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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 APIS039
Inhibited defense system
CLAN ID CLAN003
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
IMGVR_UViG_2751185776_000007|2751185776|2753238834
gene_page: 141 16050.8 3.9947 -12.5
Phage property
Phage Assembly id
IMGVR_UViG_2751185776_000007
PMID/References
PDB structures ;
Pfam domains PF03230.16
Phrog phrog_10132
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Morganella;s__Morganella psychrotolerans_B
Gene Location Start: 10487;  End: 10912;  Strand: -
Description
Note This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS007,ArdB 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_2751185776_000007 6914 7336 - IMGVR_UViG_2751185776_000007|2751185776|2753238829 140 15209.04 -9.5 4.2611 hypothetical protein
IMGVR_UViG_2751185776_000007 7431 7916 - IMGVR_UViG_2751185776_000007|2751185776|2753238830 161 17967.29 13.5 10.1417 hypothetical protein
IMGVR_UViG_2751185776_000007 8073 8540 - IMGVR_UViG_2751185776_000007|2751185776|2753238831 155 17383.10 6.0 9.6596 hypothetical protein
IMGVR_UViG_2751185776_000007 8718 9425 - IMGVR_UViG_2751185776_000007|2751185776|2753238832 235 27363.89 15.5 10.0618 predicted DNA-binding transcriptional regulator YafY phrog_13105 PF13280.9
IMGVR_UViG_2751185776_000007 9637 10473 - IMGVR_UViG_2751185776_000007|2751185776|2753238833 278 31760.34 12.0 9.9993 uncharacterized protein DUF932 phrog_12094 PF06067.14
IMGVR_UViG_2751185776_000007 10487 10912 - IMGVR_UViG_2751185776_000007|2751185776|2753238834 141 16050.82 -12.5 3.9947 antirestriction protein phrog_10132 PF03230.16
IMGVR_UViG_2751185776_000007 11004 11876 - IMGVR_UViG_2751185776_000007|2751185776|2753238835 290 32663.10 -2.5 5.8864 hypothetical protein phrog_11431 ; phrog_16468 PF01926.26
IMGVR_UViG_2751185776_000007 11938 12870 - IMGVR_UViG_2751185776_000007|2751185776|2753238836 310 36472.83 8.5 9.2282 hypothetical protein
IMGVR_UViG_2751185776_000007 13307 13885 + IMGVR_UViG_2751185776_000007|2751185776|2753238837 192 22808.02 15.5 9.9478 uncharacterized protein DUF3296 phrog_25019 PF11726.11
IMGVR_UViG_2751185776_000007 13991 14200 + IMGVR_UViG_2751185776_000007|2751185776|2753238838 69 8143.46 2.0 9.8652 AlpA family transcriptional regulator phrog_9834 ; phrog_66 ; phrog_2790 PF05930.15
IMGVR_UViG_2751185776_000007 14562 15002 - IMGVR_UViG_2751185776_000007|2751185776|2753238839 146 16592.06 -6.5 4.3904 arsenate reductase phrog_16693 PF03960.18

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.79 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-P75676-F1-model_v4 1 141 10 152 0.9559 0.9109
AF-P52139-F1-model_v4 1 141 9 152 0.9532 0.909
AF-A0A0H3GW18-F1-model_v4 1 141 1 141 0.9167 0.8995
AF-Q327Q6-F1-model_v4 2 141 15 157 0.9473 0.8897
AF-Q32HM6-F1-model_v4 1 141 38 181 0.951 0.8384
AF-Q93GQ0-F1-model_v4 7 141 7 144 0.8636 0.838
AF-A0A0H3GVF3-F1-model_v4 6 141 1 132 0.882 0.8309
AF-A0A077ZNG7-F1-model_v4 12 141 9 141 0.8676 0.829
AF-A0A0H3GZ47-F1-model_v4 2 141 35 221 0.8463 0.686

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000479619222.pdb 3 141 1 141 0.9517 0.9427
MGYP000901984350.pdb 2 141 1 138 0.9621 0.9411
MGYP000931080388.pdb 1 141 6 146 0.9653 0.9383
MGYP003365227403.pdb 1 141 3 143 0.951 0.9311
MGYP001992189960.pdb 5 141 1 134 0.9624 0.9271
MGYP001201501853.pdb 5 141 1 134 0.9598 0.9243
MGYP001037997637.pdb 3 141 1 135 0.9571 0.9242
MGYP000589756821.pdb 1 141 6 149 0.9606 0.9238
MGYP001120502683.pdb 6 141 1 133 0.9599 0.9212
MGYP001805956192.pdb 1 141 6 147 0.9529 0.9208

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS039 IMGVR_UViG_2751185776_000007|2751185776|2753238834 49 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN003

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS007 9.89E-74 2 141 14 151 restriction-modification (RM) BAF33451.1
APIS069 1.27E-25 6 141 6 144 IMGVR_UViG_3300036792_000137|3300036792|Ga0376663_0000427_343_774
APIS038 1.91E-25 4 141 8 150 IMGVR_UViG_2576861805_000002|2576861805|2579667884
APIS055 4.85E-21 2 141 2 142 OL763419_00042
APIS037 1.52E-16 10 141 7 141 IMGVR_UViG_2541047688_000003|2541047688|2543982737

