←Back to structures

NC_070885.1__YP_010661825.1__PP936_gp187__00187

Bact-Vir

NC_070885.1__YP_010661825.1__PP936_gp187__00187

Identity

Accession:
NC_070885 ↗
Kingdom:
phage

Quality

70.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Trinifflemingvirus› Rhizobium_phage_RHph_I1_9

TaxID: 2509729

Cluster

Singleton — not in a non-trivial cluster

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 7-53
PDB
Domain cluster: representative
CATH (50)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.72 57.0 4.12e-01 100.0% 30.7%
2xp1A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.71 55.0 4.42e-01 87.2% 47.4%
3f6zB01 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.71 58.0 4.98e-01 95.7% 94.9%
3cihA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.69 59.0 4.44e-01 100.0% 53.7%
2knoA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.68 52.0 4.10e-01 89.4% 67.3%
5cvmA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.68 56.0 3.49e-01 100.0% 20.1%
1ekgA00 3.30.920.10 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Frataxin/CyaY 0.67 49.0 3.81e-01 89.4% 32.8%
2kcjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 56.0 4.43e-01 100.0% 76.9%
6pxcA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.67 53.0 4.20e-01 91.5% 55.8%
2wdtC02 3.30.1490.420 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Ubiquitin carboxyl-terminal hydrolase, domain 2 0.66 54.0 4.42e-01 100.0% 75.2%
2ci9B00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.65 51.0 4.09e-01 91.5% 61.0%
2bseA00 2.60.40.1830 Mainly Beta › Sandwich › Immunoglobulin-like › Phage tail base-plate Siphoviridae RBP, head domain 0.64 51.0 4.02e-01 100.0% 40.2%
4k15A00 2.60.40.3860 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 48.0 3.59e-01 87.2% 65.9%
3i3tA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.63 52.0 3.23e-01 100.0% 91.7%
5d3xB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 52.0 3.83e-01 100.0% 64.5%
2ox7A02 2.30.30.290 Mainly Beta › Roll › SH3 type barrels. › YopX-like domains 0.63 51.0 4.64e-01 100.0% 78.3%
1m1hA02 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.62 49.0 4.21e-01 93.6% 65.9%
1wgqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 50.0 3.99e-01 100.0% 78.0%
3kyfA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.61 52.0 3.99e-01 100.0% 46.5%
3mpxA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 49.0 4.10e-01 100.0% 80.4%
2vifA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.61 47.0 3.61e-01 91.5% 59.5%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 51.0 4.01e-01 100.0% 69.4%
5u78C00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 50.0 3.89e-01 100.0% 83.6%
2elbA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 49.0 4.00e-01 100.0% 77.5%
1eazA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 49.0 3.99e-01 100.0% 84.5%
4whiA00 2.40.128.600 Mainly Beta › Beta Barrel › Lipocalin › 0.60 45.0 3.64e-01 87.2% 59.8%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 48.0 3.92e-01 100.0% 80.6%
2eobA01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.60 46.0 3.64e-01 91.5% 51.3%
2cofA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 49.0 3.91e-01 100.0% 77.6%
3fssA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 48.0 4.12e-01 100.0% 82.6%
5umsA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 49.0 3.93e-01 100.0% 70.6%
3tfmA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 47.0 3.93e-01 100.0% 88.9%
1dbhA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 48.0 3.67e-01 100.0% 71.9%
3us4A00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.58 45.0 3.71e-01 91.5% 58.8%
4gzuB03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 48.0 4.01e-01 100.0% 87.9%
3ml4A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 48.0 3.90e-01 100.0% 80.0%
1mi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 48.0 3.85e-01 100.0% 88.6%
4obiA00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.58 46.0 3.84e-01 89.4% 64.4%
5i4dA02 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.57 38.0 3.38e-01 70.2% 77.6%
3fm8D03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 47.0 3.75e-01 100.0% 81.5%
1hyoA01 2.30.30.230 Mainly Beta › Roll › SH3 type barrels. › Fumarylacetoacetase, N-terminal domain 0.57 45.0 3.48e-01 91.5% 85.8%
1qmyA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.57 47.0 3.40e-01 100.0% 95.5%
4hwmA00 2.40.128.500 Mainly Beta › Beta Barrel › Lipocalin › YedD-like protein 0.54 40.0 3.24e-01 89.4% 76.1%
1q1rA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.54 40.0 3.37e-01 87.2% 64.2%
2izvA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.54 43.0 3.13e-01 100.0% 64.4%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.44e-01 100.0% 73.4%
4fchA02 2.60.40.3610 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 40.0 3.12e-01 85.1% 70.2%
5w0kA01 3.90.380.20 Alpha Beta › Alpha-Beta Complex › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 › Herpesvirus glycoprotein H, domain D-II 0.52 41.0 2.61e-01 100.0% 56.9%
2yrtA00 4.10.1130.20 Few Secondary Structures › Irregular › btk motif of tyrosine-protein kinase itk › 0.52 36.0 3.30e-01 78.7% 68.0%
3qdfA01 2.30.30.370 Mainly Beta › Roll › SH3 type barrels. › FAH 0.51 39.0 3.85e-01 100.0% 96.6%
ECOD (66)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3826272 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.76 65.0 3.92e-01 100.0% 16.7%
3669824 386.1.1.20 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-met 0.74 59.0 5.65e-01 89.4% 76.4%
3692594 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.73 63.0 3.66e-01 100.0% 13.1%
3680084 4.2.1.4 ↗ beta barrels › SH3 › SAND › SAND › TDBD 0.72 63.0 5.41e-01 100.0% 73.3%
3719044 219.1.1.112 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH, UCH_1 0.69 57.0 3.46e-01 100.0% 18.9%
3888557 214.1.1.7 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2_1 0.69 55.0 4.06e-01 91.5% 53.1%
3399079 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.68 59.0 4.53e-01 100.0% 63.6%
