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PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00295

Bact-Vir

PLM4_65_coex_sep16_scaffold_0_prodigal-single.1__X__X__00295

Identity

Kingdom:
phage

Quality

94.9 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 33-204_233-268
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00303.25 best Thymidylat_synt 55.9 5.20e-15 81.2% 56.2%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1b5eA00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.90 73.0 6.84e-01 82.7% 73.0%
1bo7A00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.75 72.0 6.09e-01 99.5% 85.1%
1tisA00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.75 71.0 6.27e-01 99.5% 83.9%
1bkpA00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.74 70.0 6.28e-01 99.5% 79.1%
3v8hC00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.72 68.0 6.02e-01 99.5% 89.2%
2rrlA01 3.30.750.140 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.71 33.0 4.34e-01 70.2% 78.3%
3egyX00 3.30.572.10 Alpha Beta › 2-Layer Sandwich › Thymidylate Synthase; Chain A › Thymidylate synthase/dCMP hydroxymethylase domain 0.70 61.0 5.88e-01 99.0% 81.2%
2l72A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.58 32.0 4.10e-01 71.6% 93.2%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 31.0 3.99e-01 73.6% 95.1%
2ozgA02 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 32.0 3.58e-01 82.7% 78.0%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1900473 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.90 73.0 6.78e-01 82.7% 71.5%
5022688 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.88 63.0 6.52e-01 82.7% 76.4%
5046158 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.88 63.0 6.48e-01 82.7% 76.0%
5015648 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.87 64.0 6.45e-01 82.7% 75.6%
2028021 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.87 84.0 7.08e-01 100.0% 76.9%
5065331 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.86 63.0 6.15e-01 82.7% 69.5%
5031349 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.86 65.0 6.43e-01 82.7% 74.4%
4985883 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.85 60.0 6.03e-01 82.7% 70.5%
4932636 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.85 63.0 6.29e-01 82.7% 73.5%
4974926 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.85 62.0 6.17e-01 82.7% 72.1%
4998171 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.84 62.0 5.99e-01 82.7% 67.8%
4949404 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.83 63.0 6.06e-01 82.7% 69.6%
4582423 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.82 63.0 6.25e-01 82.7% 75.2%
4976145 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.82 64.0 6.26e-01 82.7% 74.2%
4938917 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.82 63.0 5.89e-01 82.7% 66.5%
4954631 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.81 66.0 6.32e-01 82.7% 77.4%
5050802 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.80 64.0 5.68e-01 82.7% 76.3%
5059575 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.78 74.0 6.51e-01 99.5% 85.5%
4937005 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.76 72.0 6.03e-01 99.5% 86.6%
4108234 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.76 72.0 6.10e-01 99.5% 85.3%
3479792 266.1.1.0 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase 0.75 72.0 6.13e-01 99.5% 77.4%
1900468 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.75 71.0 6.36e-01 99.5% 78.9%
4664958 266.1.1.0 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase 0.75 71.0 6.50e-01 99.5% 83.0%
4151800 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.75 71.0 6.15e-01 99.5% 84.9%
2540892 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.75 71.0 5.97e-01 99.5% 72.9%
3164619 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.75 71.0 6.28e-01 99.5% 83.7%
4225236 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.74 71.0 6.27e-01 99.5% 80.6%
4086625 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.74 70.0 6.24e-01 99.5% 80.4%
4599962 266.1.1.0 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase 0.74 70.0 6.24e-01 99.5% 79.6%
3824671 266.1.1.1 a+b two layers › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylate synthase/dCMP hydroxymethylase › Thymidylat_synt 0.71 68.0 6.03e-01 99.5% 81.8%
D2 medium residues 1-32_205-232
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fm0E00 3.90.1170.40 Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Molybdopterin biosynthesis MoaE subunit 0.64 45.0 3.44e-01 85.0% 31.7%
6fucA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 35.0 3.18e-01 91.7% 40.7%
3kt7A01 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.58 47.0 3.14e-01 90.0% 75.6%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.58 38.0 3.30e-01 96.7% 42.3%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 45.0 3.73e-01 88.3% 67.0%
