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MN988519.1__QIG70836.1__EVB91_285__00265

Bact-Vir

MN988519.1__QIG70836.1__EVB91_285__00265

Identity

Accession:
MN988519 ↗
Kingdom:
phage

Quality

86.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_RHph_I1_18

TaxID: 2509726

Cluster

View cluster (6 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 3-104
PDB
Domain cluster: rep: NC_031927.1__YP_009323018.1__BOW86_gp085__00085__D3-79
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 29.3 1.20e-06 90.2% 97.4%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.85 73.0 7.66e-01 93.1% 98.9%
4gr5C01 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.77 39.0 4.84e-01 89.2% 78.1%
2pstX00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.75 38.0 4.82e-01 89.2% 82.0%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.69 36.0 4.40e-01 87.3% 78.8%
3hu1A01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.62 34.0 3.51e-01 74.5% 56.2%
2kqaA00 2.40.40.10 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › RlpA-like domain 0.61 38.0 3.61e-01 100.0% 52.5%
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 30.0 3.60e-01 74.5% 80.9%
3b5mA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 34.0 3.26e-01 84.3% 54.6%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.54 32.0 2.86e-01 74.5% 42.3%
1xvsA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.53 32.0 3.02e-01 70.6% 50.4%
6w6vE01 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.52 45.0 3.87e-01 93.1% 98.7%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 38.0 3.31e-01 78.4% 93.0%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 34.0 3.56e-01 82.4% 75.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
77927 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.87 75.0 7.79e-01 94.1% 97.9%
3496147 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.84 73.0 7.46e-01 92.2% 100.0%
3505268 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.84 76.0 6.78e-01 95.1% 86.7%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.83 55.0 5.85e-01 83.3% 76.7%
3963488 821.1.1.7 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › LEM-3_GIY-YIG 0.80 72.0 6.90e-01 100.0% 85.2%
4977431 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.69 42.0 5.08e-01 93.1% 96.9%
3595003 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.60 33.0 4.12e-01 77.5% 91.7%
3596155 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 36.0 3.49e-01 74.5% 100.0%
D2 high residues 140-193
PDB
Domain cluster: rep: BML_coassembly_scaffold_37_prodigal-single.1__X__X__00338__D232-284
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.77 67.0 6.24e-01 100.0% 79.4%
1o5uA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.71 48.0 4.08e-01 100.0% 43.2%
1iyjB03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.67 43.0 3.17e-01 96.3% 24.6%
1m2oA05 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.67 41.0 3.35e-01 96.3% 31.4%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.67 56.0 5.21e-01 98.1% 81.9%
1i9gA01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.66 57.0 5.40e-01 98.1% 93.8%
5fljA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.64 45.0 3.09e-01 100.0% 22.0%
4hltA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 44.0 3.16e-01 100.0% 25.2%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.62 45.0 3.40e-01 100.0% 32.1%
1khbA03 3.90.228.20 Alpha Beta › Alpha-Beta Complex › Phosphoenolpyruvate Carboxykinase; domain 3 › 0.61 48.0 3.02e-01 98.1% 17.3%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.60 53.0 4.17e-01 96.3% 54.1%
3q34A00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.60 49.0 3.56e-01 98.1% 93.7%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.60 50.0 4.22e-01 96.3% 80.9%
3fw6A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 42.0 3.31e-01 98.1% 35.0%
4h8wC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 45.0 4.03e-01 100.0% 62.7%
1wi0A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 42.0 3.44e-01 87.0% 96.5%
2f4nB02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.55 48.0 4.01e-01 98.1% 71.3%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.55 46.0 3.61e-01 96.3% 52.1%
3gd0A01 2.60.110.10 Mainly Beta › Sandwich › Thaumatin › Thaumatin 0.54 42.0 2.81e-01 90.7% 97.6%
1wgyA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 39.0 3.59e-01 81.5% 94.7%
5escA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 46.0 3.61e-01 98.1% 45.4%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.53 41.0 3.18e-01 87.0% 66.2%
2mctA00 2.60.40.4250 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 46.0 3.80e-01 100.0% 59.8%
1ylnA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 47.0 3.72e-01 100.0% 50.0%
7sqxA02 3.30.70.2150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 41.0 3.60e-01 96.3% 83.7%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 45.0 3.49e-01 98.1% 43.5%
