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NC_025429.1__YP_009099990.1__P10VF_251__00251

Bact-Vir

NC_025429.1__YP_009099990.1__P10VF_251__00251

Identity

Accession:
NC_025429 ↗
Kingdom:
phage

Quality

80.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_vB_RleM_P10VF

TaxID: 1527770

Cluster

View cluster (3 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 2-71
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.67 50.0 4.77e-01 100.0% 68.3%
5mghA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.63 55.0 3.60e-01 98.6% 44.6%
3e1eC00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.63 43.0 3.41e-01 100.0% 35.5%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 45.0 3.51e-01 82.9% 95.2%
3cueB00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.60 48.0 3.75e-01 91.4% 78.4%
1sz7A00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.59 47.0 3.69e-01 90.0% 88.7%
4mveA00 2.40.128.580 Mainly Beta › Beta Barrel › Lipocalin › GXWXG domain 0.59 50.0 4.05e-01 100.0% 72.1%
7xr9E01 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.59 41.0 3.09e-01 75.7% 88.8%
1mu5A01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.58 41.0 3.01e-01 75.7% 71.9%
1w4tA02 2.40.128.150 Mainly Beta › Beta Barrel › Lipocalin › Cysteine proteinases 0.58 50.0 4.53e-01 100.0% 90.9%
3nuhB03 3.10.20.690 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.58 47.0 4.44e-01 92.9% 89.9%
3zi1A02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.57 39.0 3.18e-01 94.3% 34.5%
2ci8A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 39.0 4.30e-01 71.4% 98.2%
3l4gC04 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.56 46.0 3.18e-01 95.7% 40.1%
1c8uA02 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.56 39.0 3.35e-01 100.0% 45.2%
3nixB00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 45.0 2.90e-01 95.7% 83.2%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.55 48.0 4.86e-01 97.1% 100.0%
3qszA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 44.0 3.43e-01 95.7% 65.5%
3d8dA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 45.0 3.78e-01 100.0% 81.3%
3eeeA00 3.90.1520.10 Alpha Beta › Alpha-Beta Complex › H-NOX domain › H-NOX domain 0.54 43.0 3.28e-01 91.4% 67.6%
3us4A00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.54 38.0 3.37e-01 71.4% 61.9%
1azpA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 34.0 3.50e-01 97.1% 66.7%
2i6vA00 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.53 38.0 3.55e-01 75.7% 100.0%
3h6qA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.53 44.0 3.48e-01 100.0% 93.5%
1o9yC00 2.30.330.10 Mainly Beta › Roll › Surface presentation of antigens (SPOA) › SpoA-like 0.53 30.0 3.00e-01 71.4% 50.0%
3tfzB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 40.0 3.25e-01 90.0% 57.0%
2ffsA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 42.0 3.37e-01 90.0% 67.6%
1wzvA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.52 38.0 3.08e-01 100.0% 38.0%
4xrtA02 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.52 41.0 3.24e-01 90.0% 60.0%
1mknA00 2.20.60.10 Mainly Beta › Single Sheet › Heparin-binding Growth Factor, Midkine; Chain A › Pleiotrophin/Midkine, N-terminal domain 0.52 32.0 3.41e-01 95.7% 72.9%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.52 38.0 3.57e-01 82.9% 97.8%
2h2yA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.51 37.0 3.24e-01 100.0% 48.3%
2gsbA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.51 36.0 3.40e-01 74.3% 77.4%
1k32A01 2.120.10.60 Mainly Beta › 6 Propeller › Neuraminidase › Tricorn protease N-terminal domain 0.51 41.0 2.90e-01 95.7% 76.5%
3fehA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 43.0 3.67e-01 100.0% 62.9%
2it1A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 32.0 3.38e-01 92.9% 75.4%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 42.0 3.65e-01 100.0% 62.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4032324 219.1.1.6 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Acetyltransf_2 0.70 62.0 4.21e-01 100.0% 35.8%
3635675 2008.1.1.144 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF27653 0.70 45.0 3.22e-01 74.3% 22.4%
