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NC_018275.1__YP_006560568.1__B606_gp18__00018

Bact-Vir

NC_018275.1__YP_006560568.1__B606_gp18__00018

Identity

Accession:
NC_018275 ↗
Kingdom:
phage

Quality

80.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lederbergvirus› Salmonella_phage_vB_SemP_Emek

TaxID: 1168548

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 17-65
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2b6cA01 1.20.1660.10 Mainly Alpha › Up-down Bundle › ARM repeat fold › Hypothetical protein (EF3068) 0.81 73.0 5.41e-01 98.0% 41.4%
1hx8A01 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.80 64.0 4.83e-01 89.8% 43.2%
6tblB01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.76 59.0 4.47e-01 83.7% 42.3%
3hjlA03 1.20.5.2020 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.74 56.0 5.99e-01 93.9% 100.0%
1lkvX02 1.10.220.30 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Flagellar motor switch protein FliG, alpha-alpha superhelical domain 0.73 59.0 4.24e-01 87.8% 100.0%
4y5jA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.73 65.0 4.14e-01 100.0% 38.8%
2ol5A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.73 64.0 4.26e-01 98.0% 91.8%
3ix7A00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.72 52.0 3.81e-01 77.6% 41.2%
6wfqC01 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.70 59.0 4.35e-01 100.0% 74.6%
3c5wA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.70 61.0 3.94e-01 100.0% 57.5%
2vwaA00 1.20.58.1330 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Plasmodium falciparum UIS3 membrane protein 0.67 61.0 4.77e-01 100.0% 72.7%
5cwhA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.67 51.0 3.65e-01 85.7% 31.4%
4hkaA02 1.10.287.3810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.67 48.0 4.75e-01 85.7% 72.5%
2wwwC01 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.67 48.0 4.78e-01 79.6% 80.8%
4d49A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.66 54.0 3.53e-01 95.9% 70.2%
3l9tA02 1.25.40.290 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › ARM repeat domains 0.65 53.0 4.20e-01 100.0% 72.9%
3gs3A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.65 53.0 3.41e-01 93.9% 34.1%
3ppuB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 54.0 4.14e-01 100.0% 61.1%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.61 46.0 4.02e-01 91.8% 53.3%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.61 47.0 3.75e-01 91.8% 42.3%
1jqjD03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.61 41.0 3.47e-01 73.5% 39.5%
4ptsB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 53.0 3.62e-01 100.0% 38.4%
2r5sA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 48.0 4.12e-01 91.8% 86.7%
3c2gA02 1.10.10.1630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Sys-1 C-terminal domain-like 0.59 48.0 4.34e-01 91.8% 70.6%
2nwlC00 1.10.3860.10 Mainly Alpha › Orthogonal Bundle › Proton glutamate symport protein › Sodium:dicarboxylate symporter 0.59 48.0 2.89e-01 100.0% 25.6%
2au3A04 1.20.50.30 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › 0.59 42.0 4.18e-01 83.7% 76.4%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 45.0 3.21e-01 85.7% 30.3%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 51.0 3.98e-01 100.0% 57.5%
3bjdA01 1.10.1240.20 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Lytic transglycosylase, superhelical linker domain 0.57 43.0 3.73e-01 89.8% 63.6%
1hwyA01 1.10.287.140 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 43.0 4.25e-01 83.7% 92.2%
3e98B00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 42.0 3.11e-01 100.0% 81.0%
3bcvA00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.54 40.0 2.81e-01 87.8% 33.7%
1q2lA04 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.54 45.0 3.02e-01 100.0% 53.9%
5mmjn01 1.10.287.1480 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.53 42.0 3.43e-01 85.7% 67.4%
3icxA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.53 44.0 3.86e-01 93.9% 84.0%
3e22A03 1.10.287.600 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.52 41.0 4.01e-01 91.8% 79.6%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.51 39.0 3.42e-01 91.8% 53.7%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.50 44.0 3.73e-01 98.0% 69.6%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4609 109.4.1.124 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DNA_alkylation 0.81 73.0 4.66e-01 98.0% 22.5%
3575335 109.4.1.415 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RICTOR_V 0.76 58.0 3.54e-01 83.7% 15.2%
