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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 APIS107
Inhibited defense system restriction-modification (RM)
CLAN ID CLAN045
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
NP_049647.1 gene_page: dam 259 30416.80 9.2073 9.5
Phage property
Phage Assembly id
Escherichia phage T4 GCF_000836945.1
PMID/References PMID:6307815
PDB structures ;
Pfam domains PF02086.20,PF02086.20
Phrog
Host taxa d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia;
Gene Location Start: 16846;  End: 17625;  Strand: -
Description DNA adenine methylases methylate adenine residues in specific sequences, the methylation site of the host Escherichia coli dam+ methylase. Methylation protects the site against cleavage by the MboI restriction nuclease.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
NC_000866.4 14685 15026 - NP_049642.1 113 12620.65 -10.5 3.6524 Mrh.1 hypothetical protein phrog_2031
NC_000866.4 15026 15232 - NP_049643.1 68 8257.51 -1.0 5.6578 Mrh.2 hypothetical protein phrog_1873
NC_000866.4 15331 15573 - NP_049644.1 80 9117.17 0.0 6.4636 virion structural protein phrog_1715 PF16855.10
NC_000866.4 15606 16280 - NP_049645.1 224 26216.13 30.5 10.7389 SegF homing endonuclease
NC_000866.4 16270 16785 - NP_049646.1 171 20424.18 -10.5 4.5572 dUTPase PF08761.16
NC_000866.4 16846 17625 - NP_049647.1 259 30416.80 9.5 9.2073 Dam family site-specific DNA-(adenine-N6)-methyltransferase PF02086.20 ;PF02086.20
NC_000866.4 17935 18963 - NP_049648.1 342 39777.99 15.5 9.5801 DNA primase phrog_21887 PF08275.16
NC_000866.4 18966 19130 - NP_049649.1 54 5896.64 -1.0 5.0824 gp61.1 hypothetical protein phrog_2086 ; phrog_1823
NC_000866.4 19132 19758 - NP_049650.1 208 24331.57 0.0 6.4890 gp61.2 hypothetical protein phrog_4122 ; phrog_3781 ; phrog_8539
NC_000866.4 19758 20051 - NP_049651.1 97 10993.66 -3.0 4.6017 spackle periplasmic phrog_1586
NC_000866.4 20112 20369 - NP_049652.1 85 10187.10 8.5 10.4193 gp61.4 hypothetical protein phrog_12748 ; phrog_3272 ; phrog_2375 ; phrog_8921

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.87 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-Q8ZMS3-F1-model_v4 1 259 1 260 0.8634 0.8139
AF-Q32AJ9-F1-model_v4 1 259 3 268 0.8522 0.8112
AF-P0AEE8-F1-model_v4 1 259 3 268 0.8518 0.8107
AF-A0A0H3GWR3-F1-model_v4 1 259 3 270 0.847 0.8106
AF-P0DMP3-F1-model_v4 1 259 3 268 0.8509 0.8101
AF-Q58015-F1-model_v4 1 259 2 288 0.8488 0.7901
AF-P44243-F1-model_v4 1 259 23 296 0.7003 0.6346
AF-Q5F5M8-F1-model_v4 1 259 4 332 0.7305 0.6318

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

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000259042174.pdb 1 259 4 279 0.9301 0.8877
MGYP000271406668.pdb 1 259 3 279 0.9299 0.8861
MGYP000994564167.pdb 1 259 2 278 0.9274 0.886
MGYP001000926617.pdb 1 259 5 270 0.914 0.8851
MGYP003571243029.pdb 1 259 2 284 0.9349 0.8848
