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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 APIS034
Inhibited defense system O-antigen-based barrier
CLAN ID CLAN036
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
YP_009615327.1 gene_page: gnarl1 40 4963.65 9.8665 2
Phage property
Phage Assembly id
Klebsiella phage vB_KpnM_KpV79 GCF_002743875.1
PMID/References Silas et al., 2023
PDB structures ;
Pfam domains
Phrog phrog_1402,phrog_13897,phrog_23045
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Klebsiella;
Gene Location Start: 35946;  End: 36068;  Strand: -
Description Putative O-antigen modifiers, interfere with O-antigen biosynthesis.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_042041.1 32234 32644 + YP_009615322.1 136 15098.82 0.5 6.6950 hypothetical protein phrog_15451
NC_042041.1 32671 32952 + YP_009615323.1 93 10306.95 2.5 9.0828 hypothetical protein phrog_13707
NC_042041.1 32965 33552 - YP_009615324.1 195 22436.60 7.5 9.4710 DNA polymerase phrog_15833 ; phrog_1252 ; phrog_11133 ; phrog_18505
NC_042041.1 33542 34378 - YP_009615325.1 278 31552.07 22.5 9.6264 endonuclease phrog_681 ; phrog_559 PF13455.9
NC_042041.1 34375 35898 - YP_009615326.1 507 58127.38 -0.5 6.4470 DNA polymerase phrog_1252 ; phrog_34024 ; phrog_18505 ; phrog_23499
NC_042041.1 35946 36068 - YP_009615327.1 40 4963.65 2.0 9.8665 hypothetical protein phrog_23045 ; phrog_13897 ; phrog_1402
NC_042041.1 36117 36920 - YP_009615328.1 267 28844.66 1.5 6.8419 Gp2.5-like ssDNA binding protein and ssDNA annealing protein phrog_7011
NC_042041.1 37007 38131 - YP_009615329.1 374 42379.35 -3.0 6.0863 exonuclease phrog_69 PF10926.11
NC_042041.1 38136 38990 - YP_009615330.1 284 30934.77 -23.0 4.2290 hypothetical protein phrog_11133 ; phrog_27827
NC_042041.1 39131 39361 + YP_009615331.1 76 9138.29 4.0 9.1714 hypothetical protein phrog_10768 ; phrog_16432
NC_042041.1 39354 39551 + YP_009615332.1 65 7558.44 -7.0 4.0380 hypothetical protein phrog_5806 ; phrog_4173

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.53 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

No homologs found in esmfold database

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS034 YP_009615327.1 54 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN036

APIS034 has no similar APIS family.

