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SR-VP_0-2_scaffold_141_5191495_prodigal-single.1__X__X__00141

Bact-Vir

SR-VP_0-2_scaffold_141_5191495_prodigal-single.1__X__X__00141

Identity

Kingdom:
phage

Quality

62.2 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 55-136
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5jajA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.73 58.0 5.19e-01 86.6% 90.5%
4u04B01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.70 41.0 4.09e-01 100.0% 54.5%
2juaA00 1.20.1480.30 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › Designed four-helix bundle protein 0.70 55.0 5.12e-01 85.4% 100.0%
2qgmA03 1.20.1440.30 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Biosynthetic Protein domain 0.69 53.0 4.73e-01 82.9% 73.3%
2yw6B00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.67 61.0 4.94e-01 100.0% 87.3%
1sumB02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.65 44.0 3.96e-01 70.7% 71.2%
2clbA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.64 57.0 4.62e-01 100.0% 83.6%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.63 56.0 4.92e-01 100.0% 72.6%
1bgcA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.62 48.0 3.94e-01 85.4% 58.9%
2guzB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.62 44.0 4.87e-01 79.3% 95.4%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.60 46.0 4.93e-01 100.0% 95.8%
1ugoA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.60 43.0 4.05e-01 74.4% 96.0%
2a0uB01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.59 53.0 4.24e-01 98.8% 68.8%
4ag6A02 1.10.8.730 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.59 49.0 4.51e-01 93.9% 80.9%
1aluA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 45.0 3.71e-01 85.4% 61.8%
2ynqB00 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.58 46.0 3.84e-01 100.0% 48.3%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.57 46.0 4.83e-01 95.1% 98.7%
3ajfA00 1.20.1440.190 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tenuivirus movement protein 0.55 47.0 4.57e-01 98.8% 92.4%
2y8nA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.55 47.0 2.74e-01 100.0% 72.5%
5hayA02 1.25.40.440 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain 0.54 45.0 4.62e-01 93.9% 96.2%
1tjcA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 47.0 4.52e-01 100.0% 91.6%
1np7A02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 40.0 3.59e-01 100.0% 57.1%
1kn1B00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.53 41.0 3.32e-01 84.1% 100.0%
1x4qA01 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.52 39.0 4.08e-01 87.8% 93.0%
1u3dA02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.52 41.0 3.54e-01 100.0% 53.0%
1t98A02 1.20.58.590 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Chromosome partition protein MukF, middle domain 0.52 42.0 3.33e-01 86.6% 83.4%
2i6hA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 42.0 3.97e-01 90.2% 72.9%
3ujpB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.51 38.0 3.19e-01 80.5% 89.9%
2pgeA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.50 43.0 3.79e-01 96.3% 95.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3969284 633.28.1.2 ↗ alpha bundles › Bromodomain-like › Tsi6 › Tsi6 › DUF4404 0.81 63.0 6.36e-01 81.7% 100.0%
3542709 3861.1.1.1 ↗ alpha bundles › Mitochondrial translocator protein (TSPO) › Mitochondrial translocator protein (TSPO) › Mitochondrial translocator protein (TSPO) › TspO_MBR 0.78 71.0 5.61e-01 100.0% 85.5%
3733145 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.78 61.0 5.05e-01 82.9% 92.9%
3489712 103.1.1.106 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › BBS1 0.75 49.0 5.27e-01 72.0% 78.6%
4295608 633.16.1.0 ↗ alpha bundles › Bromodomain-like › PMT helical bundle domain-like › PMT helical bundle domain-like 0.69 58.0 5.63e-01 91.5% 88.9%
5072852 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.66 55.0 3.51e-01 90.2% 20.8%
3400447 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.65 61.0 4.31e-01 100.0% 54.3%
4936706 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.65 47.0 3.17e-01 90.2% 20.4%
3402481 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.64 49.0 4.33e-01 85.4% 90.0%
3261428 622.4.1.0 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.61 43.0 3.69e-01 73.2% 84.6%
4966881 2006.1.4.50 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF3368 0.60 45.0 3.58e-01 100.0% 38.8%
4994134 2006.1.4.50 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF3368 0.60 45.0 3.57e-01 100.0% 39.3%
4950367 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.60 45.0 3.82e-01 79.3% 60.0%
3177396 109.4.1.237 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Wap1 0.59 53.0 3.35e-01 97.6% 37.8%
2104833 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 51.0 4.01e-01 100.0% 54.4%
5001522 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 50.0 4.57e-01 100.0% 88.3%
5050625 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 47.0 3.87e-01 100.0% 85.2%
5009130 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.53 45.0 3.04e-01 98.8% 55.9%
5041215 2006.1.4.50 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF3368 0.52 42.0 3.43e-01 89.0% 86.9%
5040916 2006.1.4.50 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF3368 0.52 45.0 3.55e-01 96.3% 96.6%
4970118 2006.1.4.50 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › DUF3368 0.51 46.0 3.60e-01 100.0% 97.1%
3973307 2007.1.14.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.51 45.0 3.71e-01 100.0% 95.5%
4999301 4156.1.1.0 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.51 45.0 4.09e-01 100.0% 88.7%
D2 high residues 251-342
PDB
Domain cluster: representative
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ukfA00 3.90.70.20 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.67 59.0 4.76e-01 100.0% 59.0%
3zxkA02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.64 58.0 4.40e-01 100.0% 69.9%
