Back to structures

SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00290

Bact-Vir

SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00290

Identity

Kingdom:
phage

Quality

95.9 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 115-220
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14301.13 best DUF4376 58.9 9.00e-16 98.1% 87.7%
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 54.0 5.64e-01 93.4% 95.7%
3nuiA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.67 39.0 3.52e-01 80.2% 42.5%
4dveA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.66 41.0 3.38e-01 91.5% 34.4%
1egdA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.65 45.0 4.10e-01 96.2% 53.2%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 57.0 5.34e-01 97.2% 86.5%
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 56.0 5.65e-01 97.2% 94.3%
2zxeA02 1.20.1110.10 Mainly Alpha › Up-down Bundle › Calcium-transporting ATPase, transmembrane domain › Calcium-transporting ATPase, transmembrane domain 0.64 57.0 3.85e-01 99.1% 38.0%
1f02T00 4.10.820.10 Few Secondary Structures › Irregular › Translocated Intimin Receptor; Chain T › Translocated intimin receptor, central domain 0.63 39.0 4.79e-01 95.3% 100.0%
4kc9A02 1.20.120.1750 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.63 45.0 3.52e-01 86.8% 35.7%
1s7hA01 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 34.0 3.82e-01 75.5% 68.8%
5aexJ00 1.10.3430.10 Mainly Alpha › Orthogonal Bundle › Ammonium transporter fold › Ammonium transporter AmtB like domains 0.63 56.0 3.70e-01 98.1% 61.4%
3p4tA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.63 44.0 3.90e-01 89.6% 50.7%
1js3A03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.61 35.0 3.72e-01 72.6% 62.9%
3vbbE01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.61 55.0 5.26e-01 97.2% 99.2%
7wu7501 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 52.0 4.98e-01 97.2% 95.2%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.60 35.0 3.68e-01 73.6% 63.3%
2fji101 1.10.357.50 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.59 47.0 3.78e-01 97.2% 43.5%
1d8cA03 1.20.1220.12 Mainly Alpha › Up-down Bundle › Malate Synthase G; Chain: A; Domain 4 › Malate synthase, domain III 0.58 36.0 3.31e-01 75.5% 47.4%
1hciA03 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 43.0 4.15e-01 92.5% 70.8%
3pe0A01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 38.0 3.94e-01 94.3% 72.3%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.56 48.0 4.31e-01 92.5% 82.2%
5ziyA01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.54 48.0 3.90e-01 97.2% 94.8%
4pxeA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 43.0 4.22e-01 86.8% 78.6%
4oloB00 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.53 30.0 3.25e-01 83.0% 65.5%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.53 45.0 3.35e-01 94.3% 38.0%
8i3jA01 1.20.920.20 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.53 46.0 3.53e-01 98.1% 99.6%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.52 40.0 3.30e-01 90.6% 42.4%
2ce7B03 1.20.58.760 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Peptidase M41 0.52 47.0 4.01e-01 99.1% 93.5%
3ja8601 3.30.1640.10 Alpha Beta › 2-Layer Sandwich › mini-chromosome maintenance (MCM) complex, chain A, domain 1 › mini-chromosome maintenance (MCM) complex, chain A, domain 1 0.52 34.0 3.47e-01 88.7% 67.6%
5mmiG01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.52 34.0 3.78e-01 86.8% 84.5%
4i0wB01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.51 39.0 2.75e-01 80.2% 80.4%
2ixtA00 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.51 35.0 2.58e-01 71.7% 80.6%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3979390 192.2.1.5 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF4376 0.90 86.0 8.03e-01 100.0% 88.0%
3985490 192.2.1.5 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › DUF4376 0.83 78.0 7.36e-01 100.0% 91.9%
3775826 4016.1.1.0 alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase 0.76 46.0 4.13e-01 95.3% 44.8%
3538512 3892.1.1.0 alpha bundles › Transhydrogeanse domain II › Transhydrogeanse domain II › Transhydrogeanse domain II 0.74 46.0 3.94e-01 94.3% 41.2%
3394225 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.72 57.0 5.63e-01 97.2% 78.3%
4463557 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.71 58.0 6.05e-01 96.2% 96.8%
5081618 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.70 54.0 5.19e-01 97.2% 70.8%
3783976 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.70 56.0 5.97e-01 90.6% 100.0%
4027679 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.68 53.0 5.40e-01 94.3% 84.8%
3229643 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.68 55.0 5.35e-01 97.2% 78.3%
139279 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.68 54.0 5.64e-01 93.4% 95.7%
3630462 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 54.0 4.91e-01 95.3% 65.0%
5060418 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 55.0 5.27e-01 97.2% 77.5%
3931606 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 56.0 5.49e-01 97.2% 83.5%
3493963 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.67 54.0 5.56e-01 98.1% 91.0%
