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OR159669.1__WKW86691.1__SEA_KARHDO_65__00065

Bact-Vir

OR159669.1__WKW86691.1__SEA_KARHDO_65__00065

Identity

Accession:
OR159669 ↗
Kingdom:
phage

Quality

62.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Cheoctovirus› Mycobacterium_phage_Karhdo

TaxID: 3062843

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 6-75
PDB
Domain cluster: rep: NC_011285.1__YP_002241455.1__TROLL4_41__00041__D3-55
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF07411.18 best DUF1508 29.8 6.10e-07 58.6% 68.8%
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2k49A00 2.30.29.80 Mainly Beta › Roll › PH-domain like › 0.79 66.0 5.48e-01 90.0% 93.2%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.73 50.0 5.05e-01 71.4% 78.9%
2ap1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.72 61.0 4.92e-01 95.7% 96.4%
4ijaB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.70 61.0 4.71e-01 97.1% 63.7%
2w40A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 61.0 4.15e-01 100.0% 93.3%
4hkqA04 3.10.20.370 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.69 52.0 5.07e-01 81.4% 93.4%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 44.0 3.87e-01 100.0% 43.1%
4htlA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.68 59.0 5.30e-01 100.0% 95.0%
3t69A01 3.30.420.300 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, substrate binding domain 0.67 54.0 5.35e-01 90.0% 100.0%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 57.0 5.19e-01 98.6% 95.9%
4v19S00 3.30.420.80 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribosomal protein S11/S14 0.66 58.0 4.64e-01 100.0% 67.8%
1xc3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.66 56.0 5.04e-01 100.0% 94.2%
3ungC03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.65 48.0 3.97e-01 81.4% 98.5%
5umsA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 47.0 4.25e-01 91.4% 54.9%
1bqnA05 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.64 56.0 4.63e-01 100.0% 72.5%
4eo3A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.64 44.0 3.63e-01 72.9% 82.6%
2o1uB01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.62 53.0 4.11e-01 98.6% 93.3%
1fs0G01 3.40.1380.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › ATP synthase, F1 complex, gamma subunit 0.62 55.0 4.50e-01 100.0% 86.9%
3id6A01 3.30.420.220 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.62 55.0 4.79e-01 100.0% 72.6%
1vhxB00 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.61 52.0 4.25e-01 98.6% 64.5%
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.61 52.0 4.18e-01 100.0% 50.7%
3qtgA03 3.40.1380.20 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate Kinase; Chain: A, domain 1 › Pyruvate kinase, C-terminal domain 0.60 53.0 4.50e-01 98.6% 73.9%
7eqiA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.60 52.0 4.13e-01 100.0% 51.6%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.60 41.0 3.19e-01 72.9% 30.9%
3hrgA01 3.30.420.250 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, N-terminal domain 0.60 51.0 4.11e-01 98.6% 88.8%
6z9uA01 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.59 35.0 3.31e-01 98.6% 48.2%
1u6eA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.59 51.0 4.04e-01 100.0% 52.0%
2hjjA00 3.30.160.130 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › ykff protein like domains 0.58 41.0 4.19e-01 100.0% 77.3%
1wv8A00 3.30.2390.10 Alpha Beta › 2-Layer Sandwich › TTHA1013/TTHA0281-like › TTHA1013-like 0.58 46.0 4.68e-01 90.0% 91.5%
4wz9A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 43.0 4.03e-01 81.4% 98.9%
1eotA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 38.0 3.76e-01 98.6% 63.5%
4qxaB00 2.30.29.230 Mainly Beta › Roll › PH-domain like › 0.57 47.0 3.87e-01 100.0% 52.4%
1jofA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 49.0 3.12e-01 100.0% 99.2%
1a0rB00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 49.0 3.14e-01 100.0% 74.9%
3sm3A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 39.0 2.83e-01 74.3% 97.2%
7jl1B01 2.60.120.920 Mainly Beta › Sandwich › Jelly Rolls › SPRY domain 0.55 40.0 3.08e-01 98.6% 35.1%
2i5tA00 3.10.490.10 Alpha Beta › Roll › Hypothetical upf0131 protein ytfp › Gamma-glutamyl cyclotransferase-like 0.53 41.0 3.22e-01 87.1% 72.2%
3fovA00 3.40.1350.10 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.52 38.0 3.39e-01 77.1% 72.5%
1v1aA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.52 44.0 3.00e-01 100.0% 61.5%
1vm7B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 44.0 3.00e-01 100.0% 69.0%
3ljsA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 43.0 2.92e-01 100.0% 69.3%
1ikpA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 46.0 3.16e-01 97.1% 32.3%
3fgbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.51 43.0 2.81e-01 98.6% 99.7%
2byvE05 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 38.0 3.72e-01 82.9% 77.2%
2oa9B02 3.30.70.3570 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › MvaI/BcnI restriction endonuclease, recognition domain 0.51 41.0 3.40e-01 95.7% 48.8%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 43.0 3.15e-01 97.1% 51.9%
5c40B00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.50 42.0 2.85e-01 100.0% 68.6%
4o1gA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.50 41.0 2.79e-01 98.6% 58.2%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4297945 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.88 59.0 6.61e-01 70.0% 87.3%