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_3300034683_000017|3300034683|Ga0310147_000399_22219_22368 80.000 1.78e-13 65.1 100% IMGVR phrog_13897 phrog_23045
IMGVR_UViG_3300045988_027960|3300045988|Ga0495776_005869_34233_34355 97.500 2.76e-18 77.0 100% Enterobacteriaceae IMGVR phrog_1402 phrog_13897 phrog_23045
IMGVR_UViG_3300045988_050704|3300045988|Ga0495776_143500_5987_6136 80.000 1.21e-13 65.5 100% IMGVR phrog_13897 phrog_23045
IMGVR_UViG_3300045988_053044|3300045988|Ga0495776_103643_21602_21736 90.000 3.19e-16 72.0 100% Enterobacteriaceae IMGVR phrog_1402 phrog_13897 phrog_23045
IMGVR_UViG_3300045988_058156|3300045988|Ga0495776_060453_22595_22720 87.500 7.98e-16 70.9 100% Enterobacteriaceae IMGVR phrog_1402 phrog_13897 phrog_23045
IMGVR_UViG_3300045988_068412|3300045988|Ga0495776_076727_13509_13634 91.667 4.17e-14 66.6 90% IMGVR phrog_1402 phrog_13897 phrog_23045
IMGVR_UViG_3300045988_073072|3300045988|Ga0495776_104554_20632_20781 92.500 8.06e-17 73.6 100% Enterobacteriaceae IMGVR phrog_1402 phrog_13897 phrog_23045
JX866719_00054 87.500 3.23e-16 72.0 100% Klebsiella phage JD001 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
KX237516_00054 87.500 5.62e-16 71.2 100% Klebsiella phage vB_KpnM_KpV52 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MG432137_00012 87.500 3.72e-16 72.0 100% Pectinobacterium phage PEAT2 Pectobacterium INPHARED phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0189935_39 90.000 1.35e-16 72.8 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0210311_23 82.500 4.73e-14 66.6 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0218315_22 82.500 8.07e-14 65.9 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0226918_21 88.889 1.77e-13 65.1 90% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0231838_30 91.667 6.94e-14 65.9 90% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0231940_30 91.667 3.69e-14 66.6 90% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0232395_28 92.500 8.24e-17 73.6 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0239582_10 80.000 1.24e-13 65.5 100% MGV phrog_13897 phrog_23045
MGV-GENOME-0242953_29 90.000 3.26e-16 72.0 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0245115_19 100.000 6.52e-19 78.6 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0302439_51 97.500 2.81e-18 77.0 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0305001_18 87.500 8.14e-16 70.9 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0305038_39 80.000 2.20e-13 64.7 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0305165_31 87.500 6.51e-16 71.2 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0305506_48 92.500 1.10e-16 73.2 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0305591_22 86.111 1.41e-12 62.8 90% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0307383_57 86.111 8.69e-13 63.2 90% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0309124_63 90.000 1.34e-16 72.8 100% MGV phrog_1402 phrog_13897 phrog_23045
MGV-GENOME-0309228_23 85.000 1.42e-14 67.8 100% MGV phrog_1402 phrog_13897 phrog_23045
MK685667_00077 88.889 1.13e-13 65.5 90% Klebsiella phage vB_KpnM_IME346 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MN689778_00020 92.500 2.41e-17 75.1 100% Klebsiella phage vB_KpnM_15-38_KLPPOU148 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MT559528_00055 86.111 1.39e-12 62.8 90% Klebsiella phage vB_KpnM_cmc20193 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MT757392_00017 80.000 2.16e-13 64.7 100% Klebsiella phage vB_KleM_KB2 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MT894004_00036 97.222 2.92e-15 69.3 90% Klebsiella phage MEW1 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MZ374361_00055 88.889 1.01e-13 65.5 90% Klebsiella phage BUCT_49532 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MZ398021_00047 92.500 3.70e-17 74.3 100% Klebsiella phage BUCT_47333 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
MZ504995_00058 91.667 3.62e-14 66.6 90% Klebsiella phage Geezett Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
OK499978_00055 88.889 1.73e-13 65.1 90% Klebsiella phage vB_KpnM_JustaPhage Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
ON086804_00055 87.500 8.75e-16 70.9 100% Escherichia phage ZCEC13 Escherichia INPHARED phrog_1402 phrog_13897 phrog_23045
ON602758_00018 90.000 1.11e-16 73.2 100% Klebsiella phage VLCpiM12a Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
ON809560_00021 85.000 2.50e-15 69.7 100% Klebsiella phage pKp383 Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
OP114730_00026 87.500 6.34e-16 71.2 100% Klebsiella phage SBP Klebsiella INPHARED phrog_1402 phrog_13897 phrog_23045
uvig_139151_25 90.000 1.31e-16 72.8 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_224221_39 90.000 1.33e-16 72.8 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_230302_57 86.111 8.53e-13 63.2 90% GPD phrog_1402 phrog_13897 phrog_23045
uvig_244421_15 91.667 6.81e-14 65.9 90% GPD phrog_1402 phrog_13897 phrog_23045
uvig_245059_4 90.000 1.96e-16 72.4 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_247526_19 85.000 1.13e-14 68.2 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_324604_31 87.500 6.38e-16 71.2 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_332678_50 82.500 4.64e-14 66.6 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_372694_65 92.500 1.07e-16 73.2 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_438241_42 82.500 7.92e-14 65.9 100% GPD phrog_1402 phrog_13897 phrog_23045
uvig_461969_40 85.000 1.39e-14 67.8 100% GPD phrog_1402 phrog_13897 phrog_23045
YP_009615327.1 100.000 1.65e-25 78.6 100% Klebsiella phage vB_KpnM_KpV79 Klebsiella NCBI phrog_1402 phrog_13897 phrog_23045
APIS Contig Range
APIS034 NC_042041.1 32234 - 39551

Gene cluster comparison plot by clinker      Download html