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NC_003714.1__NP_620343.1__phi-6S_4__00004
Bact-VirNC_003714.1__NP_620343.1__phi-6S_4__00004
Identity
- Accession:
- NC_003714 ↗
- Kingdom:
- phage
Quality
87.1
mean pLDDT
Taxonomy
Orthornavirae›
Duplornaviricota›
Vidaverviricetes›
Mindivirales›
Cystoviridae›
Orthocystovirus›
Pseudomonas_phage_phi6
TaxID: 2928686
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
medium
residues 39-151
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF10464.15 best | Peptidase_U40 | 256.3 | 3.30e-76 | 100.0% | 53.3% |
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4dq5B00 | 1.10.530.50 | Mainly Alpha › Orthogonal Bundle › Lysozyme › Peptidase U40 | 0.97 | 76.0 | 6.56e-01 | 80.5% | 56.9% |
| 1ft9A02 | 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 | 34.0 | 3.92e-01 | 85.0% | 84.8% |
| 2rijA01 | 3.30.70.2010 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.55 | 39.0 | 3.46e-01 | 73.5% | 89.8% |
| 3nxaB00 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.54 | 36.0 | 3.90e-01 | 92.0% | 80.4% |
| 2j0nB00 | 1.20.1710.10 | Mainly Alpha › Up-down Bundle › IpaD-like › IpaD-like | 0.53 | 40.0 | 3.43e-01 | 81.4% | 71.1% |
| 1yz6A02 | 1.10.150.190 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 | 0.52 | 33.0 | 3.62e-01 | 71.7% | 81.6% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 221869 | 235.1.1.16 ↗ | a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Peptidase_U40 | 0.97 | 77.0 | 6.53e-01 | 81.4% | 54.8% |
| 3177718 | 101.1.9.0 ↗ | alpha arrays › HTH › HTH › Putative DNA-binding domain | 0.69 | 37.0 | 4.48e-01 | 81.4% | 79.7% |
| 3173849 | 101.1.9.77 ↗ | alpha arrays › HTH › HTH › Putative DNA-binding domain › PAP1 | 0.66 | 36.0 | 4.67e-01 | 80.5% | 98.3% |
| 5050045 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.63 | 48.0 | 4.42e-01 | 81.4% | 82.7% |
| 4940097 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.57 | 34.0 | 4.13e-01 | 81.4% | 95.7% |
| 2814319 | 109.2.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid | 0.54 | 38.0 | 2.57e-01 | 75.2% | 36.9% |
| 3593166 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.52 | 40.0 | 4.04e-01 | 89.4% | 82.6% |
| 3217935 | 601.2.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes | 0.50 | 38.0 | 3.76e-01 | 81.4% | 90.8% |
D2
medium
residues 152-220
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF10464.15 best | Peptidase_U40 | 150.8 | 6.30e-44 | 100.0% | 32.6% |
CATH (21)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4dq5B00 | 1.10.530.50 | Mainly Alpha › Orthogonal Bundle › Lysozyme › Peptidase U40 | 0.99 | 96.0 | 6.97e-01 | 100.0% | 43.1% |
| 3colB00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.79 | 36.0 | 2.64e-01 | 79.7% | 17.8% |
| 1jvmB00 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.72 | 54.0 | 4.76e-01 | 79.7% | 76.0% |
| 7e84A03 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.71 | 54.0 | 4.48e-01 | 82.6% | 60.2% |
| 4h33A00 | 1.10.287.70 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.70 | 52.0 | 4.75e-01 | 79.7% | 78.0% |
| 4hjzA00 | 1.10.530.10 | Mainly Alpha › Orthogonal Bundle › Lysozyme › | 0.66 | 50.0 | 3.68e-01 | 81.2% | 42.1% |
| 1bdp001 | 3.30.420.10 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H | 0.64 | 44.0 | 3.20e-01 | 88.4% | 25.3% |
| 1w36D02 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.61 | 47.0 | 3.31e-01 | 85.5% | 26.1% |
| 1uaaA02 | 1.10.10.160 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › | 0.61 | 45.0 | 4.43e-01 | 79.7% | 95.9% |
| 3o10C00 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.60 | 49.0 | 3.91e-01 | 89.9% | 52.9% |
| 1x6iB00 | 1.10.150.250 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Flavinator of succinate dehydrogenase | 0.58 | 50.0 | 4.68e-01 | 100.0% | 89.7% |
| 2iw3A02 | 1.20.1390.20 | Mainly Alpha › Up-down Bundle › PWI domain › | 0.57 | 46.0 | 4.28e-01 | 89.9% | 90.0% |
| 1ornA01 | 1.10.340.30 | Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 | 0.56 | 49.0 | 4.21e-01 | 100.0% | 68.8% |
| 7z7vF03 | 1.20.1440.230 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain | 0.56 | 40.0 | 3.79e-01 | 79.7% | 95.5% |
