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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 APIS044
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
HM144387_00160
gene_page: 247 28728.72 6.1665 -2.0
Phage property
Phage Assembly id
Bacillus phage W.Ph. HM144387
PMID/References
PDB structures ;
Pfam domains PF12706.10
Phrog phrog_392,phrog_14429
Host taxa d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;
Gene Location Start: 109111;  End: 109854;  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
HM144387 108161 108340 + HM144387_00155 59 6929.03 6929.03 4.5702 hypothetical protein phrog_2637
HM144387 108337 108507 + HM144387_00156 56 6777.53 6777.53 4.2258 hypothetical protein phrog_13947 ; phrog_5688
HM144387 108510 108770 + HM144387_00157 86 10318.77 10318.77 7.3125 hypothetical protein phrog_4388
HM144387 108770 108892 + HM144387_00158 40 4589.62 4589.62 5.8806 hypothetical protein phrog_4169
HM144387 108896 109108 + HM144387_00159 70 7553.95 7553.95 8.5062 hypothetical protein phrog_5623
HM144387 109111 109854 + HM144387_00160 247 28728.72 28728.72 6.1665 metal-dependent hydrolase phrog_35014 ; phrog_14429 ; phrog_392 PF12706.10
HM144387 109874 110092 + HM144387_00161 72 8684.76 8684.76 4.2293 hypothetical protein phrog_8000
HM144387 110104 111309 + HM144387_00162 401 47165.28 47165.28 7.8003 hypothetical protein phrog_30990 ; phrog_2475 ; phrog_13564 ; phrog_6266 ; phrog_14061
HM144387 111336 111761 + HM144387_00163 141 16203.97 16203.97 7.2776 hypothetical protein phrog_2574 ; phrog_6841
HM144387 111886 112485 + HM144387_00164 199 23582.42 23582.42 4.3065 hypothetical protein phrog_4518
HM144387 112463 112981 + HM144387_00165 172 19217.69 19217.69 5.0827 hypothetical protein phrog_10728 ; phrog_5566

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.92 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 1 245 2 243 0.8144 0.7901
AF-A0A0H3GHL8-F1-model_v4 4 245 1 237 0.8045 0.7759
AF-Q58769-F1-model_v4 1 247 4 266 0.8058 0.7557
AF-P16692-F1-model_v4 1 245 4 248 0.7805 0.752
AF-Q329H1-F1-model_v4 1 245 4 248 0.7798 0.7514
AF-A0A0H3GM29-F1-model_v4 1 245 4 248 0.7792 0.7508
AF-P50474-F1-model_v4 1 245 28 275 0.814 0.7454
AF-Q9HYM9-F1-model_v4 1 245 2 253 0.7772 0.7437
AF-K0EUK8-F1-model_v4 21 245 1 229 0.7871 0.7435
AF-A0A0P0W0M3-F1-model_v4 1 245 6 307 0.8354 0.7354

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000539623615.pdb 1 247 5 236 0.9235 0.8922
MGYP001339465194.pdb 1 247 2 242 0.914 0.888
MGYP001434148013.pdb 1 247 1 237 0.9124 0.8778
MGYP001084414565.pdb 1 247 1 240 0.908 0.8773
MGYP000970277262.pdb 1 247 1 235 0.9102 0.8736
MGYP000109510454.pdb 1 245 1 240 0.8924 0.8691
MGYP000890762165.pdb 1 247 8 244 0.8886 0.868
MGYP000867902925.pdb 1 247 1 247 0.8822 0.8653
MGYP001053807098.pdb 1 247 3 232 0.9053 0.8628
MGYP003548652537.pdb 1 243 1 240 0.8909 0.8611

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS044 HM144387_00160 9 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN001

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS001 4.00E-31 2 229 22 253 pyrimidine cyclase system for antiphage resistance (Pycsar) YP_009840594.1
APIS076 3.02E-28 2 240 8 253 IMGVR_UViG_3300044693_000096|3300044693|Ga0466961_0000159_42271_43065
APIS058 4.62E-27 2 236 18 257 IMGVR_UViG_3300022562_000702|3300022562|Ga0247387_1000200120
APIS062 2.16E-22 2 226 3 244 IMGVR_UViG_3300028374_000006|3300028374|Ga0306906_100003345
APIS060 1.47E-21 2 238 3 250 IMGVR_UViG_3300024258_000005|3300024258|Ga0233440_1000037199
APIS073 9.07E-19 2 229 25 269 IMGVR_UViG_3300042197_004918|3300042197|Ga0451494_0000046_37885_38742
APIS041 1.34E-18 2 229 4 231 IMGVR_UViG_2832702071_000001|2832702071|2832704097
APIS054 1.41E-17 2 236 5 251 IMGVR_UViG_3300014204_000482|3300014204|Ga0172381_1000105623
APIS064 4.65E-17 2 223 3 227 IMGVR_UViG_3300033145_003233|3300033145|Ga0366840_1000004654
APIS066 2.22E-14 2 228 3 262 IMGVR_UViG_3300035396_000446|3300035396|Ga0393109_006065_59543_60412

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
HM144387_00160 100.000 0.0 516 100% Bacillus phage W.Ph. Bacillus INPHARED PF12706 phrog_392 phrog_14429
IMGVR_UViG_2936514734_000001|2936514734|2936514924 42.915 3.82e-55 185 100% Priestia megaterium IMGVR PF12706 phrog_392
IMGVR_UViG_3300007790_000074|3300007790|Ga0105679_1013100840 99.595 0.0 514 99% IMGVR PF12706 phrog_392 phrog_14429
IMGVR_UViG_3300011497_000002|3300011497|Ga0120869_1002699 40.476 5.37e-49 169 98% IMGVR PF12706 phrog_392
IMGVR_UViG_3300024999_000038|3300024999|Ga0209728_1000028178 39.592 6.53e-43 154 98% IMGVR PF12706 phrog_392
IMGVR_UViG_3300026493_000016|3300026493|Ga0256786_1000025144 68.016 3.63e-121 353 100% IMGVR PF12706 phrog_392 phrog_14429
IMGVR_UViG_3300027858_000004|3300027858|Ga0209013_10000004126 40.164 5.43e-50 172 96% IMGVR PF12706 phrog_392
IMGVR_UViG_3300047323_000304|3300047323|Ga0495683_0000015_159496_160188 39.834 3.62e-49 169 98% IMGVR PF12706 phrog_392
ON366411_00087 50.826 3.93e-73 231 97% Bacillus phage vB_BceH_LY2 Bacillus INPHARED PF12706 phrog_392 phrog_14429