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SR-VP_4-6_scaffold_141_2201553_prodigal-single.1__X__X__00261

Bact-Vir

SR-VP_4-6_scaffold_141_2201553_prodigal-single.1__X__X__00261

Identity

Kingdom:
phage

Quality

89.7 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 3-146
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gmuA01 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.70 31.0 4.38e-01 75.7% 88.1%
2jsxA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.70 35.0 4.72e-01 75.0% 95.8%
1earA02 3.30.70.790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › UreE, C-terminal domain 0.67 30.0 4.15e-01 75.7% 85.5%
2cg4A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.67 35.0 4.35e-01 75.0% 83.3%
3afgB01 3.30.70.80 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptidase S8 propeptide/proteinase inhibitor I9 0.66 33.0 4.12e-01 75.7% 77.0%
2dbbA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.66 35.0 4.16e-01 75.0% 76.3%
1nm2A01 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.65 30.0 4.05e-01 75.7% 88.2%
1lq9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 41.0 4.57e-01 75.7% 81.2%
2cveA02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 31.0 4.20e-01 73.6% 97.0%
3n79A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.63 33.0 4.18e-01 75.0% 89.7%
6lxgA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 33.0 4.42e-01 74.3% 100.0%
2mq8A00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.62 40.0 4.40e-01 75.7% 82.1%
2op5B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 40.0 4.63e-01 75.0% 93.0%
2kjwA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.61 35.0 4.11e-01 75.7% 81.2%
2l3mA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 30.0 3.98e-01 73.6% 91.5%
2jpiA00 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.60 38.0 4.48e-01 77.1% 94.8%
1d5aA01 3.30.342.10 Alpha Beta › 2-Layer Sandwich › DNA Polymerase; Chain A, domain 1 › DNA Polymerase, chain B, domain 1 0.59 34.0 3.38e-01 76.4% 52.3%
1rzmA01 3.30.70.1140 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 0.59 32.0 4.10e-01 75.0% 93.8%
3bb5A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 39.0 4.44e-01 75.0% 93.2%
2jdjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 37.0 4.21e-01 75.7% 86.5%
3d68A01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.58 30.0 3.58e-01 75.7% 75.0%
1kwmA01 3.30.70.340 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Metallocarboxypeptidase-like 0.57 30.0 3.68e-01 77.1% 79.5%
4tqrA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.56 36.0 4.22e-01 93.1% 95.9%
3p3dA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 33.0 3.93e-01 77.8% 95.4%
3pm9A03 3.30.70.2190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 36.0 3.89e-01 76.4% 81.8%
6lpnA03 3.30.70.2190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 37.0 4.15e-01 76.4% 91.2%
1qltA03 3.40.462.10 Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › FAD-linked oxidases, C-terminal domain 0.53 39.0 3.35e-01 77.8% 48.9%
4hvmB01 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.52 39.0 3.58e-01 77.1% 81.4%
2cpiA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 30.0 3.67e-01 75.0% 100.0%
2cq4A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 30.0 3.45e-01 77.8% 83.5%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3651398 304.4.1.65 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › HMA 0.75 35.0 5.00e-01 75.0% 96.9%
4979734 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.71 36.0 4.47e-01 75.0% 80.0%
5050539 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.71 34.0 4.72e-01 75.7% 94.3%
4946857 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.69 32.0 4.12e-01 75.7% 74.1%
4979746 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.69 37.0 4.36e-01 75.0% 74.0%
5000232 304.7.1.0 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.69 33.0 4.45e-01 76.4% 86.7%
5036361 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.69 35.0 4.57e-01 75.0% 91.9%
5063368 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.68 30.0 4.45e-01 74.3% 98.3%
4979725 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.68 37.0 4.49e-01 75.7% 82.2%
4065299 304.162.1.1 ↗ a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH 0.68 36.0 4.80e-01 77.8% 98.7%
4942010 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 35.0 4.29e-01 75.0% 78.9%
3279154 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 34.0 4.06e-01 75.7% 70.0%
3517655 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.67 35.0 4.25e-01 75.0% 77.8%
4954322 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.67 33.0 4.52e-01 75.0% 95.7%
5027483 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.67 34.0 4.22e-01 75.7% 77.8%
4963354 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.66 34.0 4.02e-01 75.7% 71.6%
4644410 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.66 34.0 4.00e-01 75.0% 71.6%
3290613 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.66 34.0 4.16e-01 75.7% 77.8%
3423904 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.66 33.0 4.04e-01 75.7% 74.4%
5061378 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.66 33.0 4.46e-01 75.7% 97.1%
4060463 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.65 35.0 4.14e-01 75.7% 77.4%
