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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 APIS008
Inhibited defense system Gabija
CLAN ID CLAN002
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
Gad2
gene_page: Gad2 400 46527.6 4.6283 -16
Phage property
Phage Assembly id
SPbetaL7 of B. subtilis
PMID/References Yirmiya et al., 2023
PDB structures ;
Pfam domains
Phrog phrog_18122,phrog_27100,phrog_4400,phrog_25514,phrog_37109,phrog_16176
Host taxa d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus;s__Bacillus subtilis
Gene Location Start: ;  End: ;  Strand: 
Description Alphafold2 predicted that Gad2 is an enzyme with a nucleotidyltransferase protein domain, suggesting that it inhibits Gabija via a mechanism of action different than Gad1.

Predicted 3D structure by alphafold2 with pTM = 0.71 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

No homologs found in AlphaFold database

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000373333736.pdb 1 221 1 204 0.9299 0.7
MGYP003394315973.pdb 1 199 2 202 0.9177 0.6875
MGYP000999235125.pdb 3 220 1 204 0.912 0.6868
MGYP001439174798.pdb 1 229 1 230 0.8785 0.6862
MGYP003537377462.pdb 2 400 1 266 0.8166 0.6752
MGYP000376116683.pdb 1 264 2 248 0.8319 0.6687
MGYP000981939358.pdb 1 235 2 199 0.8876 0.6603
MGYP001240424264.pdb 1 228 2 229 0.8384 0.6572
MGYP001238726922.pdb 1 219 1 226 0.871 0.6473
MGYP001760742232.pdb 12 223 1 235 0.8161 0.6428

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS008 Gad2 49 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN002

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS056 2.00E-77 75 468 2 364 IMGVR_UViG_3300020049_002891|3300020049|Ga0206652_100507913
APIS059 7.46E-67 58 457 2 399 KF302034_00153
APIS089 1.00E-51 77 458 2 389 uvig_330502_68

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
Gad2 100.000 0.0 813 100% SPbetaL7 of B. subtilis Bacillus subtilis NCBI phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2547132108_000008|2547132108|2547391173 50.000 2.39e-125 376 98% Paenibacillus_G elgii IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2554235236_000002|2554235236|2555268698 65.915 0.0 554 99% Bacillus paralicheniformis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2579778832_000008|2579778832|2581159682 50.508 1.22e-124 374 98% Paenibacillaceae IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2582580961_000009|2582580961|2584062409 56.391 1.18e-150 441 98% Priestia flexa IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2600255062_000003|2600255062|2600787771 48.990 2.45e-120 363 99% Paenibacillus polymyxa_D IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2600255075_000001|2600255075|2600850457 50.000 4.36e-126 377 99% Paenibacillus_F chitinolyticus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2615840593_000003|2615840593|2616180048 48.500 2.34e-118 359 98% Lysinibacillus xylanilyticus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2645727636_000004|2645727636|2646315180 46.898 4.05e-114 348 99% Lysinibacillus sp001278875 IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2645727811_000003|2645727811|2647076456 65.915 0.0 551 99% Bacillus paralicheniformis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2654587505_000001|2654587505|2654606956 51.015 3.56e-132 396 99% Paenibacillus_G naphthalenovorans IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2660238538_000004|2660238538|2662791354 92.500 0.0 759 100% Bacillus subtilis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2744054576_000007|2744054576|2744833085 48.232 1.47e-116 353 99% Paenibacillus ottowii IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2808606540_000001|2808606540|2809656356 56.468 6.52e-153 446 98% Bacillus_AB infantis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2808606549_000001|2808606549|2809704922 45.524 1.42e-110 339 97% Mycobacterium sp001667735 IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2811995041_000004|2811995041|2812925906 68.782 0.0 580 99% Bacillus glycinifermentans IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2832702071_000001|2832702071|2832704110 43.182 4.00e-100 312 97% Paraliobacillus ryukyuensis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2841277917_000004|2841277917|2841278851 43.797 1.66e-112 343 99% Brevibacillus_B laterosporus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2879469214_000003|2879469214|2879471703 50.761 7.07e-129 385 98% Paenibacillus amylolyticus_B IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2885526491_000007|2885526491|2885531743 50.384 5.72e-127 380 98% Paenibacillus taichungensis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2897137741_000002|2897137741|2897139691 99.000 0.0 805 100% Bacillus subtilis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2901146262_000001|2901146262|2901146816 41.327 2.02e-103 320 97% Amphibacillaceae IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2904150443_000004|2904150443|2904151883 48.000 1.37e-117 357 97% Paenibacillus_B sp001894745 IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2904560550_000001|2904560550|2904561077 94.458 0.0 766 99% Bacillus velezensis IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2908369612_000002|2908369612|2908372510 96.474 0.0 785 99% Bacillus atrophaeus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2919361683_000002|2919361683|2919363014 49.747 6.81e-121 365 99% Paenibacillus polymyxa IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_2939702853_000004|2939702853|2939705507 48.101 2.16e-116 352 99% Paenibacillus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300009011_000023|3300009011|Ga0105251_1000039215 55.639 1.25e-150 441 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300017565_000003|3300017565|Ga0182745_100005758 57.323 2.17e-158 460 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300017589_000061|3300017589|Ga0134288_1000062154 43.970 2.93e-99 309 97% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300018910_000036|3300018910|Ga0193598_1000081136 69.036 0.0 582 99% Bacillus IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300021254_000066|3300021254|Ga0223824_1000067568 40.831 4.72e-76 250 96% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300022816_000020|3300022816|Ga0255657_15472635 49.746 5.97e-124 372 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300022879_000002|3300022879|Ga0213824_100003747 50.251 2.09e-123 372 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300025528_000044|3300025528|Ga0207867_100125631 56.566 1.22e-149 437 99% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300025735_000045|3300025735|Ga0207713_100073225 55.639 1.20e-150 441 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300028649_000004|3300028649|Ga0302162_1000001534 44.717 2.26e-109 335 99% IMGVR phrog_18122 phrog_1614 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300037067_006209|3300037067|Ga0378408_0000883_8146_9333 44.089 1.06e-102 318 99% IMGVR phrog_18122 phrog_1614 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300037418_002096|3300037418|Ga0395900_0000118_108376_109638 60.305 2.53e-162 471 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300042922_000937|3300042922|Ga0456363_0002333_12137_13255 45.238 2.99e-110 336 94% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300042923_000660|3300042923|Ga0456365_0001332_15013_16275 49.492 4.45e-125 376 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300042923_001106|3300042923|Ga0456365_0000168_156697_157881 52.513 7.84e-127 379 99% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300047323_000304|3300047323|Ga0495683_0000015_118164_119405 45.432 6.82e-103 319 98% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
IMGVR_UViG_3300048929_000399|3300048929|Ga0496126_0004501_9996_11159 48.111 1.04e-116 353 99% IMGVR phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
MGV-GENOME-0222383_11 42.680 1.21e-83 269 98% CAG-269 MGV phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
MT325768_00069 48.985 1.50e-129 386 99% Psychrobacillus phage Perkons Psychrobacillus INPHARED phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
OL580764_00108 91.940 0.0 753 99% Bacillus phage vB_BsuS-Goe14 Bacillus INPHARED phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
ON107264_00062 93.250 0.0 764 100% Bacillus phage BUCT083 Bacillus INPHARED phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176
uvig_179468_52 42.680 1.17e-83 269 98% GPD phrog_18122 phrog_27100 phrog_4400 phrog_25514 phrog_37109 phrog_16176