4533388 219.1.1.122 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › PF28648 0.68 56.0 3.70e-01 100.0% 22.2%
3606753 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.67 54.0 3.30e-01 100.0% 17.6%
3390398 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.66 51.0 3.77e-01 89.4% 43.5%
3418449 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.66 55.0 3.21e-01 100.0% 11.5%
3917042 214.1.1.7 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2_1 0.65 52.0 3.89e-01 93.6% 53.3%
3905631 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.65 49.0 3.88e-01 87.2% 50.9%
4030120 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 53.0 3.06e-01 100.0% 14.6%
3216674 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.65 52.0 4.01e-01 93.6% 54.8%
3496180 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 54.0 4.05e-01 100.0% 61.5%
3920610 633.23.1.2 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › GSG-1 0.63 53.0 3.62e-01 100.0% 67.6%
3530034 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.63 51.0 3.96e-01 100.0% 69.2%
3535755 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.63 46.0 3.48e-01 87.2% 42.9%
4103373 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.62 51.0 4.94e-01 100.0% 98.2%
4067146 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 48.0 4.93e-01 97.9% 95.6%
3861490 220.1.1.118 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › RHG20_PH 0.62 51.0 4.15e-01 100.0% 83.0%
3905081 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.62 47.0 3.66e-01 91.5% 45.6%
3624619 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 50.0 3.81e-01 100.0% 66.9%
3241885 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 49.0 3.81e-01 100.0% 68.0%
3261192 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 50.0 3.88e-01 100.0% 70.0%
3916025 214.1.1.0 ↗ a+b two layers › SH2 › SH2 › SH2 0.61 46.0 3.42e-01 89.4% 40.7%
3990213 220.1.1.7 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › IRS 0.61 49.0 4.06e-01 100.0% 77.0%
3412536 4.10.1.1 ↗ beta barrels › SH3 › Fumarylacetoacetate hydrolase, FAH, N-terminal domain › Fumarylacetoacetate hydrolase, FAH, N-terminal domain › FAA_hydrolase_N 0.61 51.0 3.99e-01 100.0% 87.3%
3777177 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 50.0 4.09e-01 100.0% 81.0%
3882213 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 50.0 4.21e-01 100.0% 86.7%
3860032 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 50.0 4.06e-01 100.0% 78.0%
3271586 220.1.1.12 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Myosin_TH1 0.60 48.0 3.24e-01 100.0% 38.7%
5013200 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.60 44.0 3.22e-01 80.9% 81.4%
4586498 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.60 49.0 3.74e-01 100.0% 66.2%
3971733 11.9.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › FAH › FAH 0.60 51.0 3.15e-01 100.0% 68.1%
3259130 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.60 49.0 3.99e-01 100.0% 83.0%
4614679 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.60 47.0 4.71e-01 95.7% 100.0%
3226939 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 48.0 3.97e-01 100.0% 82.0%
3937468 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 47.0 3.84e-01 100.0% 75.5%
3211867 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 47.0 3.83e-01 100.0% 73.6%
1489671 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.59 47.0 4.56e-01 100.0% 92.9%
3756645 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.59 48.0 3.65e-01 100.0% 71.5%
3513128 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.59 47.0 3.48e-01 100.0% 76.0%
3525358 220.1.1.50 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_17 0.59 47.0 3.68e-01 100.0% 69.2%
3971301 3784.1.1.4 ↗ a+b two layers › Putative lipoprotein CPF_1278-related › Putative lipoprotein CPF_1278-related › Putative lipoprotein CPF_1278-related › DUF4340 0.58 50.0 3.63e-01 100.0% 56.4%
3937758 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.58 45.0 3.58e-01 91.5% 54.0%
3515382 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 47.0 3.69e-01 100.0% 75.0%
4834236 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.58 44.0 3.41e-01 91.5% 46.5%
3797707 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 47.0 3.56e-01 100.0% 57.0%
3617381 220.1.1.80 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › RME-8_N 0.58 46.0 3.68e-01 100.0% 72.2%
3916753 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 47.0 3.40e-01 100.0% 51.9%
3255104 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.57 45.0 3.54e-01 100.0% 80.0%
4467867 3784.1.1.0 ↗ a+b two layers › Putative lipoprotein CPF_1278-related › Putative lipoprotein CPF_1278-related › Putative lipoprotein CPF_1278-related 0.57 48.0 3.49e-01 100.0% 56.6%
3940063 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.57 45.0 3.84e-01 100.0% 85.3%
4120366 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.57 44.0 4.31e-01 97.9% 92.7%
3577804 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 48.0 3.74e-01 100.0% 70.0%
3373211 3115.3.1.3 ↗ a+b two layers › GP2-like › P56 › P56 › DUF679 0.56 40.0 4.26e-01 89.4% 92.5%
4031797 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.56 44.0 4.30e-01 100.0% 98.2%
4239498 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.56 46.0 4.45e-01 100.0% 90.9%
4203469 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.55 44.0 4.27e-01 100.0% 94.5%
4389625 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.55 46.0 4.41e-01 97.9% 92.7%
4123157 375.1.1.47 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › BshC 0.54 41.0 4.05e-01 100.0% 92.7%
3722215 11.9.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › FAH › FAH › FAA_hydrolase 0.53 44.0 2.67e-01 100.0% 54.1%
3438163 4135.1.1.1 ↗ beta duplicates or obligate multimers › MAL13P1.257-like › MAL13P1.257-like › MAL13P1.257-like › CXXC_Zn-b_euk 0.53 42.0 3.06e-01 100.0% 58.2%
3932976 2484.5.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase 0.51 35.0 3.03e-01 80.9% 83.2%