160731 304.4.1.1 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.65 33.0 4.33e-01 75.0% 92.0%
3284313 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.65 33.0 4.35e-01 75.7% 92.0%
3924882 304.7.1.1 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Propep_M14 0.64 38.0 4.33e-01 75.7% 79.0%
5077608 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 35.0 4.23e-01 75.0% 82.2%
1318645 304.4.1.20 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg2 0.64 34.0 3.92e-01 75.0% 69.9%
4979741 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.64 36.0 4.20e-01 76.4% 78.0%
5041306 304.114.1.0 ↗ a+b two layers › Alpha-beta plaits › Family B DNA polymerase insertion domain › Family B DNA polymerase insertion domain 0.64 36.0 4.64e-01 91.7% 98.8%
4078055 304.7.1.2 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Inhibitor_I9 0.64 37.0 4.28e-01 76.4% 80.0%
3270398 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.63 36.0 4.32e-01 75.0% 87.6%
4986330 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 33.0 3.98e-01 75.7% 77.8%
4272341 304.7.1.2 ↗ a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Inhibitor_I9 0.63 33.0 4.45e-01 76.4% 97.3%
5035126 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.63 30.0 4.07e-01 73.6% 95.4%
5028585 304.16.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF-1beta-like › eEF-1beta-like › EF1_GNE 0.62 35.0 4.30e-01 75.7% 90.6%
5047466 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.62 34.0 4.23e-01 75.0% 88.2%
4311079 304.4.1.20 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg2 0.62 33.0 3.93e-01 75.7% 74.7%
3927357 304.6.1.1 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.61 39.0 3.44e-01 92.4% 42.4%
5011049 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.61 30.0 4.07e-01 75.0% 98.5%
166322 304.4.1.14 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Dabb 0.59 39.0 4.45e-01 75.0% 94.1%
3784456 331.2.1.0 ↗ a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain 0.57 41.0 4.23e-01 74.3% 97.1%
3279061 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.56 29.0 3.71e-01 75.7% 94.3%
3969033 304.6.1.1 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.55 44.0 3.68e-01 93.1% 49.4%
4585125 304.12.1.1 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S6 › Ribosomal protein S6 › Ribosomal_S6 0.55 34.0 3.96e-01 75.0% 88.0%
3724439 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.54 33.0 3.80e-01 72.9% 81.9%
3974758 304.6.1.1 ↗ a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.53 43.0 3.58e-01 91.7% 50.6%
None — 0.51 39.0 3.72e-01 80.6% 81.2%
D2 medium residues 147-227
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4uavA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.64 38.0 3.75e-01 93.8% 55.3%
4gmqA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.61 40.0 3.85e-01 72.8% 58.7%
1dqeA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.61 48.0 4.00e-01 84.0% 71.5%
1bgcA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.57 40.0 3.25e-01 72.8% 54.4%
1c02A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.56 39.0 3.15e-01 72.8% 47.6%
2imsA00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.55 39.0 3.19e-01 75.3% 93.3%
3u4qA02 1.10.274.50 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › 0.55 36.0 2.98e-01 98.8% 36.7%
4dvyP01 1.10.357.130 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.53 38.0 2.93e-01 75.3% 42.6%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.51 34.0 3.10e-01 91.4% 47.9%
4qhpA05 1.25.50.10 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › Peptidase M1, alanyl aminopeptidase, C-terminal domain 0.51 41.0 2.71e-01 87.7% 42.8%
4tpjA00 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.50 40.0 2.56e-01 88.9% 29.2%
2ehgA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.50 36.0 3.00e-01 76.5% 72.5%
1tujA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.50 36.0 3.26e-01 79.0% 67.5%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3959203 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.70 40.0 3.71e-01 86.4% 46.0%
3468141 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.66 46.0 3.55e-01 72.8% 42.7%
3475514 605.1.1.95 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › TADA2A-like_3rd 0.64 35.0 3.65e-01 96.3% 57.3%
3189488 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.60 35.0 3.21e-01 90.1% 42.7%
3827764 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 49.0 3.42e-01 92.6% 58.2%
4652188 171.1.1.1 ↗ alpha arrays › RNase III catalytic domain-like › RNase III catalytic domain-like › RNase III catalytic domain-like › Ribonuclease_3 0.59 48.0 3.98e-01 88.9% 54.5%
3671050 6155.1.1.5 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › ER_lumen_recept 0.59 45.0 3.49e-01 80.2% 85.3%
4085430 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.59 37.0 3.02e-01 100.0% 31.5%
3741923 109.4.1.335 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SEN1_N 0.58 44.0 3.33e-01 80.2% 93.2%
4368947 141.1.1.6 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › HEPPP_synt_1 0.58 40.0 2.85e-01 71.6% 34.4%
4015044 6155.1.1.0 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.56 43.0 3.20e-01 81.5% 68.3%
3694231 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.54 44.0 2.82e-01 92.6% 41.6%
4888660 5067.1.1.1 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › ACR_tran 0.53 47.0 3.34e-01 100.0% 56.5%