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NC_048756.1__YP_009844620.1__HWC12_gp017__00017

Bact-Vir

NC_048756.1__YP_009844620.1__HWC12_gp017__00017

Identity

Accession:
NC_048756 ↗
Kingdom:
phage

Quality

67.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Ravarandavirus› Nodularia_phage_vB_NspS-kac65v151

TaxID: 2557579

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 2-91
PDB
D2 high residues 331-443
PDB
Domain cluster: rep: MF403008.1__AUZ94854.1__X__00042__D10-155
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF18823.7 best InPase 109.1 2.10e-31 100.0% 79.3%
D3 medium residues 110-172
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF11160.14 best Hva1_TUDOR 65.9 3.90e-18 96.8% 98.3%
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mysA01 2.30.30.360 Mainly Beta › Roll › SH3 type barrels. › Myosin S1 fragment, N-terminal 0.81 54.0 6.13e-01 100.0% 91.7%
6az1E03 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.79 59.0 5.60e-01 100.0% 68.1%
2x4jA01 2.30.30.600 Mainly Beta › Roll › SH3 type barrels. › 0.79 52.0 4.38e-01 100.0% 42.2%
3j7aF03 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.79 58.0 5.60e-01 100.0% 69.0%
2gfaB01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.77 56.0 5.72e-01 100.0% 79.0%
4ii1A02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.76 53.0 5.59e-01 100.0% 82.1%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.76 53.0 5.53e-01 98.4% 79.7%
3mp6A05 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.74 52.0 5.22e-01 100.0% 73.0%
3oymA02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.74 57.0 5.47e-01 100.0% 72.9%
2fhdA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.74 57.0 5.74e-01 100.0% 83.9%
2ldmA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.69 50.0 5.38e-01 100.0% 92.5%
3urgA02 2.30.30.530 Mainly Beta › Roll › SH3 type barrels. › Calcium binding protein CcbP, beta-barrel domain 0.69 56.0 5.67e-01 100.0% 88.9%
1e0bA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.68 48.0 4.87e-01 92.1% 75.4%
1ssfA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.67 47.0 4.97e-01 100.0% 85.5%
3k2zA02 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.61 42.0 3.48e-01 100.0% 38.7%
3c6kA02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.60 44.0 4.57e-01 96.8% 87.5%
1z47A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.60 41.0 4.63e-01 98.4% 91.8%
4m0hA01 2.60.120.1440 Mainly Beta › Sandwich › Jelly Rolls › 0.60 39.0 3.09e-01 71.4% 30.2%
2e5wA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 43.0 4.48e-01 96.8% 87.5%
3o4fC01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 42.0 4.54e-01 96.8% 94.1%
2hx0A01 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.58 51.0 3.98e-01 100.0% 46.2%
3npfB01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 50.0 5.00e-01 100.0% 90.9%
2dt4A00 3.30.1330.80 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Hypothetical protein, similar to alpha- acetolactate decarboxylase; domain 2 0.57 51.0 3.89e-01 100.0% 47.6%
1iy9A02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.57 41.0 4.37e-01 96.8% 94.2%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.56 42.0 4.18e-01 96.8% 78.1%
3jcuO01 2.40.160.30 Mainly Beta › Beta Barrel › Porin › Photosystem II, cytochrome c-550 precursor 0.55 45.0 3.30e-01 93.7% 50.6%
2o07A01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.54 42.0 4.34e-01 96.8% 91.5%
2wweA01 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.54 41.0 3.46e-01 81.0% 97.1%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.52 43.0 3.55e-01 100.0% 96.2%
2bvbA00 2.60.120.710 Mainly Beta › Sandwich › Jelly Rolls › Toxoplasma gondii micronemal protein 1 TgMIC1 0.52 36.0 2.98e-01 76.2% 59.1%
2e4qA00 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.52 36.0 3.04e-01 73.0% 59.3%
1lm4A00 3.90.45.10 Alpha Beta › Alpha-Beta Complex › Peptide Deformylase › Peptide deformylase 0.51 44.0 3.20e-01 100.0% 44.7%
3v0aB03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 43.0 3.10e-01 100.0% 94.6%
3ebtA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 42.0 3.41e-01 96.8% 79.4%
6hoxA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 43.0 2.99e-01 100.0% 92.7%
2dk6A01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.50 42.0 3.81e-01 100.0% 78.7%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4241924 4.1.1.93 ↗ beta barrels › SH3 › SH3 › SH3 › 40S_S4_C 0.83 61.0 5.30e-01 100.0% 53.3%
4605602 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.82 61.0 6.11e-01 100.0% 75.4%
3741680 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.82 61.0 6.45e-01 100.0% 89.1%
3917372 4.1.1.101 ↗ beta barrels › SH3 › SH3 › SH3 › Tudor_2 0.80 58.0 5.46e-01 100.0% 64.0%
4888987 4.1.1.6 ↗ beta barrels › SH3 › SH3 › SH3 › KOW,40S_S4_C 0.79 58.0 5.67e-01 100.0% 71.0%
2675820 4.1.1.93 ↗ beta barrels › SH3 › SH3 › SH3 › 40S_S4_C 0.78 58.0 5.05e-01 100.0% 53.8%
5073368 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.77 59.0 5.70e-01 100.0% 72.9%
3591224 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.76 54.0 5.96e-01 100.0% 94.0%
3855038 4.1.1.105 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5604 0.76 55.0 4.03e-01 100.0% 30.0%
