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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 APIS069
Inhibited defense system
CLAN ID CLAN003
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774
gene_page: 143 15871.7 6.1247 -1.5
Phage property
Phage Assembly id
IMGVR_UViG_3300036792_000137
PMID/References
PDB structures ;
Pfam domains PF03230.16
Phrog phrog_10132
Host taxa
Gene Location Start: 343;  End: 774;  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 APIS007,ArdB 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_3300036792_000137 1288 1587 - IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_1288_1587 99 10715.93 -5.0 4.5468 hypothetical protein
IMGVR_UViG_3300036792_000137 1598 1840 - IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_1598_1840 80 8401.68 4.5 10.7162 hypothetical protein
IMGVR_UViG_3300036792_000137 1837 2442 - IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_1837_2442 201 22012.79 10.5 10.2799 hypothetical protein phrog_17923
IMGVR_UViG_3300036792_000137 2439 2636 - IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_2439_2636 65 7101.94 -1.0 5.5707 hypothetical protein
IMGVR_UViG_3300036792_000137 343 774 + IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774 143 15871.73 -1.5 6.1247 hypothetical protein phrog_10132 PF03230.16
IMGVR_UViG_3300036792_000137 42 218 + IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_42_218 58 6319.69 4.0 10.1264 hypothetical protein phrog_1039 ; phrog_1584 PF14373.9
IMGVR_UViG_3300036792_000137 796 1029 + IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_796_1029 77 8472.94 -0.5 5.7905 antitoxin HicB

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.77 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-Q93GQ0-F1-model_v4 1 143 5 144 0.9302 0.9149
AF-A0A077ZNG7-F1-model_v4 1 143 5 141 0.9165 0.8953
AF-A0A0H3GW18-F1-model_v4 4 143 8 141 0.8769 0.8531
AF-A0A0H3GVF3-F1-model_v4 4 143 3 132 0.8722 0.8195
AF-P52139-F1-model_v4 4 143 18 152 0.8586 0.818
AF-P75676-F1-model_v4 4 143 18 152 0.8567 0.8156
AF-Q327Q6-F1-model_v4 4 143 21 157 0.8514 0.7979
AF-A0A0H3GZ47-F1-model_v4 1 143 84 221 0.9197 0.7523
AF-Q32HM6-F1-model_v4 4 143 45 181 0.8529 0.7521

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000816921373.pdb 1 143 1 139 0.9505 0.9242
MGYP000611349549.pdb 4 143 8 145 0.9519 0.9177
MGYP000112106482.pdb 4 143 4 140 0.9387 0.917
MGYP001142107270.pdb 4 143 5 141 0.9397 0.9161
MGYP003561631401.pdb 3 143 5 142 0.9326 0.9098
MGYP002759879196.pdb 4 143 5 141 0.9348 0.9097
MGYP001611400893.pdb 6 143 1 138 0.9368 0.9088
MGYP000926023203.pdb 5 143 1 136 0.9411 0.9047
MGYP000465578469.pdb 3 143 6 143 0.9307 0.9043
MGYP001044518354.pdb 5 143 7 143 0.9261 0.9035

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS069 IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774 5 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN003

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS007 1.77E-47 2 143 18 151 restriction-modification (RM) BAF33451.1
APIS038 2.29E-40 3 143 11 150 IMGVR_UViG_2576861805_000002|2576861805|2579667884
APIS039 1.79E-25 3 143 44 179 IMGVR_UViG_2751185776_000007|2751185776|2753238834
APIS037 3.95E-25 7 143 8 141 IMGVR_UViG_2541047688_000003|2541047688|2543982737
APIS055 2.07E-23 3 143 7 142 OL763419_00042

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_2852743531_000002|2852743531|2852746060 40.299 1.06e-22 95.5 91% Paraburkholderia tuberum IMGVR PF03230 phrog_10132
IMGVR_UViG_2921707344_000004|2921707344|2921709599 40.146 1.51e-21 92.8 93% Paraburkholderia tuberum IMGVR PF03230 phrog_10132
IMGVR_UViG_2921707344_000005|2921707344|2921712269 41.606 3.63e-24 99.4 93% Paraburkholderia tuberum IMGVR PF03230 phrog_10132
IMGVR_UViG_3300033475_000967|3300033475|Ga0310811_1000048848 64.789 2.53e-59 188 99% IMGVR PF03230 phrog_10132
IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774 100.000 6.76e-101 293 100% IMGVR PF03230 phrog_10132