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PH2015_20_scaffold_1_prodigal-single.1__X__X__00317

Bact-Vir

PH2015_20_scaffold_1_prodigal-single.1__X__X__00317

Identity

Kingdom:
phage

Quality

90.0 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 2-88
PDB
Domain cluster: representative
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.69 38.0 4.29e-01 100.0% 71.2%
6s2wA01 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.66 42.0 4.34e-01 96.6% 68.3%
2n1kA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 36.0 3.35e-01 100.0% 42.5%
2v5yA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 34.0 3.30e-01 100.0% 45.3%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.63 38.0 3.08e-01 98.9% 30.5%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.63 38.0 3.79e-01 97.7% 56.5%
5utkA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 33.0 3.45e-01 100.0% 53.0%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 33.0 3.13e-01 100.0% 41.7%
2dm4A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 32.0 3.19e-01 100.0% 45.7%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 32.0 3.28e-01 100.0% 50.0%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.59 42.0 4.18e-01 75.9% 100.0%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 34.0 3.28e-01 100.0% 49.5%
3hrzC01 2.20.210.20 Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › 0.57 31.0 3.91e-01 98.9% 91.8%
5hccB02 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.55 32.0 3.20e-01 100.0% 52.6%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.55 40.0 3.13e-01 79.3% 68.6%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.55 42.0 4.00e-01 98.9% 70.0%
6kjcA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.54 47.0 3.11e-01 100.0% 86.9%
5izdA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.53 43.0 3.05e-01 89.7% 95.8%
3rq1D01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.53 41.0 3.53e-01 87.4% 81.0%
3nx3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 41.0 3.54e-01 86.2% 60.3%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.52 38.0 3.21e-01 81.6% 89.3%
4lw2A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 41.0 3.68e-01 90.8% 71.4%
3k1lA02 3.30.457.30 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.51 31.0 3.12e-01 79.3% 56.7%
1u08A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 41.0 3.50e-01 86.2% 67.6%
3hlbD00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 44.0 2.89e-01 98.9% 87.8%
4wiwA02 3.10.50.10 Alpha Beta › Roll › Chitinase A; domain 3 › 0.50 37.0 4.03e-01 93.1% 100.0%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3285401 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.72 42.0 4.50e-01 98.9% 66.7%
3724523 4121.1.1.7 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › PF26616 0.65 44.0 2.90e-01 100.0% 16.7%
3626222 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 33.0 3.08e-01 100.0% 38.2%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.63 48.0 5.36e-01 97.7% 100.0%
4027527 929.1.1.0 ↗ beta duplicates or obligate multimers › Resistin › Resistin › Resistin 0.61 34.0 3.43e-01 98.9% 52.9%
3572577 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.61 32.0 3.12e-01 100.0% 43.0%
4057632 3012.1.1.10 ↗ a+b two layers › Cof C2 cap domain › Cof C2 cap domain › Cof C2 cap domain › ISN1 0.60 41.0 4.15e-01 71.3% 100.0%
5045774 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.60 36.0 3.06e-01 100.0% 36.4%
5080205 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.58 32.0 3.93e-01 98.9% 92.0%
3992138 11.2.1.52 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain › C2_nem 0.57 50.0 4.16e-01 96.6% 96.7%
4964514 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.57 32.0 4.07e-01 100.0% 98.0%
5065878 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.56 34.0 2.88e-01 100.0% 34.2%
5020151 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.56 34.0 2.97e-01 100.0% 37.8%
2896602 4326.1.1.1 ↗ a+b two layers › ERH-like › ERH-like › ERH-like › ER 0.56 42.0 4.09e-01 98.9% 70.0%
3256398 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 33.0 3.25e-01 100.0% 55.8%
3339265 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.54 40.0 2.40e-01 79.3% 47.9%
146727 216.1.1.9 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › FANCL_d2 0.53 30.0 3.09e-01 70.1% 54.0%
4934789 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.53 31.0 3.13e-01 100.0% 55.3%
5027350 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.53 31.0 2.69e-01 100.0% 35.5%
3175641 312.1.1.6 ↗ a+b three layers › HIT-like › HIT-related › HIT-related › CwfJ_C_2,CwfJ_C_1 0.52 44.0 3.25e-01 93.1% 47.2%
2999708 223.1.1.7 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Autoind_bind 0.52 42.0 3.39e-01 88.5% 92.6%
3328617 109.4.1.1992 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, DYW_deaminase, E_motif 0.52 40.0 2.40e-01 83.9% 16.2%
3424994 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.52 40.0 2.39e-01 83.9% 16.3%
4943252 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.52 33.0 2.86e-01 100.0% 39.3%
