sublogo

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 APIS036
Inhibited defense system O-antigen-based barrier
CLAN ID CLAN034
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
YP_009850475.1 gene_page: gnarl3 78 9002.44 9.7411 6
Phage property
Phage Assembly id
Escherichia phage Mangalitsa GCF_008214915.1
PMID/References Silas et al., 2023
PDB structures ;
Pfam domains
Phrog
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;
Gene Location Start: 4208;  End: 4444;  Strand: +
Description Putative O-antigen modifiers, interfere with O-antigen biosynthesis.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_048799.1 211 2325 + YP_009850471.1 704 79302.67 -4.5 5.8932 RNA polymerase phrog_414 PF00940.22
NC_048799.1 2368 2568 + YP_009850472.1 66 7803.76 -3.5 4.9553 hypothetical protein phrog_20790
NC_048799.1 2661 2825 + YP_009850473.1 54 6259.12 -1.0 5.6316 hypothetical protein phrog_32102
NC_048799.1 3959 4207 + YP_009850474.1 82 9286.47 -5.0 4.3193 hypothetical protein phrog_23678
NC_048799.1 4208 4444 + YP_009850475.1 78 9002.44 6.0 9.7411 hypothetical protein
NC_048799.1 4446 4634 + YP_009850476.1 62 7535.48 -6.5 4.0700 hypothetical protein phrog_28706
NC_048799.1 4631 4876 + YP_009850477.1 81 9434.78 -8.0 4.0537 hypothetical protein phrog_36363
NC_048799.1 4886 5059 + YP_009850478.1 57 6733.95 2.5 8.9777 hypothetical protein phrog_30513
NC_048799.1 5155 5451 + YP_009850479.1 98 10829.37 -4.0 4.6135 hypothetical protein phrog_31855
NC_048799.1 5467 5730 + YP_009850480.1 87 9750.23 -1.0 5.6566 hypothetical protein phrog_18131

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.3 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
APIS036 YP_009850475.1 17 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN034

APIS036 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
EF460875_00004 67.532 7.32e-26 99.0 99% Escherichia phage phiEcoM-GJ1 Escherichia INPHARED phrog_
IMGVR_UViG_3300007747_000002|3300007747|Ga0101111_100007619 71.250 1.87e-33 118 100% IMGVR phrog_
MF044458_00005 89.744 3.44e-44 145 100% Escherichia phage ST32 Escherichia INPHARED phrog_
MN122072_00041 73.750 3.47e-34 120 100% Escherichia phage vB_EcoM_Bp10 Escherichia INPHARED phrog_
MT446398_00035 70.000 1.04e-32 116 100% Escherichia virus TH24 Escherichia INPHARED phrog_
MT446399_00067 89.744 5.14e-45 147 100% Escherichia virus TH25 Escherichia INPHARED phrog_
MT446400_00069 87.179 1.18e-43 144 100% Escherichia virus TH26 Escherichia INPHARED phrog_
MT446403_00021 70.732 8.67e-32 114 100% Escherichia virus TH29 Escherichia INPHARED phrog_
MT446409_00070 67.500 1.37e-31 113 100% Escherichia virus TH37 Escherichia INPHARED phrog_
MT446419_00004 92.308 1.13e-45 149 100% Escherichia virus TH53 Escherichia INPHARED phrog_
MW147601_00003 69.512 3.10e-31 112 100% Yersinia phage PYps16N Yersinia INPHARED phrog_
MW147602_00004 64.935 2.10e-24 95.1 99% Yersinia phage PYps16T Yersinia INPHARED phrog_
OK148439_00032 70.732 4.74e-32 114 100% Escherichia phage MLP1 Escherichia INPHARED phrog_
OL741059_00003 70.000 4.38e-33 117 100% Escherichia phage SKA49 Escherichia INPHARED phrog_
OP595144_00003 62.338 1.42e-23 93.2 99% Escherichia phage vB_EcoM_DE15 Escherichia INPHARED phrog_
uvig_397811_4 89.744 3.63e-44 145 100% GPD phrog_
YP_009850475.1 100.000 7.23e-58 163 100% Escherichia phage Mangalitsa Escherichia NCBI phrog_
APIS Contig Range
APIS036 NC_048799.1 211 - 5730

Gene cluster comparison plot by clinker      Download html