←Back to structures

SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00035

Bact-Vir

SR-VP_0-2_scaffold_141_6534022_prodigal-single.1__X__X__00035

Identity

Kingdom:
phage

Quality

63.3 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

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 24-95
PDB
Domain cluster: representative
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.72 53.0 4.09e-01 77.8% 77.1%
2k3nA00 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.68 60.0 4.67e-01 100.0% 55.6%
7oq4Z01 1.20.120.950 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein DUF5062 0.68 53.0 4.84e-01 84.7% 80.6%
1nigA00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.66 50.0 4.02e-01 81.9% 82.9%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.66 48.0 4.08e-01 77.8% 51.3%
3ghyA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.65 51.0 4.27e-01 84.7% 89.6%
4nt1A00 1.10.3520.10 Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein 0.65 54.0 3.98e-01 94.4% 56.5%
1szhA02 1.10.150.370 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Caenorhabditis elegans Her-1, C-terminal domain 0.65 55.0 5.30e-01 98.6% 84.1%
1rp3A01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.64 46.0 4.38e-01 75.0% 77.6%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 50.0 4.79e-01 84.7% 81.9%
1xl7A01 1.10.275.20 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Choline/Carnitine o-acyltransferase 0.64 49.0 4.46e-01 86.1% 84.5%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.64 47.0 4.08e-01 80.6% 70.1%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 54.0 4.66e-01 98.6% 94.1%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.63 43.0 3.52e-01 72.2% 64.1%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.63 47.0 3.99e-01 80.6% 63.9%
1kyqA03 1.10.3280.10 Mainly Alpha › Orthogonal Bundle › Siro heme synthase C-terminal domain-like › Siroheme synthase; domain 3 0.61 45.0 4.30e-01 79.2% 67.9%
4i1mB01 1.20.120.1700 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.60 45.0 3.73e-01 80.6% 65.1%
8d3mA02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.59 51.0 3.63e-01 100.0% 85.4%
1z19A01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.59 50.0 4.56e-01 98.6% 86.0%
4gxzD00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.58 48.0 3.71e-01 100.0% 39.4%
1zylA03 1.20.1270.170 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.58 48.0 4.30e-01 91.7% 66.0%
4btfA01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.58 46.0 4.23e-01 90.3% 68.0%
1u00A02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.58 45.0 4.15e-01 86.1% 66.7%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 41.0 4.08e-01 75.0% 77.6%
7p2yd01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.58 46.0 4.24e-01 91.7% 78.8%
2vixA02 1.10.150.630 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.57 49.0 4.60e-01 100.0% 78.7%
1gvnA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.56 41.0 3.94e-01 80.6% 81.6%
3hwrA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.56 44.0 3.74e-01 90.3% 89.9%
4qgpB00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.55 40.0 3.54e-01 76.4% 72.0%
3m7gA02 1.10.8.1010 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.55 44.0 4.06e-01 90.3% 80.0%
2jx0A00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.55 41.0 3.43e-01 81.9% 58.8%
1lq7A00 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.55 40.0 4.18e-01 86.1% 88.1%
2ot4A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.54 39.0 3.54e-01 80.6% 69.2%
6yttA01 1.10.8.190 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Carbon monoxide dehydrogenase alpha subunit. Chain M, domain 1 0.53 38.0 3.41e-01 75.0% 56.0%
3g9gA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 42.0 2.88e-01 86.1% 68.4%
5z7qA00 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.52 38.0 2.95e-01 80.6% 50.6%
1xjaB00 2.60.120.280 Mainly Beta › Sandwich › Jelly Rolls › Regulatory protein AraC 0.52 38.0 3.05e-01 79.2% 94.2%
6khjH01 1.10.645.10 Mainly Alpha › Orthogonal Bundle › Cytochrome-c3 Hydrogenase; chain B › Cytochrome-c3 Hydrogenase, chain B 0.51 44.0 2.86e-01 100.0% 87.2%
2zgyA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.51 44.0 3.62e-01 100.0% 65.7%
3caxA01 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.51 42.0 3.14e-01 100.0% 52.5%
6q9jB02 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.51 40.0 3.84e-01 91.7% 89.8%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5052922 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.68 52.0 4.35e-01 80.6% 68.3%
4979116 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.68 51.0 4.39e-01 80.6% 74.8%
3274254 1128.1.1.1 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.66 51.0 4.48e-01 83.3% 59.0%
3223278 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.65 48.0 4.24e-01 77.8% 66.7%
4028318 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.65 49.0 4.06e-01 80.6% 58.4%
