Seed protein information help

APIS family ID APIS067
Inhibited defense system
CLAN ID CLAN003
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_6069_6716
gene_page: 215 25113.60 3.9397 -29.0
Phage property
Phage Assembly id
IMGVR_UViG_3300035506_000204
PMID/References
PDB structures ;
Pfam domains PF07275.14
Phrog phrog_2059
Host taxa
Gene Location Start: 6069;  End: 6716;  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 APIS003,ardu 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_3300035506_000204 10713 11669 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_10713_11669 318 35543.45 -8.0 4.7897 hypothetical protein
IMGVR_UViG_3300035506_000204 11770 12363 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_11770_12363 197 21122.49 -6.5 4.4764 hypothetical protein
IMGVR_UViG_3300035506_000204 3654 3965 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_3654_3965 103 11771.41 -1.0 5.2600 DNA-binding XRE family transcriptional regulator phrog_38027 ; phrog_1373 ; phrog_2439 ; phrog_3 ; phrog_29047 ; phrog_6831 ; phrog_11553 ; phrog_24325 ; phrog_5823 ; phrog_2339 ; phrog_1381 PF01381.25
IMGVR_UViG_3300035506_000204 4146 4622 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_4146_4622 158 19114.97 6.0 8.9352 hypothetical protein
IMGVR_UViG_3300035506_000204 4632 4757 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_4632_4757 41 4601.38 -5.5 3.8121 hypothetical protein
IMGVR_UViG_3300035506_000204 4760 5188 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_4760_5188 142 15933.44 1.5 7.1875 hypothetical protein
IMGVR_UViG_3300035506_000204 5461 5832 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_5461_5832 123 14044.42 -2.0 5.1657 hypothetical protein
IMGVR_UViG_3300035506_000204 6069 6716 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_6069_6716 215 25113.60 -29.0 3.9397 antirestriction protein phrog_2059 PF07275.14
IMGVR_UViG_3300035506_000204 6790 7458 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_6790_7458 222 26369.84 0.5 6.6193 hypothetical protein
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 7698 9344 - IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_7698_9344 548 62551.21 -6.0 5.1316 hypothetical protein phrog_8741 PF08238.15
IMGVR_UViG_3300035506_000204 9450 10571 + IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_9450_10571 373 40537.68 -11.5 4.7223 ATP-dependent protease ClpP protease subunit phrog_94 ; phrog_1684 ; phrog_3348 ; phrog_133 ; phrog_2976 ; phrog_53 PF00574.26

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

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
AF-A0A0H3GZQ3-F1-model_v4 49 214 5 168 0.8453 0.7359

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP002619016300.pdb 6 215 1 211 0.9465 0.9277
MGYP003538369595.pdb 28 215 1 186 0.8888 0.8145
MGYP000693494289.pdb 4 215 2 205 0.8558 0.8121
MGYP002521666680.pdb 8 215 1 200 0.8541 0.8009
MGYP002519753648.pdb 21 215 1 188 0.8717 0.7998
MGYP002523803474.pdb 21 215 16 207 0.8568 0.7947
MGYP003228289826.pdb 28 215 2 190 0.8598 0.7937
MGYP003324507119.pdb 18 215 14 205 0.8442 0.7931
MGYP003510632526.pdb 24 215 1 190 0.8578 0.79
MGYP003439714399.pdb 12 215 1 208 0.8281 0.7883

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS067 IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_6069_6716 18 HMM model Member alignment

Host Taxa distribution

Length distribution

Length Distribution Bar chart

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_3300007669_000275|3300007669|Ga0105546_10007546 59.296 1.92e-76 237 92% Muribaculaceae IMGVR PF07275 phrog_2059
IMGVR_UViG_3300008268_000462|3300008268|Ga0111491_100004980 53.488 6.76e-75 233 99% Muribaculaceae IMGVR PF07275 phrog_2059
IMGVR_UViG_3300013414_001143|3300013414|Ga0177923_108916522 53.589 2.52e-68 217 92% CAG-485 IMGVR PF07275 phrog_2059
IMGVR_UViG_3300035428_000204|3300035428|Ga0247197_01065_5309_5935 53.488 3.79e-75 234 99% Muribaculaceae IMGVR PF07275 phrog_2059
IMGVR_UViG_3300035501_000804|3300035501|Ga0376455_0008063_329_934 52.821 2.37e-61 198 89% IMGVR PF07275 phrog_2059
IMGVR_UViG_3300035506_000204|3300035506|Ga0376461_0000200_6069_6716 100.000 3.87e-158 444 100% IMGVR PF07275 phrog_2059
IMGVR_UViG_3300045988_155923|3300045988|Ga0495776_113777_35447_36073 56.500 1.68e-72 227 96% Muribaculaceae IMGVR PF07275 phrog_2059
IMGVR_UViG_3300045988_165293|3300045988|Ga0495776_184413_31235_31861 53.023 7.05e-75 233 99% Muribaculaceae IMGVR PF07275 phrog_2059
IMGVR_UViG_3300045988_185973|3300045988|Ga0495776_114647_14749_15378 55.941 1.15e-68 217 96% CAG-485 IMGVR PF07275 phrog_2059
IMGVR_UViG_3300045988_187022|3300045988|Ga0495776_071467_36894_37544 65.278 3.52e-95 285 99% IMGVR PF07275 phrog_2059
MGV-GENOME-0268661_41 65.278 3.63e-95 285 99% Muribaculaceae MGV PF07275 phrog_2059
MGV-GENOME-0272767_35 56.500 1.79e-72 227 92% Muribaculaceae MGV PF07275 phrog_2059
MGV-GENOME-0290063_36 53.023 7.54e-75 233 99% Muribaculaceae MGV PF07275 phrog_2059
MGV-GENOME-0316874_15 55.941 1.22e-68 217 93% CAG-873 MGV PF07275 phrog_2059
uvig_403301_1 49.254 5.20e-59 192 93% GPD PF07275 phrog_2059
IMGVR_UViG_3300007566_000011|3300007566|Ga0104970_100006694 0.458 2.724E-40 146 % Prevotella IMGVR
IMGVR_UViG_3300045988_128334|3300045988|Ga0495776_080700_3512_4102 0.461 1.062E-40 147 % Prevotella IMGVR
MGV-GENOME-0347767_7 0.461 1.104E-40 147 % MGV