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Seed proteins  | 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 APIS055
Inhibited defense system
CLAN ID CLAN003
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
OL763419_00042
gene_page: 137 15688.8 4.381 -7.5
Phage property
Phage Assembly id
Pseudomonas phage Churro OL763419
PMID/References
PDB structures ;
Pfam domains PF03230.16
Phrog phrog_10132
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;
Gene Location Start: ;  End: ;  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.

Predicted 3D structure by alphafold2 with pTM = 0.88 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-A0A0H3GW18-F1-model_v4 1 137 6 141 0.9313 0.9039
AF-P52139-F1-model_v4 1 137 16 152 0.9259 0.8679
AF-P75676-F1-model_v4 1 137 16 152 0.9255 0.867
AF-Q93GQ0-F1-model_v4 3 137 7 144 0.8948 0.8558
AF-Q327Q6-F1-model_v4 1 137 19 157 0.9249 0.8539
AF-A0A0H3GVF3-F1-model_v4 1 137 1 132 0.8913 0.8522
AF-A0A077ZNG7-F1-model_v4 6 137 7 141 0.878 0.8488
AF-Q32HM6-F1-model_v4 1 137 43 181 0.9244 0.8028
AF-A0A0H3GZ47-F1-model_v4 3 137 87 221 0.8742 0.7011

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001248649841.pdb 1 137 1 137 0.9885 0.9841
MGYP001201501853.pdb 1 137 2 134 0.9757 0.9591
MGYP003390684032.pdb 1 137 2 135 0.9609 0.9433
MGYP000117479218.pdb 1 137 1 133 0.9646 0.939
MGYP000412510903.pdb 3 137 1 131 0.9696 0.9384
MGYP001120502683.pdb 1 137 1 133 0.9622 0.9363
MGYP001487061361.pdb 3 137 1 132 0.9652 0.9361
MGYP001335377403.pdb 2 137 1 131 0.9674 0.936
MGYP001992189960.pdb 1 137 2 134 0.9554 0.9322
MGYP003460860055.pdb 1 137 2 135 0.9462 0.9317

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS055 OL763419_00042 20 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 2.99E-39 2 142 14 151 restriction-modification (RM) BAF33451.1
APIS038 9.43E-29 4 142 8 150 IMGVR_UViG_2576861805_000002|2576861805|2579667884
APIS069 1.64E-22 7 142 7 144 IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774
APIS039 8.76E-20 2 142 39 179 IMGVR_UViG_2751185776_000007|2751185776|2753238834
APIS037 1.90E-15 12 142 9 141 IMGVR_UViG_2541047688_000003|2541047688|2543982737

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
DQ163916_00002 99.270 3.15e-98 286 100% Pseudomonas phage M6 Pseudomonas INPHARED PF03230 phrog_10132
IMGVR_UViG_2595698855_000001|2595698855|2596517448 97.810 4.06e-97 283 96% Burkholderiaceae IMGVR PF03230 phrog_10132
IMGVR_UViG_3300015607_001032|3300015607|Ga0182412_11370211 97.080 4.84e-95 278 96% IMGVR PF03230 phrog_10132
IMGVR_UViG_3300028603_000095|3300028603|Ga0265293_1000173436 94.161 2.45e-93 274 100% Gammaproteobacteria IMGVR PF03230 phrog_10132
IMGVR_UViG_3300033074_000335|3300033074|Ga0364573_111686 87.591 6.85e-86 255 100% Proteobacteria IMGVR PF03230 phrog_10132
IMGVR_UViG_641509461_000001|641509461|641514143 89.781 2.40e-87 259 96% Gammaproteobacteria IMGVR PF03230 phrog_10132
JX131330_00045 97.810 3.23e-97 283 100% Pseudomonas phage MP1412 Pseudomonas INPHARED PF03230 phrog_10132
KX198613_00078 98.540 9.44e-98 285 100% Pseudomonas phage AN14 Pseudomonas INPHARED PF03230 phrog_10132
KX961385_00071 97.810 2.46e-96 281 100% Bordetella phage LK3 Bordetella INPHARED PF03230 phrog_10132
KY000221_00043 96.350 1.54e-95 279 100% Bordetella phage CN1 Bordetella INPHARED PF03230 phrog_10132
MH791406_00059 88.321 3.55e-86 256 100% Pseudomonas phage PaSz-4 Pseudomonas INPHARED PF03230 phrog_10132
MN871456_00032 89.781 1.03e-86 257 100% Pseudomonas phage Pa-C Pseudomonas INPHARED PF03230 phrog_10132
MN871469_00034 89.781 1.97e-87 259 100% Pseudomonas phage Pa-S Pseudomonas INPHARED PF03230 phrog_10132
MN871478_00030 97.810 2.71e-97 284 100% Pseudomonas phage PaSt-2_45_61k Pseudomonas INPHARED PF03230 phrog_10132
MN871482_00028 90.511 4.02e-88 260 100% Pseudomonas virus PaSz-6 Pseudomonas INPHARED PF03230 phrog_10132
MN871486_00009 89.051 4.30e-87 258 100% Pseudomonas phage PaSz-9_45_61k Pseudomonas INPHARED PF03230 phrog_10132
MZ089741_00002 99.270 1.67e-97 284 100% Pseudomonas phage PSA39 Pseudomonas INPHARED PF03230 phrog_10132
OL763419_00042 100.000 1.11e-98 287 100% Pseudomonas phage Churro Pseudomonas INPHARED PF03230 phrog_10132
OM809160_00032 92.701 6.68e-91 268 100% Pseudomonas phage 185 Pseudomonas INPHARED PF03230 phrog_10132
ON165687_00074 97.080 2.72e-96 281 100% Sphaerotilus phage SN1 Sphaerotilus INPHARED PF03230 phrog_10132
APIS Contig Range
APIS055 -

Gene cluster comparison plot by clinker      Download html