MGYP001024232661.pdb 5 259 1 273 0.9182 0.8845
MGYP000860657186.pdb 1 259 3 282 0.9294 0.8817
MGYP000249947192.pdb 1 259 3 262 0.8967 0.8811
MGYP000042165803.pdb 1 239 2 260 0.8881 0.8785
MGYP000897117520.pdb 9 259 1 263 0.8971 0.8784

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS107 NP_049647.1 110 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN045

APIS107 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
MN871507_00003 61.400 1.907E-97 314 1.000% Aeromonas phage asfd_1h Aeromonas INPHARED PF02086 phrog_
ON042478_00093 61.400 2.612E-97 313 1.000% Aeromonas phage AhFM11 Aeromonas INPHARED PF02086 phrog_
MGV-GENOME-0377561_28 63.500 8.037E-102 326 1.000% MGV PF02086 phrog_
MGV-GENOME-0377499_93 62.900 1.367E-100 323 1.000% MGV PF02086 phrog_
OK499996_00268 62.600 6.597E-100 321 1.000% Klebsiella phage vB_KaeM_Shinkou Klebsiella INPHARED PF02086 phrog_
LR877331_00120 62.600 4.815E-100 321 1.000% Klebsiella phage vB_KpnM_311F Klebsiella INPHARED PF02086 phrog_
KY000080_00021 63.500 8.037E-102 326 1.000% Klebsiella phage KPV15 Klebsiella INPHARED PF02086 phrog_
OM337876_00278 63.500 8.037E-102 326 1.000% Klebsiella phage KP182 Klebsiella INPHARED PF02086 phrog_
IMGVR_UViG_3300045988_090046|3300045988|Ga0495776_001918_66348_67133 62.900 1.367E-100 323 1.000% IMGVR PF02086 phrog_
MH729874_00251 63.400 1.101E-101 326 1.000% Klebsiella phage KP179 Klebsiella INPHARED PF02086 phrog_
MN038175_00040 49.100 2.101E-73 244 0.996% Panteoa phage Phynn Pantoea INPHARED PF02086 phrog_
MF327006_00203 43.800 7.351E-61 208 0.996% Shigella phage Sf20 Shigella INPHARED PF02086 phrog_27806
MK962753_00065 44.200 1.120E-61 210 0.996% Shigella phage JK32 Shigella INPHARED PF02086 phrog_27806
MW748999_00192 44.200 8.181E-62 211 0.996% Escherichia phage vB_EcoM_Skers Escherichia INPHARED PF02086 phrog_27806
MN709127_00061 44.100 1.532E-61 210 0.996% Escherichia phage Ec_Makalu_002 Escherichia INPHARED PF02086 phrog_27806
OX001802_00201 44.500 2.333E-62 212 0.996% Escherichia phage vB_Eco_TB34 Escherichia INPHARED PF02086 phrog_27806
MGV-GENOME-0375882_202 44.200 1.120E-61 210 0.996% MGV PF02086 phrog_27806
ON286974_00061 44.200 1.120E-61 210 0.996% Escherichia phage W115 Escherichia INPHARED PF02086 phrog_27806
MT764208_00182 44.000 2.869E-61 209 0.996% Escherichia phage JEP8 Escherichia INPHARED PF02086 phrog_
MK573636_00071 43.300 6.603E-60 205 0.996% Escherichia phage vB_EcoM_PHB13 Escherichia INPHARED PF02086 phrog_27806
MN850615_00204 44.200 8.181E-62 211 0.996% Escherichia phage kvi Escherichia INPHARED PF02086 phrog_27806
HE978309_00063 43.700 1.006E-60 207 0.996% Enterobacteria phage GEC-3S Enterobacteria INPHARED PF02086 phrog_
uvig_374832_55 44.500 2.333E-62 212 0.996% GPD PF02086 phrog_27806
MH560358_00221 44.700 6.650E-63 214 0.996% Escherichia virus KFS-EC Escherichia INPHARED PF02086 phrog_
MN894885_00061 44.200 1.120E-61 210 0.996% Escherichia phage Ec_Makalu_001 Escherichia INPHARED PF02086 phrog_27806
