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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 APIS011
Inhibited defense system toxin-antitoxin (TA)
CLAN ID CLAN023
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_041980.1 gene_page: gp4.5 89 10091.5 10.5538 5.5
Phage property
Phage Assembly id
T7 of E. coli GCF_000844825.1
PMID/References PMID:23478446
PDB structures ;
Pfam domains PF17574.5
Phrog phrog_2254
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: 13584;  End: 13853;  Strand: +
Description Protein gp4.5 allows T7 to block Lon (protease) from degrading antitoxins (the SanTA system in E. coli), including SanaA, thereby preventing liberation of SanaT. However, beyond a possible interaction between gp4.5 and Lon in uninfected cells, this speculative model remains untested.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_001604.1 11565 13265 + NP_041975.1 566 62655.45 -11.5 5.2337 DNA primase/helicase phrog_239 ; phrog_37627 ; phrog_47 PF08273.15 ;PF13155.9 ;PF03796.18
NC_001604.1 11635 11757 + NP_041976.1 40 4397.03 4.0 10.8565 hypothetical protein phrog_20075
NC_001604.1 11754 13265 + NP_041977.1 503 55742.97 -10.0 5.2007 DNA primase/helicase phrog_239 ; phrog_37627 ; phrog_47 PF13155.9 ;PF03796.18
NC_001604.1 12988 13326 + NP_041978.1 112 12653.76 5.5 9.8477 hypothetical protein phrog_5140 PF17576.5
NC_001604.1 13352 13564 + NP_041979.1 70 7927.14 5.0 10.7019 hypothetical protein phrog_1950 PF17565.5
NC_001604.1 13584 13853 + NP_041980.1 89 10091.46 5.5 10.5538 hypothetical protein phrog_2254 PF17574.5
NC_001604.1 13927 14334 + NP_041981.1 135 15208.56 8.5 10.0361 hypothetical protein phrog_4023
NC_001604.1 14353 16467 + NP_041982.1 704 79691.65 -1.0 6.4437 DNA polymerase I phrog_24147 ; phrog_17 ; phrog_15971 ; phrog_6375 ; phrog_403 ; phrog_38876 ; phrog_9565 ; phrog_16667 PF00476.23
NC_001604.1 16483 16839 + NP_041983.1 118 13067.05 3.5 8.6691 hypothetical protein phrog_5018 PF11645.11
NC_001604.1 16851 17147 + NP_041984.1 169 18712.73 9.0 9.7615 hypothetical protein phrog_17900 ; phrog_1452 ; phrog_1334 PF11247.11
NC_001604.1 17147 17359 + NP_041984.1 169 18712.73 9.0 9.7615 hypothetical protein phrog_17900 ; phrog_1452 ; phrog_1334 PF11247.11

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.68 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 1 86 1 85 0.7503 0.7168

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS011 NP_041980.1 43 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
APIS078 6.20E-33 1 73 1 73 KX078568_00026
APIS080 6.25E-32 4 87 9 90 ON602753_00020
APIS084 5.37E-29 4 72 9 77 MW001769_00023

