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NC_055841.1__YP_010107282.1__KNU99_gp140__00140

Bact-Vir

NC_055841.1__YP_010107282.1__KNU99_gp140__00140

Identity

Accession:
NC_055841 ↗
Kingdom:
phage

Quality

75.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Heverleevirus› Agrobacterium_phage_OLIVR5

TaxID: 2723773

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 high residues 5-57
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.93 87.0 6.64e-01 100.0% 49.5%
1zmbA02 6.10.170.10 Special › Helix non-globular › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › 0.91 59.0 7.13e-01 71.7% 100.0%
6ig5A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.90 73.0 5.22e-01 88.7% 33.3%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.90 66.0 6.24e-01 77.4% 66.1%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.89 80.0 6.11e-01 100.0% 46.2%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.89 73.0 5.88e-01 88.7% 49.0%
2o5iN07 1.10.132.30 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › RNA polymerase Rpb1 funnel domain 0.88 81.0 6.12e-01 100.0% 46.6%
6vudA01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.86 76.0 5.99e-01 100.0% 49.5%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.83 68.0 5.36e-01 88.7% 44.8%
2fe1A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.83 62.0 4.54e-01 84.9% 32.3%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.82 56.0 5.26e-01 79.2% 60.3%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.81 54.0 4.80e-01 71.7% 49.3%
3iylU02 1.10.287.1520 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.81 66.0 6.66e-01 92.5% 90.6%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.80 66.0 5.07e-01 96.2% 41.2%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.79 70.0 6.71e-01 100.0% 86.7%
3zdmB00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.79 56.0 5.72e-01 75.5% 86.0%
3c8tA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.75 56.0 4.62e-01 86.8% 44.3%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.75 63.0 5.65e-01 100.0% 67.5%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 66.0 5.64e-01 100.0% 64.0%
6dv2G02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.75 57.0 3.88e-01 92.5% 23.9%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 60.0 5.94e-01 100.0% 86.0%
1wpbG01 1.10.287.680 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 52.0 5.19e-01 75.5% 72.2%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.74 59.0 5.07e-01 96.2% 56.8%
4in3B00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.73 64.0 3.64e-01 100.0% 70.1%
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.72 64.0 4.24e-01 100.0% 28.8%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.71 61.0 5.82e-01 100.0% 87.5%
1yfmA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.71 56.0 4.29e-01 88.7% 37.3%
2wglA00 1.10.4190.10 Mainly Alpha › Orthogonal Bundle › Urease accessory protein UreF › Urease accessory protein UreF 0.70 57.0 3.85e-01 90.6% 73.2%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.70 57.0 5.22e-01 100.0% 67.5%
1l5jA03 3.40.1060.10 Alpha Beta › 3-Layer(aba) Sandwich › Aconitase; Domain 2 › Aconitase, Domain 2 0.70 54.0 3.81e-01 88.7% 26.6%
3zxsC02 1.25.40.80 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.70 60.0 4.32e-01 98.1% 100.0%
1ailA00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.69 50.0 4.57e-01 77.4% 60.0%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.69 58.0 5.23e-01 94.3% 70.3%
4biuE01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.69 60.0 4.86e-01 100.0% 52.0%
2ygwA01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.69 50.0 3.58e-01 77.4% 27.5%
4cpgA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.68 48.0 4.46e-01 77.4% 63.8%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.67 50.0 4.44e-01 81.1% 54.4%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.67 50.0 3.41e-01 90.6% 21.1%
1y74A00 1.10.287.650 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › L27 domain 0.64 53.0 5.21e-01 96.2% 93.0%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.63 53.0 5.17e-01 96.2% 86.2%
4finB01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 53.0 3.41e-01 100.0% 41.5%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 54.0 4.51e-01 98.1% 94.5%
2om6A02 1.10.150.400 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.61 45.0 4.09e-01 84.9% 64.6%
2au5A00 1.20.120.590 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › EF2947-like 0.61 55.0 4.06e-01 98.1% 51.2%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.60 53.0 4.99e-01 98.1% 86.2%