1rm6A05 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.53 38.0 2.80e-01 81.5% 72.8%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 46.0 3.57e-01 98.1% 46.2%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.53 45.0 3.75e-01 96.3% 56.2%
3h8hA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 43.0 3.73e-01 98.1% 69.6%
1rfeA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 43.0 3.27e-01 98.1% 38.2%
3waiA02 2.60.40.3390 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 46.0 3.83e-01 100.0% 65.6%
1qr4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 44.0 3.77e-01 100.0% 59.8%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.51 41.0 3.75e-01 98.1% 64.5%
1mkiA01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 45.0 3.17e-01 100.0% 76.7%
7sz2A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.51 41.0 3.60e-01 98.1% 81.5%
6gh3A01 2.70.98.40 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Glycoside hydrolase, family 65, N-terminal domain 0.51 41.0 2.67e-01 100.0% 36.7%
4zciA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 45.0 3.67e-01 100.0% 59.4%
3agdA01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 44.0 2.78e-01 100.0% 86.7%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.51 44.0 3.58e-01 100.0% 62.5%
5eh1A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 45.0 3.73e-01 100.0% 60.0%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.77 67.0 6.21e-01 100.0% 78.3%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.74 62.0 5.46e-01 98.1% 67.1%
3716841 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.67 41.0 3.13e-01 96.3% 25.4%
3264763 11.2.1.50 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_GDE1 0.65 52.0 4.09e-01 94.4% 93.8%
4931715 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.65 46.0 3.74e-01 79.6% 79.1%
3621342 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.64 54.0 4.57e-01 98.1% 80.0%
3805835 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.61 54.0 3.47e-01 100.0% 27.9%
4075554 3019.1.1.0 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain 0.61 50.0 4.00e-01 98.1% 65.8%
3592956 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 51.0 4.70e-01 100.0% 81.3%
3957598 2004.1.2.1 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › PEP carboxykinase catalytic C-terminal domain › PEPCK_GTP 0.60 48.0 3.08e-01 98.1% 20.0%
3615194 73.1.1.0 ↗ beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain 0.60 50.0 3.85e-01 98.1% 97.0%
3214460 10.4.1.9 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain › CUB_2 0.60 44.0 3.41e-01 100.0% 35.8%
3427385 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.58 41.0 3.73e-01 100.0% 54.7%
5064213 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.58 47.0 2.94e-01 94.4% 76.7%
5053244 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.57 38.0 3.17e-01 98.1% 37.0%
2028252 3986.2.1.1 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd › Dmd 0.57 46.0 4.36e-01 100.0% 75.0%
5018490 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.56 41.0 3.24e-01 79.6% 74.4%
5042888 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.56 48.0 2.78e-01 98.1% 23.7%
1392732 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.56 41.0 3.37e-01 83.3% 80.9%
3260724 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.56 46.0 3.32e-01 96.3% 34.5%
3783835 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.55 46.0 2.95e-01 98.1% 18.9%
3569553 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 42.0 3.72e-01 90.7% 84.4%
3388281 3019.1.1.0 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain 0.55 46.0 3.38e-01 100.0% 62.9%
5082591 314.1.1.0 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases 0.55 43.0 2.72e-01 94.4% 74.4%
5079217 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 49.0 3.90e-01 100.0% 55.2%
1933293 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 46.0 3.80e-01 98.1% 52.5%
4941557 2487.1.1.5 ↗ a/b three-layered sandwiches › "The ""swivelling"" beta/beta/alpha domains" › "The ""swivelling"" beta/beta/alpha domain" › "The ""swivelling"" beta/beta/alpha domain" › CPSase_sm_chain 0.53 44.0 3.27e-01 96.3% 87.1%
3414820 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 45.0 3.63e-01 100.0% 48.6%
3727369 4139.1.1.1 ↗ a+b two layers › AMMECR1-like › AMMECR1-like › AMMECR1-like › AMMECR1 0.53 45.0 4.23e-01 100.0% 80.0%
5018864 11.1.1.895 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF29538 0.53 48.0 3.73e-01 100.0% 60.9%
136189 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.52 46.0 3.37e-01 100.0% 38.1%
4976909 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 46.0 3.80e-01 100.0% 63.2%
5037563 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 44.0 3.62e-01 100.0% 52.0%
3904587 11.1.1.1087 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GBD_Hemicentin 0.51 45.0 3.02e-01 100.0% 26.2%
4585632 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 45.0 3.63e-01 98.1% 53.0%