←Back to structures
NC_005856.1__YP_006489.1__P1_gp020__00019
Bact-VirNC_005856.1__YP_006489.1__P1_gp020__00019
Identity
- Accession:
- NC_005856 ↗
- Kingdom:
- phage
Quality
86.4
mean pLDDT
Taxonomy
TaxID: 2886926
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 11-131
Domain cluster:
representative
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4r80A00 | 3.10.450.630 | Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › | 0.60 | 31.0 | 3.82e-01 | 82.6% | 78.9% |
| 3bt3A01 | 3.30.1900.10 | Alpha Beta › 2-Layer Sandwich › glyoxalase-related enzyme like fold › glyoxalase-related enzyme like domain | 0.54 | 29.0 | 3.58e-01 | 91.7% | 84.7% |
| 2wiiC02 | 2.10.70.10 | Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 | 0.54 | 26.0 | 3.53e-01 | 85.1% | 91.8% |
| 1ylxA00 | 3.30.70.1480 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GK1464-like | 0.52 | 36.0 | 3.93e-01 | 82.6% | 86.9% |
| 4ksaA01 | 3.40.630.180 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › | 0.52 | 42.0 | 3.90e-01 | 86.8% | 87.1% |
| 5tkyA04 | 2.60.34.10 | Mainly Beta › Sandwich › Substrate Binding Domain Of DNAk; Chain A, domain 1 › Substrate Binding Domain Of DNAk; Chain A, domain 1 | 0.51 | 36.0 | 3.75e-01 | 74.4% | 100.0% |
ECOD (8)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3931156 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.55 | 32.0 | 3.97e-01 | 81.0% | 98.6% |
| 3961733 | 330.10.1.0 ↗ | a+b two layers › dsRBD-like › Heterocyclase TruD C-terminal domain › Heterocyclase TruD C-terminal domain | 0.53 | 34.0 | 3.80e-01 | 82.6% | 84.4% |
| 3205629 | 213.1.1.0 ↗ | a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) | 0.53 | 43.0 | 3.34e-01 | 86.0% | 65.9% |
| 3728854 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.52 | 28.0 | 3.68e-01 | 86.0% | 98.5% |
| 3271533 | 331.4.1.0 ↗ | a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 | 0.51 | 40.0 | 4.25e-01 | 100.0% | 96.3% |
| 3519114 | 330.1.1.0 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like | 0.51 | 32.0 | 3.38e-01 | 84.3% | 68.2% |
| 3788141 | 330.1.1.1 ↗ | a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm | 0.51 | 31.0 | 3.69e-01 | 90.1% | 97.3% |
| 3733642 | 213.1.1.72 ↗ | a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1, Acetyltransf_10 | 0.50 | 39.0 | 3.36e-01 | 82.6% | 85.6% |
D2
high
residues 137-200
Domain cluster:
representative
CATH (35)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4p04A01 | 2.60.40.3100 | Mainly Beta › Sandwich › Immunoglobulin-like › Arylsulphate sulphotransferase monomer, N-terminal domain | 0.65 | 51.0 | 4.31e-01 | 100.0% | 51.9% |
| 1qysA00 | 3.30.1710.10 | Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein | 0.60 | 44.0 | 3.92e-01 | 89.1% | 54.3% |
| 3ffyA00 | 3.30.950.10 | Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain | 0.59 | 42.0 | 3.57e-01 | 100.0% | 43.8% |
| 4rlqA01 | 3.40.50.980 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.59 | 40.0 | 2.75e-01 | 70.3% | 89.6% |
| 3h20A01 | 3.30.1490.240 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain | 0.59 | 45.0 | 4.51e-01 | 100.0% | 81.8% |
| 3hrzC01 | 2.20.210.20 | Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › | 0.59 | 40.0 | 4.44e-01 | 93.8% | 93.9% |
| 3kalB05 | 3.30.1490.50 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Glutathione synthase lid domain | 0.57 | 37.0 | 3.85e-01 | 100.0% | 72.9% |
| 1va0B02 | 3.30.950.10 | Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain | 0.57 | 41.0 | 3.41e-01 | 100.0% | 41.1% |
| 3orqA03 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.57 | 39.0 | 4.01e-01 | 100.0% | 74.6% |
| 5yotA03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.57 | 47.0 | 3.90e-01 | 93.8% | 88.0% |
| 1ve2B02 | 3.30.950.10 | Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain | 0.56 | 39.0 | 3.29e-01 | 100.0% | 40.9% |