| 7f16R01 | 1.20.1070.10 | Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins | 0.55 | 41.0 | 2.73e-01 | 79.7% | 20.9% |
| 4dwpA01 | 6.10.140.1780 | Special › Helix non-globular › Helix Hairpins › | 0.53 | 45.0 | 4.13e-01 | 92.8% | 80.4% |
| 2d5vA01 | 1.10.260.40 | Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains | 0.53 | 40.0 | 3.89e-01 | 89.9% | 73.4% |
| 8b70A01 | 1.20.1740.10 | Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I | 0.53 | 44.0 | 2.79e-01 | 100.0% | 92.1% |
| 7krzA02 | 1.10.8.60 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › | 0.52 | 40.0 | 3.81e-01 | 87.0% | 98.8% |
| 3gziA00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.51 | 37.0 | 2.69e-01 | 78.3% | 26.6% |
| 3mq1A01 | 1.20.58.970 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.51 | 45.0 | 4.11e-01 | 100.0% | 92.4% |
ECOD (25)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 221869 | 235.1.1.16 ↗ | a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Peptidase_U40 | 0.96 | 90.0 | 6.46e-01 | 97.1% | 39.9% |
| 3194380 | 5059.1.1.4 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Nuc_sug_transp | 0.72 | 53.0 | 3.35e-01 | 78.3% | 78.6% |
| 3404120 | 5054.1.1.0 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels | 0.72 | 54.0 | 4.25e-01 | 81.2% | 54.5% |
| 3218555 | 5054.1.1.0 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels | 0.68 | 52.0 | 4.06e-01 | 82.6% | 50.0% |
| 3587723 | 605.1.1.0 ↗ | alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase | 0.67 | 55.0 | 5.53e-01 | 88.4% | 91.4% |
| 3411768 | 627.1.1.2 ↗ | alpha complex topology › VPS9 domain › VPS9 domain › VPS9 domain › DUF5601 | 0.66 | 49.0 | 4.42e-01 | 79.7% | 97.9% |
| 3622936 | 106.1.1.0 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like | 0.64 | 47.0 | 3.64e-01 | 79.7% | 93.1% |
| 3800376 | 5059.1.1.4 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › Nuc_sug_transp | 0.63 | 55.0 | 3.59e-01 | 100.0% | 61.2% |
| 4369849 | 516.1.1.1 ↗ | alpha arrays › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › YgfY-like (DUP399, Pfam03937) › Sdh5 | 0.63 | 54.0 | 5.22e-01 | 100.0% | 95.0% |
| 3642518 | 5059.1.1.33 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA, SLC35F | 0.62 | 52.0 | 3.41e-01 | 94.2% | 65.2% |
| 3888840 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.60 | 51.0 | 3.39e-01 | 100.0% | 44.1% |
| 5050456 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.59 | 49.0 | 3.28e-01 | 97.1% | 51.1% |
| 3988228 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.58 | 50.0 | 3.30e-01 | 98.6% | 52.0% |
| 3381284 | 5059.1.1.33 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA, SLC35F | 0.58 | 50.0 | 3.29e-01 | 100.0% | 63.4% |
| 3174456 | 5059.1.1.1 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA | 0.58 | 49.0 | 3.24e-01 | 100.0% | 65.3% |
| 3485215 | 5059.1.1.5 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › UAA | 0.58 | 49.0 | 3.23e-01 | 100.0% | 63.3% |
| 3249649 | 5059.1.1.3 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › TPT | 0.57 | 49.0 | 3.21e-01 | 100.0% | 45.7% |
| 3452617 | 5059.1.1.24 ↗ | alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › PUNUT | 0.56 | 49.0 | 3.16e-01 | 100.0% | 45.1% |
| 3755586 | 3291.1.1.118 ↗ | alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › KIF9 | 0.52 | 40.0 | 3.13e-01 | 81.2% | 66.4% |
| 4456090 | 5086.1.1.94 ↗ | alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HB_LcnD | 0.52 | 40.0 | 2.74e-01 | 81.2% | 43.6% |
| 3867093 | 632.1.1.3 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid | 0.52 | 41.0 | 3.43e-01 | 84.1% | 60.0% |
| 3541873 | 3755.3.1.297 ↗ | alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF9 | 0.52 | 40.0 | 3.20e-01 | 84.1% | 86.4% |
| 3957651 | 191.1.1.11 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › TetR_C_7 | 0.51 | 45.0 | 3.64e-01 | 98.6% | 54.1% |
| 3686449 | 633.6.1.12 ↗ | alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX+ACOX_C_alpha1 | 0.51 | 42.0 | 2.84e-01 | 98.6% | 73.8% |
| 3925125 | 4207.1.1.60 ↗ | alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF31020 | 0.50 | 37.0 | 3.36e-01 | 85.5% | 88.2% |