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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 APIS075
Inhibited defense system
CLAN ID CLAN028
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
KY083726_00051
gene_page: 124 14542.9 4.2934 -9.5
Phage property
Phage Assembly id
Pectobacterium phage A38 KY083726
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_3972
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Pectobacterium;
Gene Location Start: 46194;  End: 46568;  Strand: -
Description
Note This family does not have seed protein, but we infer its function is defending broad-spectrum counter-defense because it belongs to the same clan as family APIS035 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
KY083726 44598 44984 - KY083726_00046 128 13570.71 13570.71 9.6887 lipoprotein phrog_13472 ; phrog_26640
KY083726 45050 45301 - KY083726_00047 83 8877.14 8877.14 6.8924 hypothetical protein
KY083726 45298 45660 - KY083726_00048 120 13701.81 13701.81 9.9893 endonuclease phrog_10495 ; phrog_826 ; phrog_6254 ; phrog_3593 ; phrog_1872 ; phrog_99 ; phrog_59 PF13392.9
KY083726 45657 45905 - KY083726_00049 82 9604.82 9604.82 6.0727 hypothetical protein phrog_24795
KY083726 46018 46242 + KY083726_00050 74 7905.86 7905.86 5.4312 hypothetical protein
KY083726 46194 46568 - KY083726_00051 124 14542.86 14542.86 4.2934 hypothetical protein phrog_3972 ; phrog_16544
KY083726 46568 46861 - KY083726_00052 97 10984.57 10984.57 4.7771 hypothetical protein phrog_18415
KY083726 46809 47396 - KY083726_00053 195 22084.97 22084.97 5.8722 hypothetical protein phrog_30952 ; phrog_26890
KY083726 47383 47592 - KY083726_00054 69 7993.24 7993.24 10.2883 hypothetical protein phrog_22755
KY083726 47838 48080 - KY083726_00055 80 9097.57 9097.57 8.5693 hypothetical protein phrog_24879
KY083726 48083 48325 - KY083726_00056 80 8876.36 8876.36 7.3178 hypothetical protein phrog_24414

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.69 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)
MGYP000932118009.pdb 4 102 1 96 0.7576 0.6371
MGYP003611076310.pdb 2 101 1 94 0.6402 0.5545

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS075 KY083726_00051 103 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN028

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS047 6.07E-58 1 107 20 127 IMGVR_UViG_3300009183_005911|3300009183|Ga0114974_10000105111
APIS035 8.81E-57 1 109 17 127 broad-spectrum counter-defense YP_009790938.1
APIS074 5.86E-53 2 104 5 106 IMGVR_UViG_3300042691_005779|3300042691|Ga0415385_0000706_88760_89182
APIS050 2.01E-51 1 107 1 116 IMGVR_UViG_3300010885_038456|3300010885|Ga0133913_1000088583
APIS082 7.03E-23 1 97 1 98 MGV-GENOME-0365202_107

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_2721755548_000004|2721755548|2722993784 52.475 5.75e-29 109 91% Serratia_A fonticola IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300000969_000005|3300000969|BBAY82_1000001739 36.792 1.22e-16 78.6 92% IMGVR phrog_3972
IMGVR_UViG_3300001091_000004|3300001091|JGI12218J13221_100001531 44.231 1.18e-22 93.6 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300001275_000017|3300001275|B570J13894_10000727 36.449 2.29e-16 77.8 87% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300001533_000518|3300001533|MLSed_100123794 36.893 1.15e-13 70.5 94% IMGVR phrog_3972
IMGVR_UViG_3300001869_000136|3300001869|JGI24147J20444_10060739 46.226 2.14e-20 87.8 95% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300006803_000122|3300006803|Ga0075467_1000130321 43.396 7.47e-20 85.9 97% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300006916_000092|3300006916|Ga0070750_1000006339 40.367 9.15e-18 82.0 81% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300007177_000224|3300007177|Ga0102978_101267016 41.905 3.17e-16 77.4 89% IMGVR phrog_3972
