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 APIS079
Inhibited defense system
CLAN ID CLAN031
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
MF042361_00008
gene_page: 164 17982.3 4.9286 -4
Phage property
Phage Assembly id
Pseudomonas phage Skulduggery MF042361
PMID/References
PDB structures ;
Pfam domains PF11195.11
Phrog phrog_2709,phrog_30130,phrog_872,phrog_32732,phrog_9467,phrog_1048
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas;
Gene Location Start: 4858;  End: 5352;  Strand: +
Description
Note This family does not have seed protein, but we infer its function is defending Thoeris because it belongs to the same clan as family APIS024,APIS029 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
MF042361 1415 2983 + MF042361_00003 522 60145.17 60145.17 6.9336 hypothetical protein phrog_26724 ; phrog_2472 ; phrog_38407
MF042361 2980 3450 + MF042361_00004 156 16610.59 16610.59 4.0302 hypothetical protein phrog_17424
MF042361 3456 3701 + MF042361_00005 81 8783.17 8783.17 4.5878 hypothetical protein
MF042361 3698 4513 + MF042361_00006 271 28666.30 28666.30 4.1973 hypothetical protein
MF042361 4559 4861 + MF042361_00007 100 11277.66 11277.66 4.2972 hypothetical protein
MF042361 4858 5352 + MF042361_00008 164 17982.27 17982.27 4.9286 hypothetical protein phrog_1048 ; phrog_32732 ; phrog_30130 ; phrog_872 ; phrog_2709 ; phrog_18865 ; phrog_9467 PF11195.11
MF042361 5349 5768 + MF042361_00009 139 15556.63 15556.63 4.9130 DNA methyltransferase phrog_10057
MF042361 5761 8127 + MF042361_00010 788 88929.29 88929.29 4.3944 portal protein phrog_18470 ; phrog_27974 ; phrog_156 ; phrog_24564 ; phrog_25797
MF042361 8139 9095 + MF042361_00011 318 34012.92 34012.92 3.9565 hypothetical protein phrog_8246
MF042361 9108 9293 + MF042361_00012 61 6484.84 6484.84 9.2532 CsrA-like regulator phrog_8397 PF02599.19
MF042361 9400 10494 + MF042361_00013 364 40384.66 40384.66 7.9320 major head protein phrog_13784 ; phrog_334 ; phrog_31117 PF13252.9

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.55 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)
MGYP000632396215.pdb 6 160 6 152 0.7472 0.7042
MGYP003620421190.pdb 5 161 6 142 0.7595 0.6766
MGYP001070471033.pdb 72 160 1 89 0.8799 0.6706
MGYP001121567902.pdb 76 160 1 86 0.8666 0.6511
MGYP002732175134.pdb 6 159 6 147 0.721 0.6504
MGYP002731914620.pdb 72 160 1 85 0.8676 0.6487
MGYP002777370215.pdb 10 161 2 84 0.8649 0.646
MGYP000498482146.pdb 5 160 6 172 0.6995 0.646
MGYP003665317257.pdb 5 160 9 167 0.694 0.643
MGYP003586902511.pdb 74 159 1 85 0.8568 0.642

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS079 MF042361_00008 47 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN031

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS052 1.08E-66 1 160 3 163 IMGVR_UViG_3300012991_000489|3300012991|Ga0157148_10003866
APIS029 7.84E-47 72 161 14 103 Thoeris YP_002300464.1
APIS043 4.05E-36 73 160 119 209 MH238467_00052
APIS045 3.48E-25 74 159 21 115 IMGVR_UViG_3300005805_000580|3300005805|Ga0079957_100145420
APIS070 1.71E-23 1 75 12 76 IMGVR_UViG_3300037297_000240|3300037297|Ga0394146_0000041_21955_22497

