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MK448720.1__QBX16561.1__Javan261_0001__00001

Bact-Vir

MK448720.1__QBX16561.1__Javan261_0001__00001

Identity

Accession:
MK448720 ↗
Kingdom:
phage

Quality

89.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Streptococcus_phage_Javan261

TaxID: 2548078

Cluster

View cluster (8 members)

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 17-108
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pq7A00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.63 55.0 4.58e-01 100.0% 69.4%
4etsA01 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 0.60 49.0 5.04e-01 92.4% 100.0%
6ofsA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.57 46.0 3.53e-01 89.1% 79.5%
3khkB01 1.20.1260.30 Mainly Alpha › Up-down Bundle › Ferritin › N6 adenine-specific DNA methyltransferase, N-terminal domain 0.55 45.0 3.83e-01 92.4% 98.1%
1g4wR02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.54 42.0 3.29e-01 87.0% 86.0%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.53 39.0 3.93e-01 90.2% 78.4%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.53 42.0 4.00e-01 85.9% 98.1%
8f2lE01 1.10.1740.110 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › 0.52 37.0 3.68e-01 100.0% 69.7%
4urpA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.52 45.0 3.68e-01 98.9% 73.0%
2e18A00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 44.0 3.26e-01 96.7% 94.9%
7ae2A01 1.20.120.580 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › bsu32300-like 0.52 40.0 3.62e-01 87.0% 73.0%
2bvlA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 33.0 3.47e-01 100.0% 70.9%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.51 34.0 3.21e-01 93.5% 54.6%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.51 36.0 3.89e-01 76.1% 92.4%
3ptwA01 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.50 41.0 3.18e-01 95.7% 76.0%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587332 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.92 87.0 5.91e-01 100.0% 33.0%
4034131 101.1.1.248 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DUF772 0.75 68.0 6.53e-01 100.0% 92.4%
5019256 101.1.1.248 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DUF772 0.75 61.0 6.15e-01 88.0% 90.3%
5044345 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.66 45.0 4.77e-01 77.2% 81.2%
2330433 101.1.2.25 ↗ alpha arrays › HTH › HTH › winged helix domain › FUR 0.63 54.0 4.66e-01 97.8% 62.3%
4423880 563.1.1.1 ↗ alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP 0.59 43.0 3.57e-01 79.3% 89.7%
4596379 7000.1.1.0 ↗ alpha arrays › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS › inserted region in the C-terminal domain of the archeal LeuRS 0.57 39.0 4.27e-01 72.8% 92.9%
3640621 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.56 39.0 3.90e-01 71.7% 73.7%
3733339 3324.1.1.0 ↗ extended segments › Helical arch in Ski2-like helicases › Helical arch in Ski2-like helicases › Helical arch in Ski2-like helicases 0.56 43.0 3.97e-01 83.7% 83.2%
3240699 101.1.1.75 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_48 0.55 40.0 4.47e-01 93.5% 100.0%
4026916 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.55 36.0 3.16e-01 89.1% 43.6%
4057021 605.4.1.20 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein › DUF6092 0.52 35.0 3.61e-01 88.0% 72.2%
5006970 4323.1.1.0 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C 0.52 34.0 2.96e-01 100.0% 42.9%
3965168 601.7.1.6 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase 0.51 42.0 3.45e-01 92.4% 52.6%
3887886 604.3.1.11 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › DUF155 0.51 40.0 3.01e-01 87.0% 57.6%
D2 high residues 111-261
PDB
Domain cluster: rep: KX077896.1__ANM47701.1__X__00070__D117-246_318-381
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF13612.13 best DDE_Tnp_1_3 98.1 7.40e-28 100.0% 94.2%
PF01609.28 DDE_Tnp_1 77.3 1.90e-21 100.0% 88.0%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kksB00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.77 55.0 5.57e-01 100.0% 73.0%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.75 56.0 5.66e-01 97.4% 77.9%
4py5A02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.56 51.0 4.72e-01 98.7% 82.6%
1xc3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 36.0 4.27e-01 83.4% 100.0%
3rqiA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.53 37.0 4.03e-01 88.1% 85.8%
5m1pB00 3.30.420.240 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.53 39.0 3.70e-01 96.7% 63.0%
2dstA00 3.40.50.12270 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 33.0 3.68e-01 85.4% 79.5%
3crnA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 37.0 3.95e-01 88.1% 85.3%
3kcnB00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 38.0 3.96e-01 87.4% 83.9%
4rk6A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 36.0 3.94e-01 87.4% 87.3%
3hbmA01 3.40.50.11190 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 40.0 4.18e-01 83.4% 100.0%
3otgA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.51 41.0 3.59e-01 86.1% 94.6%
1d5wA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 37.0 3.99e-01 86.8% 92.7%
2r7aB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.50 35.0 3.89e-01 86.8% 89.3%
2iyaA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 42.0 3.67e-01 90.1% 92.1%
6j31B01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 42.0 3.66e-01 88.1% 93.7%
2zsgA01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.50 37.0 4.03e-01 90.1% 91.4%
