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NC_019486.1__YP_007003217.1__F374_gp17__00017

Bact-Vir

NC_019486.1__YP_007003217.1__F374_gp17__00017

Identity

Accession:
NC_019486 ↗
Kingdom:
phage

Quality

71.2 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 412-480
PDB
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fu1A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.68 58.0 4.79e-01 91.3% 96.6%
3ge2A00 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.66 50.0 4.63e-01 95.7% 62.9%
6i8xA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.65 59.0 4.57e-01 100.0% 61.7%
3ia8A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.64 52.0 3.99e-01 89.9% 46.9%
2qqpA03 2.60.40.4260 Mainly Beta › Sandwich › Immunoglobulin-like › 0.64 55.0 4.45e-01 98.6% 87.6%
7ob9B01 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.63 52.0 3.83e-01 92.8% 33.9%
2v43A01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.62 48.0 3.58e-01 91.3% 31.7%
2knqA01 3.55.40.10 Alpha Beta › 3-Layer(bab) Sandwich › minor pseudopilin epsh fold › minor pseudopilin epsh domain 0.62 53.0 4.41e-01 100.0% 90.2%
2essA02 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.62 46.0 4.08e-01 79.7% 93.9%
2x45A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.61 50.0 4.01e-01 92.8% 50.0%
5tz6B02 3.10.129.120 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › 0.61 50.0 3.89e-01 91.3% 85.1%
4ae7A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.61 50.0 3.66e-01 91.3% 69.9%
4jpqA00 2.60.40.1190 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 47.0 3.29e-01 85.5% 43.8%
1ospO01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.59 49.0 4.33e-01 100.0% 62.9%
3u2gA02 2.60.98.40 Mainly Beta › Sandwich › Tick-borne Encephalitis virus Glycoprotein; domain 1 › DU1608 C-terminal domain 0.58 48.0 4.00e-01 100.0% 50.4%
1flgA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.57 43.0 2.59e-01 89.9% 10.0%
3e29B00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.57 46.0 3.75e-01 91.3% 85.1%
4zohB03 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.56 46.0 4.09e-01 91.3% 74.5%
5dzeA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 45.0 3.27e-01 88.4% 49.2%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.56 47.0 3.84e-01 91.3% 56.8%
4ifdE00 3.30.230.70 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › GHMP Kinase, N-terminal domain 0.56 43.0 3.06e-01 91.3% 77.2%
3riqA00 2.160.20.20 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.55 46.0 2.71e-01 91.3% 13.5%
1cwvA04 2.60.40.1080 Mainly Beta › Sandwich › Immunoglobulin-like › 0.55 44.0 4.06e-01 88.4% 95.6%
1a6zA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.55 44.0 3.36e-01 91.3% 72.6%
1t7vA01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.54 42.0 3.27e-01 91.3% 72.5%
3a58A01 2.30.29.90 Mainly Beta › Roll › PH-domain like › 0.53 42.0 3.17e-01 87.0% 49.4%
2lezA00 3.30.2450.10 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › Secreted effector protein pipB2 0.53 44.0 3.70e-01 92.8% 74.2%
2hboA01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.53 42.0 3.48e-01 89.9% 82.7%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3973700 243.19.1.0 a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.89 81.0 7.17e-01 100.0% 70.5%
2452960 520.1.1.0 beta sandwiches › gp9 N-terminal domain-like › gp9 N-terminal domain-related › gp9 N-terminal domain-related 0.81 74.0 6.71e-01 100.0% 86.7%
3974649 243.19.1.0 a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.79 73.0 6.63e-01 100.0% 78.9%
3703649 292.2.1.0 a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain 0.75 57.0 5.42e-01 91.3% 68.8%
3707862 79.1.1.0 beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.74 57.0 5.41e-01 91.3% 70.0%
3712183 101.1.12.3 alpha arrays › HTH › HTH › HTH motif inserted in other structures › SAS-6_N 0.69 57.0 4.44e-01 91.3% 89.3%
3652840 708.1.1.9 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › CG-1 0.68 47.0 4.48e-01 73.9% 78.8%
3998279 9.1.1.0 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.67 60.0 5.06e-01 97.1% 84.5%
3421095 3521.1.1.4 a+b three layers › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › Polymerase basic protein 2 cap-binding domain › SWIM 0.64 45.0 4.18e-01 75.4% 58.9%
2099169 6176.1.1.1 beta sandwiches › Insertion domain in tetravirus coat protein › Insertion domain in tetravirus coat protein › Insertion domain in tetravirus coat protein › Peptidase_A21 0.64 55.0 4.44e-01 98.6% 87.0%
3856870 708.1.1.9 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › CG-1 0.63 52.0 4.20e-01 88.4% 92.7%
3991799 708.1.1.9 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › CG-1 0.62 53.0 3.81e-01 91.3% 60.5%
2870993 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.62 52.0 4.12e-01 91.3% 74.3%
1622905 719.1.1.4 beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain › SAS-6_N 0.62 47.0 4.80e-01 82.6% 91.3%
1032776 222.1.1.12 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PS-DH 0.61 50.0 3.81e-01 91.3% 79.0%
4946507 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.60 50.0 4.91e-01 92.8% 89.3%