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
AY264776_00018 100.000 1.02e-57 181 100% Escherichia phage T7 Escherichia INPHARED PF17574 phrog_2254
AY264778_00021 97.753 9.19e-57 177 100% Escherichia phage T7 Escherichia INPHARED PF17574 phrog_2254
EU734174_00021 96.512 3.47e-53 169 97% Escherichia phage 13a Escherichia INPHARED PF17574 phrog_2254
FR667955_00018 95.506 2.51e-55 174 100% Salmonella phage Vi06 Salmonella INPHARED PF17574 phrog_2254
IMGVR_UViG_3300013307_000032|3300013307|Ga0157372_1000058425 59.740 6.33e-21 87.4 84% IMGVR PF17574 phrog_2254
IMGVR_UViG_3300045988_000100|3300045988|Ga0495776_025784_7113_7409 96.629 8.47e-56 175 100% IMGVR PF17574 phrog_2254
IMGVR_UViG_3300045988_000519|3300045988|Ga0495776_043652_12984_13274 97.701 6.20e-55 173 98% IMGVR PF17574 phrog_2254
IMGVR_UViG_3300045988_001011|3300045988|Ga0495776_127866_17262_17558 98.864 2.37e-56 177 99% IMGVR PF17574 phrog_2254
KM242061_00029 96.629 1.04e-55 175 100% Escherichia phage CICC 80001 Escherichia INPHARED PF17574 phrog_2254
MG488277_00025 96.629 1.19e-55 175 100% Escherichia phage EG1 Escherichia INPHARED PF17574 phrog_2254
MG832642_00027 97.753 1.07e-56 177 100% Escherichia phage HZ2R8 Escherichia INPHARED PF17574 phrog_2254
MG966531_00020 68.182 7.56e-37 127 99% Escherichia phage Ebrios Escherichia INPHARED PF17574 phrog_2254
MGV-GENOME-0262495_20 97.701 8.69e-55 172 98% MGV PF17574 phrog_2254
MGV-GENOME-0263483_29 97.753 3.14e-56 176 100% MGV PF17574 phrog_2254
MGV-GENOME-0265351_15 96.629 9.41e-56 175 100% MGV PF17574 phrog_2254
MH370477_00025 61.644 1.31e-23 94.4 82% Escherichia phage SRT7 Escherichia INPHARED PF17574 phrog_2254
MH382198_00028 97.701 1.04e-54 172 98% Salmonella phage 3A_8767 Salmonella INPHARED PF17574 phrog_2254
MK310182_00022 97.753 3.01e-56 176 100% Escherichia phage NC-A Escherichia INPHARED PF17574 phrog_2254
MK542821_00027 96.629 8.54e-56 175 100% Escherichia phage HZP2 Escherichia INPHARED PF17574 phrog_2254
MN184885_00032 62.500 1.25e-22 92.0 80% Erwinia phage pEp_SNUABM_09 Erwinia INPHARED PF17574 phrog_2254
MN450150_00019 63.380 1.69e-21 89.0 80% Pantoea phage vB_PagP-SK1 Pantoea INPHARED PF17574 phrog_2254
MN481365_00028 95.506 3.60e-55 173 100% Escherichia phage vB_EcoP_PHB19 Escherichia INPHARED PF17574 phrog_2254
MN481366_00020 96.629 1.17e-55 175 100% Escherichia phage vB_EcoP_PHB20 Escherichia INPHARED PF17574 phrog_2254
MT350293_00027 98.851 2.04e-55 174 98% Enterococcus phage EFA-2 Enterococcus INPHARED PF17574 phrog_2254
MT465573_00022 61.644 1.48e-23 94.0 82% Escherichia phage P1723 Escherichia INPHARED PF17574 phrog_2254
MT681669_00029 67.816 2.34e-36 126 98% Aeromonas phage PZL-Ah1 Aeromonas INPHARED PF17574 phrog_2254
MW074885_00011 95.506 4.53e-55 173 100% Escherichia phage JB01 Escherichia INPHARED PF17574 phrog_2254
MZ220766_00022 95.402 1.86e-53 169 98% Edwardsiella phage PVN09 Edwardsiella INPHARED PF17574 phrog_2254
MZ375287_00015 98.876 3.57e-57 179 100% Escherichia phage T7 Escherichia INPHARED PF17574 phrog_2254
MZ501081_00028 98.864 1.12e-56 177 99% Escherichia phage JeanTinguely Escherichia INPHARED PF17574 phrog_2254
MZ833439_00021 95.506 2.24e-55 174 100% Enterobacteria phage AH67C600_Q5 Enterobacteria INPHARED PF17574 phrog_2254
NP_041980.1 100.000 2.78e-64 180 100% T7 of E. coli Escherichia coli NCBI PF17574 phrog_2254
OK042080_00019 95.402 5.01e-53 168 98% Yersinia phage vB_YenP_Rambo Yersinia INPHARED PF17574 phrog_2254
OM630586_00042 97.753 7.88e-57 177 100% Escherichia phage vB_EcoP_LNA7 Escherichia INPHARED PF17574 phrog_2254
ON528716_00023 100.000 3.96e-56 176 98% Shigella phage ESh2 Shigella INPHARED PF17574 phrog_2254
ON528719_00030 94.382 4.12e-54 171 100% Shigella phage ESh6 Shigella INPHARED PF17574 phrog_2254
ON715521_00019 59.155 1.48e-22 91.7 80% Erwinia phage Stepyanka Erwinia INPHARED PF17574 phrog_2254
ON886116_00048 97.753 2.50e-56 176 100% Salmonella phage PSP2-22 Salmonella INPHARED PF17574 phrog_2254
OP331230_00040 98.876 5.25e-57 178 100% Escherichia phage 04922B Escherichia INPHARED PF17574 phrog_2254
OQ507919_00016 70.000 1.95e-28 106 89% Escherichia phage vB_Ec_Tarrare Escherichia INPHARED PF17574 phrog_2254
uvig_395422_28 96.629 3.79e-56 176 100% GPD PF17574 phrog_2254
uvig_481475_20 97.701 8.43e-55 172 98% GPD PF17574 phrog_2254
uvig_557579_21 97.753 7.88e-57 177 100% GPD PF17574 phrog_2254
APIS Contig Range
APIS011 NC_001604.1 11565 - 17359

Gene cluster comparison plot by clinker      Download html