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rifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00191
Bact-Virrifoxyb1_full_scaffold_4_prodigal-single.1__X__X__00191
Identity
- Kingdom:
- phage
Quality
82.1
mean pLDDT
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
high
residues 201-385
Domain cluster:
rep: IMGVR_UViG_3300028840_006907-3300028840-Ga0309773_1000015396__D229-404
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2cw8A03 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.86 | 72.0 | 7.57e-01 | 88.1% | 93.5% |
| 7qssA01 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.85 | 80.0 | 7.97e-01 | 100.0% | 95.2% |
| 3hyiA01 | 3.10.28.10 | Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases | 0.77 | 59.0 | 5.88e-01 | 89.2% | 75.9% |
| 2gukA00 | 3.30.2190.10 | Alpha Beta › 2-Layer Sandwich › PG1857-like › PG1857-like | 0.65 | 24.0 | 3.11e-01 | 85.4% | 56.8% |
| 1y0hB00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.60 | 29.0 | 3.96e-01 | 72.4% | 86.7% |
| 4oj3B00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.59 | 27.0 | 3.59e-01 | 73.0% | 80.0% |
| 3gkuA03 | 3.30.1370.50 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain | 0.58 | 23.0 | 3.61e-01 | 86.5% | 94.4% |
| 3lnlB02 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.57 | 26.0 | 3.55e-01 | 71.4% | 86.4% |
| 2ek0A00 | 3.30.110.20 | Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › Alba-like domain | 0.56 | 27.0 | 3.71e-01 | 81.1% | 91.1% |
| 2uvaG03 | 3.30.70.3320 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.56 | 28.0 | 3.61e-01 | 97.8% | 82.4% |
| 6lpnA04 | 3.30.70.2740 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.54 | 28.0 | 3.80e-01 | 75.7% | 97.9% |
| 2ctkA00 | 3.30.1370.10 | Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 | 0.54 | 30.0 | 3.80e-01 | 97.8% | 94.2% |
| 1fpqA02 | 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 | 32.0 | 3.75e-01 | 73.0% | 90.7% |
ECOD (13)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4142602 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.90 | 47.0 | 6.63e-01 | 88.1% | 98.0% |
| 4979525 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.88 | 74.0 | 7.32e-01 | 100.0% | 82.6% |
| 4996524 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.87 | 73.0 | 7.16e-01 | 90.8% | 82.1% |
| 4993734 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.85 | 73.0 | 6.83e-01 | 89.2% | 84.1% |
| 5027652 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.83 | 43.0 | 6.12e-01 | 78.9% | 100.0% |
| 4977674 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.82 | 73.0 | 6.84e-01 | 92.4% | 82.7% |
| 5052153 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.76 | 45.0 | 5.60e-01 | 76.8% | 93.0% |
| 4937053 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.75 | 41.0 | 5.62e-01 | 76.8% | 100.0% |
| 5028135 | 242.1.1.0 ↗ | a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases | 0.74 | 45.0 | 5.73e-01 | 76.8% | 99.1% |
| 4982458 | 304.162.1.2 ↗ | a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › FLAD1_M | 0.65 | 27.0 | 4.27e-01 | 72.4% | 100.0% |
| 5620 | 320.3.1.1 ↗ | a+b two layers › R3H domain-like › PG1857-like › PG1857-like › DUF2023 | 0.65 | 24.0 | 3.11e-01 | 85.4% | 56.8% |
| 3609340 | 306.3.1.1 ↗ | a+b two layers › Glucose permease domain IIB-like › eIF1-like › eIF1-like › SUI1 | 0.61 | 30.0 | 4.13e-01 | 77.8% | 92.6% |
| 4443601 | 304.28.1.0 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain | 0.56 | 26.0 | 3.64e-01 | 73.5% | 91.8% |
D2
medium
residues 15-61_433-482
D3
medium
residues 483-621
Domain cluster:
rep: KX119204.1__ANT43181.1__X__00011__D99-235
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08275.18 best | DNAG_N | 40.4 | 4.10e-10 | 82.0% | 76.6% |
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2au3A02 | 3.90.980.10 | Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain | 0.81 | 68.0 | 7.13e-01 | 95.0% | 96.9% |
