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BML_08182015_6_5m_scaffold_1_prodigal-single.1__X__X__00038

Bact-Vir

BML_08182015_6_5m_scaffold_1_prodigal-single.1__X__X__00038

Identity

Kingdom:
phage

Quality

86.6 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 2-54
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jr7A03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.70 56.0 4.33e-01 90.6% 52.8%
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.70 58.0 4.61e-01 98.1% 79.7%
2q18X01 3.10.330.40 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.68 50.0 4.59e-01 94.3% 60.0%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.65 56.0 5.18e-01 100.0% 81.7%
7yh1A01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.64 51.0 4.02e-01 100.0% 40.4%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.64 43.0 3.98e-01 84.9% 53.7%
1sfeA01 3.30.160.70 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Methylated DNA-protein cysteine methyltransferase domain 0.62 50.0 4.43e-01 92.5% 97.5%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.62 51.0 4.11e-01 100.0% 47.9%
2re3A02 2.30.270.10 Mainly Beta › Roll › duf1285 protein fold › duf1285 protein 0.62 40.0 3.69e-01 73.6% 50.0%
1gqyB02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.62 50.0 3.40e-01 100.0% 23.5%
4bg8A01 3.30.420.430 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.62 48.0 3.71e-01 88.7% 50.4%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 43.0 4.01e-01 90.6% 59.1%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 47.0 4.01e-01 90.6% 50.5%
1f9qD00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.60 41.0 3.86e-01 84.9% 57.6%
2nqlA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.60 48.0 3.59e-01 100.0% 53.6%
3msyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 48.0 3.97e-01 100.0% 53.2%
5hy7B02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 45.0 2.89e-01 88.7% 23.2%
1h8mA00 3.30.450.50 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Longin domain 0.58 50.0 3.74e-01 100.0% 43.6%
1eigA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 39.0 3.54e-01 84.9% 50.7%
5umsA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 45.0 3.73e-01 88.7% 47.1%
3buxB03 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.57 43.0 3.81e-01 98.1% 53.5%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 42.0 3.52e-01 90.6% 43.7%
4z32C02 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.56 47.0 3.93e-01 98.1% 55.6%
2h8lA02 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.56 45.0 3.73e-01 100.0% 89.3%
4gyiA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.56 40.0 3.28e-01 77.4% 85.7%
1eotA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 39.0 3.56e-01 88.7% 54.1%
4geqB00 3.30.160.430 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.55 40.0 3.98e-01 98.1% 74.1%
3cetB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 42.0 3.44e-01 88.7% 44.5%
1nbwA04 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 41.0 3.27e-01 92.5% 67.4%
1icwB00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 39.0 3.66e-01 90.6% 62.1%
2ch5B02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 42.0 2.99e-01 94.3% 67.5%
1e3hA01 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.53 44.0 2.95e-01 98.1% 65.7%
2uz8A01 3.40.30.90 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › 0.53 36.0 3.59e-01 98.1% 68.5%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.53 41.0 3.37e-01 100.0% 60.3%
3gkeA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.53 40.0 3.22e-01 92.5% 48.5%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 41.0 3.64e-01 98.1% 56.4%
7szeB01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.53 42.0 3.49e-01 94.3% 55.1%
1s3aA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.53 43.0 3.81e-01 100.0% 96.5%
2xcmC00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 40.0 3.47e-01 88.7% 51.1%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 33.0 3.15e-01 83.0% 50.8%
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.51 40.0 3.14e-01 94.3% 46.7%
3a0oA03 2.70.98.70 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 40.0 2.70e-01 100.0% 87.5%
4fnfA00 2.40.50.50 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 44.0 3.67e-01 100.0% 57.1%
1b44D00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 44.0 3.57e-01 100.0% 55.7%
4dapA01 2.40.50.580 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 36.0 3.30e-01 81.1% 87.5%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 39.0 4.03e-01 100.0% 91.8%
1amiA04 3.20.19.10 Alpha Beta › Alpha-Beta Barrel › Aconitase; domain 4 › Aconitase, domain 4 0.50 38.0 2.55e-01 83.0% 33.5%
3deeA02 3.90.930.50 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › 0.50 41.0 3.35e-01 96.2% 76.3%
ECOD (66)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4961481 4325.1.1.0 mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.77 63.0 5.76e-01 90.6% 70.0%
4297945 4325.1.1.1 mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.75 60.0 6.03e-01 92.5% 89.1%
4944977 301.13.1.0 a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.72 57.0 4.35e-01 90.6% 52.3%
5023580 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.69 50.0 4.69e-01 88.7% 63.1%
4944860 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.69 52.0 3.94e-01 100.0% 32.1%
3921576 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.69 52.0 3.83e-01 83.0% 30.7%
5027344 1170.1.1.0 beta barrels › IL8-related › IL8-related › IL8 0.68 44.0 4.42e-01 83.0% 65.5%
5041236 375.13.1.1 few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Toprim_C_rpt 0.67 51.0 5.07e-01 86.8% 81.8%
3631791 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 48.0 3.58e-01 83.0% 64.4%
3680934 386.1.1.0 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.66 44.0 4.78e-01 96.2% 92.5%
5041229 375.13.1.0 few secondary structure elements › Rubredoxin-like › Mycobacterium tuberculosis Topoisomerase I C-terminal domain › Mycobacterium tuberculosis Topoisomerase I C-terminal domain 0.65 51.0 4.98e-01 92.5% 78.3%