IMGVR_UViG_3300008090_000003|3300008090|Ga0114309_10013032 39.048 1.76e-15 75.5 91% Haemophilus_D IMGVR phrog_3972
IMGVR_UViG_3300008345_000042|3300008345|Ga0115409_10053230 39.048 6.43e-16 76.6 91% Haemophilus_D IMGVR phrog_3972
IMGVR_UViG_3300008450_000014|3300008450|Ga0114880_1000019103 50.909 1.13e-29 111 99% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300009158_000214|3300009158|Ga0114977_1000066026 38.182 1.91e-15 75.5 93% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300009164_000005|3300009164|Ga0114975_1000008141 45.631 1.06e-24 99.0 90% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300009180_000200|3300009180|Ga0114979_1000050529 37.615 5.56e-16 77.0 93% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300010151_000882|3300010151|Ga0098061_10017273 35.897 1.84e-16 78.6 95% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300010885_048571|3300010885|Ga0133913_1000270143 33.010 2.36e-20 70.9 92% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300010943_000078|3300010943|Ga0138502_10013510 51.852 9.83e-28 106 98% IMGVR phrog_3972
IMGVR_UViG_3300014203_000112|3300014203|Ga0172378_1000098215 49.515 4.85e-26 102 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300014720_000308|3300014720|Ga0172376_1000389413 38.835 1.93e-15 75.9 80% IMGVR phrog_3972
IMGVR_UViG_3300014888_000001|3300014888|Ga0135444_1000371 47.664 2.31e-22 92.8 97% IMGVR phrog_3972
IMGVR_UViG_3300016474_000281|3300016474|Ga0186779_100287131 44.954 2.52e-21 90.1 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300017598_000427|3300017598|Ga0187366_114585014 43.810 4.36e-21 89.4 97% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020042_002824|3300020042|Ga0206640_100000374 39.286 1.04e-18 84.0 92% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020044_006151|3300020044|Ga0206656_100111727 40.741 2.14e-19 85.5 95% IMGVR phrog_3972
IMGVR_UViG_3300020044_011212|3300020044|Ga0206656_100267710 46.078 3.79e-20 87.4 89% IMGVR phrog_3972
IMGVR_UViG_3300020044_011668|3300020044|Ga0206656_100000955 42.342 2.13e-18 82.8 90% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020045_001587|3300020045|Ga0206662_100003190 51.852 1.24e-31 116 99% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020045_002431|3300020045|Ga0206662_100076811 43.137 7.21e-19 83.6 93% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020045_002690|3300020045|Ga0206662_10112476 40.000 3.39e-17 79.7 95% IMGVR phrog_3972
IMGVR_UViG_3300020045_005258|3300020045|Ga0206662_100022661 42.857 6.08e-19 84.3 92% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020045_006557|3300020045|Ga0206662_10138285 38.318 1.85e-16 78.2 90% IMGVR phrog_3972
IMGVR_UViG_3300020047_001679|3300020047|Ga0206650_100002653 43.810 2.03e-19 85.5 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020047_003453|3300020047|Ga0206650_10062084 42.342 1.28e-18 83.2 95% IMGVR phrog_3972
IMGVR_UViG_3300020047_004590|3300020047|Ga0206650_100151419 48.077 4.80e-24 97.4 89% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020047_004641|3300020047|Ga0206650_100031419 61.111 4.05e-30 95.5 64% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300020048_000041|3300020048|Ga0207193_1000128130 37.383 4.68e-22 76.3 78% IMGVR phrog_3972
IMGVR_UViG_3300020161_000771|3300020161|Ga0211726_1050413178 39.252 1.19e-17 81.3 88% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300021140_000006|3300021140|Ga0214168_100001327 36.449 2.22e-16 77.8 88% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300022178_004414|3300022178|Ga0196887_100166020 43.396 7.20e-20 85.9 98% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300022918_000053|3300022918|Ga0247814_1000577412 39.450 1.71e-17 80.1 97% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300022924_000012|3300022924|Ga0247808_1000016953 45.098 2.68e-21 90.1 96% IMGVR phrog_3972
