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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 APIS009
Inhibited defense system restriction-modification (RM)
CLAN ID CLAN013
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_040622.1 gene_page: Ral 66 7603.86 8.51 3
Phage property
Phage Assembly id
Lambda of E. coli GCF_000840245.1
PMID/References PMID:3023633
PDB structures ;
Pfam domains PF11058.11
Phrog phrog_1055,phrog_17610
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: 34087;  End: 34287;  Strand: -
Description Ral of phage λ can activate the activity of the MTase and thereby accelerate protection of the phage DNA.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_001416.1 32025 32810 - NP_040617.1 261 29688.64 -6.5 4.8663 RecT-like ssDNA annealing protein phrog_2760 ; phrog_8375 ; phrog_17377 ; phrog_12233 ; phrog_2449 ; phrog_10056 ; phrog_252 PF03837.17 ;PF03837.17
NC_001416.1 32816 33232 - NP_040618.1 138 16346.28 -3.5 5.7699 gam-like host nuclease inhibitor phrog_259 ; phrog_26899 PF06064.14
NC_001416.1 33187 33330 - NP_040619.1 47 5518.58 3.5 10.2786 Kil protein for bacterial septation inhibition phrog_3924 ; phrog_2055 ; phrog_20024 ; phrog_2461 PF06301.14
NC_001416.1 33299 33463 - NP_040620.1 54 6046.92 2.0 9.0019 CIII anti-termination phrog_35423 ; phrog_550 ; phrog_2461 PF02061.19
NC_001416.1 33536 33904 - NP_040621.1 122 13780.39 -12.0 4.0718 hypothetical protein phrog_646 PF10800.11
NC_001416.1 34087 34287 - NP_040622.1 66 7603.86 3.0 8.5100 restriction alleviation ral phrog_1055 ; phrog_17610 PF11058.11
NC_001416.1 34271 34357 - NP_040623.1 28 3698.81 -11.5 3.2418 hypothetical protein phrog_16060
NC_001416.1 35037 35438 - NP_040625.1 133 15373.80 18.0 11.3155 anti-termination protein N-like phrog_271 PF11438.11
NC_001416.1 35825 36259 - NP_040626.1 144 15967.15 6.5 9.3071 RexB-like exclusion protein phrog_14878 PF15968.8
NC_001416.1 36275 37114 - NP_040627.1 279 31254.91 6.5 8.8440 RexA-like exclusion protein phrog_12654 PF15969.8
NC_001416.1 34482 35036 + NP_597779.1 184 21557.37 7.0 9.6932 SieB superinfection exclusion phrog_6399 PF14163.9

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.53 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
APIS009 NP_040622.1 22 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN013

APIS009 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
CP000711_00047 98.485 7.00e-42 138 100% Enterobacteria phage CUS-3 Enterobacteria INPHARED PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2541047938_000001|2541047938|2545222551 98.485 4.27e-42 139 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2563366999_000007|2563366999|2565053676 98.485 5.50e-42 138 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2663763159_000003|2663763159|2665890424 98.485 5.81e-42 138 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2671180427_000015|2671180427|2672728354 100.000 2.92e-42 139 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2740892042_000001|2740892042|2741640100 98.485 4.27e-42 139 100% Escherichia marmotae IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2778261351_000002|2778261351|2779781704 98.485 7.64e-42 138 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2778261419_000004|2778261419|2780045228 96.970 7.47e-42 138 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_2913177423_000002|2913177423|2913180150 98.485 6.41e-42 138 100% Escherichia sp005843885 IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_3300023488_000025|3300023488|Ga0257039_114265 98.485 6.62e-42 138 100% Salmonella IMGVR PF11058 phrog_1055 phrog_17610
IMGVR_UViG_648276669_000002|648276669|648356650 98.485 5.32e-42 139 100% Escherichia coli IMGVR PF11058 phrog_1055 phrog_17610
JQ086370_00045 98.485 5.81e-42 138 100% Enterobacteria phage HK140 Enterobacteria INPHARED PF11058 phrog_1055 phrog_17610
LR595866_00043 98.485 5.50e-42 138 100% Escherichia phage 2G7b Escherichia INPHARED PF11058 phrog_1055 phrog_17610
MGV-GENOME-0218688_37 98.485 7.19e-42 138 100% Escherichia MGV PF11058 phrog_1055 phrog_17610
MGV-GENOME-0263200_45 100.000 1.48e-42 140 100% Escherichia MGV PF11058 phrog_1055 phrog_17610
MGV-GENOME-0268506_20 98.485 4.74e-42 139 100% Escherichia MGV PF11058 phrog_1055 phrog_17610
NP_040622.1 100.000 3.71e-49 140 100% Lambda of E. coli Escherichia coli NCBI PF11058 phrog_1055 phrog_17610
uvig_161343_15 98.485 4.41e-42 139 100% GPD PF11058 phrog_1055 phrog_17610
uvig_223775_27 100.000 6.48e-42 138 98% GPD PF11058 phrog_1055 phrog_17610
uvig_236230_11 98.485 3.50e-42 139 100% GPD PF11058 phrog_1055 phrog_17610
uvig_297278_17 98.485 7.23e-42 138 100% GPD PF11058 phrog_1055 phrog_17610
uvig_423186_41 98.485 4.61e-42 139 100% GPD PF11058 phrog_1055 phrog_17610
APIS Contig Range
APIS009 NC_001416.1 32025 - 35036

Gene cluster comparison plot by clinker      Download html