3261143 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.64 50.0 3.72e-01 83.3% 79.3%
4158879 632.22.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.64 50.0 4.66e-01 84.7% 83.3%
4350211 192.29.1.161 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › FlbT 0.64 42.0 4.13e-01 80.6% 61.3%
3236562 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.63 47.0 3.71e-01 79.2% 65.2%
4934784 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.63 49.0 4.66e-01 84.7% 82.4%
5036615 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.63 45.0 4.09e-01 75.0% 80.0%
3931994 632.15.1.10 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › IQ 0.62 48.0 4.02e-01 84.7% 58.4%
3615391 3671.1.1.0 ↗ alpha duplicates or obligate multimers › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain 0.61 37.0 3.83e-01 80.6% 62.9%
4003102 633.5.1.0 ↗ alpha bundles › Bromodomain-like › LemA-like › LemA-like 0.61 50.0 4.11e-01 94.4% 51.7%
4940598 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.61 46.0 4.55e-01 81.9% 90.7%
4935665 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.61 47.0 4.61e-01 84.7% 88.7%
5042303 1203.1.2.19 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › LPG_synthase_TM 0.60 51.0 3.61e-01 100.0% 74.6%
3524877 1203.1.2.1 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › ASD2 0.60 50.0 3.53e-01 93.1% 49.4%
3971690 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.60 45.0 3.79e-01 80.6% 49.6%
3808173 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.60 45.0 4.44e-01 81.9% 81.3%
4322565 632.15.1.4 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › HSP70 0.59 45.0 4.27e-01 81.9% 71.8%
3923707 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.59 50.0 4.61e-01 94.4% 81.1%
3456088 601.1.2.74 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Rx_N 0.59 44.0 3.69e-01 81.9% 68.9%
1674680 4085.1.1.1 ↗ alpha arrays › RbcX-like › RbcX-like › RbcX-like › RbcX 0.59 50.0 4.35e-01 100.0% 78.8%
4946174 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 44.0 4.11e-01 80.6% 64.4%
3725618 601.26.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › YppE-like › YppE-like 0.59 43.0 3.63e-01 80.6% 63.7%
3221571 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.59 47.0 4.04e-01 91.7% 68.8%
3937465 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.59 49.0 3.66e-01 100.0% 40.9%
3239857 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.59 46.0 4.20e-01 84.7% 73.7%
5013258 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.59 45.0 3.81e-01 84.7% 63.2%
4096686 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.58 43.0 4.16e-01 81.9% 81.2%
3277781 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.58 43.0 3.65e-01 100.0% 47.5%
3353814 529.1.1.0 ↗ few secondary structure elements › Anaphylotoxins (complement system) › Anaphylotoxins (complement system) › Anaphylotoxins (complement system) 0.58 48.0 4.53e-01 100.0% 86.3%
4318044 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.57 46.0 4.30e-01 88.9% 74.4%
3907116 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 47.0 3.73e-01 91.7% 90.7%
3721596 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.56 45.0 3.76e-01 90.3% 55.4%
3732950 601.1.2.95 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › PigL_N 0.56 45.0 3.63e-01 90.3% 55.2%
4192155 601.1.1.43 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Serendipity_A 0.55 39.0 3.28e-01 73.6% 75.0%
4025084 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.55 46.0 3.09e-01 97.2% 78.4%
3715999 3817.1.1.1 ↗ alpha bundles › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Pex19 0.54 42.0 3.86e-01 87.5% 74.0%
4020948 611.9.1.0 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain 0.53 44.0 3.79e-01 91.7% 61.7%
None — 0.53 45.0 3.05e-01 97.2% 81.8%
3585716 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.52 42.0 3.61e-01 93.1% 87.2%
5073702 633.29.1.13 ↗ alpha bundles › Bromodomain-like › Putative uncharacterized protein PAV1-137 › Putative uncharacterized protein PAV1-137 › DUF2096_N 0.52 45.0 4.13e-01 100.0% 99.0%
4593075 5059.1.1.9 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Sugar_transport 0.52 44.0 3.02e-01 97.2% 81.8%
3246869 212.1.1.0 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.52 45.0 3.17e-01 100.0% 62.5%
4194448 5068.1.1.1 ↗ alpha bundles › a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) › Cytochrom_B_C 0.52 38.0 3.40e-01 80.6% 69.1%
4121445 4177.2.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › Inhibitor of kappaB kinase beta dimerization domain › Inhibitor of kappaB kinase beta dimerization domain 0.51 37.0 2.72e-01 81.9% 60.8%
3474226 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.50 40.0 3.30e-01 88.9% 66.4%
3801706 3817.1.1.1 ↗ alpha bundles › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Peroxisomal biogenesis factor 19 › Pex19 0.50 42.0 3.59e-01 98.6% 88.4%