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SRR1747035_scaffold_3_prodigal-single.1__X__X__00289

Bact-Vir

SRR1747035_scaffold_3_prodigal-single.1__X__X__00289

Identity

Kingdom:
phage

Quality

75.5 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 5-127
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2bjoA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.68 34.0 3.89e-01 98.4% 62.8%
2ql8A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.65 33.0 3.17e-01 98.4% 41.4%
1s3rA04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.64 34.0 3.54e-01 78.0% 55.0%
5e1qA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.60 27.0 3.09e-01 71.5% 53.1%
5wm1A05 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 36.0 3.72e-01 74.0% 63.2%
2jwyA01 2.60.40.1620 Mainly Beta › Sandwich › Immunoglobulin-like › Lipoprotein YajI-like 0.57 32.0 3.16e-01 75.6% 48.9%
1h2cA00 2.70.20.20 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Matrix protein VP40, N-terminal domain 0.55 42.0 4.22e-01 81.3% 98.4%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.55 37.0 4.32e-01 72.4% 100.0%
4hsaF02 2.60.40.2150 Mainly Beta › Sandwich › Immunoglobulin-like › Interleukin-17 receptor A/B, fibronectin-III-like domain 2 0.53 32.0 3.38e-01 91.1% 66.7%
5k8mA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 39.0 3.87e-01 78.9% 100.0%
1hq6B00 3.50.20.10 Alpha Beta › 3-Layer(bba) Sandwich › Pyruvoyl-Dependent Histidine Decarboxylase; Chain B › Pyruvoyl-Dependent Histidine Decarboxylase, subunit B 0.51 42.0 3.51e-01 96.7% 48.7%
4dyoA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.51 41.0 3.96e-01 87.0% 77.0%
6w6vE01 3.30.70.3250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribonuclease P, Pop5 subunit 0.50 46.0 4.23e-01 99.2% 96.8%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4128974 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.73 44.0 5.30e-01 90.2% 91.3%
2741079 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.72 41.0 5.21e-01 76.4% 95.8%
3508212 3115.1.1.6 a+b two layers › GP2-like › RplX-like › RplX-like › DUF4494 0.72 39.0 5.04e-01 77.2% 94.3%
3892842 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.69 37.0 4.84e-01 74.0% 96.9%
3885857 223.1.1.0 a+b three layers › Profilin-like › sensor domains › sensor domains 0.65 28.0 3.45e-01 93.5% 62.7%
3999001 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.62 35.0 3.80e-01 75.6% 65.7%
3593809 304.31.1.0 a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase 0.62 33.0 3.54e-01 96.7% 57.3%
4971888 512.1.1.1 a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.61 30.0 2.44e-01 94.3% 24.3%
3577792 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.60 33.0 3.43e-01 76.4% 55.8%
4003316 10.7.1.0 beta sandwiches › jelly-roll › Hypothetical protein TM1070 › Hypothetical protein TM1070 0.60 34.0 3.40e-01 77.2% 54.4%
3891753 3369.1.1.1 beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.58 44.0 3.72e-01 78.0% 83.5%
3519901 3369.1.1.0 beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 0.58 44.0 3.97e-01 78.9% 92.1%
4021088 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.56 39.0 3.78e-01 74.8% 62.9%
5040494 264.2.1.0 beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.55 42.0 3.96e-01 82.1% 98.0%
3938345 11.1.1.909 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Gpi16 0.54 31.0 2.98e-01 77.2% 49.3%
3268123 192.15.1.184 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › RA 0.53 29.0 3.15e-01 86.2% 60.0%
4042627 5084.1.1.10 beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like › OMP_b-brl 0.53 39.0 3.55e-01 77.2% 99.4%
3223598 11.10.1.6 beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › MATH 0.51 32.0 3.07e-01 78.0% 54.3%
D2 high residues 155-229
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01541.31 best GIY-YIG 31.1 3.20e-07 100.0% 89.7%
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.83 76.0 7.09e-01 100.0% 87.0%
5ja1B00 3.90.820.10 Alpha Beta › Alpha-Beta Complex › Rubredoxin-like › Structural Genomics, Unknown Function 30-nov-00 1gh9 Mol_id 0.72 44.0 4.72e-01 100.0% 71.2%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.72 55.0 4.19e-01 82.7% 47.7%
1qr4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.72 45.0 4.31e-01 89.3% 55.2%
4iauA01 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.70 36.0 3.58e-01 77.3% 46.2%
2yn5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 41.0 4.09e-01 89.3% 57.0%
3pjyA00 2.60.120.1140 Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF192 0.66 47.0 3.94e-01 74.7% 94.6%
2d93A00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.65 38.0 3.13e-01 78.7% 32.8%
3rj2X00 2.60.120.1150 Mainly Beta › Sandwich › Jelly Rolls › 0.65 40.0 3.28e-01 78.7% 35.3%
2v3sA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.64 45.0 4.13e-01 73.3% 99.0%
4kncA02 2.60.120.1380 Mainly Beta › Sandwich › Jelly Rolls › C-terminal carbohydrate-binding module 0.63 44.0 3.77e-01 78.7% 47.0%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.62 38.0 3.77e-01 78.7% 57.5%
