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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 APIS080
Inhibited defense system
CLAN ID CLAN023
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
ON602753_00020
gene_page: 103 11273.8 10.3987 5
Phage property
Phage Assembly id
Klebsiella phage VLCpiA3d ON602753
PMID/References
PDB structures ;
Pfam domains PF17574.5
Phrog phrog_2254
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;
Gene Location Start: ;  End: ;  Strand: 
Description
Note This family does not have seed protein, but we infer its function is defending toxin-antitoxin (TA) because it belongs to the same clan as family APIS011 which has seed protein.

Predicted 3D structure by alphafold2 with pTM = 0.73 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)
MGYP003595835577.pdb 8 96 3 89 0.7983 0.7126

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS080 ON602753_00020 39 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN023

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS011 5.48E-32 9 86 26 103 toxin-antitoxin (TA) NP_041980.1
APIS084 8.32E-26 6 77 7 78 MW001769_00023
APIS078 2.51E-23 9 74 5 70 KX078568_00026

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_3300045988_000298|3300045988|Ga0495776_113816_26626_26937 92.857 2.15e-60 188 95% IMGVR PF17574 phrog_2254
IMGVR_UViG_3300045988_001943|3300045988|Ga0495776_046194_7165_7476 88.119 1.81e-58 183 98% IMGVR PF17574 phrog_2254
MGV-GENOME-0149923_11 92.157 3.76e-60 187 97% MGV PF17574 phrog_2254
MGV-GENOME-0189393_13 88.119 1.89e-58 183 97% MGV PF17574 phrog_2254
MGV-GENOME-0265429_14 93.069 4.12e-62 192 97% MGV PF17574 phrog_2254
MGV-GENOME-0266883_34 90.099 1.53e-59 186 97% MGV PF17574 phrog_2254
MGV-GENOME-0269628_21 94.175 7.61e-63 194 98% MGV PF17574 phrog_2254
MGV-GENOME-0271769_13 91.000 1.32e-60 188 96% MGV PF17574 phrog_2254
MGV-GENOME-0271873_37 92.157 6.42e-61 189 97% MGV PF17574 phrog_2254
MGV-GENOME-0271896_27 88.119 3.00e-58 182 97% MGV PF17574 phrog_2254
MGV-GENOME-0272093_12 92.857 2.24e-60 188 94% MGV PF17574 phrog_2254
MGV-GENOME-0272520_27 89.320 1.99e-59 185 98% MGV PF17574 phrog_2254
MGV-GENOME-0274788_15 91.176 2.37e-60 187 97% MGV PF17574 phrog_2254
MGV-GENOME-0275239_15 92.079 6.50e-60 187 97% MGV PF17574 phrog_2254
MGV-GENOME-0276411_33 89.109 6.74e-59 184 97% MGV PF17574 phrog_2254
MH059637_00020 70.370 9.81e-41 121 79% Pectobacterium phage Jarilo Pectobacterium INPHARED PF17574 phrog_2254
MK795385_00033 94.175 7.30e-63 194 99% Klebsiella phage IME304 Klebsiella INPHARED PF17574 phrog_2254
MT813141_00017 92.929 1.67e-60 188 96% Klebsiella phage NL_ZS_2 Klebsiella INPHARED PF17574 phrog_2254
MT966872_00022 90.000 5.23e-60 187 97% Klebsiella phage P510 Klebsiella INPHARED PF17574 phrog_2254
MW042791_00025 90.722 1.64e-58 183 94% Klebsiella phage 066023 Klebsiella INPHARED PF17574 phrog_2254
MW042800_00047 91.000 1.27e-60 188 97% Klebsiella phage 066037 Klebsiella INPHARED PF17574 phrog_2254
MW042812_00012 90.196 5.35e-60 187 98% Klebsiella phage 066134 Klebsiella INPHARED PF17574 phrog_2254
OM194189_00019 93.069 3.96e-62 192 98% Klebsiella phage Shaphc-9226R Klebsiella INPHARED PF17574 phrog_2254
ON602753_00020 100.000 1.08e-67 206 100% Klebsiella phage VLCpiA3d Klebsiella INPHARED PF17574 phrog_2254
ON602755_00024 91.000 8.58e-60 186 97% Klebsiella phage VLCpiA3c Klebsiella INPHARED PF17574 phrog_2254
ON880501_00029 92.079 1.19e-61 191 98% Klebsiella phage vB_KpnP1 Klebsiella INPHARED PF17574 phrog_2254
OP256047_00028 93.137 2.09e-54 172 99% Klebsiella phage BUCT-3589 Klebsiella INPHARED PF17574 phrog_2254
OQ579029_00019 92.000 9.70e-54 171 97% Klebsiella phage Saitama Klebsiella INPHARED PF17574 phrog_2254
OQ579030_00020 89.109 9.52e-52 166 98% Klebsiella phage Emom Klebsiella INPHARED PF17574 phrog_2254
OX335390_00021 87.129 2.67e-50 162 98% Klebsiella phage cp7 Klebsiella INPHARED PF17574 phrog_2254
OX335398_00022 88.119 6.15e-51 164 98% Klebsiella phage cp8 Klebsiella INPHARED PF17574 phrog_2254
uvig_225801_27 89.320 1.91e-59 185 99% GPD PF17574 phrog_2254
uvig_234063_32 88.119 2.88e-58 182 98% GPD PF17574 phrog_2254
uvig_241747_16 93.137 1.35e-61 191 98% GPD PF17574 phrog_2254
uvig_282596_29 98.058 1.69e-64 198 99% GPD PF17574 phrog_2254
uvig_320142_31 91.176 2.27e-60 187 98% GPD PF17574 phrog_2254
uvig_325023_26 92.079 6.24e-60 187 98% GPD PF17574 phrog_2254
uvig_328834_17 90.099 1.47e-59 186 98% GPD PF17574 phrog_2254
uvig_472708_11 92.157 3.60e-60 187 98% GPD PF17574 phrog_2254
APIS Contig Range
APIS080 -

Gene cluster comparison plot by clinker      Download html