uvig_100047_108 44.200 1.120E-61 210 0.996% GPD PF02086 phrog_27806
MN882349_00061 44.300 3.192E-62 212 1.000% Escherichia phage Ec_Makalu_003 Escherichia INPHARED PF02086 phrog_27806
uvig_589117_33 44.000 2.097E-61 209 0.996% GPD PF02086 phrog_
MZ504878_00062 44.300 5.978E-62 211 0.996% Enterobacteria phage Whisky Enterobacteria INPHARED PF02086 phrog_
MZ504877_00064 44.500 2.333E-62 212 0.996% Enterobacteria phage Cognac Enterobacteria INPHARED PF02086 phrog_
MZ504876_00060 44.300 5.978E-62 211 0.996% Enterobacteria phage Brandy Enterobacteria INPHARED PF02086 phrog_27806
OP114734_00205 43.800 7.351E-61 208 0.996% Escherichia phage vB_EcoM-pEE20 Escherichia INPHARED PF02086 phrog_
KY683735_00065 44.700 6.650E-63 214 0.996% Escherichia phage ECD7 Escherichia INPHARED PF02086 phrog_
MT478991_00246 44.300 5.978E-62 211 0.996% Escherichia phage vB_EcoM_011D4 Escherichia INPHARED PF02086 phrog_27806
MK327947_00065 44.000 2.097E-61 209 0.996% Escherichia phage vB_EcoM_G5211 Escherichia INPHARED PF02086 phrog_
MK327935_00064 44.200 1.120E-61 210 0.996% Escherichia phage vB_EcoM_G2494 Escherichia INPHARED PF02086 phrog_27806
AY343333_00062 44.100 1.532E-61 210 0.996% Escherichia phage RB49 Escherichia INPHARED PF02086 phrog_27806
MGV-GENOME-0374910_27 54.000 2.808E-82 270 0.992% MGV PF02086 phrog_
OP684128_00242 54.000 2.808E-82 270 0.992% Klebsiella phage pR7_1 Klebsiella INPHARED PF02086 phrog_
MW021756_00241 52.900 3.140E-80 264 0.996% Cronobacter phage vB_CsaM_SemperBestia Cronobacter INPHARED PF02086 phrog_
OL551674_00260 53.300 3.476E-81 267 0.996% Enterobacter phage vB_EcRAM-01 Enterobacter INPHARED PF02086 phrog_
MW021749_00167 51.400 4.338E-77 255 0.996% Citrobacter phage vB_Cfr_Xman Citrobacter INPHARED PF02086 phrog_
OQ571799_00156 51.700 9.009E-78 257 0.996% Enterobacter phage phi5 Enterobacter INPHARED PF02086 phrog_
OX335407_00186 54.100 1.497E-82 271 0.992% Klebsiella phage mtp7 Klebsiella INPHARED PF02086 phrog_
JN882287_00242 53.300 3.476E-81 267 0.996% Cronobacter phage vB_CsaM_GAP161 Cronobacter INPHARED PF02086 phrog_
MZ612130_00055 54.100 2.051E-82 270 0.992% Klebsiella phage vB_KpnM-VAC66 Klebsiella INPHARED PF02086 phrog_
MH823906_00246 53.100 1.223E-80 265 0.996% Citrobacter phage Maroon Citrobacter INPHARED PF02086 phrog_
KT321315_00245 53.600 1.853E-81 267 0.992% Enterobacter phage phiEap-3 Enterobacter INPHARED PF02086 phrog_
MN508624_00245 53.700 5.268E-82 269 0.996% Enterobacter phage EC-F2 Enterobacter INPHARED PF02086 phrog_
MN101224_00030 54.100 2.051E-82 270 0.992% Klebsiella phage KMI10 Klebsiella INPHARED PF02086 phrog_
HE858210_00249 52.200 9.977E-79 259 0.996% Pseudotevenvirus RB43 Unspecified INPHARED PF02086 phrog_
uvig_581689_78 53.300 3.476E-81 267 0.996% GPD PF02086 phrog_
OP970827_00082 53.300 4.760E-81 266 0.996% Klebsiella phage Kp_GWPR59 Klebsiella INPHARED PF02086 phrog_