2cmzA03 2.30.29.130 Mainly Beta › Roll › PH-domain like › 0.57 39.0 3.43e-01 71.7% 89.2%
3g12B00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.56 30.0 2.45e-01 86.7% 24.8%
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 44.0 3.85e-01 88.3% 62.8%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 45.0 3.79e-01 91.7% 59.4%
4byfC01 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.55 41.0 3.67e-01 83.3% 94.4%
1ce7A02 4.10.470.10 Few Secondary Structures › Irregular › Ricin (A Subunit), domain 2 › Ricin (A Subunit), domain 2 0.54 41.0 3.78e-01 81.7% 62.0%
6ptrB01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.54 42.0 3.54e-01 90.0% 73.5%
3u9sE04 3.30.700.40 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.54 43.0 3.43e-01 88.3% 63.2%
4p16A02 1.10.8.1190 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Papain-like viral protease, thumb domain 0.54 37.0 3.04e-01 73.3% 55.9%
1y2mD01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.54 44.0 3.03e-01 93.3% 40.0%
5i92F01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 36.0 2.57e-01 71.7% 26.1%
2od0A00 3.30.1460.30 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › YgaC/TfoX-N like chaperone 0.53 36.0 3.10e-01 71.7% 79.6%
3vtiA06 3.30.420.560 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.52 27.0 2.22e-01 95.0% 27.6%
1cyyA02 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.52 42.0 3.44e-01 95.0% 75.2%
3r4iA02 6.10.140.960 Special › Helix non-globular › Helix Hairpins › 0.51 38.0 3.88e-01 83.3% 83.3%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3464642 2004.1.1.51 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_1 0.62 42.0 2.69e-01 71.7% 65.1%
5035483 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.60 48.0 3.52e-01 88.3% 49.4%
4953241 3755.3.1.127 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › NFACT_N 0.59 47.0 3.60e-01 93.3% 65.6%
3711991 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.58 45.0 3.58e-01 86.7% 62.3%
4181293 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.57 46.0 3.75e-01 88.3% 53.6%
4177935 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.57 45.0 3.69e-01 88.3% 53.9%
3935332 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.57 45.0 3.56e-01 88.3% 46.2%
60305 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.57 45.0 3.76e-01 88.3% 68.9%
4025452 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.57 45.0 3.68e-01 88.3% 51.3%
3458699 376.1.2.2 few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_2 0.57 40.0 3.05e-01 78.3% 54.6%
5022727 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 40.0 3.03e-01 75.0% 58.7%
5078448 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.56 45.0 3.71e-01 88.3% 54.5%
5028765 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.56 44.0 3.40e-01 90.0% 44.0%
3828336 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.56 44.0 3.64e-01 88.3% 52.6%
3420717 2004.1.1.51 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Sulfotransfer_1 0.56 38.0 2.94e-01 73.3% 86.9%
4271212 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.55 44.0 3.57e-01 91.7% 51.2%
5048568 4294.1.1.2 few secondary structure elements › Trm112p-like › Trm112p-like › Trm112p-like › Trm112p 0.54 45.0 3.14e-01 95.0% 27.8%
3603208 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.54 43.0 4.15e-01 90.0% 81.4%
3781291 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.53 40.0 3.53e-01 88.3% 91.0%
4963446 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.53 36.0 3.59e-01 76.7% 67.7%
3925708 2004.1.1.183 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_9 0.53 38.0 3.03e-01 81.7% 47.9%
None 0.53 37.0 2.59e-01 73.3% 71.7%
3283640 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.52 37.0 2.33e-01 80.0% 13.4%
4162390 4121.1.1.2 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.52 42.0 2.74e-01 90.0% 18.9%
3475436 386.1.1.1 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.52 37.0 3.56e-01 75.0% 90.0%
4948745 2006.1.1.3 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Trehalose_PPase 0.52 37.0 2.46e-01 76.7% 96.6%
4996608 2007.9.1.4 a/b three-layered sandwiches › Flavodoxin-like › Toll/Interleukin receptor TIR domain › Toll/Interleukin receptor TIR domain › TIR_2 0.52 39.0 2.88e-01 88.3% 89.0%
3721249 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.52 32.0 3.36e-01 71.7% 67.3%
3622481 604.29.1.1 alpha bundles › Spectrin repeat-like › Trehalose-6-phosphate phosphatase N-terminal helical bundle › Trehalose-6-phosphate phosphatase N-terminal helical bundle › T6PP_N 0.51 39.0 3.26e-01 88.3% 45.2%
3481690 241.10.1.1 a+b two layers › Type III secretory system chaperone-like › GAS2 domain › GAS2 domain › GAS2 0.51 36.0 3.20e-01 93.3% 52.4%
4995271 2.10.1.1 beta barrels › OB-fold › CheW › CheW › CheW 0.51 38.0 3.32e-01 88.3% 67.3%
5077331 229.1.1.0 a+b two layers › Cdc48 domain 2-like › Cdc48 domain 2-like › Cdc48 domain 2-like 0.51 37.0 3.23e-01 76.7% 71.1%