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MT114166.1__QIQ63677.1__SEA_NIKE_97__00097

Bact-Vir

MT114166.1__QIQ63677.1__SEA_NIKE_97__00097

Identity

Accession:
MT114166 ↗
Kingdom:
phage

Quality

75.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Squashvirus› Microbacterium_phage_Nike

TaxID: 2719203

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 medium residues 4-75
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e7wA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.74 45.0 3.86e-01 88.9% 38.7%
3cqyB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 58.0 4.32e-01 93.1% 78.3%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 49.0 4.35e-01 76.4% 67.6%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 41.0 3.61e-01 79.2% 42.7%
3k6qA02 3.30.160.620 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.67 52.0 4.86e-01 84.7% 95.5%
1w1hD00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.67 38.0 3.07e-01 80.6% 29.9%
2yt4A03 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.66 45.0 4.00e-01 75.0% 50.0%
1w6kA01 6.20.120.20 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 32.0 3.66e-01 93.1% 68.0%
1ynjJ02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.61 38.0 4.11e-01 77.8% 74.2%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.60 45.0 3.71e-01 83.3% 97.9%
2hj1A00 3.10.20.280 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RnfH-like 0.60 44.0 4.31e-01 81.9% 74.0%
3js6A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 50.0 3.75e-01 100.0% 87.6%
1okjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 51.0 4.26e-01 98.6% 79.5%
7oode01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.58 39.0 4.07e-01 70.8% 100.0%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 48.0 3.83e-01 100.0% 88.1%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.56 48.0 4.20e-01 100.0% 78.1%
4chjA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 37.0 3.17e-01 80.6% 40.3%
3l09A02 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 0.56 41.0 3.98e-01 80.6% 92.9%
8oqxA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 43.0 3.86e-01 94.4% 87.7%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 47.0 4.38e-01 98.6% 90.1%
2aehA03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 43.0 3.75e-01 91.7% 57.7%
2y8nB02 2.20.70.100 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.53 30.0 3.47e-01 81.9% 86.4%
2cs7A00 3.10.50.90 Alpha Beta › Roll › Chitinase A; domain 3 › 0.53 29.0 3.25e-01 83.3% 69.1%
3zmdA00 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 0.53 38.0 3.05e-01 76.4% 50.7%
7whgG02 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 40.0 3.75e-01 84.7% 94.6%
3v3kD00 1.20.1260.90 Mainly Alpha › Up-down Bundle › Ferritin › 0.52 35.0 2.74e-01 70.8% 68.3%
1el6A03 3.90.1160.10 Alpha Beta › Alpha-Beta Complex › Baseplate Structural Protein Gp11; Chain: A, domain 3 › Baseplate structural protein gp11, finger domain 0.51 42.0 3.81e-01 97.2% 80.7%
2qq6A01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 44.0 3.83e-01 100.0% 95.7%
2yyzA02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.51 33.0 3.55e-01 79.2% 79.3%
8dvhB01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 36.0 2.80e-01 77.8% 52.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.50 39.0 3.04e-01 86.1% 63.5%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3267918 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.72 45.0 5.08e-01 86.1% 83.6%
3319893 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.68 46.0 4.17e-01 70.8% 72.0%
3518065 220.1.1.2 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › WH1 0.68 40.0 3.19e-01 80.6% 31.1%
4992470 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.68 39.0 4.25e-01 80.6% 68.3%
4376375 2484.1.1.49 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydant_A_N 0.67 59.0 4.70e-01 98.6% 92.4%
3934686 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.67 48.0 4.36e-01 75.0% 67.4%
3930408 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.66 50.0 4.91e-01 83.3% 88.7%
3926600 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.64 39.0 3.42e-01 79.2% 40.0%
5001332 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.63 50.0 3.04e-01 90.3% 53.0%
3861121 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.62 39.0 3.34e-01 79.2% 40.0%
4874839 880.1.1.4 ↗ a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › PF30495 0.62 42.0 2.76e-01 70.8% 80.2%
5013176 4100.1.1.0 ↗ a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.62 47.0 4.65e-01 90.3% 81.3%
3520779 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.61 38.0 3.26e-01 79.2% 38.3%
5067321 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 51.0 4.83e-01 98.6% 93.3%
3699329 70.3.1.1 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.60 43.0 2.75e-01 97.2% 15.2%
3512572 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.60 50.0 3.93e-01 100.0% 44.8%
4249934 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.60 50.0 4.33e-01 98.6% 93.3%
4225322 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.60 38.0 4.00e-01 83.3% 72.3%
4967222 3115.1.1.1 ↗ a+b two layers › GP2-like › RplX-like › RplX-like › Ribosomal_L18A 0.59 44.0 4.70e-01 84.7% 95.0%
5042618 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.58 39.0 4.05e-01 100.0% 76.9%
3906424 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.56 43.0 3.45e-01 93.1% 42.1%
3891866 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.56 42.0 3.36e-01 91.7% 41.4%
