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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 APIS013
Inhibited defense system toxin-antitoxin (TA)
CLAN ID CLAN027
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_049653.1 gene_page: Dmd 60 7027.25 4.9813 -1
Phage property
Phage Assembly id
T4 of E. coli GCF_000836945.1
PMID/References PMID:22403819
PDB structures 5I8J;
Pfam domains PF17587.5
Phrog phrog_2102
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: 20371;  End: 20553;  Strand: -
Description T4 produces Dmd, an antitoxin that inhibits E. coli RnlA and LsoA toxins. Dmd differs from the RnlB or LsoB antitoxins, suggesting it evolved independently, which is highlighted by its different toxin neutralization mechanism.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_000866.4 17935 18963 - NP_049648.1 342 39777.99 15.5 9.5801 DNA primase phrog_21887 ; phrog_47
NC_000866.4 18966 19130 - NP_049649.1 54 5896.64 -1.0 5.0824 hypothetical protein phrog_1823 ; phrog_2086 PF07068.14
NC_000866.4 19132 19758 - NP_049650.1 208 24331.57 0.0 6.4890 hypothetical protein phrog_8539 ; phrog_4122 ; phrog_3781
NC_000866.4 19758 20051 - NP_049651.1 97 10993.66 -3.0 4.6017 spackle periplasmic phrog_1586
NC_000866.4 20112 20369 - NP_049652.1 85 10187.10 8.5 10.4193 hypothetical protein phrog_3272 ; phrog_8921 ; phrog_2375 ; phrog_12748
NC_000866.4 20371 20553 - NP_049653.1 60 7027.25 -1.0 4.9813 Dmd discriminator of mRNA degradation phrog_2102 PF17587.5
NC_000866.4 20612 22039 - NP_049654.1 475 53601.01 -6.5 5.2884 AAA family ATPase phrog_19 PF03796.18
NC_000866.4 22049 22393 - NP_049655.1 114 13290.24 -6.0 4.6272 head vertex assembly chaperone phrog_999 PF11113.11
NC_000866.4 22386 23561 - NP_049656.2 391 43998.29 -6.5 5.0416 recombinase phrog_8337 ; phrog_18112 ; phrog_97 ; phrog_31060 PF00154.24
NC_000866.4 23570 24235 - NP_049657.1 221 25339.15 25.0 10.5097 homing endonuclease phrog_19446 ; phrog_37840 ; phrog_314 PF01541.27 ;PF07460.14 ;PF07460.14
NC_000866.4 24400 25455 - NP_049658.1 351 40665.95 8.5 9.5504 beta-glucosyltransferase phrog_26084 ; phrog_7922 PF09198.13

Seed genomic context- JBrowse     

PDB structure: 5I8J ; Download help

Full Sequence      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)
MGYP000576321089.pdb 1 64 2 61 0.9267 0.8872
MGYP003042793297.pdb 1 63 7 69 0.9447 0.8838

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS013 NP_049653.1 74 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN027

