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MT778839.1__QNH71827.1__P9VFCI_165__00165

Bact-Vir

MT778839.1__QNH71827.1__P9VFCI_165__00165

Identity

Accession:
MT778839 ↗
Kingdom:
phage

Quality

84.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_P9VFCI

TaxID: 2763531

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 6-122
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2af0A02 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.66 36.0 4.22e-01 70.1% 76.2%
2a72A00 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.61 42.0 4.05e-01 88.0% 61.7%
7ep1B01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.60 45.0 3.55e-01 77.8% 58.3%
4l7mA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.58 41.0 3.24e-01 85.5% 33.3%
3fp3A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 41.0 3.96e-01 84.6% 75.6%
3sl9B00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.51 40.0 3.62e-01 86.3% 81.2%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.50 36.0 3.46e-01 74.4% 77.0%
4gx0A01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.50 33.0 3.53e-01 94.9% 76.7%
2jexA01 1.10.287.30 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1 0.50 34.0 3.70e-01 76.1% 85.4%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3576858 109.4.1.1145 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IQ 0.65 45.0 2.89e-01 96.6% 14.3%
3587782 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.64 33.0 3.40e-01 70.9% 52.7%
3657338 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.62 43.0 4.96e-01 73.5% 98.8%
3890937 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.61 51.0 4.09e-01 91.5% 75.0%
1283911 109.4.1.280 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PSD13_N 0.60 47.0 3.65e-01 100.0% 36.0%
3439387 109.4.1.359 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Exo70_C 0.59 44.0 3.13e-01 77.8% 43.6%
3588616 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.54 41.0 4.28e-01 96.6% 87.6%
3294846 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 43.0 3.62e-01 91.5% 79.5%
3901933 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.52 45.0 3.32e-01 95.7% 74.0%
5036323 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.51 35.0 3.68e-01 82.9% 79.0%
D2 medium residues 211-261
PDB
Domain cluster: rep: ON526839.1__URG17631.1__GRN51_150__00015__D54-100
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF22083.3 best I-HmuI_NUMOD-like 30.4 3.10e-07 84.3% 89.1%
CATH (31)
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 0.92 83.0 7.49e-01 98.0% 73.5%
3oouA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.69 48.0 4.68e-01 72.5% 70.9%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.66 46.0 4.50e-01 100.0% 66.7%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.64 52.0 4.83e-01 100.0% 79.2%
2mtzA01 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.63 45.0 4.54e-01 74.5% 94.0%
3bcwA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 42.0 3.34e-01 100.0% 33.7%
1br2A03 1.20.120.720 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain 0.61 45.0 3.65e-01 78.4% 60.0%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.60 36.0 3.32e-01 98.0% 43.9%
2i45D00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 39.0 3.20e-01 100.0% 36.4%
2yvsA01 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.58 47.0 3.58e-01 100.0% 39.5%
5c8qB02 3.10.350.10 Alpha Beta › Roll › Membrane-bound Lytic Murein Transglycosylase D; Chain A › LysM domain 0.58 44.0 4.60e-01 82.4% 100.0%
1wdiA02 2.40.10.240 Mainly Beta › Beta Barrel › Thrombin, subunit H › QueA-like 0.58 40.0 3.63e-01 74.5% 98.6%
1wi0A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 45.0 3.58e-01 90.2% 83.2%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.57 37.0 3.72e-01 100.0% 66.0%
1f39A00 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.57 47.0 3.75e-01 100.0% 46.5%
4nlcA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 44.0 2.89e-01 90.2% 56.9%
2cyjA00 3.40.1230.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Mth938; Chain: A, › MTH938-like 0.56 44.0 3.51e-01 92.2% 81.2%
1hskA01 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.56 42.0 3.19e-01 100.0% 33.1%
3waiA02 2.60.40.3390 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 44.0 3.63e-01 100.0% 48.4%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.55 44.0 3.56e-01 90.2% 86.0%
3me8B00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 45.0 3.30e-01 100.0% 62.2%
1s6lA01 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 0.53 41.0 4.10e-01 84.3% 94.2%