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_2511231170_000001|2511231170|2511870096 47.020 2.78e-35 129 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2529292882_000013|2529292882|2530356395 47.552 6.08e-37 132 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2529293076_000023|2529293076|2531131775 50.382 4.14e-36 130 91% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2534682236_000019|2534682236|2537093308 48.201 2.85e-37 133 96% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2534682325_000015|2534682325|2537385693 49.265 5.79e-37 132 94% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2537562092_000001|2537562092|2539773385 46.853 2.70e-36 130 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047498_000018|2541047498|2543234824 48.889 6.65e-36 129 94% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047684_000005|2541047684|2543962383 47.682 6.57e-37 132 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047721_000001|2541047721|2544145901 47.020 1.95e-35 128 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047742_000006|2541047742|2544253806 48.344 1.15e-39 139 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047802_000015|2541047802|2544556426 50.382 4.21e-36 130 91% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047851_000005|2541047851|2544797335 46.358 4.49e-34 125 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2541047893_000009|2541047893|2545003977 46.154 2.64e-35 128 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2547132277_000010|2547132277|2548114485 49.265 5.99e-37 132 94% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2547132398_000002|2547132398|2548602399 51.064 2.28e-43 148 99% Cronobacter sakazakii IMGVR PF03230 phrog_10132
IMGVR_UViG_2548876858_000014|2548876858|2550148890 48.529 2.34e-36 130 94% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2562617085_000012|2562617085|2562934603 48.529 1.63e-36 131 94% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2563366805_000004|2563366805|2564130911 55.319 9.16e-46 154 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2565956581_000001|2565956581|2566253699 51.799 4.63e-43 147 99% Yersinia similis IMGVR PF03230 phrog_10132
IMGVR_UViG_2571042794_000002|2571042794|2573734993 48.936 4.67e-39 137 99% Enterobacter hormaechei IMGVR PF03230 phrog_10132
IMGVR_UViG_2579778730_000001|2579778730|2580747249 50.355 1.82e-41 143 99% Siccibacter colletis IMGVR PF03230 phrog_10132
IMGVR_UViG_2579778842_000011|2579778842|2581214126 45.833 9.68e-36 129 100% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2627854164_000002|2627854164|2630474902 49.645 9.88e-42 144 99% Citrobacter_A amalonaticus_C IMGVR PF03230 phrog_10132
IMGVR_UViG_2636416160_000022|2636416160|2639573815 46.617 3.79e-36 130 94% Yersinia pestis IMGVR PF03230 phrog_10132
IMGVR_UViG_2639763134_000006|2639763134|2642124910 47.552 4.50e-39 137 99% Salmonella enterica IMGVR PF03230 phrog_10132
IMGVR_UViG_2671180458_000011|2671180458|2672855773 48.252 1.07e-39 139 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2690316149_000015|2690316149|2692446076 46.479 4.49e-37 132 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2718218402_000003|2718218402|2721315463 48.951 2.42e-40 140 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2721755658_000005|2721755658|2723459047 51.064 6.15e-44 149 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2721755711_000001|2721755711|2723685156 52.672 1.50e-39 139 91% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2721755725_000016|2721755725|2723748035 48.252 1.14e-39 139 99% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2744054944_000002|2744054944|2746270176 93.617 6.84e-97 283 100% Providencia rettgeri_A IMGVR PF03230 phrog_10132
IMGVR_UViG_2751185776_000007|2751185776|2753238834 100.000 2.02e-102 297 100% Morganella psychrotolerans_B IMGVR PF03230 phrog_10132
IMGVR_UViG_2751185922_000002|2751185922|2753877244 50.355 3.11e-41 143 93% Enterobacter chengduensis IMGVR PF03230 phrog_10132
IMGVR_UViG_2802429241_000010|2802429241|2804655210 51.773 6.31e-42 144 93% Escherichia marmotae IMGVR PF03230 phrog_10132
IMGVR_UViG_2802429245_000006|2802429245|2804670716 49.007 2.00e-40 141 96% Escherichia marmotae IMGVR PF03230 phrog_10132
IMGVR_UViG_2872185964_000007|2872185964|2872187687 50.000 5.16e-40 139 100% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2874927903_000002|2874927903|2874928327 50.000 4.94e-40 140 86% Escherichia coli IMGVR PF03230 phrog_10132
IMGVR_UViG_2878868365_000004|2878868365|2878870336 50.355 9.87e-42 144 93% Citrobacter braakii IMGVR PF03230 phrog_10132
IMGVR_UViG_2922317101_000007|2922317101|2922321092 50.355 1.33e-41 144 93% Citrobacter braakii IMGVR PF03230 phrog_10132
IMGVR_UViG_3300011617_000014|3300011617|Ga0120835_1000499 51.064 2.35e-43 148 99% Enterobacteriaceae IMGVR PF03230 phrog_10132
IMGVR_UViG_3300011754_000012|3300011754|Ga0122284_10010317 47.143 1.76e-37 133 99% Serratia IMGVR PF03230 phrog_10132
IMGVR_UViG_3300011875_000025|3300011875|Ga0121110_10002051 50.355 1.06e-41 144 99% Enterobacter IMGVR PF03230 phrog_10132
IMGVR_UViG_3300017814_000038|3300017814|Ga0183095_107935 53.901 1.18e-44 151 99% Enterobacteriaceae IMGVR PF03230 phrog_10132
IMGVR_UViG_651053023_000006|651053023|651239028 48.951 2.12e-40 141 89% Escherichia IMGVR PF03230 phrog_10132
MGV-GENOME-0167262_5 50.355 5.65e-42 144 99% Escherichia MGV PF03230 phrog_10132
MGV-GENOME-0272743_7 50.355 1.05e-41 144 99% Escherichia MGV PF03230 phrog_10132
uvig_327479_5 50.355 1.02e-41 144 99% GPD PF03230 phrog_10132
uvig_577415_2 50.355 1.03e-41 144 99% GPD PF03230 phrog_10132