Back to structures

KY206887.1__APQ42000.1__CloPEP1_0055__00055

Bact-Vir

KY206887.1__APQ42000.1__CloPEP1_0055__00055

Identity

Accession:
KY206887 ↗
Kingdom:
phage

Quality

65.0 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 403-451
PDB
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6pw7A02 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.61 41.0 3.70e-01 71.4% 87.3%
3futA02 1.10.8.100 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › rRNA adenine dimethylase, C-terminal domain 0.59 48.0 4.50e-01 100.0% 87.7%
2wcuA01 3.40.1650.10 Alpha Beta › 3-Layer(aba) Sandwich › RbsD-like fold › RbsD-like domain 0.55 43.0 3.25e-01 91.8% 76.3%
2oqmB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.54 42.0 3.11e-01 100.0% 80.5%
2hsbA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.53 45.0 3.44e-01 100.0% 66.7%
6wilA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.52 44.0 3.80e-01 100.0% 63.1%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.52 41.0 3.27e-01 89.8% 67.0%
1e7lA02 1.10.720.10 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.50 38.0 3.71e-01 85.7% 72.7%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3664931 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.83 66.0 6.58e-01 100.0% 86.0%
3579672 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.82 66.0 6.42e-01 100.0% 80.0%
4390858 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.79 66.0 6.58e-01 100.0% 90.0%
4215938 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.79 66.0 6.00e-01 100.0% 69.2%
4401871 101.1.9.8 alpha arrays › HTH › HTH › Putative DNA-binding domain › IF2_N 0.77 62.0 5.98e-01 100.0% 80.0%
4218351 101.1.9.8 alpha arrays › HTH › HTH › Putative DNA-binding domain › IF2_N 0.76 60.0 5.81e-01 100.0% 78.2%
2876157 101.1.9.105 alpha arrays › HTH › HTH › Putative DNA-binding domain › PF30176 0.74 62.0 6.09e-01 100.0% 88.7%
3164063 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.74 65.0 5.82e-01 100.0% 77.1%
3839973 101.1.9.0 alpha arrays › HTH › HTH › Putative DNA-binding domain 0.70 58.0 5.57e-01 100.0% 83.3%
4375315 101.1.9.16 alpha arrays › HTH › HTH › Putative DNA-binding domain › HTH_17 0.69 57.0 5.69e-01 100.0% 92.0%
3899147 376.1.1.22 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-C3HC4_3 0.68 39.0 3.50e-01 93.9% 40.0%
4966133 2.1.1.377 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF25948 0.67 50.0 3.36e-01 83.7% 22.5%
3403940 377.1.1.18 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › zf-AD 0.65 55.0 4.77e-01 100.0% 61.3%
3224524 103.1.1.0 alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.61 47.0 4.75e-01 100.0% 90.0%
3960391 101.1.4.0 alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.55 42.0 3.84e-01 93.9% 88.0%
4026045 101.1.4.85 alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › HTH_3, PF28877 0.55 46.0 4.41e-01 100.0% 83.3%
D2 medium residues 2-73
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2il5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.75 58.0 4.44e-01 83.3% 90.7%
1kfiA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.70 55.0 4.65e-01 87.5% 100.0%
3pcoB06 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.69 57.0 5.28e-01 91.7% 95.7%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.68 50.0 4.92e-01 97.2% 73.7%
3io1A02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 60.0 5.08e-01 97.2% 95.7%
2b9wA03 3.30.70.1990 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 58.0 5.29e-01 97.2% 93.7%
2fe0A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.66 51.0 4.48e-01 97.2% 56.1%
2rhqB06 3.30.70.380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ferrodoxin-fold anticodon-binding domain 0.66 50.0 4.86e-01 84.7% 100.0%
2zw2A00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.65 58.0 5.49e-01 97.2% 94.1%
5koxA02 3.30.70.2450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 54.0 5.14e-01 94.4% 100.0%
3q6aB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.64 48.0 4.00e-01 83.3% 92.5%
2wbmA03 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 56.0 5.67e-01 98.6% 100.0%
1b37A02 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.62 53.0 3.87e-01 100.0% 45.9%
3gz7B00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 54.0 4.88e-01 100.0% 98.0%
2ebeA00 3.30.70.2290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Protein of unknown function (DUF3208) 0.60 49.0 4.41e-01 93.1% 92.5%
3e8oB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 50.0 4.57e-01 94.4% 92.0%
1ksiA03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.60 45.0 2.83e-01 81.9% 44.0%
2d73A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 42.0 3.63e-01 100.0% 48.7%
5l09B00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.58 41.0 3.17e-01 81.9% 32.3%
1b33N01 3.30.1490.170 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Allophycocyanin linker chain (domain) 0.58 41.0 4.55e-01 97.2% 98.2%
2zuoA06 2.30.30.560 Mainly Beta › Roll › SH3 type barrels. › Major vault protein, N-terminal structural repeat domain 0.58 36.0 4.09e-01 95.8% 88.2%
1t4aA00 3.30.1280.10 Alpha Beta › 2-Layer Sandwich › Mth169; Chain: A , › Phosphoribosylformylglycinamidine synthase subunit PurS 0.58 48.0 4.74e-01 95.8% 97.5%
2dr1A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 44.0 3.58e-01 81.9% 84.4%
3q8pB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.57 45.0 4.03e-01 95.8% 60.2%
2kc5A01 3.30.1460.40 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › [NiFe]-hydrogenase assembly chaperone, HybE 0.57 40.0 3.36e-01 76.4% 57.4%
