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SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00172

Bact-Vir

SR-VP_2-4_scaffold_141_2952615_prodigal-single.1__X__X__00172

Identity

Kingdom:
phage

Quality

68.8 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 (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xzmO02 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.75 44.0 4.91e-01 80.5% 74.3%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.68 35.0 3.96e-01 92.0% 65.2%
4hcsA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.67 35.0 3.94e-01 86.2% 65.7%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.66 38.0 4.14e-01 73.6% 67.6%
3zfnA02 2.30.140.40 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Pestivirus Npro endopeptidase C53, interaction domain 0.66 33.0 3.95e-01 95.4% 71.9%
2eyqA05 2.40.10.170 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.65 37.0 4.32e-01 96.6% 81.4%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.61 49.0 4.23e-01 87.4% 75.0%
1icwB00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 34.0 3.86e-01 90.8% 71.2%
1txdA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 41.0 3.65e-01 70.1% 97.5%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.60 37.0 4.09e-01 77.0% 80.6%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.60 42.0 3.87e-01 88.5% 57.8%
4hasA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.59 43.0 4.07e-01 100.0% 64.4%
6cz7A01 2.20.25.90 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ADC-like domains 0.59 33.0 3.84e-01 93.1% 77.4%
3mkcA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 49.0 4.17e-01 92.0% 70.1%
1xlyA00 1.20.200.20 Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › She2 domain 0.58 52.0 3.88e-01 100.0% 89.7%
3pvlA04 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 42.0 4.07e-01 96.6% 66.7%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.58 33.0 4.11e-01 97.7% 100.0%
4qxaB00 2.30.29.230 Mainly Beta › Roll › PH-domain like › 0.58 39.0 3.34e-01 70.1% 59.2%
1e0bA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 30.0 3.44e-01 93.1% 70.5%
1gutA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.56 38.0 4.28e-01 98.9% 92.5%
3fdjA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.56 38.0 3.41e-01 71.3% 79.7%
1rl2A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 32.0 3.76e-01 88.5% 85.7%
2czoA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.55 47.0 4.21e-01 98.9% 96.9%
2fhdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.54 31.0 3.59e-01 97.7% 79.0%
3ei3A02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 44.0 2.96e-01 87.4% 99.4%
3n4eA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 45.0 4.30e-01 92.0% 92.3%
6bm0A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.54 44.0 2.89e-01 88.5% 97.9%
1x1fA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.54e-01 85.1% 61.1%
8gq6A01 2.120.10.80 Mainly Beta › 6 Propeller › Neuraminidase › Kelch-type beta propeller 0.52 43.0 3.00e-01 90.8% 99.7%
3ddmA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 44.0 3.95e-01 93.1% 86.4%
3oajA02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.52 32.0 2.79e-01 88.5% 37.5%
2wweA01 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.52 42.0 3.97e-01 88.5% 100.0%
4bwgD00 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 36.0 3.51e-01 87.4% 64.9%
2gdqA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 4.04e-01 90.8% 89.7%
1x6oA02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.52 37.0 3.90e-01 96.6% 86.1%
2db2A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 36.0 3.54e-01 98.9% 67.0%
3msyA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.97e-01 90.8% 89.2%
4dxkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.52 43.0 3.80e-01 90.8% 72.0%
3i6eA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 44.0 4.15e-01 93.1% 94.2%
2wfwB02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 32.0 3.54e-01 96.6% 82.1%
5aigA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 38.0 3.41e-01 100.0% 54.8%
2oqhA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 43.0 3.93e-01 92.0% 80.7%
4jn7A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 42.0 3.81e-01 90.8% 77.3%
1vkdA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 38.0 2.65e-01 82.8% 44.5%
1d8cA03 1.20.1220.12 Mainly Alpha › Up-down Bundle › Malate Synthase G; Chain: A; Domain 4 › Malate synthase, domain III 0.50 37.0 3.22e-01 100.0% 50.4%
5cxbA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.50 36.0 2.46e-01 75.9% 63.2%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5023580 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.71 43.0 4.89e-01 87.4% 81.5%
3259095 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 44.0 3.90e-01 87.4% 49.2%
3891033 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.65 35.0 3.86e-01 88.5% 63.0%
1094905 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.64 36.0 3.94e-01 88.5% 67.1%
4093535 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.64 45.0 3.90e-01 88.5% 48.5%
4014812 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.64 34.0 3.98e-01 90.8% 73.3%
3924597 330.16.1.0 ↗ a+b two layers › dsRBD-like › ODA16 N-terminal domain › ODA16 N-terminal domain 0.64 38.0 4.13e-01 87.4% 72.9%
3483806 295.1.1.3 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › PurA 0.63 51.0 4.30e-01 88.5% 78.7%
