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NC_070967.1__YP_010671382.1__PQC17_gp233__00233
Bact-VirNC_070967.1__YP_010671382.1__PQC17_gp233__00233
Identity
- Accession:
- NC_070967 ↗
- Kingdom:
- phage
Quality
84.4
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Kleczkowskaviridae›
Cuauhnahuacvirus›
Rhizobium_phage_RHph_Y65
TaxID: 2509785
Cluster
View cluster (44 members)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 3-158_252-294
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF02739.23 best | 5_3_exonuc_N | 53.0 | 4.80e-14 | 84.9% | 89.6% |
CATH (20)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3zdbA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.89 | 63.0 | 7.09e-01 | 78.4% | 91.1% |
| 1xo1A02 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.80 | 62.0 | 6.94e-01 | 85.9% | 98.1% |
| 1tfrA01 | 3.40.50.1010 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease | 0.79 | 75.0 | 7.42e-01 | 99.0% | 98.5% |
| 8bkdA01 | 3.40.50.850 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like | 0.62 | 48.0 | 4.62e-01 | 78.4% | 86.4% |
| 4g65A03 | 3.40.50.720 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain | 0.62 | 35.0 | 4.28e-01 | 78.4% | 83.6% |
| 2q5cA01 | 3.40.50.2300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator | 0.61 | 29.0 | 3.99e-01 | 78.4% | 90.7% |
| 4gicA01 | 3.40.50.1980 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain | 0.61 | 36.0 | 4.15e-01 | 75.9% | 79.9% |
| 1q77A00 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.57 | 38.0 | 4.51e-01 | 75.4% | 97.1% |
| 4rw0A00 | 3.40.50.1110 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase | 0.57 | 34.0 | 3.55e-01 | 85.9% | 63.6% |
| 3ot4A00 | 3.40.50.850 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like | 0.57 | 43.0 | 4.36e-01 | 78.4% | 86.4% |
| 3hgmA00 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.56 | 40.0 | 4.62e-01 | 74.9% | 98.0% |
| 7paxA01 | 3.40.1180.10 | Alpha Beta › 3-Layer(aba) Sandwich › Undecaprenyl pyrophosphate synthetase › Decaprenyl diphosphate synthase-like | 0.56 | 44.0 | 4.07e-01 | 82.9% | 95.5% |
| 6xl1A01 | 3.40.50.10770 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Hypothetical protein VC1899 like domain (Restriction endonuclease-like) | 0.56 | 41.0 | 4.63e-01 | 95.5% | 96.8% |
| 1mjhB00 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.56 | 38.0 | 4.46e-01 | 76.4% | 95.8% |
| 3iprA00 | 3.40.50.510 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component | 0.54 | 34.0 | 4.10e-01 | 82.4% | 92.0% |
| 2ox6D00 | 1.10.3100.10 | Mainly Alpha › Orthogonal Bundle › Putative cytoplasmic protein › Putative cytoplasmic protein | 0.53 | 31.0 | 3.39e-01 | 73.4% | 68.3% |
| 3eefA00 | 3.40.50.850 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Isochorismatase-like | 0.52 | 42.0 | 4.54e-01 | 99.0% | 98.8% |
| 3nd5A00 | 3.40.50.620 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs | 0.52 | 36.0 | 4.12e-01 | 95.0% | 92.8% |
| 6wctD01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.50 | 33.0 | 3.78e-01 | 71.9% | 88.4% |
| 4dqlA03 | 3.40.50.80 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module | 0.50 | 37.0 | 4.06e-01 | 75.9% | 92.5% |
ECOD (47)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4031881 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.88 | 68.0 | 7.28e-01 | 78.4% | 91.4% |
| 3942272 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.88 | 67.0 | 7.32e-01 | 78.4% | 94.1% |
| 4040391 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.87 | 67.0 | 7.08e-01 | 78.4% | 93.3% |
| 4238071 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.87 | 67.0 | 7.16e-01 | 78.4% | 93.1% |
