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PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00135

Bact-Vir

PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00135

Identity

Kingdom:
phage

Quality

90.5 mean pLDDT

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 171-275
PDB
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1t0fA01 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.85 78.0 6.67e-01 98.1% 82.7%
4qboA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.73 54.0 5.79e-01 81.0% 89.1%
2couA01 3.40.50.10190 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › BRCT domain 0.62 36.0 3.91e-01 81.9% 66.3%
3vpbA01 3.40.50.20 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 40.0 4.09e-01 73.3% 67.3%
3gr0D01 3.30.70.1780 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 27.0 3.87e-01 73.3% 100.0%
5k2mA01 3.40.50.20 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 38.0 3.98e-01 75.2% 67.7%
5g4kA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 46.0 3.48e-01 81.9% 81.4%
2ziuB01 3.40.50.10130 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 46.0 4.16e-01 88.6% 84.6%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.56 49.0 3.90e-01 97.1% 65.8%
1a3cA00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 42.0 3.64e-01 80.0% 61.4%
1z2lA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.55 49.0 3.60e-01 100.0% 90.9%
6p66D01 3.40.91.30 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.55 47.0 4.69e-01 96.2% 91.7%
2py6A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 41.0 4.00e-01 81.9% 76.7%
3gnlA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 40.0 3.51e-01 80.0% 80.6%
6b10A00 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.54 41.0 2.99e-01 82.9% 86.4%
4qtzA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 43.0 3.09e-01 89.5% 72.0%
6yb3A01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 42.0 3.33e-01 89.5% 95.8%
3vasA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 41.0 3.11e-01 89.5% 91.5%
ECOD (70)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4936462 2008.1.1.78 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_endonuc 0.78 71.0 6.21e-01 100.0% 80.6%
4032115 2008.1.1.102 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF1829 0.78 60.0 5.76e-01 81.0% 95.0%
4947491 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.77 71.0 6.14e-01 100.0% 78.1%
4033074 2008.1.1.83 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF1064 0.76 69.0 6.44e-01 97.1% 87.6%
3972736 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.76 63.0 5.28e-01 89.5% 81.7%
5073529 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.74 57.0 5.76e-01 81.9% 85.7%
4962258 2008.1.1.219 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF790 0.71 53.0 5.21e-01 79.0% 93.9%
4998336 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.70 54.0 4.80e-01 81.0% 84.1%
3976034 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.70 53.0 5.17e-01 80.0% 86.1%
4935477 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.69 54.0 4.12e-01 81.9% 92.6%
5036859 2008.1.1.3 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Hjc 0.69 48.0 5.52e-01 79.0% 100.0%
4939656 2008.1.1.102 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF1829 0.68 62.0 5.79e-01 97.1% 96.0%
4955318 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.68 51.0 4.81e-01 80.0% 85.9%
4297114 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.68 52.0 4.53e-01 81.0% 85.2%
4634054 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.67 52.0 4.89e-01 81.9% 95.2%
4995781 2008.1.1.17 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF559 0.67 50.0 5.29e-01 79.0% 91.6%
4951715 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.67 51.0 4.95e-01 81.0% 95.7%
5062060 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.65 56.0 5.85e-01 95.2% 100.0%
4494448 2008.1.1.183 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF27227 0.65 59.0 5.43e-01 100.0% 92.6%
4977249 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.65 49.0 4.57e-01 80.0% 85.2%
5031791 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.65 48.0 4.86e-01 78.1% 97.1%
4963143 2008.1.1.228 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF5787 0.64 56.0 4.68e-01 96.2% 64.4%
4945329 2008.1.1.107 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.63 55.0 4.38e-01 96.2% 89.3%
5060677 2008.1.1.114 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.63 57.0 5.72e-01 97.1% 99.0%
4931670 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.63 55.0 4.14e-01 97.1% 93.7%
4947646 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 46.0 4.35e-01 77.1% 96.8%
3164196 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.62 55.0 4.14e-01 97.1% 95.2%
3270711 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.62 54.0 5.03e-01 94.3% 82.3%