4wz2C00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.53 40.0 3.59e-01 96.1% 58.1%
3ewlB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 45.0 3.37e-01 100.0% 65.7%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.52 40.0 3.53e-01 100.0% 56.6%
1et9A01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 40.0 3.29e-01 92.2% 92.7%
2l6oA01 2.40.10.320 Mainly Beta › Beta Barrel › Thrombin, subunit H › Uncharacterised protein PF13642 yp_926445, N-terminal domain 0.51 40.0 3.65e-01 98.0% 63.9%
2mctA00 2.60.40.4250 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 40.0 3.28e-01 90.2% 68.6%
2iciA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.51 41.0 3.04e-01 96.1% 79.9%
4pytA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.50 40.0 3.08e-01 92.2% 49.2%
3glkA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.50 37.0 3.60e-01 100.0% 71.2%
ECOD (37)
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 0.92 83.0 7.44e-01 98.0% 72.5%
1030873 101.1.14.1 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-TevI_DNA-bd 0.76 55.0 5.15e-01 100.0% 63.5%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.76 64.0 5.48e-01 98.0% 61.2%
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.70 58.0 5.38e-01 98.0% 78.3%
3587703 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.68 55.0 5.56e-01 92.2% 92.0%
3296049 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.68 55.0 3.69e-01 96.1% 33.5%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.67 53.0 5.38e-01 92.2% 100.0%
153859 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.66 46.0 4.50e-01 100.0% 66.7%
3264763 11.2.1.50 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_GDE1 0.62 51.0 3.91e-01 98.0% 89.2%
4932732 275.1.1.0 ↗ a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase 0.59 43.0 4.24e-01 98.0% 72.7%
3805835 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.59 51.0 3.26e-01 100.0% 21.9%
1392732 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.59 46.0 3.62e-01 88.2% 80.9%
1096061 3375.1.1.1 ↗ beta barrels › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › DdrB 0.59 42.0 3.21e-01 100.0% 31.2%
3621342 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.59 48.0 4.09e-01 100.0% 74.7%
None — 0.57 43.0 2.43e-01 82.4% 14.2%
3333626 822.1.1.0 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.57 44.0 4.20e-01 100.0% 73.3%
2389420 2003.1.2.18 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.56 38.0 2.42e-01 76.5% 13.0%
3641395 226.1.1.3 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › Skp1,Skp1_POZ 0.56 42.0 3.17e-01 92.2% 30.3%
4614734 308.2.1.0 ↗ a+b two layers › ClpS-like › Penicillin binding protein ClpS-like domain › Penicillin binding protein ClpS-like domain 0.55 41.0 3.67e-01 82.4% 90.7%
3572307 4.1.1.405 ↗ beta barrels › SH3 › SH3 › SH3 › CCDC174_GRSR 0.55 32.0 3.72e-01 86.3% 93.3%
3404558 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.54 43.0 4.41e-01 100.0% 92.0%
3838348 110.2.1.0 ↗ alpha arrays › DEATH domain › Replication modulator SeqA-C › Replication modulator SeqA-C 0.53 42.0 3.38e-01 94.1% 90.4%
3972386 10.12.1.85 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_6 0.52 44.0 3.09e-01 100.0% 76.7%
3460381 376.1.1.20 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_UBOX 0.52 43.0 3.98e-01 98.0% 72.3%
3233859 226.1.1.5 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › Skp1_POZ 0.52 43.0 3.21e-01 92.2% 34.8%
3502158 221.1.1.6 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA 0.52 42.0 3.17e-01 100.0% 67.1%
None — 0.52 41.0 3.91e-01 98.0% 75.0%
3269939 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.52 41.0 3.50e-01 96.1% 52.9%
3520111 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.52 42.0 3.93e-01 98.0% 73.4%
3398736 226.1.1.5 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › Skp1_POZ 0.51 40.0 3.10e-01 94.1% 36.2%
3196947 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 37.0 2.12e-01 78.4% 9.8%
4135543 221.1.1.17 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Stap_Strp_tox_C 0.51 42.0 3.29e-01 96.1% 89.9%
4226244 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 44.0 3.43e-01 100.0% 93.9%
4485358 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.51 42.0 3.22e-01 100.0% 53.3%
3416706 376.1.1.1 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4 0.51 39.0 3.69e-01 96.1% 69.2%
3561251 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.50 42.0 3.88e-01 98.0% 71.4%
3608311 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 38.0 3.06e-01 100.0% 41.0%