4410759 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 58.0 5.71e-01 97.2% 87.8%
3785619 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 55.0 5.44e-01 98.1% 83.5%
3538408 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.67 55.0 5.77e-01 97.2% 100.0%
3771989 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.66 57.0 5.26e-01 95.3% 73.3%
3244401 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.65 55.0 5.40e-01 97.2% 84.3%
3933404 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.65 55.0 4.89e-01 97.2% 64.0%
3927319 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.65 55.0 5.72e-01 91.5% 99.0%
4025072 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.64 55.0 5.37e-01 96.2% 86.1%
3718200 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.64 54.0 5.19e-01 97.2% 79.2%
3974474 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.63 41.0 4.37e-01 84.0% 76.7%
5000789 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.62 51.0 5.20e-01 97.2% 91.4%
4441223 4018.1.1.2 a+b two layers › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › a+b domain in carbohydrate phosphatases › Inositol_P 0.61 37.0 3.29e-01 92.5% 42.7%
4033043 616.1.1.41 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.61 41.0 4.40e-01 83.0% 80.0%
4965179 5040.1.1.0 extended segments › Cytochrome c oxidase subunit II-like, transmembrane region › Cytochrome c oxidase subunit II-like, transmembrane region › Cytochrome c oxidase subunit II-like, transmembrane region 0.59 39.0 4.52e-01 97.2% 96.0%
3669260 192.2.1.35 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Hobbit 0.59 45.0 4.93e-01 95.3% 100.0%
3532393 5050.1.1.6 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › OATP 0.59 48.0 3.48e-01 87.7% 82.3%
2409293 601.51.1.1 alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N 0.59 49.0 3.98e-01 89.6% 100.0%
3920955 5050.1.1.6 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › OATP 0.58 50.0 3.84e-01 94.3% 92.2%
3876425 5050.1.1.6 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › OATP 0.57 49.0 3.63e-01 93.4% 88.9%
3709367 633.6.1.0 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.56 40.0 3.20e-01 84.9% 36.7%
3789167 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 0.55 44.0 3.40e-01 85.8% 62.1%
3873955 7016.1.1.0 extended segments › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain 0.55 45.0 3.99e-01 92.5% 61.3%
3722440 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 0.55 47.0 3.47e-01 93.4% 90.5%
3593102 1016.1.1.0 alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 0.55 38.0 3.63e-01 72.6% 75.4%
4116357 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 0.54 49.0 4.01e-01 98.1% 68.9%
4632513 5045.1.1.1 alpha bundles › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › F1F0 ATP synthase subunit A › ATP-synt_A 0.54 48.0 3.67e-01 97.2% 61.6%
3321176 5051.1.1.6 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Aa_trans 0.54 46.0 3.14e-01 96.2% 77.3%
3929085 109.4.1.87 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec6 0.54 47.0 2.86e-01 96.2% 16.9%
5027632 5104.1.1.1 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › DHHA1 0.54 27.0 2.64e-01 77.4% 39.2%
3985268 5085.1.1.1 a+b duplicates or obligate multimers › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) › OEP 0.52 46.0 3.48e-01 97.2% 65.9%
3283276 2484.1.1.1 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.52 46.0 3.84e-01 97.2% 56.8%
3530824 101.1.2.267 alpha arrays › HTH › HTH › winged helix domain › Nse4_C 0.52 24.0 2.77e-01 94.3% 53.8%
3304698 320.4.1.0 a+b two layers › R3H domain-like › PUB domain › PUB domain 0.52 40.0 3.79e-01 83.0% 77.7%
3378382 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 40.0 3.69e-01 83.0% 72.1%
5001040 2499.1.1.1 a/b three-layered sandwiches › Subtilisin-like › Subtilisin-like › Subtilisin-like › Peptidase_S8 0.52 40.0 2.85e-01 81.1% 82.0%
4025011 650.1.1.0 alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.51 38.0 3.68e-01 77.4% 68.3%
5020806 3646.1.1.1 alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › CbiQ 0.51 44.0 3.34e-01 93.4% 85.9%
3529791 601.1.3.1 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › A middle domain of Talin 1 › Talin_middle 0.51 39.0 3.33e-01 100.0% 50.0%
3373766 7.1.1.7 beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ_3 0.50 35.0 3.17e-01 71.7% 92.0%
3717247 4106.1.1.1 few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.50 42.0 3.28e-01 89.6% 46.4%
D2 medium residues 2-64
PDB
D3 medium residues 71-113
PDB
Domain cluster: representative
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3253917 389.1.1.0 few secondary structure elements › EGF-like › EGF-related › EGF/Laminin 0.67 43.0 4.44e-01 100.0% 70.0%
3397119 389.1.1.50 few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › EGF_PEAR1L 0.58 35.0 3.75e-01 100.0% 65.7%
3938491 394.1.1.0 few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins 0.55 41.0 4.13e-01 95.3% 83.7%
4327466 394.1.1.1 few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.53 44.0 4.22e-01 95.3% 86.0%
3515835 394.1.1.1 few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14 0.50 38.0 3.83e-01 95.3% 84.4%