1z05A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.50 41.0 4.08e-01 91.4% 84.4%
4d6yA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.50 36.0 3.90e-01 84.8% 90.9%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587332 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.91 87.0 6.80e-01 100.0% 52.6%
4958315 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.84 81.0 6.24e-01 100.0% 54.0%
3587330 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.84 80.0 5.64e-01 100.0% 63.2%
3590948 105.1.1.0 ↗ alpha duplicates or obligate multimers › HLH-like › HLH, helix-loop-helix DNA-binding domain › HLH, helix-loop-helix DNA-binding domain 0.83 77.0 6.28e-01 100.0% 57.3%
5061579 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 79.0 5.78e-01 100.0% 66.4%
4966198 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.82 65.0 5.37e-01 100.0% 49.4%
4932086 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.82 72.0 6.49e-01 100.0% 70.0%
5017703 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.81 76.0 5.79e-01 100.0% 68.3%
5017696 2484.1.1.336 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4277 0.81 76.0 5.55e-01 100.0% 56.5%
4010299 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.81 77.0 5.88e-01 100.0% 50.6%
5058150 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.80 76.0 6.11e-01 100.0% 58.5%
5002528 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.79 76.0 6.14e-01 100.0% 61.2%
5020443 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.79 75.0 5.85e-01 100.0% 56.9%
4332913 2484.1.1.146 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_Tn3 0.79 72.0 5.50e-01 100.0% 46.5%
4662521 2484.1.1.146 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_Tn3 0.79 62.0 4.88e-01 100.0% 43.2%
4586139 2484.1.1.146 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_Tn3 0.78 74.0 5.47e-01 100.0% 52.6%
5019203 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.78 72.0 6.13e-01 100.0% 63.9%
4514424 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.78 73.0 5.65e-01 100.0% 53.9%
4375215 2484.1.1.146 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_Tn3 0.78 74.0 5.58e-01 100.0% 50.2%
4962044 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.77 70.0 5.63e-01 100.0% 53.3%
4961488 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.77 73.0 5.22e-01 100.0% 57.2%
3970986 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.77 73.0 5.57e-01 100.0% 51.6%
5040335 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.77 73.0 6.47e-01 100.0% 77.6%
3949341 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.76 73.0 5.80e-01 100.0% 58.9%
4518542 2484.1.1.146 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_Tn3 0.76 72.0 5.45e-01 100.0% 50.2%
4961867 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.76 72.0 5.20e-01 100.0% 59.5%
4149684 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.76 71.0 5.75e-01 100.0% 73.3%
3934892 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.75 57.0 5.56e-01 100.0% 72.1%
5027997 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.74 70.0 5.75e-01 100.0% 62.2%
4934684 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.74 56.0 6.25e-01 82.8% 98.3%
3924799 2484.1.1.107 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_IS1595 0.73 59.0 5.82e-01 100.0% 79.4%
4940124 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.73 69.0 5.37e-01 100.0% 53.1%
4974444 2484.1.1.18 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1 0.73 65.0 5.25e-01 100.0% 53.2%
3920719 2484.1.1.145 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_1_7 0.72 67.0 5.24e-01 100.0% 83.3%
3254993 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.69 56.0 4.51e-01 100.0% 46.7%
4933288 3407.1.1.0 ↗ mixed a+b and a/b › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.66 49.0 5.26e-01 98.0% 89.2%
4263690 2484.1.1.48 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.63 42.0 4.29e-01 98.7% 69.7%
3940128 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 57.0 5.19e-01 100.0% 82.1%
4956541 7597.1.1.0 ↗ a/b three-layered sandwiches › Endolysin C-terminal domain › Endolysin C-terminal domain › Endolysin C-terminal domain 0.58 32.0 4.20e-01 72.2% 100.0%
4043193 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.56 38.0 4.38e-01 88.1% 94.5%
3781312 2484.1.1.205 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27035 0.56 42.0 4.11e-01 99.3% 70.6%
3589803 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.56 32.0 3.81e-01 74.2% 84.0%
5019894 2484.1.1.48 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.55 42.0 4.05e-01 98.7% 70.6%
5083931 2484.1.1.77 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Terminase_6C 0.54 40.0 3.85e-01 96.7% 66.9%
4980198 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 41.0 4.06e-01 98.7% 75.6%
4900638 2007.1.14.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like › Oxidored_nitro 0.53 33.0 3.46e-01 85.4% 66.7%
3990327 2484.1.1.205 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27035 0.52 39.0 3.92e-01 99.3% 75.5%
3279380 2007.1.14.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.51 37.0 3.97e-01 90.1% 86.2%
3973032 2007.1.14.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Chelatase-like 0.51 35.0 3.89e-01 86.8% 89.2%
3982042 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.51 35.0 3.78e-01 90.7% 83.1%
4995715 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 46.0 3.82e-01 98.7% 71.8%