401_000034|3300020401|Ga0211617_1000015246 90.200 0.000E+00 1154 0.851% IMGVR PF07728 PF00004 phrog_249