3qnmA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.60 48.0 4.12e-01 90.6% 100.0%
2wmmA01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.59 47.0 4.83e-01 90.6% 93.9%
2qkdA02 2.60.120.1040 Mainly Beta › Sandwich › Jelly Rolls › ZPR1, A/B domain 0.58 46.0 3.51e-01 94.3% 50.0%
3k3oA02 1.20.58.1360 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 48.0 4.16e-01 96.2% 60.7%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2772104 103.1.1.13 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RNA_pol_Rpo13 0.93 73.0 7.96e-01 83.0% 100.0%
3198228 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.93 86.0 5.58e-01 100.0% 26.3%
3842812 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.92 79.0 5.07e-01 96.2% 22.8%
3769584 4146.1.1.4 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like › FAM216B 0.91 70.0 5.97e-01 81.1% 53.8%
3821967 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.91 64.0 5.58e-01 79.2% 52.0%
4868479 4959.1.1.1 ↗ a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 0.91 83.0 6.25e-01 100.0% 45.4%
3511354 4146.1.1.0 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.90 64.0 7.26e-01 77.4% 100.0%
3720672 109.4.1.1591 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U-box 0.88 80.0 4.93e-01 100.0% 19.6%
4419476 4958.1.1.1 ↗ a+b complex topology › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › second helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_5,RNA_pol_Rpb1_4 0.88 80.0 5.44e-01 100.0% 30.9%
3691750 376.1.1.8 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.88 80.0 5.66e-01 100.0% 36.9%
5036455 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 0.88 71.0 4.31e-01 90.6% 15.9%
3455580 10.12.1.1 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › cNMP_binding 0.85 74.0 4.67e-01 96.2% 20.4%
4231910 4168.1.1.1 ↗ alpha duplicates or obligate multimers › HAMP domain › HAMP domain › HAMP domain › HAMP 0.84 76.0 5.91e-01 100.0% 50.0%
3700089 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 0.83 70.0 6.52e-01 100.0% 75.4%
3187337 630.1.1.0 ↗ a+b complex topology › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain › RuBisCo LSMT C-terminal, substrate-binding domain 0.83 75.0 5.09e-01 100.0% 29.0%
5055565 192.15.1.224 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › SHOCT 0.82 72.0 5.36e-01 100.0% 40.0%
3988447 5043.1.1.0 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.81 67.0 6.64e-01 90.6% 87.3%
5065070 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.81 64.0 6.02e-01 88.7% 70.8%
4984022 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.80 70.0 5.44e-01 100.0% 45.6%
3410594 4177.1.1.6 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3_WASP_bdg 0.78 68.0 4.56e-01 100.0% 79.5%
3317228 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.78 67.0 5.75e-01 96.2% 65.9%
3486312 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.78 69.0 5.33e-01 100.0% 46.2%
4971062 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.78 66.0 5.64e-01 96.2% 58.8%
5054079 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.78 70.0 6.07e-01 100.0% 68.8%
3735607 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.77 67.0 5.89e-01 100.0% 66.3%
2636640 192.15.1.3 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Vps23_core 0.77 68.0 6.01e-01 100.0% 68.8%
3377698 192.15.1.2 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Mod_r 0.76 64.0 4.99e-01 96.2% 44.5%
3476064 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 66.0 5.10e-01 100.0% 44.2%
5051746 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.75 65.0 5.64e-01 96.2% 65.0%
5039692 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 0.75 66.0 5.44e-01 100.0% 57.9%
4124570 1054.1.1.1 ↗ alpha bundles › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arginine decarboxylase C-terminal helical extension › Arg_decarbox_C 0.74 55.0 5.80e-01 86.8% 95.6%
3838083 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.73 62.0 5.65e-01 94.3% 74.3%
4175809 5086.1.1.88 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_CyaD 0.73 61.0 4.32e-01 94.3% 31.5%
3941960 5086.1.1.86 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_YBHG 0.72 59.0 4.54e-01 94.3% 41.6%
3973283 325.1.7.27 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif › HH_AprE 0.70 59.0 4.02e-01 94.3% 26.7%
3403130 4323.1.1.1 ↗ 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 › V_ATPase_I 0.68 58.0 4.14e-01 100.0% 31.5%
3783055 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.65 55.0 4.46e-01 100.0% 50.0%