3691227 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.67 46.0 4.00e-01 74.3% 45.2%
4178727 314.1.1.11 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA_synthFbeta 0.62 53.0 3.78e-01 98.6% 55.1%
3966067 219.1.1.6 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Acetyltransf_2 0.61 52.0 3.56e-01 100.0% 32.3%
3964724 3675.1.1.1 ↗ a+b complex topology › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › DNA gyrase subunit B insertion domain › GyrB_insert 0.60 47.0 3.77e-01 90.0% 51.0%
3592742 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 41.0 3.80e-01 71.4% 70.0%
4945021 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.59 50.0 4.40e-01 100.0% 69.1%
4269457 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.57 44.0 3.65e-01 85.7% 72.4%
3286312 642.1.1.1 ↗ a+b three layers › Suppressor of Fused, N-terminal domain › Suppressor of Fused, N-terminal domain › Suppressor of Fused, N-terminal domain › SUFU 0.57 40.0 3.05e-01 75.7% 53.2%
4972821 523.1.1.3 ↗ a+b two layers › Ribosomal protein L9 C-domain › Ribosomal protein L9 C-domain › Ribosomal protein L9 C-domain › PF29994 0.57 45.0 3.90e-01 91.4% 74.2%
4026812 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.56 45.0 3.52e-01 90.0% 58.7%
3630575 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.56 38.0 2.61e-01 70.0% 44.5%
3497120 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 40.0 3.67e-01 78.6% 55.8%
3578188 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 46.0 3.49e-01 100.0% 38.5%
4948719 101.1.2.28 ↗ alpha arrays › HTH › HTH › winged helix domain › eIF-5_eIF-2B 0.55 33.0 2.96e-01 81.4% 41.0%
3619070 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.54 42.0 3.37e-01 90.0% 57.0%
3495619 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.54 43.0 3.80e-01 100.0% 57.3%
5066760 330.6.1.1 ↗ a+b two layers › dsRBD-like › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain › LeuA_dimer 0.54 41.0 3.56e-01 87.1% 79.0%
1679996 11.2.1.5 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › IcmF_C 0.54 47.0 4.12e-01 100.0% 96.4%
3883097 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.54 40.0 4.00e-01 78.6% 90.0%
None — 0.54 43.0 3.02e-01 91.4% 92.5%
3420881 5.1.3.252 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › PF27637 0.54 28.0 3.47e-01 88.6% 97.1%
3789706 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.54 42.0 3.30e-01 90.0% 55.3%
3591998 220.1.1.11 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rpn13_ADRM1_Pru 0.54 47.0 4.07e-01 100.0% 73.6%
4026643 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 39.0 3.71e-01 80.0% 67.1%
4988770 2006.1.3.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain 0.53 37.0 2.87e-01 91.4% 29.7%
3960039 2003.1.5.151 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23, Methyltransf_25 0.53 44.0 3.05e-01 92.9% 73.9%
3918879 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 46.0 3.65e-01 100.0% 49.3%
3633647 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.53 34.0 3.49e-01 98.6% 69.2%
3169943 719.1.1.7 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › PF30203 0.53 45.0 3.66e-01 100.0% 54.5%
3591940 223.2.1.19 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Intu_longin_1 0.53 40.0 3.08e-01 87.1% 72.1%
3744190 220.1.1.43 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SIN1_PH 0.53 43.0 3.79e-01 100.0% 66.7%
3549045 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.53 39.0 3.46e-01 82.9% 59.1%
5042846 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.52 44.0 2.81e-01 98.6% 82.0%
4018808 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.52 45.0 3.86e-01 100.0% 60.0%
3798262 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 44.0 3.55e-01 100.0% 57.3%
4407599 227.1.1.3 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › DNA_pol3_beta 0.52 39.0 3.22e-01 100.0% 45.6%
3682205 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.51 38.0 3.19e-01 85.7% 77.9%
4952060 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 36.0 3.86e-01 75.7% 90.0%
3500755 304.55.1.14 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Y2_Tnp 0.51 34.0 2.47e-01 70.0% 61.4%
3558744 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.50 43.0 3.62e-01 100.0% 63.2%