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 APIS041
Inhibited defense system
CLAN ID CLAN030
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_2832702071_000001|2832702071|2832704097
gene_page: 247 28994 6.2226 -2
Phage property
Phage Assembly id
IMGVR_UViG_2832702071_000001
PMID/References
PDB structures ;
Pfam domains PF00753.30
Phrog phrog_392
Host taxa d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus;s__Paraliobacillus ryukyuensis
Gene Location Start: 923901;  End: 924644;  Strand: -
Description
Note This family does not have seed protein, but we infer its function is defending pyrimidine cyclase system for antiphage resistance (Pycsar) because it belongs to the same clan as family APIS001 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_2832702071_000001 920815 921990 - IMGVR_UViG_2832702071_000001|2832702071|2832704092 391 45191.84 -22.5 4.5291 hypothetical protein
IMGVR_UViG_2832702071_000001 922073 922561 - IMGVR_UViG_2832702071_000001|2832702071|2832704093 162 18578.57 0.0 6.4832 hypothetical protein
IMGVR_UViG_2832702071_000001 922619 922801 - IMGVR_UViG_2832702071_000001|2832702071|2832704094 60 6990.80 -7.5 4.0377 hypothetical protein
IMGVR_UViG_2832702071_000001 922943 923491 - IMGVR_UViG_2832702071_000001|2832702071|2832704095 182 22218.17 0.5 6.7472 hypothetical protein
IMGVR_UViG_2832702071_000001 923525 923761 - IMGVR_UViG_2832702071_000001|2832702071|2832704096 78 9357.76 5.0 10.0248 hypothetical protein
IMGVR_UViG_2832702071_000001 923901 924644 - IMGVR_UViG_2832702071_000001|2832702071|2832704097 247 28993.97 -2.0 6.2226 ribonuclease BN (tRNA processing enzyme) phrog_392 PF00753.30
IMGVR_UViG_2832702071_000001 924780 925136 - IMGVR_UViG_2832702071_000001|2832702071|2832704098 118 14238.48 7.5 9.6145 hypothetical protein
IMGVR_UViG_2832702071_000001 925151 925423 - IMGVR_UViG_2832702071_000001|2832702071|2832704099 90 10338.59 -5.0 4.3228 hypothetical protein
IMGVR_UViG_2832702071_000001 925463 926035 - IMGVR_UViG_2832702071_000001|2832702071|2832704100 190 21654.57 -4.5 5.0067 O-acetyl-ADP-ribose deacetylase (regulator of RNase III) phrog_2613 ; phrog_14717 PF01661.24
IMGVR_UViG_2832702071_000001 925463 926035 - IMGVR_UViG_2832702071_000001|2832702071|2832704100 190 21654.57 -4.5 5.0067 O-acetyl-ADP-ribose deacetylase (regulator of RNase III) phrog_2613 ; phrog_14717 PF20016.2
IMGVR_UViG_2832702071_000001 926112 926648 - IMGVR_UViG_2832702071_000001|2832702071|2832704101 178 21055.73 -14.0 4.2159 hypothetical protein phrog_2259 PF16473.8
IMGVR_UViG_2832702071_000001 926689 926868 - IMGVR_UViG_2832702071_000001|2832702071|2832704102 59 6943.91 -2.0 4.6691 hypothetical protein

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.93 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-A0A133CTF0-F1-model_v4 2 247 1 246 0.8379 0.8175
AF-A0A0H3GHL8-F1-model_v4 6 247 1 240 0.8327 0.8037
AF-P9WGC1-F1-model_v4 1 247 17 269 0.8469 0.7915
AF-Q58769-F1-model_v4 1 247 2 255 0.8313 0.7828
AF-A0A0H3GM29-F1-model_v4 1 247 2 251 0.8049 0.7784
AF-P50474-F1-model_v4 1 247 26 278 0.847 0.7782
AF-P16692-F1-model_v4 1 247 2 251 0.8039 0.777
AF-Q329H1-F1-model_v4 1 247 2 251 0.8029 0.7769
AF-O74545-F1-model_v4 1 247 5 299 0.8586 0.7697
AF-Q9HYM9-F1-model_v4 2 247 1 256 0.7995 0.7671

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP001278173685.pdb 2 247 1 252 0.9257 0.9025
MGYP003194564429.pdb 2 247 1 252 0.9256 0.9024
MGYP001047755842.pdb 2 247 1 248 0.9009 0.884
MGYP001450167839.pdb 2 247 1 247 0.905 0.8826
MGYP001093182360.pdb 2 247 1 255 0.8957 0.8647
MGYP000919716965.pdb 2 247 1 252 0.8964 0.8605
MGYP000754846076.pdb 1 247 2 245 0.879 0.8601
MGYP001157950379.pdb 1 247 2 247 0.8703 0.854
MGYP000856702051.pdb 1 247 2 267 0.9038 0.8532
MGYP003452926687.pdb 1 247 1 265 0.8956 0.8522

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS041 IMGVR_UViG_2832702071_000001|2832702071|2832704097 4 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN030

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS001 1.00E-44 1 247 19 270 pyrimidine cyclase system for antiphage resistance (Pycsar) YP_009840594.1
APIS058 6.47E-37 2 247 16 268 IMGVR_UViG_3300022562_000702|3300022562|Ga0247387_1000200120
APIS076 3.10E-31 2 246 6 258 IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065
APIS062 3.11E-29 2 247 1 263 IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345
APIS073 2.60E-28 2 247 23 285 IMGVR_UViG_3300042197_004918|3300042197|Ga0451494_0000046_37885_38742
APIS054 4.48E-26 2 246 3 261 IMGVR_UViG_3300014204_000482|3300014204|Ga0172381_1000105623
APIS066 1.23E-25 2 247 1 293 IMGVR_UViG_3300035396_000446|3300035396|Ga0393109_006065_59543_60412
APIS064 1.12E-23 2 247 1 258 IMGVR_UViG_3300033145_003233|3300033145|Ga0366840_1000004654
APIS060 3.65E-23 2 247 1 259 IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199
APIS044 3.48E-19 4 236 2 233 HM144387_00160

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_2582580961_000009|2582580961|2584062426 49.565 8.86e-73 230 92% Priestia flexa IMGVR PF00753 phrog_392
IMGVR_UViG_2832702071_000001|2832702071|2832704097 100.000 0.0 512 100% Paraliobacillus ryukyuensis IMGVR PF00753 phrog_392
IMGVR_UViG_3300009011_000023|3300009011|Ga0105251_1000039243 47.200 1.14e-76 240 100% IMGVR PF00753 phrog_392
IMGVR_UViG_3300025735_000016|3300025735|Ga0207713_100037673 47.200 1.10e-76 240 100% IMGVR PF00753 phrog_392