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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 APIS023
Inhibited defense system RecBCD
CLAN ID CLAN022
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_041987.1 gene_page: gp5.9 52 6044.63 3.8516 -8.0
Phage property
Phage Assembly id
T7 of E. coli GCF_000844825.1
PMID/References PMID:36533901
PDB structures 8B1R;
Pfam domains
Phrog phrog_9014
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: ;  End: ;  Strand: 
Description Gp5.9 completely inhibits RecBCD by preventing it from binding to DNA. The RecBCD-gp5.9 structure shows that gp5.9 acts by substrate mimicry, binding predominantly to the RecB arm domain and competing sterically for the DNA binding site.

PDB structure: 8B1R ; Download help

Full Sequence      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-Q32CA1-F1-model_v4 1 1170 5 1174 0.979 0.972
AF-Q32C99-F1-model_v4 1 1121 1 1121 0.9758 0.972
AF-Q8ZMB4-F1-model_v4 1 1121 1 1121 0.9744 0.97
AF-A0A0H3GX23-F1-model_v4 1 1121 1 1121 0.9664 0.9601
AF-A0A0H3GSM0-F1-model_v4 1 1163 5 1162 0.9662 0.9588
AF-Q8ZMB6-F1-model_v4 1 1170 5 1174 0.9648 0.9556
AF-P07648-F1-model_v4 1 1121 1 1121 0.9411 0.9329
AF-P45157-F1-model_v4 1 1168 4 1211 0.9208 0.8991
AF-Q5F9M3-F1-model_v4 1 1167 5 1200 0.8987 0.8814
AF-Q9HWB5-F1-model_v4 1 1121 13 1167 0.8917 0.8651

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001323249337.pdb 1 1121 1 1078 0.8954 0.8697
MGYP000343347791.pdb 1 1121 3 1078 0.8914 0.866
MGYP000296227853.pdb 1 1121 2 1064 0.8962 0.866
MGYP001220130095.pdb 1 1121 1 1073 0.8893 0.8638
MGYP000048607859.pdb 1 346 1 354 0.8811 0.8633
MGYP001350262151.pdb 30 354 1 329 0.906 0.8606
MGYP003689255157.pdb 7 1121 1 1087 0.8797 0.8599
MGYP001051269506.pdb 1 1121 1 1101 0.8749 0.8579
MGYP003971195195.pdb 1 1121 2 1098 0.8758 0.8577
MGYP000608793603.pdb 1 1121 2 1088 0.8787 0.8575

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS023 NP_041987.1 24 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN022

APIS023 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
FR667955_00024 80.769 8.13e-22 87.0 100% Salmonella phage Vi06 Salmonella INPHARED phrog_9014
MG488277_00031 88.462 2.87e-25 95.5 100% Escherichia phage EG1 Escherichia INPHARED phrog_9014
MG832642_00032 92.157 3.68e-26 97.8 98% Escherichia phage HZ2R8 Escherichia INPHARED phrog_9014
MGV-GENOME-0262495_14 90.385 2.74e-26 98.2 100% MGV phrog_9014
MGV-GENOME-0263483_34 98.077 4.43e-29 105 100% MGV phrog_9014
MGV-GENOME-0265351_20 90.385 3.57e-26 97.8 100% MGV phrog_9014
MH382198_00033 90.385 3.41e-26 97.8 100% Salmonella phage 3A_8767 Salmonella INPHARED phrog_9014
MH717099_00028 90.385 3.49e-26 97.8 100% Escherichia phage C5 Escherichia INPHARED phrog_9014
MK310182_00028 94.231 8.69e-28 102 100% Escherichia phage NC-A Escherichia INPHARED phrog_9014
MK542821_00033 90.385 5.06e-26 97.4 100% Escherichia phage HZP2 Escherichia INPHARED phrog_9014
MN098329_00025 96.154 2.25e-28 103 100% Serratia phage Pila Serratia INPHARED phrog_9014
MT350293_00022 90.385 1.41e-25 96.3 100% Enterococcus phage EFA-2 Enterococcus INPHARED phrog_9014
MW074885_00016 90.385 6.04e-26 97.4 100% Escherichia phage JB01 Escherichia INPHARED phrog_9014
MW883060_00022 96.154 1.40e-28 103 100% Escherichia phage vB_EcoP_SYGE1 Escherichia INPHARED phrog_9014
MZ220766_00026 90.385 4.25e-26 97.8 100% Edwardsiella phage PVN09 Edwardsiella INPHARED phrog_9014
MZ375257_00021 98.077 3.94e-28 102 100% Escherichia phage T7 Escherichia INPHARED phrog_9014
NP_041987.1 100.000 3.59e-36 106 100% T7 of E. coli Escherichia coli NCBI phrog_9014
OM630586_00048 98.077 4.33e-29 105 100% Escherichia phage vB_EcoP_LNA7 Escherichia INPHARED phrog_9014
ON528716_00028 94.231 1.96e-27 100 100% Shigella phage ESh2 Shigella INPHARED phrog_9014
ON528717_00024 92.308 9.85e-27 99.4 100% Shigella phage ESh3 Shigella INPHARED phrog_9014
ON528719_00035 92.308 6.56e-27 99.8 100% Shigella phage ESh6 Shigella INPHARED phrog_9014
ON568193_00030 94.231 1.79e-27 101 100% Cedecea phage Yanou Cedecea INPHARED phrog_9014
OP331230_00045 88.462 8.77e-26 97.1 100% Escherichia phage 04922B Escherichia INPHARED phrog_9014
uvig_481475_14 90.385 2.68e-26 98.2 100% GPD phrog_9014
APIS Contig Range
APIS023 NC_001604.1 -

Gene cluster comparison plot by clinker      Download html