2f4nB02 2.40.30.90 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Bacterial fluorinating enzyme like 0.61 44.0 4.05e-01 74.7% 69.1%
1u1sA00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.60 39.0 4.16e-01 77.3% 75.8%
3wdhA01 2.60.40.2320 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 39.0 3.59e-01 74.7% 52.1%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.60 46.0 4.04e-01 84.0% 56.9%
6julA02 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.59 43.0 3.95e-01 80.0% 59.4%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.59 38.0 3.99e-01 73.3% 72.7%
1xvsA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.59 42.0 3.55e-01 80.0% 45.5%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 47.0 3.73e-01 88.0% 89.8%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.58 41.0 3.54e-01 78.7% 48.3%
3in6A02 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 42.0 3.67e-01 84.0% 50.4%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.57 37.0 3.69e-01 78.7% 63.2%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.57 40.0 3.30e-01 84.0% 39.4%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.57 41.0 3.46e-01 80.0% 46.7%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 41.0 3.24e-01 77.3% 42.3%
2bkfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 41.0 3.99e-01 77.3% 89.2%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.56 37.0 3.53e-01 78.7% 56.5%
3vzbB02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.56 43.0 3.15e-01 82.7% 99.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.55 36.0 2.88e-01 78.7% 31.1%
1p8jA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 40.0 3.32e-01 77.3% 43.9%
1wmdA02 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.54 38.0 3.32e-01 80.0% 47.9%
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 0.54 38.0 4.01e-01 89.3% 80.9%
6hj2A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.54 40.0 2.80e-01 81.3% 80.3%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.54 37.0 3.51e-01 77.3% 57.4%
2mlbA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 38.0 3.77e-01 74.7% 83.5%
2lw3A00 2.60.40.2880 Mainly Beta › Sandwich › Immunoglobulin-like › MmpS1-5, C-terminal soluble domain 0.54 32.0 3.09e-01 78.7% 48.9%
1o54A01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.53 39.0 4.05e-01 98.7% 81.9%
3h8hA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 38.0 3.59e-01 76.0% 93.5%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.53 39.0 3.19e-01 80.0% 43.1%
2lrwA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.53 38.0 3.77e-01 76.0% 82.1%
1alo006 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.51 40.0 3.48e-01 90.7% 96.8%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4344289 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.83 76.0 6.24e-01 100.0% 64.6%
3505268 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.83 77.0 6.20e-01 100.0% 80.0%
4158495 821.1.1.1 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.79 70.0 6.54e-01 100.0% 80.0%
5001166 301.1.1.2 a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.66 47.0 3.83e-01 93.3% 40.7%
4990637 3115.1.1.1 a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.65 50.0 4.89e-01 88.0% 75.9%
3958896 4187.2.1.0 a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.62 37.0 4.10e-01 72.0% 75.0%
3216210 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.61 39.0 4.53e-01 78.7% 98.0%
4012131 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.61 44.0 3.75e-01 77.3% 50.4%
3705532 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.60 45.0 3.76e-01 80.0% 53.1%
3959955 304.163.1.3 a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain › PF31118 0.60 36.0 4.33e-01 80.0% 100.0%
4004704 3115.6.1.2 a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.60 36.0 4.22e-01 76.0% 100.0%
3194295 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.60 43.0 3.71e-01 77.3% 50.4%
4946583 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.59 43.0 3.76e-01 77.3% 54.8%
3593981 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.59 43.0 3.83e-01 81.3% 55.2%
4002865 10.32.1.6 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › P_proprotein 0.56 41.0 3.34e-01 78.7% 41.4%
3440477 2484.1.1.15 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › GDA1_CD39 0.56 40.0 3.74e-01 76.0% 65.3%
3941506 2002.1.1.16 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Bac_luciferase 0.54 41.0 2.80e-01 88.0% 95.8%
3231131 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 44.0 4.04e-01 94.7% 91.4%
3783481 11.1.1.642 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.53 40.0 3.38e-01 80.0% 56.7%
5022263 322.1.1.2 a+b two layers › HPr-like › HPr-like › HPr-like › 3H 0.53 36.0 3.26e-01 72.0% 51.8%
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 0.52 46.0 3.23e-01 97.3% 71.3%
3677917 109.3.1.320 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › DYW_deaminase 0.51 36.0 3.03e-01 76.0% 68.9%
5052968 109.4.1.192 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.50 36.0 2.38e-01 77.3% 27.2%
3643305 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.50 41.0 3.46e-01 93.3% 85.2%