5004718 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 52.0 4.32e-01 90.8% 53.5%
3547409 604.1.1.153 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF4455 0.63 38.0 2.95e-01 77.0% 26.0%
2095508 1170.1.2.4 ↗ beta barrels › IL8-related › IL8-related › chemokine-related domain in glycoprotein L (gL) › Gp_UL130 0.62 34.0 3.64e-01 93.1% 60.8%
4140296 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.62 45.0 3.79e-01 87.4% 47.1%
3508714 295.1.1.29 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › YjeJ 0.61 52.0 4.28e-01 94.3% 78.8%
4483150 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.61 51.0 4.19e-01 100.0% 50.0%
3942738 295.1.1.29 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › YjeJ 0.61 49.0 4.06e-01 87.4% 76.8%
4674129 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 42.0 3.95e-01 88.5% 60.0%
3241447 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.60 44.0 3.96e-01 78.2% 100.0%
4077485 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 40.0 4.59e-01 96.6% 93.8%
4932378 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.59 32.0 3.71e-01 92.0% 75.0%
3629460 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.59 40.0 2.81e-01 70.1% 39.6%
3889863 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.59 49.0 4.44e-01 100.0% 66.7%
5011439 802.1.1.0 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 0.59 48.0 4.08e-01 89.7% 97.9%
3933293 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 31.0 3.67e-01 88.5% 75.9%
4985853 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.58 47.0 4.02e-01 88.5% 75.7%
4203238 220.1.1.217 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH, GRAM 0.57 45.0 3.23e-01 83.9% 85.6%
3694693 4.8.1.2 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_shadow 0.57 32.0 3.55e-01 92.0% 70.8%
3810543 220.1.1.20 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_TFIIH 0.56 41.0 3.83e-01 88.5% 60.9%
3705072 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.56 45.0 4.12e-01 87.4% 87.0%
3546312 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.56 46.0 4.25e-01 88.5% 100.0%
3627778 220.1.1.64 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C1_MyoVII 0.56 40.0 3.91e-01 96.6% 66.0%
4399169 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.56 32.0 3.79e-01 89.7% 83.3%
4977784 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.56 38.0 2.89e-01 81.6% 26.4%
3935835 2.1.1.68 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › RMI1_C 0.56 41.0 3.58e-01 79.3% 70.7%
4973274 2.1.1.2 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Ribosomal_L2 0.55 31.0 3.74e-01 85.1% 87.3%
3718148 2484.8.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) 0.55 44.0 3.14e-01 89.7% 31.9%
4971091 802.1.1.1 ↗ a+b two layers › Hypothetical protein TM0160 › Hypothetical protein TM0160 › Hypothetical protein TM0160 › BFN_dom 0.55 47.0 4.02e-01 92.0% 77.0%
4667221 2003.1.2.8 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2,Pyr_redox_2 0.54 48.0 3.71e-01 97.7% 93.3%
3933294 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.54 41.0 3.89e-01 90.8% 67.6%
5057564 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.54 40.0 3.37e-01 81.6% 70.6%
3257603 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.53 43.0 3.89e-01 88.5% 92.5%
3793797 5.1.5.93 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Beta-prop_EMC1_N 0.53 39.0 2.70e-01 78.2% 47.8%
3930846 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.53 29.0 3.20e-01 89.7% 62.9%
4002892 109.4.1.2561 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FATC 0.53 36.0 2.21e-01 87.4% 10.1%
3601482 5.1.4.17 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A,MMS1_N 0.53 42.0 2.43e-01 86.2% 45.1%
3412753 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 43.0 2.86e-01 89.7% 95.5%
3787501 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.53 45.0 3.94e-01 98.9% 100.0%
3439990 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.52 37.0 3.71e-01 87.4% 71.1%
3478410 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 39.0 2.57e-01 100.0% 20.0%
3542914 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.52 43.0 3.98e-01 95.4% 90.8%
3247746 5.1.4.303 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › BBS2_N, BBS2_Mid 0.52 38.0 2.67e-01 78.2% 49.5%
3742938 4.1.1.102 ↗ beta barrels › SH3 › SH3 › SH3 › Tudor_3 0.52 30.0 3.38e-01 97.7% 75.4%
3485043 267.1.1.3 ↗ a+b complex topology › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Metal cation-transporting ATPase, ATP-binding domain › Cation_ATPase 0.52 43.0 3.19e-01 93.1% 47.8%
3744517 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.52 40.0 3.70e-01 86.2% 91.7%
3914347 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.51 41.0 3.60e-01 88.5% 89.6%
4110527 5.1.4.322 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, ANAPC4_WD40, Beta-prop_IFT122_1st 0.51 42.0 2.95e-01 92.0% 95.1%
3894035 5.1.4.12 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Sema 0.51 43.0 2.80e-01 100.0% 41.1%
3880705 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.51 45.0 4.02e-01 100.0% 100.0%
4346865 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.50 42.0 4.16e-01 92.0% 97.9%
3364309 220.1.1.76 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_2 0.50 36.0 3.16e-01 87.4% 50.8%
3924612 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.50 35.0 3.16e-01 75.9% 53.3%