| 4edgA01 | 3.90.980.10 | Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain | 0.79 | 70.0 | 7.12e-01 | 96.4% | 97.0% |
| 5w36B01 | 3.90.980.10 | Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain | 0.77 | 69.0 | 7.05e-01 | 97.1% | 97.0% |
| 1eqnB01 | 3.90.980.10 | Alpha Beta › Alpha-Beta Complex › DNA primase DNAg catalytic core, N-terminal domain › DNA primase, catalytic core, N-terminal domain | 0.75 | 63.0 | 6.61e-01 | 92.1% | 96.8% |
| 2p5tA00 | 1.10.8.130 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › | 0.63 | 29.0 | 3.58e-01 | 98.6% | 66.3% |
| 3teqB00 | 1.10.287.3550 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.60 | 31.0 | 3.65e-01 | 100.0% | 70.3% |
| 4v1gA00 | 1.20.20.10 | Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C | 0.54 | 32.0 | 4.00e-01 | 99.3% | 95.3% |
| 4nphA02 | 1.20.1270.330 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.52 | 28.0 | 3.81e-01 | 90.6% | 100.0% |
| 1u00A02 | 1.20.1270.10 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.52 | 30.0 | 3.56e-01 | 88.5% | 83.3% |
| 1ugiD00 | 3.10.450.20 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor | 0.50 | 30.0 | 3.79e-01 | 89.9% | 100.0% |
ECOD (23)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4434598 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.83 | 73.0 | 7.62e-01 | 97.8% | 98.5% |
| 4157635 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.82 | 70.0 | 7.34e-01 | 93.5% | 97.6% |
| 4186968 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.82 | 71.0 | 7.38e-01 | 99.3% | 97.7% |
| 4096247 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.81 | 69.0 | 7.24e-01 | 97.8% | 98.4% |
| 4099289 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.81 | 71.0 | 7.35e-01 | 98.6% | 98.5% |
| 1407259 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.81 | 68.0 | 7.14e-01 | 95.0% | 97.6% |
| 4467859 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.80 | 68.0 | 7.21e-01 | 94.2% | 99.2% |
| 4345683 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.77 | 63.0 | 6.66e-01 | 92.8% | 96.0% |
| 3387388 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.77 | 63.0 | 6.64e-01 | 92.1% | 96.0% |
| 4431937 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.76 | 70.0 | 7.07e-01 | 100.0% | 97.9% |
| 4206082 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.76 | 65.0 | 6.76e-01 | 95.0% | 96.9% |
| 3589490 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.76 | 66.0 | 6.78e-01 | 92.8% | 96.3% |
| 4043621 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.76 | 70.0 | 6.96e-01 | 98.6% | 97.2% |
| 4588732 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.75 | 67.0 | 6.84e-01 | 94.2% | 99.3% |
| 3074400 | 4023.1.1.0 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core | 0.72 | 51.0 | 5.88e-01 | 93.5% | 100.0% |
| 5003469 | 4023.1.1.1 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › DNAG_N | 0.72 | 66.0 | 6.63e-01 | 96.4% | 99.3% |
| 3948312 | 4023.1.1.0 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core | 0.70 | 48.0 | 5.59e-01 | 90.6% | 97.0% |
| 3511263 | 4023.1.1.0 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core | 0.70 | 41.0 | 4.86e-01 | 97.1% | 84.2% |
| 4537309 | 4023.1.1.0 ↗ | a+b two layers › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core › N-terminal a+b domain in DNA primase core | 0.65 | 44.0 | 5.12e-01 | 92.8% | 98.9% |
| 3476001 | 331.4.1.1 ↗ | a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › KA1 | 0.58 | 28.0 | 3.34e-01 | 71.9% | 65.6% |
| 3990074 | 101.15.1.1 ↗ | alpha arrays › HTH › LysM domain › LysM domain › LysM | 0.58 | 39.0 | 4.33e-01 | 84.2% | 88.6% |
| 5044962 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.55 | 30.0 | 3.54e-01 | 84.2% | 76.8% |
| 4494025 | 632.22.1.0 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats | 0.50 | 35.0 | 4.00e-01 | 87.8% | 94.3% |
D4
medium
residues 622-798
