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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 APIS093
Inhibited defense system
CLAN ID CLAN035
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
MN450150_00001
gene_page: 154 17223.32 4.8782 -5.0
Phage property
Phage Assembly id
Pantoea phage vB_PagP-SK1 MN450150
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_2226
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteralesl;f__Erwiniaceae;g__Pantoea;
Gene Location Start: 937;  End: 1401;  Strand: +
Description
Note This family does not have seed protein, but we infer its function is defending restriction-modification (RM);bacteriophage exclusion (BREX) because it belongs to the same clan as family APIS091 which has seed protein.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
MN450150 937 1401 + MN450150_00001 154 17223.32 -5.0 4.8782 SAM-dependent methyltransferase
MN450150 1401 1622 + MN450150_00002 73 8253.92 9.0 10.3708 hypothetical protein
MN450150 1794 1976 + MN450150_00003 60 6976.49 16.5 12.4343 hypothetical protein
MN450150 2014 3306 + MN450150_00004 430 48326.62 22.0 10.0312 serine-threonine kinase
MN450150 3380 6037 + MN450150_00005 885 99251.61 10.5 7.7043 RNA polymerase phrog_36028 ; phrog_2166 ; phrog_2051 ; phrog_414 PF14700.9 ;PF00940.22
MN450150 6159 6659 + MN450150_00006 166 19539.50 10.5 9.7511 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.82 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)
MGYP000057980695.pdb 5 154 5 152 0.8711 0.8512
MGYP001570296396.pdb 5 154 5 154 0.874 0.8482
MGYP003287343591.pdb 7 154 7 155 0.8573 0.8373
MGYP000138540675.pdb 10 154 1 137 0.8866 0.8194
MGYP003114451701.pdb 4 154 1 138 0.826 0.761
MGYP000148811234.pdb 7 154 6 143 0.8104 0.7598
MGYP001360985504.pdb 6 151 6 154 0.7833 0.7588
MGYP000505594169.pdb 4 154 5 130 0.7592 0.6944

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS093 MN450150_00001 11 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN035

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS091 6.28E-60 1 154 15 164 RecBCD YP_009792928.1

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_3300013307_000032|3300013307|Ga0157372_1000058444 69.935 1.29e-79 223 99% IMGVR phrog_2226
MK903277_00001 46.452 4.22e-41 125 99% Escherichia phage Pisces Escherichia INPHARED phrog_2226
MN013085_00001 52.903 6.98e-51 150 99% Klebsiella phage vB_KpnP_NahiliMali Klebsiella INPHARED phrog_2226
MN184885_00003 53.247 1.66e-52 154 99% Erwinia phage pEp_SNUABM_09 Erwinia INPHARED phrog_2226
MN450150_00001 100.000 1.94e-117 318 100% Pantoea phage vB_PagP-SK1 Pantoea INPHARED phrog_2226
MT822285_00003 53.896 5.58e-53 155 99% Erwinia phage pEp_SNUABM_04 Erwinia INPHARED phrog_2226
MT822286_00003 52.597 1.30e-51 152 99% Erwinia phage pEp_SNUABM_10 Erwinia INPHARED phrog_2226
MT822287_00003 53.896 4.69e-52 153 99% Erwinia phage pEp_SNUABM_11 Erwinia INPHARED phrog_2226
MT822288_00008 53.205 2.40e-50 148 99% Erwinia phage pEp_SNUABM_12 Erwinia INPHARED phrog_2226
OL856139_00001 54.140 2.24e-54 159 100% Rahnella phage Sarma103 Rahnella INPHARED phrog_2226
ON715521_00040 84.967 2.60e-100 275 99% Erwinia phage Stepyanka Erwinia INPHARED phrog_2226