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 APIS037
Inhibited defense system
CLAN ID CLAN003
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_2541047688_000003|2541047688|2543982737
gene_page: 141 16245.5 4.7142 -6
Phage property
Phage Assembly id
IMGVR_UViG_2541047688_000003
PMID/References
PDB structures ;
Pfam domains PF03230.16
Phrog phrog_10132
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;s__Escherichia coli
Gene Location Start: 142165;  End: 142590;  Strand: +
Description
Note This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS007,ArdB 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
IMGVR_UViG_2541047688_000003 138994 139197 + IMGVR_UViG_2541047688_000003|2541047688|2543982732 67 7305.88 -12.5 3.3580 hypothetical protein phrog_37043
IMGVR_UViG_2541047688_000003 139581 140264 + IMGVR_UViG_2541047688_000003|2541047688|2543982733 227 25436.93 8.0 9.2535 site-specific DNA-methyltransferase (adenine-specific) phrog_23085 ; phrog_3008 ; phrog_18293 ; phrog_6025 ; phrog_498 ; phrog_6952 ; phrog_8769 ; phrog_23148 ; phrog_67 ; phrog_12862 PF01555.21
IMGVR_UViG_2541047688_000003 140265 140486 + IMGVR_UViG_2541047688_000003|2541047688|2543982734 73 8674.86 -2.0 5.1002 hypothetical protein phrog_4830
IMGVR_UViG_2541047688_000003 140500 140934 + IMGVR_UViG_2541047688_000003|2541047688|2543982735 144 16127.30 -7.5 4.4673 Protein of unknown function (DUF1380) phrog_9024 PF07128.15
IMGVR_UViG_2541047688_000003 140979 141749 + IMGVR_UViG_2541047688_000003|2541047688|2543982736 256 28725.97 -1.0 6.1331 hypothetical protein phrog_8919
IMGVR_UViG_2541047688_000003 142165 142590 + IMGVR_UViG_2541047688_000003|2541047688|2543982737 141 16245.46 -6.0 4.7142 Antirestriction protein phrog_10132 PF03230
IMGVR_UViG_2541047688_000003 142637 143059 + IMGVR_UViG_2541047688_000003|2541047688|2543982738 140 15641.69 -14.5 4.1242 Protein of unknown function (DUF1380)
IMGVR_UViG_2541047688_000003 143056 143247 + IMGVR_UViG_2541047688_000003|2541047688|2543982739 63 7264.29 3.5 9.9914 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.7 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

Structure homologs against by afdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
AF-Q93GQ0-F1-model_v4 3 141 6 144 0.9678 0.9404
AF-A0A077ZNG7-F1-model_v4 5 141 5 141 0.9703 0.9367
AF-A0A0H3GW18-F1-model_v4 7 141 10 141 0.8924 0.8519
AF-A0A0H3GVF3-F1-model_v4 7 141 5 132 0.8497 0.8024
AF-P52139-F1-model_v4 7 141 20 152 0.8506 0.7993
AF-P75676-F1-model_v4 7 141 20 152 0.8455 0.793
AF-Q327Q6-F1-model_v4 7 141 23 157 0.8383 0.78
AF-A0A0H3GZ47-F1-model_v4 3 141 83 221 0.9301 0.7593
AF-Q32HM6-F1-model_v4 7 141 47 181 0.8393 0.7351

Structure homologs against by esmdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001142107270.pdb 6 141 6 141 0.9716 0.9314
MGYP003561631401.pdb 6 141 7 142 0.9718 0.9286
MGYP000112106482.pdb 7 141 6 140 0.9681 0.9223
MGYP002759879196.pdb 7 141 7 141 0.9676 0.9186
MGYP000816921373.pdb 6 141 5 139 0.9509 0.9134
MGYP000926023203.pdb 6 141 1 136 0.9402 0.912
MGYP000465578469.pdb 6 141 8 143 0.9545 0.9041
MGYP001044518354.pdb 7 141 8 143 0.9428 0.9006
MGYP000611349549.pdb 7 141 10 145 0.9557 0.9005
MGYP000014743116.pdb 7 141 9 143 0.9549 0.8977

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS037 IMGVR_UViG_2541047688_000003|2541047688|2543982737 3 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN003

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS007 1.98E-30 5 141 20 151 restriction-modification (RM) BAF33451.1
APIS069 5.96E-27 4 141 7 144 IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774
APIS038 9.50E-21 4 141 11 150 IMGVR_UViG_2576861805_000002|2576861805|2579667884
APIS039 2.94E-17 6 141 46 179 IMGVR_UViG_2751185776_000007|2751185776|2753238834
APIS055 2.42E-15 12 141 16 142 OL763419_00042

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_2541047688_000003|2541047688|2543982737 100.000 3.62e-102 296 100% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2609460178_000003|2609460178|2611808575 65.248 2.38e-63 198 100% Klebsiella pneumoniae IMGVR PF03230 phrog_10132
uvig_397292_14 98.582 4.82e-101 293 100% Escherichia coli GPD PF03230 phrog_10132