3ijtB00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 42.0 3.48e-01 83.3% 93.7%
3n40P04 2.60.40.2400 Mainly Beta › Sandwich › Immunoglobulin-like › Alphavirus E2 glycoprotein, domain C 0.56 35.0 3.53e-01 100.0% 60.3%
3uezC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 44.0 4.24e-01 97.2% 75.9%
3ix3A00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.55 36.0 2.93e-01 81.9% 30.7%
3dkxA01 3.40.1310.30 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.55 46.0 3.84e-01 97.2% 63.4%
3s2cJ01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 42.0 3.44e-01 84.7% 76.4%
2hr0B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 3.76e-01 100.0% 58.7%
4mt4A00 1.20.1600.10 Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP) 0.53 39.0 2.34e-01 76.4% 41.7%
2ap1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 44.0 3.67e-01 100.0% 69.1%
5u8rA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 45.0 3.99e-01 100.0% 65.7%
1ex0A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 45.0 3.88e-01 100.0% 64.0%
3qdhA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 40.0 3.54e-01 90.3% 92.2%
2z5bB01 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 37.0 3.13e-01 81.9% 46.2%
1l9nA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 43.0 3.80e-01 100.0% 63.2%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3856140 331.2.1.0 a+b two layers › TBP-like › Phosphoglucomutase, C-terminal domain › Phosphoglucomutase, C-terminal domain 0.78 65.0 5.17e-01 90.3% 99.3%
4936297 304.48.1.32 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › TiaS-FLD 0.72 62.0 4.78e-01 100.0% 64.0%
4942818 3115.1.1.0 a+b two layers › GP2-like › RplX-like › RplX-like 0.72 54.0 4.32e-01 97.2% 41.4%
3593924 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.70 55.0 4.67e-01 97.2% 51.7%
3987406 3115.6.1.1 a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › RpoY 0.70 53.0 5.28e-01 97.2% 77.3%
3590783 302.1.1.1 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.70 55.0 4.39e-01 97.2% 42.8%
3268447 304.39.1.0 a+b two layers › Alpha-beta plaits › Mechanosensitive channel protein MscS (YggB), C-terminal domain › Mechanosensitive channel protein MscS (YggB), C-terminal domain 0.69 54.0 4.85e-01 87.5% 90.5%
5083482 12.1.1.22 beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › GH97_C 0.68 46.0 4.18e-01 95.8% 52.6%
3729534 821.1.1.0 a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.65 52.0 4.20e-01 95.8% 44.8%
3333290 10.32.1.203 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin 0.64 55.0 4.16e-01 97.2% 65.6%
4350613 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.64 57.0 4.99e-01 100.0% 67.6%
3923666 304.7.1.0 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors 0.64 51.0 4.76e-01 88.9% 90.0%
3787850 304.159.1.0 a+b two layers › Alpha-beta plaits › Alpha-beta plait domain in NisB › Alpha-beta plait domain in NisB 0.63 54.0 4.79e-01 98.6% 100.0%
5037616 886.1.1.2 a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › GyrI-like 0.62 40.0 3.12e-01 72.2% 29.4%
3701221 304.43.1.0 a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 0.61 50.0 4.53e-01 95.8% 90.5%
3251475 4114.1.1.2 a+b two layers › PHP14-like › PHP14-like › PHP14-like › Ocnus 0.60 53.0 4.47e-01 100.0% 69.6%
4956201 304.6.1.1 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › FAD-oxidase_C 0.60 53.0 3.75e-01 100.0% 39.1%
2841932 331.3.1.0 a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.60 43.0 3.67e-01 77.8% 98.4%
4321964 304.6.1.3 a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE 0.59 49.0 3.39e-01 98.6% 39.3%
3089702 807.1.1.1 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.59 46.0 4.23e-01 100.0% 66.0%
4308194 330.4.1.1 a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.59 45.0 4.32e-01 86.1% 71.8%
4671096 304.4.1.54 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › Amnionless 0.58 48.0 4.10e-01 97.2% 80.0%
4386705 5.1.2.20 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › BMT 0.58 46.0 2.76e-01 84.7% 34.8%
2794904 807.1.1.1 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.57 42.0 4.40e-01 98.6% 89.4%
4179225 807.1.1.0 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) 0.57 38.0 4.21e-01 95.8% 100.0%
3854107 207.2.1.92 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Amnionless 0.56 46.0 3.67e-01 97.2% 55.3%
3645719 223.1.1.79 a+b three layers › Profilin-like › sensor domains › sensor domains › GAF_NLP 0.56 45.0 3.38e-01 91.7% 39.0%
4237265 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.55 46.0 4.07e-01 100.0% 62.7%
3824339 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 44.0 3.30e-01 98.6% 37.0%
3446878 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.53 39.0 3.58e-01 77.8% 94.7%
3701090 244.1.1.0 a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.53 43.0 3.58e-01 94.4% 87.9%
3472190 2492.1.1.4 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.53 45.0 3.04e-01 100.0% 29.5%
3485482 10.1.1.10 beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › MAM 0.53 43.0 3.28e-01 97.2% 56.5%
3623001 284.2.1.0 a+b two layers › FKBP-like › Chitinase insertion domain › Chitinase insertion domain 0.52 43.0 4.26e-01 97.2% 97.5%
4029036 11.1.4.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.51 43.0 4.10e-01 100.0% 80.0%
4930528 11.1.1.1432 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF26259 0.51 37.0 3.25e-01 100.0% 47.5%
5049198 2492.1.1.18 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › Prok-JAB 0.50 42.0 3.37e-01 100.0% 65.0%
D3 medium residues 197-288
PDB