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NC_048876.1__YP_009859486.1__HWD32_gp76__00076

Bact-Vir

NC_048876.1__YP_009859486.1__HWD32_gp76__00076

Identity

Accession:
NC_048876 ↗
Kingdom:
phage

Quality

84.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Secretariatvirus› Gordonia_phage_Secretariat

TaxID: 2725616

Cluster

Singleton — not in a non-trivial cluster

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 7-96
PDB
Domain cluster: rep: NC_048751.1__YP_009843702.1__HWC07_gp021__00021__D19-110
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF24043.2 best DUF7352 31.1 3.00e-07 100.0% 87.8%
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3gbnL02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 28.0 3.67e-01 81.1% 92.7%
5lf5A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 42.0 4.23e-01 75.6% 77.4%
3towA00 2.100.10.50 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › 0.57 49.0 4.15e-01 96.7% 91.4%
3hm0A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.56 39.0 3.56e-01 73.3% 88.1%
1v05A00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 37.0 3.63e-01 76.7% 65.6%
2fbjH02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 36.0 3.95e-01 88.9% 86.3%
4q9bA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 39.0 3.79e-01 78.9% 73.3%
6aqgD02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.53 47.0 3.16e-01 100.0% 75.7%
3u83A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.64e-01 75.6% 70.3%
1fp5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.66e-01 75.6% 75.0%
4o5lL02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.58e-01 75.6% 69.2%
7k0xA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 3.68e-01 75.6% 80.8%
1dn0D02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.67e-01 75.6% 78.7%
2p4gA00 3.40.430.10 Alpha Beta › 3-Layer(aba) Sandwich › Dihydrofolate Reductase, subunit A › Dihydrofolate Reductase, subunit A 0.51 35.0 2.62e-01 71.1% 98.8%
4e2aA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.50 40.0 3.25e-01 85.6% 56.5%
2w59A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 36.0 3.54e-01 75.6% 74.0%
1cl7I00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 38.0 3.93e-01 98.9% 89.0%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5044384 306.3.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like 0.80 42.0 4.35e-01 88.9% 55.3%
3624088 2484.1.1.32 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_C 0.66 36.0 2.63e-01 88.9% 19.6%
4107647 243.18.1.1 ↗ a+b two layers › Cystatin-like › Maltokinase N-terminal domain › Maltokinase N-terminal domain › Mak_N_cap 0.58 42.0 4.16e-01 100.0% 71.6%
3321290 11.1.1.902 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_GEX2_N 0.58 43.0 3.94e-01 76.7% 68.7%
1935147 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.55 37.0 3.49e-01 88.9% 56.8%
3884911 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.53 38.0 3.74e-01 75.6% 74.0%
4109774 11.1.5.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.53 38.0 3.19e-01 74.4% 88.1%
2138593 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.53 38.0 3.74e-01 75.6% 70.6%
3896293 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.53 41.0 4.04e-01 100.0% 78.0%
138151 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.52 37.0 3.61e-01 75.6% 68.3%
2755161 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.52 37.0 3.36e-01 75.6% 55.8%
3273082 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 36.0 3.57e-01 78.9% 68.4%
141424 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.51 37.0 3.52e-01 75.6% 67.3%
4353523 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.51 36.0 3.54e-01 75.6% 70.0%
3567054 11.1.1.96 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C1-set 0.51 36.0 3.14e-01 75.6% 48.0%
D2 high residues 103-172
PDB
Domain cluster: rep: NC_048825.1__YP_009853943.1__HWC81_gp80__00080__D2-66
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3eehA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.64 51.0 4.32e-01 87.1% 75.9%
4ojmX02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.63 50.0 4.38e-01 85.7% 73.3%
3majA01 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 40.0 2.66e-01 70.0% 18.4%
3mq0B02 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.58 44.0 3.38e-01 84.3% 60.5%
1tbxB00 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 0.57 43.0 4.00e-01 81.4% 83.3%
4ne4A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.57 42.0 3.31e-01 82.9% 92.8%
6pcoC00 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 0.56 40.0 3.25e-01 97.1% 40.2%
3jzyA00 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.56 48.0 4.06e-01 100.0% 95.2%
5flmA02 3.30.1360.140 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.55 43.0 3.59e-01 88.6% 69.9%
3pqkA00 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 0.55 39.0 3.48e-01 97.1% 52.5%
4z7eA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.55 40.0 3.19e-01 82.9% 94.6%
3lmbA01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.54 50.0 3.78e-01 100.0% 51.0%
2dqlA00 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 0.54 42.0 3.65e-01 87.1% 76.5%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.54 40.0 3.12e-01 84.3% 60.8%
4hqeA00 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 0.54 41.0 3.64e-01 98.6% 56.2%
2bv6A00 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 0.54 43.0 3.44e-01 87.1% 71.3%
2mlgA00 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 0.53 40.0 3.92e-01 97.1% 74.0%
4g9yA00 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 0.53 39.0 3.19e-01 97.1% 41.2%