OP045497_00016 53.700 1.353E-81 268 0.992% Klebsiella phage 150040 Klebsiella INPHARED PF02086 phrog_
MN508622_00233 52.800 4.301E-80 263 0.996% Enterobacter phage EC-W2 Enterobacter INPHARED PF02086 phrog_
OK210075_00075 53.600 7.214E-82 269 0.996% Citrobacter phage KKP_3664 Citrobacter INPHARED PF02086 phrog_
IMGVR_UViG_2974557979_000001|2974557979|2974558229 52.000 3.206E-65 220 0.857% Enterobacteriaceae IMGVR PF02086 phrog_
HM134276_00240 53.300 3.476E-81 267 0.996% Escherichia phage RB16 Escherichia INPHARED PF02086 phrog_
IMGVR_UViG_2974587579_000001|2974587579|2974587826 53.300 2.340E-71 238 0.900% IMGVR PF02086 phrog_
IMGVR_UViG_648936715_000001|648936715|648937927 51.200 7.395E-64 216 0.857% IMGVR PF02086 phrog_
MW250785_00039 53.100 1.223E-80 265 0.996% Escherichia phage UPEC03 Escherichia INPHARED PF02086 phrog_
HQ918180_00241 53.700 9.880E-82 268 0.992% Klebsiella phage KP27 Klebsiella INPHARED PF02086 phrog_
AY967407_00253 51.600 1.689E-77 256 0.996% Escherichia phage RB43 Escherichia INPHARED PF02086 phrog_
MGV-GENOME-0378091_26 54.000 2.808E-82 270 0.992% MGV PF02086 phrog_
MGV-GENOME-0375107_27 53.300 3.476E-81 267 0.996% MGV PF02086 phrog_
MGV-GENOME-0378171_221 54.200 1.093E-82 271 0.992% MGV PF02086 phrog_
KC801932_00237 52.300 7.285E-79 260 0.996% Escherichia phage Lw1 Escherichia INPHARED PF02086 phrog_
OP617746_00184 54.000 2.808E-82 270 0.992% Klebsiella phage KP13MC5-1 Klebsiella INPHARED PF02086 phrog_
KX245890_00240 51.100 2.089E-76 253 0.996% Citrobacter phage vB_CfrM_CfP1 Citrobacter INPHARED PF02086 phrog_
ON157416_00242 53.100 1.223E-80 265 0.996% Cronobacter phage Dev_CS701 Cronobacter INPHARED PF02086 phrog_
OL539470_00021 52.800 4.301E-80 263 0.996% Cronobacter phage vB_CsaM_Invicta Cronobacter INPHARED PF02086 phrog_
MN508817_00198 50.100 1.242E-74 248 1.000% Yersinia phage JC221 Yersinia INPHARED PF02086 phrog_
KX443552_00251 53.400 2.538E-81 267 0.996% Cronobacter phage vB_CsaM_leE Cronobacter INPHARED PF02086 phrog_
KR869820_00232 51.500 3.168E-77 255 0.996% Citrobacter phage IME-CF2 Citrobacter INPHARED PF02086 phrog_
IMGVR_UViG_3300015157_000003|3300015157|Ga0181864_12499820 54.200 1.093E-82 271 0.992% IMGVR PF02086 phrog_
LR746310_00257 53.800 7.214E-82 269 0.992% Klebsiella phage vB_KpnM_05F Klebsiella INPHARED PF02086 phrog_
MW448170_00246 54.100 1.497E-82 271 0.992% Klebsiella phage vB_KpnM_M1 Klebsiella INPHARED PF02086 phrog_
KX431559_00246 53.500 1.353E-81 268 0.996% Cronobacter phage vB_CsaM_leB Cronobacter INPHARED PF02086 phrog_
IMGVR_UViG_3300045988_041714|3300045988|Ga0495776_110494_15088_15939 54.000 2.808E-82 270 0.992% IMGVR PF02086 phrog_
MT334653_00251 52.300 7.285E-79 260 0.996% Buttiauxella phage vB_ButM_GuL6 Buttiauxella INPHARED PF02086 phrog_
OQ267591_00256 53.700 1.353E-81 268 0.992% Klebsiella phage phi_KPN_S3 Klebsiella INPHARED PF02086 phrog_
ON515458_00244 54.200 1.093E-82 271 0.992% Klebsiella phage BL02 Klebsiella INPHARED PF02086 phrog_