5046181 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 46.0 4.16e-01 79.0% 98.0%
3969514 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 55.0 4.25e-01 96.2% 65.8%
5047640 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.62 46.0 3.99e-01 79.0% 100.0%
4400584 192.8.1.474 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › RmuC 0.61 54.0 3.79e-01 96.2% 44.8%
4944802 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.61 54.0 4.01e-01 97.1% 90.2%
4065705 2008.1.1.96 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RmuC 0.61 55.0 4.54e-01 97.1% 81.1%
4927057 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 53.0 4.99e-01 96.2% 96.2%
4476235 2008.1.1.96 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RmuC 0.61 54.0 3.97e-01 97.1% 53.8%
4028756 2008.1.1.86 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RAP 0.61 53.0 4.56e-01 99.0% 61.3%
4620053 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 53.0 4.47e-01 100.0% 57.1%
4314348 2008.1.1.59 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.61 46.0 3.82e-01 81.0% 55.8%
4107946 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.60 54.0 4.22e-01 100.0% 54.2%
5078654 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.60 44.0 4.24e-01 77.1% 95.0%
5073133 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.60 52.0 4.65e-01 96.2% 84.0%
4972924 2008.1.1.16 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.60 51.0 4.95e-01 93.3% 97.4%
5036081 2008.1.1.15 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › HSDR_N 0.60 52.0 3.92e-01 96.2% 84.3%
199740 2008.1.1.22 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › MmcB-like 0.59 52.0 4.68e-01 97.1% 71.2%
4929290 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 53.0 5.00e-01 98.1% 97.6%
5076904 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 52.0 4.72e-01 98.1% 93.1%
5049141 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 52.0 4.29e-01 98.1% 92.1%
2715553 2008.1.1.34 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Card1_endonuc 0.59 51.0 4.95e-01 96.2% 100.0%
5031240 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 51.0 4.86e-01 96.2% 96.0%
3838750 2008.1.1.59 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PDDEXK_1 0.59 50.0 4.60e-01 97.1% 97.2%
4009365 2008.1.1.162 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF30170 0.59 52.0 4.23e-01 96.2% 91.1%
3198801 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 40.0 3.49e-01 70.5% 85.5%
4627062 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 52.0 4.42e-01 100.0% 92.6%
5072639 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 52.0 4.55e-01 100.0% 91.8%
4017555 7514.1.1.0 a/b three-layered sandwiches › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain › Ferredoxin reductase-like, C-terminal NADP-linked domain 0.58 42.0 3.66e-01 76.2% 86.7%
5080539 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 51.0 4.59e-01 100.0% 94.8%
4583141 2008.1.1.134 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › XhoI 0.58 49.0 4.25e-01 94.3% 75.9%
3268851 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 52.0 3.99e-01 100.0% 89.4%
4547181 2008.1.1.134 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › XhoI 0.58 51.0 3.93e-01 98.1% 79.2%
3952449 2008.1.1.114 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF4143 0.58 50.0 4.98e-01 97.1% 97.3%
2983287 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.58 51.0 4.72e-01 98.1% 90.2%
5030620 2008.1.1.5 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NucS_C 0.57 50.0 4.51e-01 96.2% 93.8%
4934478 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 50.0 4.65e-01 98.1% 91.9%
3661035 2007.1.3.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.55 28.0 3.42e-01 76.2% 83.6%
4565932 2008.1.1.71 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › CdiA_C_tRNase 0.54 44.0 3.94e-01 89.5% 82.6%
4934112 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.53 46.0 4.37e-01 98.1% 96.9%
None 0.53 40.0 3.15e-01 80.0% 55.3%
None 0.53 44.0 3.38e-01 89.5% 93.8%
4299161 7512.1.1.23 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_52 0.51 39.0 3.68e-01 82.9% 91.0%
D2 medium residues 110-170
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24308.2 best DUF7487 41.2 2.40e-10 100.0% 26.4%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qgiA01 3.30.386.10 Alpha Beta › 2-Layer Sandwich › Chitosanase; Chain A, domain 2 › Chitosanase, subunit A, domain 2 0.52 38.0 3.01e-01 82.0% 76.2%
5fmgG00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.50 37.0 2.58e-01 78.7% 42.9%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3706618 101.1.6.0 alpha arrays › HTH › HTH › TrpR 0.62 41.0 3.84e-01 72.1% 54.7%
3678733 633.16.1.0 alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like 0.55 33.0 3.21e-01 70.5% 51.4%
4973696 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.52 36.0 3.25e-01 75.4% 88.9%