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MN988556.1__QIG76677.1__EVC28_053__00053

Bact-Vir

MN988556.1__QIG76677.1__EVC28_053__00053

Identity

Accession:
MN988556 ↗
Kingdom:
phage

Quality

92.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_I1_23

TaxID: 2509727

Cluster

View cluster (7 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 2-91
PDB
Domain cluster: rep: NC_027299.1__YP_009146220.1__SUFP_046__00046__D4-101
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF10544.16 best T5orf172 30.3 6.90e-07 91.1% 89.8%
PF13455.13 MUG113 32.9 1.10e-07 73.3% 89.0%
D2 high residues 111-178
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h3mA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.75 50.0 4.55e-01 72.1% 52.8%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.72 49.0 3.98e-01 70.6% 44.8%
2wyhB04 1.20.1270.50 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Glycoside hydrolase family 38, central domain 0.72 64.0 5.61e-01 100.0% 80.2%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.72 49.0 4.22e-01 70.6% 59.8%
1o3uA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.69 61.0 5.07e-01 100.0% 78.3%
1gnlA01 1.20.1270.20 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.69 60.0 4.80e-01 100.0% 49.6%
2ozbB01 1.10.287.4070 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 47.0 3.81e-01 72.1% 84.0%
5ha6B00 1.10.287.210 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 47.0 4.47e-01 72.1% 73.4%
6vddA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.66 46.0 3.83e-01 72.1% 84.3%
1td6A03 1.10.472.40 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Hypothetical protein mg237 homolog; domain 3 0.65 50.0 4.61e-01 95.6% 63.0%
1wncB00 1.20.5.300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.65 45.0 4.26e-01 72.1% 86.4%
5z5mA01 1.10.3330.10 Mainly Alpha › Orthogonal Bundle › UraD-like › Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase 0.64 42.0 3.32e-01 97.1% 30.9%
4hz4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 44.0 3.73e-01 72.1% 51.8%
1dxrL02 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.63 43.0 3.68e-01 70.6% 51.9%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 42.0 4.04e-01 70.6% 73.8%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.62 43.0 4.49e-01 72.1% 83.9%
3ckdA02 1.20.58.360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Shigella T3SS effector IpaH defines 0.62 47.0 3.95e-01 85.3% 62.9%
3bg2A03 1.10.3410.10 Mainly Alpha › Orthogonal Bundle › putative deoxyguanosinetriphosphate triphosphohydrolase fold › putative deoxyguanosinetriphosphate triphosphohydrolase like domain 0.61 52.0 4.73e-01 100.0% 95.8%
2etdA00 1.20.1440.20 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › LemA-like domain 0.60 50.0 4.13e-01 100.0% 53.2%
3cxbA03 1.10.1740.30 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › Secreted effector protein SifA helical domain 0.60 51.0 4.86e-01 97.1% 79.0%
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.57 47.0 4.82e-01 100.0% 98.5%
5afdA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 44.0 3.01e-01 94.1% 95.3%
2ah5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.55 38.0 3.88e-01 98.5% 75.4%
3e9lA02 1.20.80.40 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › Prp8 RNase H domain, fingers region 0.54 44.0 4.04e-01 100.0% 68.4%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.52 46.0 3.85e-01 100.0% 56.9%
3iieB03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.52 45.0 4.17e-01 95.6% 78.8%
4neoA00 1.10.1200.10 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › ACP-like 0.52 46.0 4.30e-01 94.1% 94.0%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.51 44.0 3.89e-01 100.0% 81.6%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.51 44.0 3.99e-01 95.6% 79.1%
3nvoB02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.51 46.0 3.82e-01 98.5% 79.3%
2oikA00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.51 45.0 3.58e-01 100.0% 79.1%
3rcyB01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 34.0 2.80e-01 72.1% 77.3%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5029782 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.78 71.0 6.42e-01 100.0% 94.4%
5031855 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.75 69.0 6.49e-01 100.0% 90.0%
4959289 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.74 50.0 4.46e-01 70.6% 100.0%
3716758 206.1.1.11 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH 0.74 66.0 3.99e-01 100.0% 43.0%
3725619 2004.1.1.366 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NPHP3_N 0.73 65.0 4.20e-01 100.0% 23.2%
5054405 606.1.1.1 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.73 50.0 4.37e-01 72.1% 97.0%
5069997 606.1.1.1 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.71 48.0 4.17e-01 70.6% 89.5%
4010416 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.71 49.0 3.96e-01 72.1% 93.6%
4339359 4044.1.1.1 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.70 62.0 5.03e-01 100.0% 56.2%
3944006 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 49.0 3.92e-01 72.1% 80.0%
3009331 4044.1.1.1 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.70 61.0 5.74e-01 100.0% 85.5%
55361 4044.1.1.1 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Prismane 0.69 60.0 5.15e-01 100.0% 61.3%
5076440 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 0.68 60.0 5.32e-01 100.0% 83.0%
3386925 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.68 58.0 4.70e-01 100.0% 82.9%
3615262 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 45.0 2.90e-01 70.6% 26.3%
3483300 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.66 58.0 4.09e-01 100.0% 90.5%
3731997 3831.1.1.0 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 0.66 59.0 4.81e-01 100.0% 91.2%
3170621 3755.3.1.305 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Rad50_zn_hook 0.65 44.0 3.88e-01 72.1% 79.0%
3990099 2007.5.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase 0.64 47.0 3.34e-01 88.2% 25.7%
3616267 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.64 54.0 4.05e-01 94.1% 81.8%
4346887 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.63 43.0 4.20e-01 70.6% 72.0%
3842608 1128.1.1.2 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR_2 0.63 51.0 4.61e-01 94.1% 68.0%
2970331 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.63 51.0 3.85e-01 92.6% 77.3%
3333792 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.61 50.0 3.80e-01 94.1% 82.3%
3225449 621.1.1.0 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain 0.59 41.0 3.99e-01 72.1% 65.3%
3572526 386.1.1.377 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › DUF4662 0.59 35.0 3.82e-01 83.8% 72.7%
3993742 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.58 38.0 2.99e-01 97.1% 33.3%
4994067 5054.1.1.8 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 0.58 44.0 3.85e-01 80.9% 78.0%
4997208 2004.1.1.146 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.58 51.0 3.33e-01 100.0% 24.1%
5011442 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.57 46.0 4.60e-01 95.6% 88.6%
5065130 633.12.1.0 ↗ alpha bundles › Bromodomain-like › Ta0600-like › Ta0600-like 0.55 48.0 4.51e-01 100.0% 81.2%
4957980 2484.1.1.341 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Salactin 0.55 43.0 3.16e-01 83.8% 42.8%
4361196 102.1.3.8 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › Mab-21_C 0.55 45.0 4.05e-01 91.2% 71.6%
3580212 4970.1.1.2 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_A 0.52 45.0 3.92e-01 89.7% 89.5%
5012274 2004.1.1.233 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Cas3-like_C_2 0.51 44.0 2.73e-01 100.0% 22.2%
1346260 604.28.1.1 ↗ alpha bundles › Spectrin repeat-like › E3 ubiquitin-protein ligase SHPRH second helical domain › E3 ubiquitin-protein ligase SHPRH second helical domain › SHPRH_helical-2nd 0.50 42.0 3.37e-01 95.6% 95.9%