APIS013 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
AP019521_00035 59.016 5.24e-15 70.5 97% Escherichia phage KIT01 Escherichia INPHARED PF17587 phrog_2102
EU863409_00037 56.667 1.59e-14 69.3 95% Escherichia phage JS10 Escherichia INPHARED PF17587 phrog_2102
HE956711_00040 98.333 5.09e-35 120 100% Yersinia phage phiD1 Yersinia INPHARED PF17587 phrog_2102
HM563683_00041 58.333 2.41e-15 71.2 95% Escherichia phage vB_EcoM_VR7 Escherichia INPHARED PF17587 phrog_2102
IMGVR_UViG_2974735146_000001|2974735146|2974735365 100.000 1.64e-30 109 87% IMGVR PF17587 phrog_2102
IMGVR_UViG_3300010279_000005|3300010279|Ga0129313_100005819 96.667 1.07e-34 120 100% IMGVR PF17587 phrog_2102
IMGVR_UViG_3300029310_000146|3300029310|Ga0134545_10057502 57.627 1.30e-14 69.3 95% IMGVR PF17587 phrog_2102
IMGVR_UViG_3300045988_061624|3300045988|Ga0495776_119604_40396_40608 55.738 4.25e-15 70.9 98% IMGVR PF17587 phrog_2102
IMGVR_UViG_3300045988_086346|3300045988|Ga0495776_001670_4739_4948 56.667 8.73e-15 70.1 97% IMGVR PF17587 phrog_2102
JX536493_00143 56.667 1.01e-14 69.7 97% Escherichia phage HX01 Escherichia INPHARED PF17587 phrog_2102
KF208315_00036 98.333 1.28e-34 119 100% Yersinia phage PST Yersinia INPHARED PF17587 phrog_2102
KM501444_00050 96.667 4.95e-34 118 100% Shigella phage pSs-1 Shigella INPHARED PF17587 phrog_2102
KM607000_00039 68.254 5.00e-20 83.2 100% Enterobacteria phage RB27 Enterobacteria INPHARED PF17587 phrog_2102
KP007361_00042 58.333 1.30e-15 72.0 95% Escherichia phage vB_EcoM_VR25 Escherichia INPHARED PF17587 phrog_2102
KR269718_00165 98.333 8.91e-35 120 100% Escherichia phage HY03 Escherichia INPHARED PF17587 phrog_2102
KX130865_00020 63.333 8.83e-18 77.4 95% Shigella phage SHSML-52-1 Shigella INPHARED PF17587 phrog_2102
KY703222_00150 57.627 1.09e-14 69.7 95% Escherichia phage phiC120 Escherichia INPHARED PF17587 phrog_2102
LC348379_00041 96.667 2.08e-34 119 100% Escherichia phage PP01 Escherichia INPHARED PF17587 phrog_2102
LR877332_00037 98.333 1.49e-34 119 100% Shigella phage vB_SsoM_JK08 Shigella INPHARED PF17587 phrog_2102
MF044457_00078 56.667 4.29e-15 70.5 97% Escherichia phage ST0 Escherichia INPHARED PF17587 phrog_2102
MF327007_00037 96.667 1.04e-34 120 100% Shigella phage Sf21 Shigella INPHARED PF17587 phrog_2102
MGV-GENOME-0371733_83 96.667 1.85e-34 119 100% MGV PF17587 phrog_2102
MGV-GENOME-0373836_53 100.000 5.87e-36 123 100% MGV PF17587 phrog_2102
MGV-GENOME-0377517_57 56.667 5.19e-15 70.5 97% MGV PF17587 phrog_2102
MGV-GENOME-0377569_212 98.333 3.52e-35 121 100% MGV PF17587 phrog_2102
MGV-GENOME-0377573_11 57.627 1.11e-14 69.7 95% MGV PF17587 phrog_2102
MGV-GENOME-0377591_83 62.903 1.71e-18 79.3 98% MGV PF17587 phrog_2102
MGV-GENOME-0377637_166 61.667 6.98e-16 72.8 95% MGV PF17587 phrog_2102
MH837626_00148 96.667 1.65e-34 119 100% Escherichia phage vB_vPM_PD112 Escherichia INPHARED PF17587 phrog_2102
MK327928_00039 98.333 2.33e-35 121 100% Escherichia phage vB_EcoM_G2133 Escherichia INPHARED PF17587 phrog_2102
MK327934_00036 58.333 7.02e-16 72.4 97% Escherichia phage vB_EcoM_G2469 Escherichia INPHARED PF17587 phrog_2102
MK327936_00038 98.333 1.45e-35 122 100% Escherichia phage vB_EcoM_G2540 Escherichia INPHARED PF17587 phrog_2102
MK327942_00038 96.667 6.55e-35 120 100% Escherichia phage vB_EcoM_G50 Escherichia INPHARED PF17587 phrog_2102
MK373778_00036 62.903 5.20e-19 80.5 98% Escherichia phage vB_EcoM_WFbE185 Escherichia INPHARED PF17587 phrog_2102
MK373779_00039 95.000 9.05e-34 117 100% Escherichia phage vB_EcoM_G9062 Escherichia INPHARED PF17587 phrog_2102
MK373785_00038 98.333 2.55e-35 121 100% Escherichia phage vB_EcoM_OE5505 Escherichia INPHARED PF17587 phrog_2102
MK962754_00036 58.333 2.20e-15 71.2 97% Shigella phage JK36 Shigella INPHARED PF17587 phrog_2102
MN850651_00058 62.903 4.88e-18 78.2 98% Escherichia phage moskry Escherichia INPHARED PF17587 phrog_2102
