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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 APIS065
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
KJ018209_00009
gene_page: 348 39989.1 6.1114 -2
Phage property
Phage Assembly id
Shewanella sp. phage 1/4 KJ018209
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_20113
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella;
Gene Location Start: 4179;  End: 5225;  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
KJ018209 1802 2935 - KJ018209_00004 377 43373.85 43373.85 9.7898 hypothetical protein phrog_16315 ; phrog_8470 ; phrog_36382 ; phrog_7484 PF14284.9
KJ018209 2946 3062 - KJ018209_00005 38 4657.75 4657.75 10.4720 hypothetical protein
KJ018209 3167 3283 - KJ018209_00006 38 4356.96 4356.96 3.7700 hypothetical protein
KJ018209 3328 3627 - KJ018209_00007 99 11515.12 11515.12 5.6523 hypothetical protein
KJ018209 3851 4177 - KJ018209_00008 108 12712.33 12712.33 4.4194 hypothetical protein phrog_11684
KJ018209 4179 5225 - KJ018209_00009 348 39989.06 39989.06 6.1114 hypothetical protein phrog_20113
KJ018209 5280 5528 - KJ018209_00010 82 9856.11 9856.11 6.2119 hypothetical protein phrog_15762 ; phrog_29978
KJ018209 5630 5866 - KJ018209_00011 78 9419.68 9419.68 4.5175 hypothetical protein phrog_38582
KJ018209 5863 6228 - KJ018209_00012 121 14139.36 14139.36 7.3147 hypothetical protein phrog_38754
KJ018209 6319 6450 - KJ018209_00013 43 4686.48 4686.48 9.5737 hypothetical protein
KJ018209 6438 7010 - KJ018209_00014 190 20826.68 20826.68 8.2455 DprA-like DNA recombination-mediator protein phrog_768 PF02481.18

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.71 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
APIS065 KJ018209_00009 11 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
APIS071 2.97E-116 5 351 4 346 IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751
APIS046 7.32E-78 4 351 1 335 IMGVR_UViG_3300009034_000088|3300009034|Ga0115863_100105265
APIS068 1.28E-63 4 341 1 330 IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844
APIS083 1.78E-63 2 342 19 342 CP067347_00056
APIS057 4.56E-55 7 344 1 322 IMGVR_UViG_3300021167_000128|3300021167|Ga0216365_13592277
APIS005 3.23E-54 5 342 7 303 Gabija APD21271.1
APIS088 4.55E-32 5 343 5 304 uvig_218805_40
APIS053 4.03E-26 7 341 80 374 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_3300007538_000027|3300007538|Ga0099851_100001233 74.928 0.0 545 98% IMGVR phrog_20113
IMGVR_UViG_3300008255_000114|3300008255|Ga0100403_1000053103 74.352 0.0 547 99% IMGVR phrog_20113
IMGVR_UViG_3300022200_000029|3300022200|Ga0196901_100001173 74.928 0.0 545 99% IMGVR phrog_20113
IMGVR_UViG_3300022690_000006|3300022690|Ga0247388_100100481 37.015 2.95e-69 228 97% IMGVR phrog_20113
IMGVR_UViG_3300023100_000003|3300023100|Ga0247738_1000004971 39.169 2.32e-71 234 95% IMGVR phrog_20113
IMGVR_UViG_3300025018_000107|3300025018|Ga0210043_1000053108 74.352 0.0 547 99% IMGVR phrog_20113
IMGVR_UViG_3300027861_000034|3300027861|Ga0233415_100000439 38.138 1.02e-53 188 96% IMGVR phrog_20113
IMGVR_UViG_3300033997_000035|3300033997|Ga0310131_000137_6247_7305 67.052 9.28e-169 482 98% IMGVR phrog_20113
IMGVR_UViG_3300037424_000713|3300037424|Ga0395806_0005169_4599_5585 41.298 9.46e-73 237 99% IMGVR phrog_20113
KJ018209_00009 100.000 0.0 722 100% Shewanella sp. phage 1/4 Shewanella INPHARED phrog_20113
MG592537_00069 45.797 2.61e-85 270 96% Vibrio phage 1.170.O._10N.261.52.C3 Vibrio INPHARED phrog_20113
APIS Contig Range
APIS065 KJ018209 1802 - 7010

Gene cluster comparison plot by clinker      Download html