3557649 4.8.1.20 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › PWP3A-B_N 0.74 59.0 4.91e-01 100.0% 51.4%
3933293 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.72 48.0 5.06e-01 90.5% 75.9%
3687350 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.66 48.0 5.11e-01 100.0% 89.1%
3907870 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.66 53.0 4.95e-01 100.0% 69.6%
4505316 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 49.0 5.01e-01 100.0% 86.7%
4941512 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.64 46.0 4.46e-01 100.0% 68.6%
3744811 4.11.1.2 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S26 0.62 53.0 4.09e-01 100.0% 43.2%
3679362 4.1.1.351 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_ISE2 0.62 54.0 4.95e-01 100.0% 94.1%
3991065 4.1.1.334 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1, SH3_2 0.60 54.0 5.00e-01 100.0% 87.5%
3532406 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.60 42.0 3.14e-01 76.2% 44.4%
3175036 4.11.1.2 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S26 0.60 49.0 3.90e-01 100.0% 46.7%
3639196 3256.1.1.0 ↗ a+b two layers › DUF2233 N-terminal domain › DUF2233 N-terminal domain › DUF2233 N-terminal domain 0.59 41.0 4.51e-01 92.1% 93.9%
5056181 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.56 41.0 4.32e-01 95.2% 90.9%
3266698 4.11.1.2 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S26 0.56 47.0 3.78e-01 100.0% 51.1%
5014301 56.1.1.0 ↗ beta sandwiches › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N › Epsilon subunit of F1F0-ATP synthase-N 0.55 49.0 4.16e-01 98.4% 95.0%
3300506 4286.1.1.1 ↗ beta complex topology › At5g01610-like › At5g01610-like › At5g01610-like › DUF538 0.54 41.0 3.29e-01 85.7% 57.9%
3413864 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.54 44.0 3.29e-01 100.0% 35.8%
4203743 3338.2.1.0 ↗ a+b two layers › Fragilysin-3 prodomain-like › Type II secretion chaperone CpaB › Type II secretion chaperone CpaB 0.52 44.0 3.43e-01 95.2% 42.8%
3942848 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 46.0 3.20e-01 100.0% 97.1%
D4 medium residues 240-316
PDB
Domain cluster: representative
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1b06A01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.65 47.0 4.99e-01 84.4% 89.6%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.62 37.0 3.78e-01 83.1% 60.5%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.61 48.0 4.75e-01 85.7% 81.5%
4gczA03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.61 45.0 4.78e-01 87.0% 93.8%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 51.0 5.04e-01 96.1% 88.9%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 50.0 4.61e-01 94.8% 73.8%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 53.0 4.22e-01 100.0% 62.6%
2etnB01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.59 40.0 4.06e-01 87.0% 69.7%
3ctwB00 1.10.8.930 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Protein of unknown function DUF1465 0.58 46.0 3.97e-01 90.9% 55.0%
1vw4T01 6.10.330.20 Special › Helix non-globular › Monooxygenase › 0.56 44.0 3.93e-01 87.0% 69.6%
5xtck00 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 40.0 3.76e-01 77.9% 59.8%
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.55 41.0 3.92e-01 87.0% 69.3%
2i0mA02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.55 45.0 4.13e-01 90.9% 83.2%
1z0xA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.54 41.0 4.34e-01 81.8% 97.0%
1zbtA01 6.10.140.1950 Special › Helix non-globular › Helix Hairpins › 0.53 36.0 3.60e-01 83.1% 66.3%
4dllB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.53 41.0 3.52e-01 85.7% 61.5%
2n8lA00 3.30.310.210 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.51 40.0 3.02e-01 84.4% 84.3%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.50 41.0 3.57e-01 88.3% 86.8%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5018716 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.68 40.0 4.19e-01 92.2% 64.3%
3602612 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 33.0 3.46e-01 89.6% 50.0%
1145753 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.65 50.0 5.14e-01 94.8% 85.3%
4013585 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.63 46.0 4.86e-01 88.3% 85.7%
4660205 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.60 51.0 4.25e-01 94.8% 97.8%
3590987 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.58 46.0 4.70e-01 88.3% 89.3%
4032379 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.57 48.0 4.91e-01 93.5% 100.0%
3933048 4992.1.1.12 ↗ extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.57 49.0 4.51e-01 96.1% 76.0%
1288932 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.52 39.0 3.96e-01 89.6% 84.2%
3965811 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.52 39.0 3.52e-01 81.8% 61.5%
3455900 4044.1.1.12 ↗ alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › RH_dom 0.52 37.0 3.39e-01 74.0% 61.0%
3448469 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.50 32.0 2.56e-01 79.2% 31.2%
3456216 4163.1.2.1 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF2 C-terminal domain-like › Sld5 0.50 41.0 3.71e-01 93.5% 77.3%
D5 medium residues 482-533
PDB