1jvaB02 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.53 37.0 3.24e-01 74.3% 59.1%
1jgsA00 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 0.53 39.0 3.15e-01 97.1% 40.6%
3bj6B00 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 0.52 39.0 3.06e-01 98.6% 37.1%
1p4xA01 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 0.52 40.0 3.29e-01 97.1% 45.7%
8agaA01 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 0.52 39.0 3.21e-01 97.1% 44.4%
7jgsG02 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 0.52 41.0 3.77e-01 90.0% 89.8%
1sd4A01 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 0.52 38.0 3.99e-01 100.0% 89.1%
2ethA00 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 0.52 39.0 3.10e-01 97.1% 39.7%
1sh8B00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.52 46.0 3.62e-01 100.0% 47.7%
3g3zA02 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 0.52 38.0 3.98e-01 98.6% 87.5%
1s3jA02 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 0.52 39.0 4.04e-01 98.6% 89.1%
2hoeA01 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 0.52 37.0 3.96e-01 97.1% 93.1%
7dvrA01 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 0.52 40.0 3.20e-01 98.6% 41.8%
2mh2A00 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 0.52 39.0 4.00e-01 100.0% 90.6%
1ulyA01 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 0.51 38.0 3.58e-01 97.1% 64.0%
1ku9B01 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 0.51 42.0 3.98e-01 92.9% 96.6%
2co5A00 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 0.51 38.0 3.53e-01 82.9% 87.0%
5f7qC01 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 0.51 39.0 3.92e-01 97.1% 82.9%
2jt1A00 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 0.51 38.0 3.84e-01 97.1% 81.7%
3r0aA00 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 0.51 38.0 3.26e-01 98.6% 48.3%
2p4wA01 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 0.50 37.0 3.34e-01 97.1% 55.3%
3hozA02 3.30.1360.140 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.50 38.0 3.45e-01 85.7% 83.5%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4966192 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.56 44.0 3.83e-01 88.6% 82.6%
4358890 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.55 44.0 3.82e-01 90.0% 79.1%
5029327 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.54 41.0 3.49e-01 82.9% 80.0%
4943285 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 43.0 3.56e-01 90.0% 72.6%
4943364 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 40.0 3.42e-01 82.9% 74.0%
3602531 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.54 41.0 3.54e-01 97.1% 52.7%
5030563 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.54 40.0 3.67e-01 97.1% 60.0%
4672256 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.54 42.0 3.65e-01 88.6% 79.1%
3739675 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.53 42.0 3.74e-01 90.0% 80.0%
4487383 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.53 42.0 3.68e-01 90.0% 81.8%
5016950 101.1.2.31 ↗ alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.53 40.0 3.72e-01 97.1% 64.4%
4927759 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.53 40.0 3.08e-01 97.1% 36.3%
5065786 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.53 41.0 3.44e-01 84.3% 75.8%
5081950 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.53 40.0 3.44e-01 82.9% 76.5%
3289766 101.1.2.110 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_IclR 0.52 39.0 3.83e-01 97.1% 74.7%
4976847 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.52 39.0 3.36e-01 97.1% 50.9%
4957324 101.1.2.920 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_TbsP_C 0.52 42.0 3.54e-01 91.4% 86.4%
3602589 101.1.2.150 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_45 0.52 39.0 3.49e-01 97.1% 57.0%
4961841 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.52 41.0 3.45e-01 90.0% 74.6%
5003874 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.52 41.0 3.53e-01 90.0% 81.7%
4975513 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.52 39.0 3.44e-01 82.9% 79.1%
None — 0.52 38.0 3.86e-01 97.1% 80.0%
4032381 101.1.2.231 ↗ alpha arrays › HTH › HTH › winged helix domain › Staph_reg_Sar_Rot 0.52 40.0 3.49e-01 98.6% 53.0%
5025840 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 38.0 3.48e-01 82.9% 82.0%
4562581 101.1.2.110 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_IclR 0.51 38.0 3.80e-01 97.1% 80.0%
4961822 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 37.0 3.50e-01 97.1% 62.2%
4999154 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.51 38.0 3.63e-01 98.6% 67.1%
3964741 101.1.2.368 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_36 0.51 40.0 3.62e-01 97.1% 61.0%
4999286 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.51 40.0 3.03e-01 87.1% 82.2%
4988184 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.51 40.0 3.74e-01 97.1% 68.9%
4958024 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.50 41.0 3.74e-01 97.1% 67.4%
4981949 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 40.0 3.85e-01 97.1% 76.2%
5071948 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 38.0 3.57e-01 97.1% 67.1%
4988512 101.1.2.14 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.50 37.0 2.83e-01 97.1% 32.0%
4980377 101.1.2.136 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_20 0.50 37.0 2.71e-01 97.1% 27.1%
3473498 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.50 42.0 3.98e-01 98.6% 77.6%
4961270 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.50 38.0 3.41e-01 84.3% 85.7%