3817532 109.4.1.2179 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, DYW_deaminase, E_motif 0.52 40.0 2.46e-01 85.1% 18.5%
223777 3115.4.1.1 ↗ a+b two layers › GP2-like › Uncharacterized conserved protein Il1583 › Uncharacterized conserved protein Il1583 › DUF1543 0.51 27.0 2.92e-01 98.9% 58.7%
4472409 223.1.1.7 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › Autoind_bind 0.51 39.0 3.25e-01 85.1% 93.5%
4944787 304.3.1.0 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.51 39.0 4.02e-01 85.1% 90.0%
3671718 109.4.1.2659 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, DYW_deaminase, E_motif, TPR_24 0.51 39.0 2.37e-01 85.1% 16.7%
3330921 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.51 39.0 2.59e-01 85.1% 28.1%
3385387 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.50 38.0 2.39e-01 85.1% 19.8%
D2 high residues 98-187
PDB
Domain cluster: representative
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2aehA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.77 42.0 3.91e-01 75.6% 44.1%
2r55A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 50.0 3.86e-01 94.4% 58.2%
3qszA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 49.0 3.96e-01 95.6% 67.8%
1p9rA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 43.0 4.02e-01 90.0% 65.8%
2x6hA02 3.30.1010.10 Alpha Beta › 2-Layer Sandwich › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 4 0.56 36.0 2.99e-01 81.1% 37.6%
1w0pA02 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.55 46.0 3.18e-01 100.0% 93.4%
3c6kA01 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.53 38.0 3.79e-01 75.6% 79.8%
3mx7A00 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.53 36.0 3.67e-01 71.1% 98.9%
2v7sA00 3.30.2030.20 Alpha Beta › 2-Layer Sandwich › TBP-like › 0.52 46.0 3.79e-01 98.9% 54.4%
4zrlA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.52 44.0 4.10e-01 94.4% 88.9%
2x0qA01 3.30.310.280 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.52 41.0 3.61e-01 83.3% 88.0%
2f5tX01 3.30.870.10 Alpha Beta › 2-Layer Sandwich › Endonuclease; Chain A › Endonuclease Chain A 0.52 42.0 3.69e-01 88.9% 69.1%
5fl3A01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 41.0 3.97e-01 90.0% 77.0%
5cw7B00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.52 39.0 3.84e-01 78.9% 74.5%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.51 43.0 3.97e-01 92.2% 74.1%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 37.0 3.80e-01 100.0% 79.3%
1qqgA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 39.0 3.74e-01 100.0% 71.2%
2gzaA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 39.0 3.75e-01 92.2% 70.4%
6eugA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 43.0 3.01e-01 100.0% 86.2%
2pt7C01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.51 41.0 3.98e-01 91.1% 77.4%
1dglA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 43.0 3.26e-01 96.7% 87.3%
3u12A00 2.30.29.180 Mainly Beta › Roll › PH-domain like › Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain 0.51 40.0 3.83e-01 100.0% 75.0%
1h4rA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 35.0 3.50e-01 100.0% 71.4%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
154344 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.80 43.0 3.98e-01 74.4% 44.0%
3916003 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.79 43.0 3.98e-01 78.9% 42.6%
3222570 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.77 36.0 3.28e-01 73.3% 34.8%
4964505 244.2.1.7 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › Rubredoxin_C 0.64 38.0 3.76e-01 88.9% 55.9%
5053926 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.64 32.0 3.44e-01 70.0% 52.5%
3487132 244.2.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain › FAD/NAD-linked reduatases, dimerisation (C-terminal) domain 0.62 42.0 4.06e-01 92.2% 62.0%
3615114 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 35.0 3.04e-01 92.2% 34.3%
3929502 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.59 36.0 3.61e-01 93.3% 57.4%
3486278 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 46.0 4.39e-01 100.0% 74.3%
4994897 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.55 41.0 3.62e-01 80.0% 97.8%
4976853 220.5.1.1 ↗ beta barrels › PH domain-like › NucS N-terminal domain › NucS N-terminal domain › NucS_N 0.54 44.0 4.04e-01 100.0% 66.7%
5049089 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 39.0 3.63e-01 76.7% 97.5%
5029231 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.54 42.0 2.64e-01 90.0% 14.7%
3609794 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 44.0 3.07e-01 100.0% 93.0%
5054338 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.52 41.0 2.72e-01 90.0% 19.3%
3684873 109.4.1.681 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans_2 0.52 44.0 2.83e-01 95.6% 59.6%
5029609 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 40.0 2.66e-01 88.9% 18.4%
3767975 220.1.1.38 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › UCH_N 0.51 42.0 3.96e-01 100.0% 73.6%
3498572 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.50 41.0 2.81e-01 92.2% 45.8%