MT129652_00176 56.667 1.41e-14 69.3 95% Escherichia phage MN01 Escherichia INPHARED PF17587 phrog_2102
MT176426_00038 96.667 1.20e-34 119 100% Serratia phage PhiZZ30 Serratia INPHARED PF17587 phrog_2102
MT446390_00236 56.667 5.06e-15 70.5 97% Escherichia phage TH12 Escherichia INPHARED PF17587 phrog_2102
MT828552_00149 98.333 1.28e-34 119 100% Yersinia phage PYps5T Yersinia INPHARED PF17587 phrog_2102
MW149274_00203 57.377 2.86e-15 71.2 97% Salmonella phage vB_SalM_ABTNLsp5 Salmonella INPHARED PF17587 phrog_2102
MW250787_00259 56.667 1.37e-14 69.3 95% Escherichia phage UPEC07 Escherichia INPHARED PF17587 phrog_2102
MW679410_00038 60.000 1.15e-15 72.0 95% Escherichia phage C6 Escherichia INPHARED PF17587 phrog_2102
MZ150757_00040 98.333 2.16e-35 121 100% Salmonella phage Lv5cm Salmonella INPHARED PF17587 phrog_2102
MZ189261_00034 55.738 1.75e-15 71.6 98% Escherichia phage S143_2 Escherichia INPHARED PF17587 phrog_2102
MZ234018_00056 98.333 4.36e-35 120 100% Escherichia phage vB_EcoM-101117BS1 Escherichia INPHARED PF17587 phrog_2102
MZ234025_00059 55.000 1.10e-14 69.7 97% Escherichia phage vB_EcoM-172859UKE1 Escherichia INPHARED PF17587 phrog_2102
MZ234038_00056 96.667 2.29e-34 119 100% Escherichia phage vB_EcoM-G3F10 Escherichia INPHARED PF17587 phrog_2102
MZ501089_00148 96.667 7.40e-35 120 100% Escherichia phage KarlGJung Escherichia INPHARED PF17587 phrog_2102
MZ502380_00036 98.333 2.41e-35 121 100% Escherichia phage vB_EcoM_Nami Escherichia INPHARED PF17587 phrog_2102
NP_049653.1 100.000 1.47e-42 123 100% T4 of E. coli Escherichia coli NCBI PF17587 phrog_2102
OL960580_00041 96.667 5.06e-34 118 100% Escherichia phage vB_EcoM_SA21RB Escherichia INPHARED PF17587 phrog_2102
OL960581_00037 98.333 1.50e-35 122 100% Escherichia phage vB_EcoM_SA20RB Escherichia INPHARED PF17587 phrog_2102
ON210139_00242 96.667 1.80e-34 119 100% Escherichia phage EC128 Escherichia INPHARED PF17587 phrog_2102
ON528735_00027 96.667 2.24e-34 119 100% Shigella phage ESh25 Shigella INPHARED PF17587 phrog_2102
ON528737_00125 55.000 6.03e-15 70.1 97% Shigella phage ESh27 Shigella INPHARED PF17587 phrog_2102
ON528743_00029 98.333 2.05e-35 121 100% Shigella phage ESh33 Shigella INPHARED PF17587 phrog_2102
ON528745_00209 98.276 2.50e-33 116 97% Shigella phage ESH35 Shigella INPHARED PF17587 phrog_2102
OP172786_00050 96.667 2.22e-34 119 100% Escherichia phage ECO07P3 Escherichia INPHARED PF17587 phrog_2102
OP555982_00039 96.667 1.17e-34 119 100% Escherichia phage vB_EcoM-UFV11 Escherichia INPHARED PF17587 phrog_2102
OP611477_00026 98.333 2.69e-35 121 100% Escherichia virus CAM-21 Escherichia INPHARED PF17587 phrog_2102
OP870144_00038 66.667 5.83e-20 82.8 100% Escherichia phage vB_Eco_F25 Escherichia INPHARED PF17587 phrog_2102
OP870146_00038 56.667 8.57e-15 69.7 97% Escherichia phage vB_Eco_F27 Escherichia INPHARED PF17587 phrog_2102
OP870147_00035 55.000 9.96e-15 69.7 97% Escherichia phage vB_Eco_F31 Escherichia INPHARED PF17587 phrog_2102
OQ174500_00210 98.333 1.42e-35 122 100% Escherichia phage REP1 Escherichia INPHARED PF17587 phrog_2102
OQ446694_00064 96.667 1.19e-34 119 100% Escherichia phage Killian Escherichia INPHARED PF17587 phrog_2102
OQ466432_00080 98.333 3.32e-35 121 100% Escherichia phage ADUt Escherichia INPHARED PF17587 phrog_2102
OQ599309_00038 98.333 3.43e-35 121 100% Escherichia phage 107 Escherichia INPHARED PF17587 phrog_2102
OQ599310_00076 61.667 6.81e-16 72.8 95% Escherichia phage 55 Escherichia INPHARED PF17587 phrog_2102
OQ703618_00190 58.333 9.76e-16 72.4 97% Escherichia phage GADS24 Escherichia INPHARED PF17587 phrog_2102
uvig_174995_58 62.903 2.34e-17 76.3 98% GPD PF17587 phrog_2102
uvig_175339_83 62.903 1.67e-18 79.3 98% GPD PF17587 phrog_2102
APIS Contig Range
APIS013 NC_000866.4 17935 - 25455

Gene cluster comparison plot by clinker      Download html