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NC_049431.1__YP_009880039.1__HYP58_gp53__00053

Bact-Vir

NC_049431.1__YP_009880039.1__HYP58_gp53__00053

Identity

Accession:
NC_049431 ↗
Kingdom:
phage

Quality

76.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Schitoviridae› Dorisvirus› Vibrio_phage_1.097.O._10N.286.49.B3

TaxID: 1881383

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 7-54
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1khiA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.68 49.0 4.22e-01 77.1% 60.0%
2i9wA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 46.0 3.16e-01 75.0% 33.5%
1x67A01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.65 49.0 3.59e-01 83.3% 80.5%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.64 46.0 4.14e-01 77.1% 60.9%
3wa1A01 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.62 46.0 3.30e-01 83.3% 60.0%
4gaaA01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.62 44.0 2.95e-01 77.1% 67.4%
2e2dC02 2.40.50.120 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.61 52.0 4.28e-01 100.0% 88.3%
2xq0A01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.60 43.0 2.98e-01 77.1% 69.3%
3p2aA01 2.30.30.380 Mainly Beta › Roll › SH3 type barrels. › Zn-finger domain of Sec23/24 0.60 40.0 4.51e-01 70.8% 100.0%
3f02B02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.59 41.0 3.35e-01 77.1% 70.0%
5c0pA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.58 44.0 2.83e-01 87.5% 18.3%
4axvA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.58 47.0 3.05e-01 91.7% 90.9%
1w7cA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 44.0 3.39e-01 85.4% 59.8%
2rajA02 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.57 47.0 3.58e-01 97.9% 73.0%
5c17A00 3.30.450.410 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.57 48.0 3.24e-01 100.0% 44.7%
4me3A03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.57 43.0 4.13e-01 97.9% 72.7%
2crfA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 44.0 3.35e-01 89.6% 51.2%
4ntqB00 3.30.2450.20 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.56 42.0 3.05e-01 83.3% 87.6%
5sviB00 3.30.40.100 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › 0.55 46.0 4.46e-01 91.7% 83.0%
8a9nA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.55 43.0 3.19e-01 87.5% 51.1%
4f0fA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 44.0 3.52e-01 87.5% 71.0%
4tllC01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.54 43.0 3.38e-01 100.0% 57.4%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.54 37.0 3.74e-01 93.8% 72.0%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 40.0 3.20e-01 87.5% 41.0%
3sluA02 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 40.0 2.99e-01 83.3% 31.4%
1pfsA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 43.0 3.72e-01 93.8% 75.6%
3gxwC00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.53 38.0 3.08e-01 100.0% 38.0%
4bs9A04 3.30.40.250 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › 0.53 35.0 2.95e-01 70.8% 85.6%
6u7jA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.17e-01 79.2% 79.8%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.52 41.0 3.12e-01 100.0% 97.3%
1cyyA02 2.70.20.10 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Topoisomerase I, domain 3 0.52 40.0 3.19e-01 97.9% 53.6%
5cmlA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 40.0 2.73e-01 97.9% 96.7%
5fbhA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.52 39.0 2.63e-01 81.2% 28.9%
4l8nA03 3.30.160.670 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 41.0 3.02e-01 100.0% 53.0%
6fezA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 41.0 3.28e-01 87.5% 71.3%
1wfqA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 40.0 3.57e-01 89.6% 58.9%
3io5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 35.0 2.28e-01 77.1% 91.5%
4qiwB04 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 0.51 40.0 2.94e-01 100.0% 47.2%
2eo6A01 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.50 36.0 2.99e-01 89.6% 37.0%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004198 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.78 53.0 5.93e-01 72.9% 97.1%
3337279 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.74 50.0 5.56e-01 70.8% 100.0%
5004690 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.72 49.0 5.38e-01 72.9% 97.1%
4305218 375.6.1.1 ↗ few secondary structure elements › Rubredoxin-like › FlhC-like › FlhC-like › FlhC 0.69 48.0 5.43e-01 89.6% 97.1%