3531915 221.4.1.25 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › PF31008 0.55 45.0 3.53e-01 94.4% 88.8%
4144736 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.55 47.0 4.11e-01 100.0% 92.2%
3966122 4035.1.1.1 ↗ a+b three layers › N-terminal a+b domain in adenylylcyclase toxin › N-terminal a+b domain in adenylylcyclase toxin › N-terminal a+b domain in adenylylcyclase toxin › Anthrax_toxA 0.55 49.0 3.49e-01 100.0% 63.8%
3720090 221.4.1.25 ↗ a+b two layers › beta-Grasp › Nudix › Nudix › PF31008 0.54 45.0 3.37e-01 93.1% 83.7%
3556135 220.1.1.49 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Carm_PH 0.54 42.0 3.30e-01 91.7% 40.0%
3386854 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 47.0 3.45e-01 98.6% 92.7%
3391824 220.1.1.60 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › ECT2_PH 0.54 45.0 3.63e-01 100.0% 46.9%
4091986 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 47.0 4.06e-01 100.0% 93.9%
3197622 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.53 38.0 3.35e-01 75.0% 75.2%
4013529 7579.1.1.0 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.53 46.0 3.13e-01 98.6% 81.3%
4861971 4099.1.1.3 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Spc24 0.53 35.0 4.01e-01 75.0% 100.0%
3238074 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.53 44.0 3.10e-01 91.7% 43.6%
3678667 304.31.1.1 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase › HMG-CoA_red 0.52 41.0 3.93e-01 87.5% 80.0%
3287739 304.48.1.48 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › GGDEF_2 0.52 40.0 3.22e-01 86.1% 70.3%
4626818 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.51 44.0 3.95e-01 100.0% 94.3%
4297114 2008.1.1.107 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NERD 0.51 41.0 3.21e-01 91.7% 40.6%
2966283 224.1.1.2 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like › Gelsolin 0.51 40.0 3.46e-01 87.5% 73.1%
4980224 324.1.1.1 ↗ a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC 0.51 37.0 3.14e-01 77.8% 63.2%
3242105 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.51 43.0 3.12e-01 93.1% 61.5%
3262357 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 37.0 2.91e-01 76.4% 63.3%
D2 medium residues 79-115
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1xqrA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.74 51.0 3.03e-01 73.0% 25.5%
7c4sB01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.70 55.0 3.28e-01 89.2% 33.0%
2r18A02 1.10.8.880 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Birnavirus VP3 protein, domain 2 0.69 58.0 5.12e-01 100.0% 74.6%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 51.0 3.83e-01 83.8% 34.8%
4bzaA01 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.65 55.0 4.59e-01 100.0% 63.2%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.64 48.0 4.53e-01 81.1% 73.3%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.62 49.0 4.14e-01 94.6% 52.5%
2nrkA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 50.0 3.28e-01 91.9% 83.6%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.59 51.0 4.03e-01 100.0% 68.4%
4a64A01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.59 46.0 3.19e-01 83.8% 23.5%
2i06A02 3.30.54.10 Alpha Beta › 2-Layer Sandwich › Replication Terminator Protein; Chain A, domain 2 › 0.58 49.0 3.87e-01 94.6% 46.8%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3798353 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.68 52.0 3.43e-01 83.8% 52.0%
5030243 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.68 55.0 4.85e-01 100.0% 60.0%
3969538 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.67 50.0 4.42e-01 81.1% 94.5%
3283657 4177.1.1.142 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › WXG100 0.67 50.0 3.14e-01 83.8% 14.4%
3602408 4271.1.1.0 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like 0.66 52.0 3.39e-01 100.0% 22.0%
5038847 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.65 49.0 3.92e-01 81.1% 52.9%
4062237 604.11.1.1 ↗ alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S 0.63 48.0 3.96e-01 83.8% 52.9%
3189639 4146.1.1.0 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.63 54.0 4.57e-01 100.0% 96.9%
3394141 601.6.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › TMV-like viral coat proteins › TMV-like viral coat proteins › TMV_coat 0.63 56.0 3.69e-01 100.0% 57.7%
4416633 604.11.1.1 ↗ alpha bundles › Spectrin repeat-like › XseB-like › XseB-like › Exonuc_VII_S 0.62 49.0 4.14e-01 94.6% 53.3%
3742339 1128.1.1.3 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › UQCC2_CBP6 0.62 52.0 4.55e-01 100.0% 96.7%
3821485 2004.1.1.71 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › IPPT 0.61 51.0 3.02e-01 100.0% 19.0%
3961960 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.60 51.0 3.87e-01 97.3% 43.3%
3634542 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.59 52.0 3.38e-01 100.0% 92.1%
3685719 316.1.1.36 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.59 44.0 3.00e-01 100.0% 41.1%
3315337 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.58 49.0 3.08e-01 100.0% 17.4%
4094062 3877.1.1.1 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP 0.58 46.0 2.97e-01 100.0% 17.3%
3968853 2498.4.1.0 ↗ mixed a+b and a/b › Zincin-like › HSP90 C-terminal domain (C-terminal part of Pfam 00183) › HSP90 C-terminal domain (C-terminal part of Pfam 00183) 0.55 47.0 3.18e-01 100.0% 69.3%
4643887 1079.1.1.1 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › DsbD 0.53 47.0 2.84e-01 100.0% 17.3%
3930451 386.1.1.10 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › MAT1 0.53 44.0 3.86e-01 97.3% 85.0%