3284714 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.88 60.0 6.29e-01 71.4% 77.8%
7726 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.87 59.0 6.46e-01 71.4% 84.5%
4188237 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.87 59.0 6.63e-01 71.4% 89.1%
5075465 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.85 58.0 6.22e-01 71.4% 81.7%
3954708 4325.1.1.9 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › PF26003 0.79 52.0 6.09e-01 70.0% 96.0%
4952072 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.78 52.0 5.92e-01 70.0% 96.0%
119245 252.3.1.1 ↗ a+b two layers › DNA-binding domain › Uncharacterized protein yaiA › Uncharacterized protein yaiA › YaiA 0.73 50.0 5.05e-01 71.4% 78.9%
4584783 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 0.72 54.0 4.82e-01 92.9% 57.0%
4156379 2484.1.1.41 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › AnmK 0.71 63.0 4.77e-01 98.6% 97.6%
3977273 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.70 61.0 4.87e-01 98.6% 70.7%
4944977 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.69 60.0 4.98e-01 100.0% 98.5%
4345436 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.68 63.0 6.15e-01 100.0% 100.0%
5047317 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.68 58.0 5.48e-01 95.7% 96.5%
1307002 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 0.67 59.0 4.96e-01 98.6% 81.0%
4420316 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.67 58.0 4.23e-01 98.6% 65.0%
4485089 2484.1.1.8 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › ROK 0.67 59.0 4.66e-01 100.0% 66.7%
5005971 304.48.1.31 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Cas10-Cmr2_palm2 0.67 51.0 2.96e-01 82.9% 27.4%
3954516 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.67 57.0 4.83e-01 97.1% 63.3%
3716107 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 0.67 47.0 4.85e-01 80.0% 80.3%
4431514 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.65 56.0 4.49e-01 97.1% 60.7%
3719687 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 48.0 4.73e-01 91.4% 74.7%
3971108 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 54.0 5.01e-01 95.7% 95.6%
4930787 315.1.1.0 ↗ a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF 0.64 45.0 3.87e-01 100.0% 47.3%
5032371 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 0.64 46.0 4.66e-01 81.4% 78.6%
4639619 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.63 53.0 4.25e-01 97.1% 80.7%
3217858 220.1.1.37 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_13 0.62 43.0 3.24e-01 74.3% 32.6%
3349450 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.62 49.0 4.20e-01 98.6% 52.5%
3250619 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 44.0 3.87e-01 100.0% 49.1%
None — 0.61 51.0 3.79e-01 98.6% 77.4%
4307499 2484.1.1.40 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvX 0.61 52.0 4.21e-01 98.6% 60.7%
4948156 2004.5.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain 0.61 54.0 3.73e-01 100.0% 49.4%
3961445 7581.1.1.12 ↗ a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › ACP_syn_III_C 0.61 53.0 5.15e-01 100.0% 91.3%
3692758 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.60 50.0 3.02e-01 90.0% 27.3%
3510425 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.58 43.0 3.34e-01 100.0% 35.5%
4274357 244.2.1.6 ↗ 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 › Rbx_binding 0.57 38.0 3.89e-01 70.0% 100.0%
3227570 220.1.1.47 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_16 0.56 41.0 3.16e-01 97.1% 32.4%
4392365 5.1.4.35 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Lactonase 0.56 50.0 3.21e-01 100.0% 100.0%
3630687 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 43.0 3.40e-01 100.0% 39.3%
4169299 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.56 48.0 4.22e-01 100.0% 66.1%
3523477 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.55 43.0 3.18e-01 100.0% 31.9%
3778135 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.55 43.0 3.38e-01 100.0% 39.3%
3618917 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 38.0 3.36e-01 91.4% 46.4%
4994452 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.55 37.0 3.35e-01 70.0% 77.9%
4591449 7556.1.1.1 ↗ a/b three-layered sandwiches › Fe-only hydrogenase › Fe-only hydrogenase › Fe-only hydrogenase › Fe_hyd_lg_C 0.55 45.0 2.86e-01 97.1% 43.2%
3411578 220.1.1.115 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_19 0.55 38.0 3.10e-01 100.0% 35.9%
3671478 2492.1.1.2 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.54 44.0 3.89e-01 94.3% 87.3%
3773546 810.1.1.3 ↗ a+b two layers › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › BtrG-like (Pfam 03674) › AIG2_2 0.54 42.0 3.25e-01 87.1% 70.5%
4019053 11.1.1.837 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › TAF2_3rd 0.54 43.0 3.55e-01 92.9% 97.1%
3515139 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.53 41.0 3.14e-01 100.0% 33.9%
4965204 7523.1.1.0 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II 0.53 45.0 3.82e-01 100.0% 55.8%
4041349 7573.1.1.2 ↗ a/b three-layered sandwiches › PRTase-like › PRTase-like › PRTase-like › Pribosyltran_N 0.53 44.0 3.50e-01 97.1% 91.0%
4028996 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 41.0 3.30e-01 90.0% 42.1%
3413902 2008.2.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › tRNA-intron endonuclease catalytic domain-like › tRNA-intron endonuclease catalytic domain-like 0.52 40.0 3.61e-01 87.1% 98.0%
4991263 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.50 41.0 3.13e-01 94.3% 43.8%