3351704 109.4.1.2950 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_EZ, Importin_rep_4, TPR_IMB1, TPR_IPO5 0.75 63.0 3.45e-01 100.0% 5.9%
4545374 3054.1.1.0 ↗ alpha arrays › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol › Insert all-alpha domain in prim-pol 0.74 65.0 5.08e-01 100.0% 48.4%
3404865 109.4.1.1406 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT, Vac14_Fab1_bd 0.74 64.0 4.24e-01 100.0% 48.3%
3819254 109.4.1.765 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Vac14_Fab1_bd 0.73 64.0 4.25e-01 100.0% 70.0%
3338557 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.72 52.0 5.56e-01 79.6% 100.0%
3368785 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.72 60.0 4.61e-01 95.9% 71.3%
3682624 109.4.1.3042 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sec7-like_HDS, Sec7-like_HUS, Mon2_C, DCB 0.71 60.0 3.26e-01 100.0% 5.5%
4887352 4246.1.1.4 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_2, RNA_pol_Rpb1_1 0.71 53.0 3.25e-01 83.7% 36.2%
3234964 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.70 49.0 3.71e-01 91.8% 32.7%
3454770 109.4.1.621 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_3 0.70 58.0 3.64e-01 98.0% 18.2%
5027916 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.68 50.0 3.86e-01 85.7% 35.5%
3798486 7583.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like domain in AF1104-like proteins › Rossmann-like domain in AF1104-like proteins › Rossmann-like domain in AF1104-like proteins 0.68 57.0 3.55e-01 98.0% 52.4%
4942626 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.67 50.0 3.90e-01 85.7% 39.0%
4128454 7583.1.1.1 ↗ a/b three-layered sandwiches › Rossmann-like domain in AF1104-like proteins › Rossmann-like domain in AF1104-like proteins › Rossmann-like domain in AF1104-like proteins › ARMT1-like_dom 0.67 57.0 3.54e-01 98.0% 56.1%
3279424 632.2.1.34 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › OmdA 0.67 49.0 4.76e-01 77.6% 73.6%
3629293 109.4.1.1222 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_PSME4 0.66 56.0 3.70e-01 100.0% 48.0%
3510767 3343.1.1.2 ↗ alpha complex topology › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › gamma-tubulin complex protein 4 (GCP4) › GCP_C_terminal,GCP_N_terminal 0.66 55.0 3.12e-01 100.0% 21.1%
3204035 1.1.17.4 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Peptidase_S64 0.66 46.0 2.83e-01 77.6% 45.0%
5040578 604.9.1.0 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 0.65 50.0 4.56e-01 83.7% 69.2%
3289740 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.65 42.0 3.95e-01 85.7% 55.0%
3222404 109.4.1.414 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MMS19_N 0.64 57.0 3.40e-01 100.0% 15.3%
3708600 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.64 53.0 3.09e-01 100.0% 58.4%
3938475 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.63 51.0 4.64e-01 100.0% 70.7%
4964878 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 0.62 49.0 4.29e-01 93.9% 58.6%
3375617 192.5.1.30 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › DUF641 0.62 45.0 3.89e-01 77.6% 48.8%
3864403 226.1.1.1 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › BTB 0.60 51.0 3.66e-01 100.0% 63.9%
3704038 574.1.1.1 ↗ alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp 0.60 48.0 4.42e-01 98.0% 80.0%
3608747 574.1.1.0 ↗ alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) 0.59 48.0 4.63e-01 100.0% 91.7%
3252622 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.59 50.0 4.09e-01 100.0% 86.3%
4344316 109.40.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › DNA polymerase alpha-binding protein Ctf4 C-terminal domain › Hira 0.58 49.0 3.61e-01 100.0% 91.0%
4803705 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.58 43.0 3.94e-01 91.8% 60.6%
3283532 2004.1.1.85 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ArsA_ATPase 0.57 50.0 3.03e-01 95.9% 18.4%
4010395 622.4.1.26 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › HisKA 0.57 45.0 4.05e-01 87.8% 98.6%
3982421 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.57 45.0 3.94e-01 87.8% 92.0%
5055924 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.57 48.0 3.61e-01 95.9% 89.6%
3285577 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 41.0 2.95e-01 85.7% 73.9%
3941249 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 47.0 3.72e-01 98.0% 87.0%
3278304 103.18.1.0 ↗ alpha arrays › RuvA-C 0.52 35.0 3.69e-01 75.5% 75.6%
3922338 101.1.2.512 ↗ alpha arrays › HTH › HTH › winged helix domain › PF25877 0.51 37.0 3.41e-01 91.8% 67.5%