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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 APIS071
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751
gene_page: 343 39700.1 7.1914 3.5
Phage property
Phage Assembly id
IMGVR_UViG_3300037628_000643
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_20113
Host taxa
Gene Location Start: 90720;  End: 91751;  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_3300037628_000643 86259 87203 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_86259_87203 314 35358.84 -5.5 5.0064 ribonucleoside-diphosphate reductase alpha chain phrog_84 ; phrog_3987 PF00317.24
IMGVR_UViG_3300037628_000643 86259 87203 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_86259_87203 314 35358.84 -5.5 5.0064 ribonucleoside-diphosphate reductase alpha chain phrog_84 ; phrog_3987 PF02867.18
IMGVR_UViG_3300037628_000643 87398 89005 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_87398_89005 535 60398.50 -8.0 5.3682 ribonucleoside-diphosphate reductase alpha chain phrog_3844 ; phrog_84 ; phrog_3987 ; phrog_367 PF02867.18
IMGVR_UViG_3300037628_000643 89040 89414 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89040_89414 124 14731.86 -7.5 4.5097 hypothetical protein
IMGVR_UViG_3300037628_000643 89488 90135 - IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89488_90135 215 24550.85 15.0 9.9016 group I intron endonuclease phrog_655 ; phrog_314 ; phrog_19446 PF07460.14
IMGVR_UViG_3300037628_000643 89488 90135 - IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_89488_90135 215 24550.85 15.0 9.9016 group I intron endonuclease phrog_655 ; phrog_314 ; phrog_19446 PF07460.14
IMGVR_UViG_3300037628_000643 90308 90727 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90308_90727 139 16143.93 -9.5 4.3326 hypothetical protein phrog_98 ; phrog_21205 PF09643.13
IMGVR_UViG_3300037628_000643 90720 91751 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 343 39700.05 3.5 7.1914 hypothetical protein phrog_20113
IMGVR_UViG_3300037628_000643 91748 92182 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_91748_92182 144 16265.24 -9.0 4.4963 hypothetical protein
IMGVR_UViG_3300037628_000643 92193 92393 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92193_92393 66 7334.27 -4.5 4.3297 hypothetical protein
IMGVR_UViG_3300037628_000643 92390 92827 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92390_92827 145 16210.75 -2.5 4.8947 hypothetical protein phrog_30914 ; phrog_335
IMGVR_UViG_3300037628_000643 92824 93186 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_92824_93186 120 14217.32 5.5 9.4221 hypothetical protein
IMGVR_UViG_3300037628_000643 93173 93331 + IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_93173_93331 52 5814.65 -5.0 4.2829 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.7 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
APIS071 IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 8 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
APIS065 4.85E-117 1 343 4 350 KJ018209_00009
APIS046 3.01E-81 1 341 1 333 IMGVR_UViG_3300009034_000088|3300009034|Ga0115863_100105265
APIS068 1.95E-63 1 333 1 330 IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844
APIS083 8.42E-62 2 334 22 342 CP067347_00056
APIS057 1.03E-55 4 336 1 322 IMGVR_UViG_3300021167_000128|3300021167|Ga0216365_13592277
APIS005 1.80E-50 2 334 7 303 Gabija APD21271.1
APIS088 5.23E-35 2 335 5 304 uvig_218805_40
APIS053 4.40E-29 5 333 81 374 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_3300006192_000111|3300006192|Ga0075011_100015277 41.593 5.39e-82 261 97% IMGVR phrog_20113
IMGVR_UViG_3300007988_000001|3300007988|Ga0100402_100016990 43.636 1.52e-76 247 95% IMGVR phrog_20113
IMGVR_UViG_3300008005_000001|3300008005|Ga0100385_1000211103 43.333 2.04e-75 244 95% IMGVR phrog_20113
IMGVR_UViG_3300020047_003347|3300020047|Ga0206650_100312810 41.813 3.94e-87 274 99% IMGVR phrog_20113
IMGVR_UViG_3300022690_003208|3300022690|Ga0247388_100048132 43.917 2.67e-94 292 97% IMGVR phrog_20113
IMGVR_UViG_3300025018_000005|3300025018|Ga0210043_100013681 43.636 1.04e-76 247 95% IMGVR phrog_20113
IMGVR_UViG_3300037587_000320|3300037587|Ga0310923_0000225_16300_17337 37.982 8.07e-70 230 95% IMGVR phrog_20113
IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751 100.000 0.0 705 100% IMGVR phrog_20113