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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 APIS012
Inhibited defense system toxin-antitoxin (TA)
CLAN ID CLAN022
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_049652.1 gene_page: tifA 85 10187.1 10.4193 8.5
Phage property
Phage Assembly id
T4 of E. coli GCF_000836945.1
PMID/References PMID:35924892
PDB structures ;
Pfam domains
Phrog phrog_8921,phrog_2375,phrog_3272,phrog_12748
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: 20112;  End: 20369;  Strand: -
Description Original gene 61.4, experimentally evolved T4 phage to overcome a phage-defensive toxin-antitoxin system (toxIN) in E. coli. Through recombination, T4 rapidly acquires segmental amplifications of a previously uncharacterized gene, now named tifA, encoding an inhibitor of the toxin, ToxN.

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 16846 17625 - NP_049647.1 259 30416.80 9.5 9.2073 Dam family site-specific DNA-(adenine-N6)-methyltransferase phrog_56 PF02086.18
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

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.57 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

No homologs found in esmfold database

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS012 NP_049652.1 73 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN022

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS086 2.51E-59 1 92 2 93 ON229909_00228

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
AP018814_00038 96.471 2.83e-54 171 100% Enterobacteria phage T6 Enterobacteria INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
AP018932_00039 96.471 3.92e-55 173 100% Escherichia phage KIT03 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
DQ904452_00036 96.512 3.81e-53 168 100% Escherichia phage RB32 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
IMGVR_UViG_3300010279_000005|3300010279|Ga0129313_100005818 97.647 7.07e-55 172 100% IMGVR phrog_8921 phrog_2375 phrog_3272 phrog_12748
IMGVR_UViG_3300045988_132814|3300045988|Ga0495776_001669_138774_139070 98.824 1.31e-55 175 100% IMGVR phrog_8921 phrog_2375 phrog_3272 phrog_12748
KM501444_00049 96.471 2.83e-54 171 100% Shigella phage pSs-1 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KM607000_00038 97.647 6.28e-55 172 100% Enterobacteria phage RB27 Enterobacteria INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KR233165_00101 95.294 3.45e-54 171 100% Escherichia phage PEC04 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KT184308_00222 98.824 2.21e-55 174 100% Enterobacteria phage Aplg8 Enterobacteria INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KT184312_00076 96.471 4.70e-53 168 100% Enterobacteria phage Kha5h Enterobacteria INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KU867876_00039 96.053 9.33e-47 152 89% Escherichia phage vB_EcoM-UFV13 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KX009778_00038 96.471 2.59e-54 171 100% Escherichia phage UFV-AREG1 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KX130862_00138 97.468 3.88e-50 160 93% Shigella phage SHFML-26 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
KX828711_00036 96.053 9.33e-47 152 89% Shigella phage SH7 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
LC465543_00068 97.647 6.49e-55 172 100% Shigella phage SfPhi01 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
LR215723_00036 96.471 9.06e-54 169 100% Yersinia phage fPS-90 Yersinia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
LR746311_00104 96.471 2.80e-54 171 100% Shigella phage vB_SsoM_113 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
LR990704_00180 96.471 1.79e-53 169 100% Escherichia phage vB_Eco_NR1 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MF158045_00221 97.647 1.46e-54 172 100% Shigella phage Sf22 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MF327009_00165 96.471 1.48e-54 172 100% Shigella phage Sf25 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MG775043_00264 97.647 1.90e-54 171 100% Citrobacter phage vB_CroM_CrRp10 Citrobacter INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MGV-GENOME-0371733_84 97.647 2.38e-55 174 100% MGV phrog_8921 phrog_2375 phrog_3272 phrog_12748
MGV-GENOME-0373836_52 100.000 9.69e-56 174 100% MGV phrog_8921 phrog_2375 phrog_3272 phrog_12748
MGV-GENOME-0377341_189 97.647 8.21e-54 170 100% MGV phrog_8921 phrog_2375 phrog_3272 phrog_12748
MGV-GENOME-0377569_213 98.824 1.52e-55 174 100% MGV phrog_8921 phrog_2375 phrog_3272 phrog_12748
MGV-GENOME-0377588_86 96.471 2.53e-54 171 100% MGV phrog_8921 phrog_2375 phrog_3272 phrog_12748
MK327928_00038 97.647 2.13e-54 171 100% Escherichia phage vB_EcoM_G2133 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MK373781_00039 98.824 3.59e-55 173 100% Escherichia phage vB_EcoM_KAW1E185 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MN022785_00037 97.647 3.43e-55 173 100% Escherichia phage VEc20 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MN580668_00037 97.647 7.83e-55 172 100% Salmonella phage pSe_SNUABM_01 Salmonella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MN895434_00050 97.647 4.88e-55 173 100% Escherichia phage teqhad Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MN895438_00060 96.471 1.55e-53 169 100% Escherichia phage teqdroes Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MT682709_00240 94.737 1.45e-45 149 89% Escherichia phage vB_EcoM_SP1 Escherichia INPHARED phrog_2375 phrog_3272 phrog_12748