3321067 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 40.0 3.27e-01 95.8% 31.1%
3435685 376.1.3.6 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › FYVE/PHD zinc finger › zf-CW 0.65 52.0 4.57e-01 89.6% 65.8%
3466584 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.65 49.0 4.43e-01 81.2% 86.2%
4946993 4.1.1.479 ↗ beta barrels › SH3 › SH3 › SH3 › eIF-5a 0.64 46.0 4.09e-01 77.1% 60.0%
4943301 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 43.0 4.25e-01 72.9% 66.0%
3574854 375.1.1.267 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Mcm10, zf-CCCH_Mcm10 0.63 52.0 4.41e-01 95.8% 78.8%
4521197 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.63 45.0 4.28e-01 79.2% 91.7%
4997059 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.62 44.0 3.91e-01 77.1% 54.7%
4931072 4.1.1.139 ↗ beta barrels › SH3 › SH3 › SH3 › IF5A-like_N 0.62 43.0 3.92e-01 77.1% 60.0%
3504912 1194.1.1.1 ↗ few secondary structure elements › C4H2C2-type zinc finger › C4H2C2-type zinc finger › C4H2C2-type zinc finger › PF31216 0.61 48.0 3.48e-01 89.6% 72.7%
4929448 2484.1.1.107 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_Tnp_IS1595 0.61 45.0 3.32e-01 83.3% 31.0%
4202305 312.1.1.0 ↗ a+b three layers › HIT-like › HIT-related › HIT-related 0.61 50.0 3.11e-01 100.0% 86.5%
5044393 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.60 42.0 3.95e-01 75.0% 63.3%
4968552 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.60 49.0 3.40e-01 97.9% 76.7%
3623942 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.58 41.0 3.90e-01 75.0% 69.0%
3703176 64.1.1.0 ↗ beta meanders › WW domain-like › WW domain › WW domain 0.58 38.0 3.94e-01 77.1% 75.0%
3273263 5.1.4.169 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RSE1_2nd 0.57 37.0 2.23e-01 70.8% 7.7%
3743386 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.57 45.0 3.06e-01 87.5% 30.3%
4028728 375.1.1.21 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 0.57 44.0 4.30e-01 87.5% 90.9%
3975926 2.4.1.17 ↗ beta barrels › OB-fold › MOP-like › MOP-like › DUF7765 0.55 44.0 3.68e-01 87.5% 80.0%
3507809 1.1.1.1 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp 0.55 43.0 4.18e-01 89.6% 79.2%
3476815 4184.1.1.1 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat › DM9 0.55 38.0 3.47e-01 75.0% 70.0%
3190757 375.1.1.21 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 0.54 40.0 3.82e-01 85.4% 85.0%
3179468 330.1.1.18 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › DSRM_DHX29 0.54 41.0 3.11e-01 100.0% 72.5%
3468705 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 38.0 2.29e-01 79.2% 20.6%
4138663 4099.1.1.3 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Spc24 0.53 39.0 3.64e-01 83.3% 75.4%
3937984 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 42.0 3.54e-01 100.0% 57.0%
3518948 214.1.1.9 ↗ a+b two layers › SH2 › SH2 › SH2 › DUF7063 0.53 43.0 3.70e-01 95.8% 89.4%
3300995 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.53 39.0 3.04e-01 87.5% 99.3%
5001270 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.53 40.0 3.54e-01 91.7% 57.5%
5052071 7528.1.1.0 ↗ a/b three-layered sandwiches › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains › Phosphoglucomutase, first 3 domains 0.52 37.0 2.67e-01 81.2% 32.9%
1068683 7503.1.1.8 ↗ a/b three-layered sandwiches › TolB, N-terminal domain › TolB, N-terminal domain › TolB, N-terminal domain › DUF4136 0.51 41.0 2.88e-01 100.0% 43.5%
4267022 330.10.1.1 ↗ a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain › YcaO 0.51 40.0 2.86e-01 95.8% 78.9%
4609498 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 0.51 37.0 3.26e-01 83.3% 66.3%
3538297 375.1.1.191 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_GRF 0.50 38.0 3.18e-01 87.5% 85.3%
1095153 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.50 42.0 2.50e-01 100.0% 12.8%
D2 high residues 63-202
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 35.5 8.10e-09 29.3% 69.6%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1c4zA01 3.90.1750.10 Alpha Beta › Alpha-Beta Complex › Hect, E3 ligase catalytic domain fold › Hect, E3 ligase catalytic domains 0.55 39.0 3.71e-01 70.7% 98.1%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5011299 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 36.0 3.92e-01 82.1% 72.2%
4319999 101.1.2.111 ↗ alpha arrays › HTH › HTH › winged helix domain › RQC 0.58 29.0 3.42e-01 70.7% 68.4%
4026891 101.1.15.1 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain › MOZ_SAS 0.51 26.0 3.11e-01 95.0% 71.1%