| 4157264 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.86 | 67.0 | 7.03e-01 | 78.4% | 91.1% |
| 3969358 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.86 | 65.0 | 7.29e-01 | 78.4% | 95.6% |
| 3261281 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.86 | 65.0 | 7.10e-01 | 78.4% | 91.7% |
| 4031817 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 66.0 | 7.14e-01 | 78.4% | 92.4% |
| 3283240 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.85 | 66.0 | 6.68e-01 | 78.4% | 88.2% |
| 4995752 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 64.0 | 7.08e-01 | 78.4% | 93.9% |
| 3387660 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 64.0 | 6.93e-01 | 78.4% | 90.6% |
| 4125023 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.84 | 65.0 | 7.01e-01 | 78.4% | 92.4% |
| 4322588 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.83 | 69.0 | 7.24e-01 | 84.4% | 98.9% |
| 3964138 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.81 | 69.0 | 7.23e-01 | 86.9% | 99.4% |
| 3838580 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.80 | 63.0 | 6.65e-01 | 80.9% | 94.4% |
| 4355422 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.79 | 66.0 | 7.09e-01 | 100.0% | 98.3% |
| 3596632 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.79 | 60.0 | 5.51e-01 | 78.4% | 85.6% |
| 4324598 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.78 | 66.0 | 6.86e-01 | 86.4% | 93.0% |
| 4165496 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.77 | 69.0 | 7.17e-01 | 100.0% | 98.4% |
| 4299585 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.76 | 67.0 | 7.01e-01 | 100.0% | 98.4% |
| 3739745 | 2006.1.4.20 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I_2 | 0.76 | 61.0 | 5.48e-01 | 83.4% | 89.1% |
| 3942445 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.75 | 67.0 | 6.93e-01 | 100.0% | 97.8% |
| 3719108 | 2006.1.4.5 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XRN_N | 0.74 | 62.0 | 5.34e-01 | 86.4% | 74.9% |
| 3683988 | 2006.1.4.1 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I | 0.74 | 57.0 | 5.55e-01 | 78.4% | 83.2% |
| 4136793 | 2006.1.4.4 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N | 0.73 | 69.0 | 6.79e-01 | 98.0% | 96.2% |
| 3484303 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.72 | 55.0 | 5.69e-01 | 78.4% | 82.1% |
| 3716763 | 2006.1.4.0 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like | 0.69 | 60.0 | 5.45e-01 | 89.9% | 85.1% |
| 4988271 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.62 | 44.0 | 5.05e-01 | 74.9% | 99.3% |
| 4983833 | 2005.1.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains | 0.60 | 38.0 | 4.66e-01 | 73.4% | 100.0% |
| 5042296 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.59 | 39.0 | 4.70e-01 | 75.9% | 100.0% |
| 4961979 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.58 | 36.0 | 4.28e-01 | 75.9% | 88.6% |
| 138354 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.56 | 40.0 | 4.62e-01 | 74.9% | 98.0% |
| 4951031 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.56 | 40.0 | 4.53e-01 | 75.9% | 96.7% |
| 4300793 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.54 | 34.0 | 3.85e-01 | 95.0% | 82.8% |
| 4988572 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.54 | 39.0 | 4.48e-01 | 75.9% | 98.7% |
| 3972419 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.54 | 38.0 | 4.35e-01 | 76.4% | 96.0% |
| 4999143 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.53 | 40.0 | 4.34e-01 | 76.4% | 98.2% |
| 4403263 | 2003.1.1.48 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › YjeF_N | 0.53 | 38.0 | 3.80e-01 | 73.4% | 90.0% |
| 3821203 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.52 | 38.0 | 4.31e-01 | 76.4% | 96.1% |