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_2529292723_000020|2529292723|2529718555 59.748 2.00e-67 210 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2529293139_000011|2529293139|2531345721 60.377 2.00e-67 210 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2541047878_000002|2541047878|2544928132 59.748 9.47e-67 208 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2556921007_000002|2556921007|2556950327 51.875 7.74e-54 176 97% Microvirgula aerodenitrificans IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2576861092_000011|2576861092|2577208822 60.377 8.52e-68 211 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2585427736_000016|2585427736|2586429403 59.748 8.24e-68 211 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2690316184_000005|2690316184|2692603718 60.377 3.83e-68 212 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2740892230_000034|2740892230|2742592482 60.377 1.25e-67 211 88% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2767802355_000002|2767802355|2769871653 51.875 4.68e-54 176 97% Microvirgula aerodenitrificans IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2778261515_000018|2778261515|2780394986 59.748 6.11e-67 209 100% Escherichia coli IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_2916216219_000002|2916216219|2916217846 50.633 8.29e-51 168 96% Citrobacter braakii IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300011547_000021|3300011547|Ga0121204_10000158 59.748 3.18e-66 207 99% Salmonella IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300012177_000098|3300012177|Ga0153943_100011011 44.654 6.72e-41 143 97% Enterobacteriaceae IMGVR PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300022745_000088|3300022745|Ga0228698_100035516 50.318 1.43e-49 165 95% IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_9467 phrog_1048
IMGVR_UViG_3300029288_000212|3300029288|Ga0265297_1000146775 40.415 3.50e-46 141 97% IMGVR PF11195 phrog_18865 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300044551_000122|3300044551|Ga0455787_00272_16383_16865 51.899 3.89e-52 171 96% Enterobacteriaceae IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300044630_002347|3300044630|Ga0453703_0013641_4573_5067 42.500 3.08e-39 139 95% IMGVR PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300045973_000315|3300045973|Ga0485830_0007101_5693_6178 44.720 2.24e-42 147 98% IMGVR PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300046684_000100|3300046684|Ga0495669_0009738_1957_2445 55.000 4.26e-58 187 99% IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300047317_000108|3300047317|Ga0495604_0021516_747_1232 55.625 3.43e-58 187 97% IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300049019_000006|3300049019|Ga0498751_000020_2991_3476 55.696 1.05e-56 183 96% IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300049460_000031|3300049460|Ga0495682_0002753_6414_6899 53.797 6.68e-56 181 96% IMGVR PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
IMGVR_UViG_3300050196_000059|3300050196|Ga0501166_017721_324_815 42.857 1.23e-39 140 96% IMGVR PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MF042361_00008 100.000 1.87e-116 334 100% Pseudomonas phage Skulduggery Pseudomonas INPHARED PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0136053_21 60.377 4.59e-68 212 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0156300_2 60.377 1.09e-68 213 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0167741_20 59.748 3.05e-67 210 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0172692_19 43.396 1.11e-39 140 97% Enterobacteriaceae MGV PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0184490_21 59.748 1.91e-67 210 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0201091_25 59.748 1.02e-67 211 94% Klebsiella MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0213226_19 59.748 8.83e-67 209 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0247302_22 59.748 4.06e-67 209 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0270912_40 60.377 5.18e-68 212 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
MGV-GENOME-0293369_25 60.377 8.76e-68 211 99% Escherichia MGV PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
OM022251_00046 60.377 4.55e-68 212 97% Escherichia phage HZ41 Escherichia INPHARED PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_145486_5 60.377 1.05e-68 213 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_202925_20 59.119 4.31e-67 209 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_241115_15 60.377 4.98e-68 212 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_260595_48 59.748 5.92e-67 209 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_285902_11 59.748 1.83e-67 210 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_314811_27 60.377 8.43e-68 211 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_317483_25 59.748 9.77e-68 211 94% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_318904_26 43.396 1.07e-39 140 97% GPD PF11195 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_336113_19 59.748 8.49e-67 209 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_395284_33 61.006 6.27e-68 211 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_464652_22 59.748 3.90e-67 209 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048
uvig_67729_23 59.748 2.94e-67 210 100% GPD PF11195 phrog_2709 phrog_30130 phrog_872 phrog_32732 phrog_9467 phrog_1048