IMGVR_UViG_3300023082_000010|3300023082|Ga0247730_100009330 45.872 1.45e-23 95.5 98% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300025118_000481|3300025118|Ga0208790_10010771 36.792 3.39e-16 77.4 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300025195_000001|3300025195|Ga0208062_10002725 44.231 1.13e-22 93.6 97% Mesonia IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300025575_000055|3300025575|Ga0209430_100123011 46.226 2.06e-20 87.8 95% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300025759_014240|3300025759|Ga0208899_10077356 40.367 7.73e-18 82.4 84% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300025896_000100|3300025896|Ga0208916_1000015246 43.750 8.29e-21 88.2 98% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300027733_000033|3300027733|Ga0209297_100002596 36.449 5.59e-21 73.6 78% IMGVR phrog_3972
IMGVR_UViG_3300027749_000131|3300027749|Ga0209084_100020886 40.000 2.63e-17 63.2 53% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300027749_004167|3300027749|Ga0209084_100029150 40.171 8.45e-17 79.3 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300027762_000059|3300027762|Ga0209288_1000032031 42.424 9.98e-21 88.6 91% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300027763_000072|3300027763|Ga0209088_1000013267 45.631 1.02e-24 99.0 91% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300027777_000023|3300027777|Ga0209829_1000000353 40.000 8.95e-19 83.6 95% IMGVR phrog_3972
IMGVR_UViG_3300027782_000092|3300027782|Ga0209500_100001607 43.158 1.64e-18 83.2 82% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300028388_002472|3300028388|Ga0307031_100101416 41.748 1.22e-14 72.8 92% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300028559_000074|3300028559|Ga0247831_100149342 49.091 4.96e-26 102 87% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300028595_000014|3300028595|Ga0272440_100013621 55.769 2.12e-21 72.8 54% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300031707_000842|3300031707|Ga0315291_100351403 46.535 1.62e-22 93.2 95% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300032092_000031|3300032092|Ga0315905_1000023631 35.514 1.96e-15 75.5 88% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300032291_001823|3300032291|Ga0335297_161688316 42.424 8.51e-22 91.3 91% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300032302_000191|3300032302|Ga0335315_115944320 40.000 2.33e-18 82.4 95% IMGVR phrog_3972
IMGVR_UViG_3300033074_000798|3300033074|Ga0364573_1014668 43.396 1.15e-24 98.6 98% IMGVR phrog_3972
IMGVR_UViG_3300033980_000276|3300033980|Ga0334981_0001330_14561_14866 39.048 2.81e-17 79.7 99% IMGVR phrog_3972
IMGVR_UViG_3300034022_000402|3300034022|Ga0335005_0000019_10417_10734 46.078 7.90e-23 94.0 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300034355_001008|3300034355|Ga0335039_0000003_189666_190013 38.333 9.25e-17 61.6 52% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300035661_000114|3300035661|Ga0373633_0001144_1107_1454 53.763 6.80e-32 100 77% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300037042_004016|3300037042|Ga0393277_0000699_269_598 45.872 1.20e-25 101 100% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300037067_008087|3300037067|Ga0378408_0000573_10926_11255 37.383 1.08e-18 83.6 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300037418_000343|3300037418|Ga0395900_0016987_3707_4024 48.571 2.07e-23 95.5 93% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300037634_002275|3300037634|Ga0394429_000524_340_708 35.897 1.78e-16 78.6 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042343_001567|3300042343|Ga0453919_0000110_12772_13113 32.692 1.47e-17 63.5 88% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042351_000564|3300042351|Ga0453931_0000018_23620_23958 36.449 1.77e-16 78.2 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042445_003239|3300042445|Ga0453054_0000082_3671_3958 46.226 9.99e-20 85.5 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042446_001701|3300042446|Ga0454391_0000823_17467_17778 45.794 9.56e-21 88.6 89% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042463_000409|3300042463|Ga0453057_0000081_29126_29458 34.343 6.58e-14 71.2 85% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042540_000683|3300042540|Ga0453068_0000416_25599_25913 46.154 1.00e-25 101 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042564_001032|3300042564|Ga0453070_0000216_62576_62923 33.654 4.77e-16 77.0 86% IMGVR phrog_3972
IMGVR_UViG_3300042691_024438|3300042691|Ga0415385_0011970_17975_18298 46.667 5.83e-25 99.4 95% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042862_000163|3300042862|Ga0453095_0000021_8590_8904 46.154 2.20e-23 95.1 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042890_003866|3300042890|Ga0453678_0000328_46800_47141 40.000 2.08e-17 63.2 53% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300042907_002003|3300042907|Ga0453086_0000037_65216_65557 33.333 1.47e-17 63.5 88% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300043391_000853|3300043391|Ga0451672_0000018_71190_71510 42.268 2.69e-20 87.4 90% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300043436_001870|3300043436|Ga0453108_0000054_15954_16262 40.000 9.63e-18 80.9 98% IMGVR phrog_3972
IMGVR_UViG_3300044259_000026|3300044259|Ga0456009_000084_56657_56992 47.664 9.30e-26 101 93% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300044712_000083|3300044712|Ga0453684_0000742_325_645 54.206 2.30e-30 113 97% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300044844_000928|3300044844|Ga0453102_0000004_17081_17494 37.383 8.60e-23 78.2 78% IMGVR phrog_3972
IMGVR_UViG_3300044846_000602|3300044846|Ga0453141_0001336_17124_17495 50.000 7.42e-25 99.8 80% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300044898_000031|3300044898|Ga0467063_0000111_19954_20286 40.741 2.51e-20 87.8 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300045588_000058|3300045588|Ga0466452_000002_56130_56447 49.020 3.65e-27 104 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300046011_007074|3300046011|Ga0485186_0000040_19646_20059 36.449 2.77e-21 74.3 78% IMGVR phrog_3972
IMGVR_UViG_3300046323_000202|3300046323|Ga0456308_0000019_35112_35453 41.284 7.86e-18 81.6 91% IMGVR phrog_3972
IMGVR_UViG_3300046352_000068|3300046352|Ga0456340_000002_7909_8226 45.631 3.28e-21 89.7 94% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300046820_001017|3300046820|Ga0485288_000585_3077_3406 38.667 2.01e-16 60.5 69% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300047284_000355|3300047284|Ga0466488_000142_4452_4748 47.170 5.74e-23 94.0 100% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300047476_001403|3300047476|Ga0485304_000529_10037_10432 41.748 1.04e-20 89.4 83% IMGVR phrog_3972
IMGVR_UViG_3300047557_001637|3300047557|Ga0485255_000863_2285_2599 47.664 1.05e-26 103 98% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_3300047557_002560|3300047557|Ga0485255_000074_37257_37628 39.837 1.05e-20 89.4 96% IMGVR phrog_3972 phrog_16544
IMGVR_UViG_7000000563_000040|7000000563|SRS014124_WUGC_scaffold_45771__gene_57704 39.048 1.70e-15 75.5 92% Pasteurellaceae IMGVR phrog_3972
IMGVR_UViG_7000000599_000006|7000000599|C2671273__gene_126369 39.048 6.21e-16 76.6 92% Pasteurellaceae IMGVR phrog_3972
ivig_3256_87 39.640 1.80e-19 85.9 97% Butyricimonas synergistica GPD phrog_3972
KY083726_00051 100.000 1.41e-88 261 100% Pectobacterium phage A38 Pectobacterium INPHARED phrog_3972
uvig_279207_48 39.048 1.16e-15 75.9 92% GPD phrog_3972