| 5082342 | 2005.1.1.3 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp | 0.52 | 37.0 | 4.25e-01 | 74.9% | 98.6% |
| 3837439 | 2005.1.1.43 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd | 0.52 | 38.0 | 4.05e-01 | 76.4% | 89.4% |
| 3803179 | 2005.1.1.0 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains | 0.52 | 39.0 | 4.23e-01 | 78.4% | 92.4% |
| 3645022 | 2005.1.1.43 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd | 0.51 | 38.0 | 4.17e-01 | 76.4% | 95.8% |
| 3925925 | 300.1.1.9 ↗ | a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › MIT_C | 0.51 | 37.0 | 3.93e-01 | 78.4% | 82.2% |
| 3583806 | 7590.1.1.6 ↗ | a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › ArgoMid | 0.51 | 32.0 | 3.45e-01 | 86.4% | 73.5% |
| 3680038 | 2005.1.1.43 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd | 0.50 | 41.0 | 4.23e-01 | 99.0% | 90.0% |
| 3320604 | 2005.1.1.43 ↗ | a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd | 0.50 | 37.0 | 3.95e-01 | 76.4% | 93.3% |
D2
high
residues 160-244
Domain cluster:
representative
CATH (14)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2y0nC00 | 1.10.274.30 | Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › MRG domain | 0.66 | 48.0 | 3.84e-01 | 76.5% | 73.8% |
| 7b7tA01 | 1.20.1270.30 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.62 | 44.0 | 3.57e-01 | 74.1% | 49.7% |
| 1e1dA02 | 1.20.1270.20 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.61 | 36.0 | 3.69e-01 | 75.3% | 59.5% |
| 4fxdA04 | 3.90.1600.10 | Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain | 0.61 | 37.0 | 3.06e-01 | 100.0% | 33.3% |
| 6elqA01 | 1.20.1270.30 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.59 | 42.0 | 3.37e-01 | 75.3% | 73.3% |
| 4rg8A04 | 1.10.287.1240 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.59 | 33.0 | 3.76e-01 | 91.8% | 74.2% |
| 3on3B00 | 3.40.920.10 | Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 0.58 | 49.0 | 3.96e-01 | 96.5% | 97.1% |
| 2xrfC00 | 3.40.50.1580 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain | 0.58 | 44.0 | 3.05e-01 | 81.2% | 53.1% |
| 5grqA00 | 1.10.8.810 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Daxx helical bundle domain | 0.57 | 38.0 | 3.83e-01 | 70.6% | 88.9% |
| 2p8tA01 | 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 | 36.0 | 3.86e-01 | 80.0% | 77.3% |
| 4h33A00 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.54 | 36.0 | 3.58e-01 | 72.9% | 64.8% |
| 1m62A00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.53 | 34.0 | 3.42e-01 | 100.0% | 62.1% |
| 4hr1A00 | 1.20.1270.410 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.52 | 39.0 | 3.54e-01 | 81.2% | 72.9% |
| 3rguB00 | 1.20.5.420 | Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C | 0.51 | 38.0 | 3.85e-01 | 80.0% | 85.1% |
ECOD (6)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3918763 | 101.1.1.117 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › CHDCT2 | 0.56 | 42.0 | 3.97e-01 | 78.8% | 95.0% |
| 3972755 | 601.1.2.99 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › DAGK_prokar | 0.54 | 40.0 | 3.63e-01 | 80.0% | 57.6% |
| 3869337 | 150.3.1.1 ↗ | alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › Hormone_1 | 0.53 | 39.0 | 2.86e-01 | 76.5% | 96.4% |
| 3462649 | 148.1.3.205 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_At3g28540 | 0.52 | 37.0 | 3.67e-01 | 75.3% | 90.0% |
| 4136484 | 206.1.1.11 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › APH | 0.52 | 42.0 | 3.02e-01 | 94.1% | 49.7% |
| 5012928 | 4044.1.1.0 ↗ | alpha bundles › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins › Helical bundle domain in prismane-like proteins | 0.51 | 37.0 | 3.55e-01 | 76.5% | 83.0% |