5020511 3338.2.1.0 a+b two layers › Fragilysin-3 prodomain-like › Type II secretion chaperone CpaB › Type II secretion chaperone CpaB 0.59 50.0 4.35e-01 100.0% 59.1%
3946213 295.1.1.0 a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.59 47.0 3.75e-01 89.9% 70.7%
3995220 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 47.0 3.62e-01 92.8% 85.0%
4027263 4.1.1.104 beta barrels › SH3 › SH3 › SH3 › KN17_SH3 0.56 41.0 3.47e-01 88.4% 45.0%
4430793 222.1.1.12 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PS-DH 0.56 45.0 3.90e-01 91.3% 87.0%
3600523 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.56 43.0 2.71e-01 84.1% 18.8%
4175473 5087.3.1.1 beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › Vit_open_b-sht 0.56 45.0 2.97e-01 91.3% 40.9%
4971928 2003.1.5.81 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.56 45.0 3.01e-01 89.9% 75.7%
3928430 4.1.1.223 beta barrels › SH3 › SH3 › SH3 › KIF2A-like_1st 0.53 38.0 3.83e-01 85.5% 75.7%
3207081 4.1.1.92 beta barrels › SH3 › SH3 › SH3 › SH3_9 0.53 40.0 4.11e-01 82.6% 89.2%
3491785 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.53 41.0 3.57e-01 88.4% 54.8%
4882197 219.1.1.28 a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › CHAP 0.51 38.0 3.36e-01 88.4% 50.8%
D2 medium residues 72-193
PDB
Domain cluster: representative
D3 medium residues 694-779
PDB
Domain cluster: representative
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4xmeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.62 45.0 3.49e-01 75.6% 45.7%
1shyB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 41.0 2.63e-01 77.9% 74.7%
3afcA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 48.0 3.08e-01 100.0% 68.8%
3ke6B01 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.56 40.0 3.04e-01 76.7% 66.1%
3fcxB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 43.0 3.05e-01 84.9% 99.6%
4fwwA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 47.0 3.02e-01 100.0% 54.4%
1wznA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.52 32.0 3.83e-01 75.6% 94.6%
3holA03 2.40.128.240 Mainly Beta › Beta Barrel › Lipocalin › 0.51 32.0 3.21e-01 79.1% 60.7%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4956163 71.1.1.0 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.66 45.0 3.49e-01 75.6% 33.3%
3965134 9.1.1.0 beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.65 45.0 4.07e-01 70.9% 57.4%
2362 71.2.1.1 beta meanders › Lipoprotein localization factors LolAB › PA1994-like › PA1994-like › Glycolipid_bind 0.63 51.0 3.88e-01 84.9% 41.4%
2491359 243.19.1.0 a+b two layers › Cystatin-like › Phi ETA orf 56-like protein C-terminal domains › Phi ETA orf 56-like protein C-terminal domains 0.61 44.0 3.77e-01 74.4% 73.5%
3914972 10.1.1.17 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.59 44.0 3.38e-01 77.9% 60.5%
3512529 216.1.1.2 a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.58 42.0 3.40e-01 75.6% 85.0%
4996269 844.1.1.0 beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain 0.57 48.0 3.65e-01 96.5% 56.0%
3230630 2003.1.5.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 50.0 3.45e-01 100.0% 85.5%
3607940 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 41.0 2.74e-01 79.1% 52.0%
4068344 7579.1.1.6 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1 0.55 42.0 2.89e-01 81.4% 99.7%
3262671 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 47.0 2.78e-01 96.5% 12.8%
5026249 2004.1.1.87 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.54 37.0 2.64e-01 72.1% 35.8%
4486484 2004.1.1.799 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_27, AAA_29 0.54 37.0 2.57e-01 72.1% 31.4%
3230598 216.1.1.0 a+b two layers › UBC-like › UBC-like › UBC-like 0.54 38.0 3.21e-01 74.4% 60.7%
3221575 2003.1.5.13 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Spermine_synth 0.54 44.0 3.09e-01 91.9% 88.0%
5032886 2004.1.1.293 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.53 42.0 2.47e-01 84.9% 17.1%
4982005 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 42.0 2.62e-01 84.9% 26.8%
4933430 4041.1.1.1 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.52 45.0 3.59e-01 95.3% 69.7%
3897847 216.1.1.2 a+b two layers › UBC-like › UBC-like › UBC-like › Autophagy_act_C 0.52 37.0 3.07e-01 76.7% 66.9%
4363296 330.11.1.1 a+b two layers › dsRBD-like › Anti-lipopolysaccharide factor (ALF) › Anti-lipopolysaccharide factor (ALF) › Anti-LPS-SCYG 0.52 36.0 3.49e-01 73.3% 70.0%
3675483 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 44.0 2.94e-01 100.0% 46.8%
3587744 9.9.1.1 beta barrels › Lipocalins/Streptavidin › Hypothetical protein YwiB › Hypothetical protein YwiB › DUF1934 0.52 45.0 3.91e-01 100.0% 67.9%
4958749 4041.1.1.1 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.51 42.0 3.36e-01 95.3% 63.7%
4994698 4041.1.1.0 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase 0.50 42.0 3.34e-01 95.3% 61.5%
4973001 4041.1.1.0 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase 0.50 42.0 3.33e-01 95.3% 71.1%
4980641 4041.1.1.0 a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase 0.50 42.0 3.35e-01 95.3% 70.3%
D4 medium residues 881-970
PDB