MZ322895_00079 53.800 7.214E-82 269 0.992% Klebsiella phage vB_KpnM_VAC13 Klebsiella INPHARED PF02086 phrog_
KY971610_00204 52.900 3.508E-78 258 0.992% Pseudomonas phage PspYZU05 Pseudomonas INPHARED PF02086 phrog_
MGV-GENOME-0377602_140 95.700 4.115E-170 523 1.000% MGV PF02086 phrog_
KR269718_00173 96.300 2.410E-171 527 1.000% Escherichia phage HY03 Escherichia INPHARED PF02086 phrog_
OM135583_00028 95.700 4.115E-170 523 1.000% Escherichia phage EP01 Escherichia INPHARED PF02086 phrog_
MK373785_00030 95.700 4.115E-170 523 1.000% Escherichia phage vB_EcoM_OE5505 Escherichia INPHARED PF02086 phrog_
OQ599309_00030 96.000 8.506E-171 525 1.000% Escherichia phage 107 Escherichia INPHARED PF02086 phrog_
NP_049647.1 100.000 9.098E-175 537 1.000% Escherichia phage T4 Escherichia NCBI PF02086 PF02086 phrog_
OL964735_00031 96.900 1.030E-172 531 1.000% Escherichia phage T4 Escherichia INPHARED PF02086 phrog_
MG867727_00030 96.000 1.166E-170 525 1.000% Escherichia phage vB_EcoM-G28 Escherichia INPHARED PF02086 phrog_
MF001354_00203 96.300 2.410E-171 527 1.000% Salmonella phage SG1 Salmonella INPHARED PF02086 phrog_
uvig_585812_256 95.800 3.002E-170 524 1.000% GPD PF02086 phrog_
MW822011_00276 95.600 7.730E-170 522 1.000% Shigella phage TB004 Shigella INPHARED PF02086 phrog_
ON528734_00172 96.000 1.166E-170 525 1.000% Shigella phage ESh24 Shigella INPHARED PF02086 phrog_
MZ501089_00141 95.500 1.060E-169 522 1.000% Escherichia phage KarlGJung Escherichia INPHARED PF02086 phrog_
ON229909_00235 96.100 4.528E-171 526 1.000% Escherichia phage vB_EcoM_CE1 Escherichia INPHARED PF02086 phrog_
KX130861_00215 96.100 4.528E-171 526 1.000% Shigella phage SHFML-11 Shigella INPHARED PF02086 phrog_
OL362041_00032 95.600 5.640E-170 523 1.000% Escherichia phage vB_Eco_OMNI12 Escherichia INPHARED PF02086 phrog_
IMGVR_UViG_3300006879_000208|3300006879|Ga0079226_100114192 95.900 1.598E-170 524 1.000% IMGVR PF02086 phrog_
ON528727_00058 94.700 4.658E-168 517 1.000% Shigella phage ESh17 Shigella INPHARED PF02086 phrog_
KU878969_00027 75.600 2.889E-127 400 1.000% Escherichia phage MX01 Escherichia INPHARED PF02086 phrog_
KU925172_00237 95.100 7.025E-169 520 1.000% Escherichia phage PE37 Escherichia INPHARED PF02086 phrog_
IMGVR_UViG_3300019879_000001|3300019879|Ga0193723_100006840 43.200 1.006E-60 207 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300031418_000373|3300031418|Ga0308166_10137639 43.100 2.577E-60 206 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_067560|3300045988|Ga0495776_014908_94011_94832 54.700 7.983E-83 271 1.000% IMGVR PF02086 phrog_
MGV-GENOME-0378626_206 55.000 2.269E-83 273 1.000% MGV PF02086 phrog_
OM638103_00097 55.000 2.269E-83 273 1.000% Cronobacter phage LPCS28 Cronobacter INPHARED PF02086 phrog_
MT560058_00035 52.200 4.804E-78 258 1.000% Pectobacterium phage POP12 Pectobacterium INPHARED PF02086 phrog_