3196233 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 52.0 3.80e-01 90.6% 64.5%
5049640 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 52.0 4.53e-01 88.7% 58.2%
4093535 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.64 52.0 3.90e-01 90.6% 36.2%
3789602 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 46.0 3.60e-01 83.0% 33.6%
5045959 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.64 49.0 4.12e-01 100.0% 45.5%
5001324 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 47.0 3.77e-01 90.6% 40.0%
2124201 220.3.1.2 beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.64 45.0 3.23e-01 100.0% 25.3%
3949336 220.1.1.216 beta barrels › PH domain-like › PH domain-like › PH domain-like › Helicase_IV_N 0.63 47.0 3.81e-01 84.9% 40.0%
3591459 220.1.1.8 beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.62 46.0 3.98e-01 83.0% 50.6%
3945142 252.2.1.7 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › PF30395 0.62 49.0 5.07e-01 94.3% 98.0%
3216714 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.62 35.0 4.06e-01 71.7% 82.9%
4997112 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.62 47.0 3.70e-01 100.0% 36.2%
3954708 4325.1.1.9 mixed a+b and a/b › YegP-like › YegP-like › YegP-like › PF26003 0.61 51.0 5.23e-01 88.7% 94.0%
3786015 5.1.5.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.60 48.0 2.72e-01 94.3% 9.2%
4280539 109.21.1.8 alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › WD40 0.60 48.0 2.72e-01 94.3% 8.5%
3282813 268.1.1.0 a+b two layers › Sterol carrier protein-like › Sterol carrier protein, SCP-related › Sterol carrier protein, SCP-related 0.60 36.0 3.20e-01 75.5% 38.7%
3737927 220.1.1.294 beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26663 0.60 42.0 3.38e-01 73.6% 60.9%
3478371 214.1.1.1 a+b two layers › SH2 › SH2 › SH2 › SH2 0.59 53.0 4.15e-01 100.0% 50.9%
5073342 2484.1.1.4 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.59 47.0 3.91e-01 98.1% 46.5%
3501861 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 46.0 3.69e-01 84.9% 43.8%
4398495 109.21.1.8 alpha superhelices › Repetitive alpha hairpins › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › Nucleoporin NUP85/Nucleoporin NUP145 C-terminal domain › WD40 0.59 50.0 2.78e-01 98.1% 13.8%
4072904 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.59 42.0 4.17e-01 92.5% 74.5%
5000609 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.58 45.0 3.67e-01 100.0% 40.8%
5051943 2004.1.1.159 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.58 46.0 3.11e-01 100.0% 21.3%
5038844 330.2.1.0 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.58 46.0 4.19e-01 98.1% 76.2%
4988423 4210.1.1.0 a+b two layers › WGR domain › WGR domain › WGR domain 0.58 46.0 4.05e-01 88.7% 65.0%
4945655 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 42.0 3.52e-01 83.0% 42.0%
3963958 2484.2.1.0 mixed a+b and a/b › Ribonuclease H-like › Methylated DNA-protein cysteine methyltransferase domain › Methylated DNA-protein cysteine methyltransferase domain 0.58 42.0 3.86e-01 100.0% 57.3%
3346566 1.1.7.85 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › BRX 0.58 40.0 3.99e-01 73.6% 81.8%
3231308 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.58 44.0 2.91e-01 83.0% 29.3%
3439434 3521.1.1.3 a+b three layers › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › BRX 0.57 41.0 4.06e-01 75.5% 83.6%
4408024 325.1.7.3 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › Apocytochr_F_C 0.57 44.0 4.25e-01 94.3% 75.0%
4320111 218.1.1.8 a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.57 46.0 3.92e-01 100.0% 93.0%
3164555 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 44.0 3.31e-01 98.1% 31.3%
3924597 330.16.1.0 a+b two layers › dsRBD-like › ODA16 N-terminal domain › ODA16 N-terminal domain 0.56 42.0 3.94e-01 98.1% 65.7%
3971108 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 45.0 3.92e-01 98.1% 55.6%
4977878 223.2.1.5 a+b three layers › Profilin-like › profilin-like › profilin-like › Robl_LC7 0.56 43.0 3.56e-01 100.0% 42.5%
2464208 220.3.1.2 beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Baculo_gp64 0.56 39.0 2.85e-01 100.0% 25.0%
3387142 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 41.0 3.00e-01 90.6% 27.4%
3601996 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 46.0 2.90e-01 100.0% 76.5%
5064976 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 45.0 3.29e-01 98.1% 81.9%
4978622 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 42.0 3.67e-01 98.1% 54.0%
3419193 5.1.3.118 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.54 44.0 3.00e-01 94.3% 33.3%
4940035 223.2.1.0 a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 42.0 3.48e-01 94.3% 49.1%
3933293 4.8.1.0 beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.53 36.0 3.49e-01 86.8% 62.1%
5056316 2002.1.1.120 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.53 40.0 2.58e-01 92.5% 96.6%
5061404 219.1.1.0 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 44.0 2.84e-01 98.1% 57.4%
3971431 241.11.1.0 a+b two layers › Type III secretory system chaperone-like › YjbR-like › YjbR-like 0.53 40.0 3.63e-01 96.2% 57.1%
4461866 3326.1.1.1 alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.53 43.0 3.56e-01 100.0% 82.7%
3475200 223.2.1.33 a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_3 0.52 43.0 3.44e-01 100.0% 48.5%
3439990 220.1.1.76 beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.52 41.0 3.54e-01 96.2% 54.4%
3978292 2484.1.1.251 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF26691 0.51 41.0 2.55e-01 100.0% 60.0%
4462824 2003.1.5.174 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_15 0.51 39.0 2.47e-01 92.5% 25.6%
4373832 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.51 39.0 3.24e-01 88.7% 67.6%
3719687 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 40.0 3.64e-01 96.2% 65.3%