2wsuB02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.63 54.0 4.71e-01 95.7% 87.5%
2ox7A02 2.30.30.290 Mainly Beta › Roll › SH3 type barrels. › YopX-like domains 0.62 42.0 4.62e-01 85.9% 92.8%
2jkdB00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.61 47.0 4.07e-01 83.7% 74.0%
5nldB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 54.0 4.71e-01 98.9% 89.1%
4ozxA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 52.0 3.76e-01 100.0% 67.7%
4agrB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 52.0 4.53e-01 97.8% 86.8%
4azpA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.59 40.0 3.52e-01 72.8% 47.8%
1h30A01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.57 50.0 3.95e-01 100.0% 83.7%
3u1xA00 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.57 50.0 3.87e-01 100.0% 71.0%
3ligA02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.57 50.0 4.09e-01 97.8% 83.4%
1o70A01 2.30.180.10 Mainly Beta › Roll › FAS1 domain › FAS1 domain 0.56 39.0 3.41e-01 71.7% 75.0%
1u17A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.56 45.0 3.67e-01 89.1% 92.4%
1w2tA02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.56 49.0 4.34e-01 97.8% 79.1%
1pz7A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 48.0 3.86e-01 98.9% 77.1%
1srqA01 3.30.1120.160 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.55 39.0 3.44e-01 73.9% 58.7%
2nvnA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.54 37.0 3.46e-01 72.8% 96.7%
2v43A01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.53 42.0 3.46e-01 88.0% 86.9%
1z24A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 42.0 3.41e-01 89.1% 67.7%
4f78A01 3.30.200.180 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › 0.52 36.0 3.49e-01 73.9% 62.5%
2rcqA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 41.0 3.68e-01 90.2% 97.2%
3mazA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.52 42.0 4.14e-01 94.6% 84.8%
7u6rA01 2.60.120.960 Mainly Beta › Sandwich › Jelly Rolls › Spike glycoprotein, N-terminal domain 0.51 44.0 3.25e-01 100.0% 77.6%
2rrfA00 2.30.29.160 Mainly Beta › Roll › PH-domain like › Zinc finger FYVE domain-containing protein 21, C-terminal 0.51 37.0 3.23e-01 76.1% 72.3%
5ay6A01 2.60.98.20 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › Flagellar hook protein FlgE 0.51 41.0 3.38e-01 89.1% 97.1%
4dq2A03 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 27.0 3.46e-01 75.0% 100.0%
2wzoA01 3.30.160.360 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.50 44.0 3.92e-01 97.8% 89.5%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2582130 219.1.1.117 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › PF30660 0.71 64.0 4.59e-01 100.0% 45.7%
2526334 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.66 58.0 4.66e-01 100.0% 55.0%
3427234 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.60 54.0 3.95e-01 100.0% 88.2%
3734714 2008.1.1.143 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7924 0.59 45.0 3.32e-01 82.6% 79.6%
3228242 4210.1.1.1 ↗ a+b two layers › WGR domain › WGR domain › WGR domain › WGR 0.59 44.0 4.31e-01 79.3% 97.0%
3607434 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.59 49.0 4.34e-01 91.3% 91.1%
3735680 2008.1.1.143 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7924 0.59 50.0 3.53e-01 93.5% 63.4%
3287652 3844.2.1.1 ↗ a+b two layers › hydrogenase expression protein-like › MybT EspG5 chaperone › MybT EspG5 chaperone › ESX-1_EspG 0.59 42.0 3.06e-01 75.0% 50.0%
3179238 3504.3.1.1 ↗ beta barrels › MutM N-terminal domain-like › Fibrinogen binding protein N-terminal domain › Fibrinogen binding protein N-terminal domain › NFACT_N 0.58 41.0 3.34e-01 75.0% 46.1%
3627339 10.1.1.1 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_1 0.58 50.0 3.94e-01 97.8% 62.0%
3787118 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.58 52.0 3.49e-01 100.0% 66.0%
159262 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.58 50.0 3.96e-01 98.9% 69.3%
5002658 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 51.0 4.09e-01 100.0% 74.6%
3712908 9.1.1.4 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › META 0.57 41.0 3.95e-01 77.2% 100.0%
3279607 9.3.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like 0.57 41.0 4.04e-01 77.2% 98.0%
3710203 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.56 50.0 3.25e-01 100.0% 73.0%
4928923 4200.1.1.0 ↗ beta barrels › YmcC-like › YmcC-like › YmcC-like 0.56 44.0 3.56e-01 85.9% 97.9%
3614247 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 39.0 3.57e-01 75.0% 87.2%
3927305 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 37.0 3.56e-01 70.7% 90.0%
5038023 206.1.3.41 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_Ter 0.54 46.0 3.21e-01 98.9% 26.7%
3946522 9.1.1.36 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › DUF3833 0.54 43.0 3.72e-01 89.1% 100.0%
3600529 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.54 40.0 3.83e-01 77.2% 100.0%
3401140 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.54 47.0 3.00e-01 95.7% 94.4%
3323208 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.54 44.0 3.47e-01 88.0% 67.4%
3722420 2008.1.1.143 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7924 0.54 41.0 3.48e-01 82.6% 83.1%
3999814 3131.1.1.1 ↗ a+b two layers › FYR domain › FYR domain › FYR domain › FYRN,FYRC 0.54 48.0 3.86e-01 97.8% 86.3%
3491787 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.53 38.0 2.94e-01 75.0% 65.2%
3209857 2008.1.1.143 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › DUF7924 0.53 42.0 3.43e-01 87.0% 67.2%
3163979 71.1.1.4 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › MucB_RseB 0.53 42.0 3.40e-01 88.0% 84.7%
3463325 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.53 47.0 3.45e-01 100.0% 67.1%
3804264 64.1.1.8 ↗ beta meanders › WW domain-like › WW domain › WW domain › DUF7028 0.50 39.0 4.11e-01 84.8% 94.1%
4298074 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.50 44.0 3.58e-01 97.8% 89.1%
D3 high residues 382-512
PDB