Domain cluster:
rep: IMGVR_UViG_3300042256_000037-3300042256-Ga0451646_00357_7329_9968__D263-392
Pfam (3)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF13155.13 best | Toprim_2 | 51.3 | 1.80e-13 | 59.9% | 98.9% |
| PF13662.13 | Toprim_4 | 38.5 | 1.50e-09 | 53.7% | 83.1% |
| PF01751.29 | Toprim | 24.8 | 2.80e-05 | 53.7% | 88.5% |
D5
medium
residues 935-965_1133-1202
Domain cluster:
representative
CATH (7)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2yh9B00 | 3.30.1450.10 | Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › | 0.58 | 29.0 | 3.45e-01 | 87.1% | 69.1% |
| 6gmhI02 | 2.20.25.10 | Mainly Beta › Single Sheet › N-terminal domain of TfIIb › | 0.55 | 32.0 | 3.72e-01 | 79.2% | 82.6% |
| 3po3S02 | 2.20.25.10 | Mainly Beta › Single Sheet › N-terminal domain of TfIIb › | 0.54 | 29.0 | 3.23e-01 | 82.2% | 66.2% |
| 3f6gA02 | 3.30.160.340 | Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › | 0.53 | 30.0 | 3.59e-01 | 89.1% | 87.3% |
| 3nqnA00 | 3.30.530.70 | Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › Uncharacterised protein PF12723, DUF3809 | 0.53 | 31.0 | 2.74e-01 | 86.1% | 39.1% |
| 4ebgA00 | 3.10.450.560 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.53 | 42.0 | 4.30e-01 | 94.1% | 90.7% |
| 1nw1A01 | 3.30.200.20 | Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 | 0.51 | 38.0 | 3.95e-01 | 83.2% | 84.4% |
ECOD (20)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3801858 | 252.1.1.0 ↗ | a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD | 0.72 | 34.0 | 4.27e-01 | 84.2% | 75.0% |
| 4028728 | 375.1.1.21 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 | 0.67 | 35.0 | 4.46e-01 | 87.1% | 90.9% |
| 4949036 | 375.1.1.21 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 | 0.66 | 35.0 | 4.56e-01 | 87.1% | 100.0% |
| 4014830 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.64 | 34.0 | 4.38e-01 | 88.1% | 92.7% |
| 3190757 | 375.1.1.21 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-ZPR1 | 0.63 | 36.0 | 4.32e-01 | 91.1% | 91.7% |
| 3705742 | 375.1.1.7 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIS_C | 0.58 | 32.0 | 3.83e-01 | 85.1% | 89.7% |
| 3589900 | 243.3.1.0 ↗ | a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin | 0.57 | 41.0 | 4.39e-01 | 81.2% | 88.2% |
| 4030033 | 331.4.1.0 ↗ | a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 | 0.57 | 30.0 | 3.40e-01 | 81.2% | 66.7% |
| 3189324 | 375.1.1.319 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Saf4_Yju2 | 0.55 | 37.0 | 4.30e-01 | 84.2% | 100.0% |
| 3990414 | 216.1.1.0 ↗ | a+b two layers › UBC-like › UBC-like › UBC-like | 0.54 | 35.0 | 3.21e-01 | 84.2% | 47.9% |
| 4945758 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.54 | 35.0 | 3.96e-01 | 89.1% | 94.3% |
| 3258377 | 331.23.1.0 ↗ | a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain | 0.53 | 31.0 | 3.27e-01 | 82.2% | 63.3% |
| 3507295 | 304.166.1.9 ↗ | a+b two layers › Alpha-beta plaits › Nup54 ferredoxin-like domain › Nup54 ferredoxin-like domain › PF29949 | 0.53 | 32.0 | 3.23e-01 | 96.0% | 59.0% |
| 3781791 | 5.1.4.1 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 | 0.53 | 46.0 | 3.08e-01 | 99.0% | 88.2% |
| 3621358 | 375.1.1.7 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › TFIIS_C | 0.52 | 33.0 | 3.83e-01 | 92.1% | 98.5% |
| 3487047 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.52 | 30.0 | 3.63e-01 | 85.1% | 95.0% |
| 3941717 | 243.3.1.0 ↗ | a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin | 0.51 | 39.0 | 4.17e-01 | 83.2% | 93.2% |
| 3995515 | 5.1.4.1 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 | 0.51 | 45.0 | 3.21e-01 | 98.0% | 43.8% |
| 3825573 | 5.1.5.184 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Beta-prop_WDR11_2nd | 0.51 | 44.0 | 3.00e-01 | 99.0% | 42.0% |
| 3953439 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.50 | 31.0 | 3.56e-01 | 90.1% | 90.0% |