MT682713_00040 94.737 1.77e-45 149 89% Escherichia phage vB_EcoM_Ozark Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MW749001_00035 97.647 2.50e-55 174 100% Escherichia phage vB_EcoM_Kelasse Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ170040_00274 96.471 2.83e-54 171 100% Escherichia phage vB_EcoM_FJ1 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ417521_00037 94.737 1.40e-46 151 89% Escherichia phage 132 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ501046_00145 98.824 1.47e-55 174 100% Escherichia phage AdolfPortmann Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ501050_00145 98.824 3.88e-55 173 100% Escherichia phage AndreasVesalius Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ501089_00147 96.471 1.41e-53 169 100% Escherichia phage KarlGJung Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
MZ753803_00037 96.471 2.86e-54 171 100% Escherichia phage U115 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
NP_049652.1 100.000 2.42e-62 174 100% T4 of E. coli Escherichia coli NCBI phrog_8921 phrog_2375 phrog_3272 phrog_12748
OK274152_00039 97.647 1.74e-54 171 100% Escherichia phage APTC-EC-2A Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OK331996_00265 98.824 1.47e-55 174 100% Escherichia phage vB_EcoM-G157lw Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OL770073_00063 97.647 2.31e-55 174 100% Escherichia phage vB_EcoM-RPN226 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OL960581_00036 94.737 1.04e-45 149 89% Escherichia phage vB_EcoM_SA20RB Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
ON528727_00051 97.647 5.88e-55 172 100% Shigella phage ESh17 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
ON528734_00165 96.471 3.85e-54 171 100% Shigella phage ESh24 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
ON528743_00030 97.647 3.30e-54 171 100% Shigella phage ESh33 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
ON528746_00046 94.118 1.11e-52 167 100% Shigella phage ESh36 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
ON645936_00035 97.647 6.08e-55 172 100% Escherichia phage N2 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP137232_00060 96.471 1.39e-54 172 100% Shigella phage S2_01 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP172788_00048 96.471 1.08e-54 172 100% Escherichia phage ECO07P5 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP197928_00039 95.294 1.12e-53 169 100% Shigella phage A2 Shigella INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP557970_00221 97.647 5.69e-55 172 100% Escherichia phage ph0021 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP611477_00027 96.471 3.33e-54 171 100% Escherichia virus CAM-21 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP856590_00039 97.368 1.94e-47 154 89% Escherichia phage Ec_MI-02 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP870144_00037 96.053 8.64e-47 152 89% Escherichia phage vB_Eco_F25 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OP978391_00148 96.471 1.99e-54 171 100% Escherichia phage HP3.2 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ067375_00146 96.053 9.85e-47 152 89% Escherichia phage a48 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ067376_00143 97.647 4.88e-55 173 100% Escherichia phage a51 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ174503_00134 96.053 3.11e-47 153 89% Escherichia phage REP4 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ223305_00053 97.647 3.43e-55 173 100% Escherichia phage EO1 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ349392_00240 96.053 9.12e-47 152 89% Escherichia phage KIT06 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ446694_00063 97.647 7.25e-55 172 100% Escherichia phage Killian Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ466432_00081 97.647 6.86e-55 172 100% Escherichia phage ADUt Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ599309_00037 95.294 7.54e-53 167 100% Escherichia phage 107 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
OQ721911_00037 97.647 2.50e-55 174 100% Escherichia phage vB_VIPECOOM03 Escherichia INPHARED phrog_8921 phrog_2375 phrog_3272 phrog_12748
uvig_175033_184 96.471 2.45e-54 171 100% GPD phrog_8921 phrog_2375 phrog_3272 phrog_12748
uvig_249051_107 95.294 6.17e-54 170 100% GPD phrog_8921 phrog_2375 phrog_3272 phrog_12748
uvig_35225_189 97.647 7.96e-54 170 100% GPD phrog_8921 phrog_2375 phrog_3272 phrog_12748
uvig_585812_247 94.737 1.72e-46 151 89% GPD phrog_8921 phrog_2375 phrog_3272 phrog_12748
uvig_70837_1 97.647 9.56e-55 172 100% GPD phrog_8921 phrog_2375 phrog_3272 phrog_12748
APIS Contig Range
APIS012 NC_000866.4 16846 - 24235

Gene cluster comparison plot by clinker      Download html