| 4mamA02 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.56 | 40.0 | 3.77e-01 | 100.0% | 60.5% |
| 2iabA01 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 44.0 | 3.50e-01 | 100.0% | 39.9% |
| 2q9kA00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.56 | 47.0 | 3.66e-01 | 100.0% | 42.2% |
| 4gwmA02 | 2.60.120.200 | Mainly Beta › Sandwich › Jelly Rolls › | 0.56 | 46.0 | 3.47e-01 | 100.0% | 36.6% |
| 5z9sA03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 47.0 | 3.85e-01 | 96.9% | 88.6% |
| 2qsdA01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.55 | 40.0 | 4.02e-01 | 100.0% | 77.6% |
| 3db0B00 | 2.30.110.10 | Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A | 0.55 | 44.0 | 3.60e-01 | 100.0% | 46.8% |
| 3o4lD01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 46.0 | 4.01e-01 | 98.4% | 92.3% |
| 1s4dE02 | 3.30.950.10 | Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain | 0.54 | 41.0 | 3.23e-01 | 100.0% | 38.1% |
| 2r0hA00 | 2.60.120.200 | Mainly Beta › Sandwich › Jelly Rolls › | 0.54 | 44.0 | 3.47e-01 | 100.0% | 67.5% |
| 1vwxS01 | 3.10.20.10 | Alpha Beta › Roll › Ubiquitin-like (UB roll) › | 0.54 | 43.0 | 4.19e-01 | 100.0% | 81.7% |
| 3ethA03 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.54 | 38.0 | 3.92e-01 | 100.0% | 79.0% |
| 2vzwB00 | 3.30.450.40 | Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain | 0.53 | 40.0 | 3.12e-01 | 82.8% | 44.3% |
| 1dikA01 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.53 | 44.0 | 3.48e-01 | 100.0% | 54.9% |
| 3k5iA02 | 3.30.1490.20 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain | 0.52 | 38.0 | 3.73e-01 | 100.0% | 71.4% |
| 7ox5A01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 43.0 | 3.75e-01 | 93.8% | 93.2% |
| 5kfzA04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.52 | 44.0 | 3.67e-01 | 100.0% | 63.4% |
| 4yokA01 | 2.60.40.1120 | Mainly Beta › Sandwich › Immunoglobulin-like › Carboxypeptidase-like, regulatory domain | 0.51 | 40.0 | 3.57e-01 | 100.0% | 59.6% |
| 7bi2A02 | 2.60.40.150 | Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain | 0.51 | 42.0 | 3.49e-01 | 100.0% | 95.5% |
| 5tf0B03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.51 | 42.0 | 3.66e-01 | 100.0% | 71.2% |
| 6p3xB01 | 3.40.140.10 | Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 | 0.51 | 39.0 | 3.03e-01 | 92.2% | 52.0% |
| 3hvnA01 | 3.90.840.10 | Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain | 0.51 | 44.0 | 3.29e-01 | 100.0% | 47.1% |
| 5o60c00 | 2.20.28.120 | Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › Ribosomal protein L33 | 0.50 | 36.0 | 3.86e-01 | 92.2% | 100.0% |
| 2a90A01 | 3.30.720.50 | Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › | 0.50 | 40.0 | 3.68e-01 | 98.4% | 80.6% |
ECOD (35)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4103289 | 3435.1.1.3 ↗ | a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › CENP-L | 0.68 | 60.0 | 3.94e-01 | 100.0% | 27.0% |
| 3924910 | 633.21.1.0 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 | 0.65 | 54.0 | 4.12e-01 | 96.9% | 75.2% |
| 3781646 | 3435.1.1.0 ↗ | a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC | 0.65 | 55.0 | 3.73e-01 | 100.0% | 26.5% |
| 3249139 | 304.128.1.0 ↗ | a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB | 0.61 | 51.0 | 4.33e-01 | 100.0% | 92.5% |
| 1937092 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.60 | 42.0 | 3.56e-01 | 100.0% | 42.9% |
| 4944833 | 304.48.1.31 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Cas10-Cmr2_palm2 | 0.60 | 42.0 | 3.16e-01 | 76.6% | 51.1% |
| 3250018 | 633.23.1.0 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin | 0.60 | 48.0 | 3.57e-01 | 92.2% | 73.9% |
| 4964937 | 821.1.1.15 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › DUF7508 | 0.59 | 38.0 | 3.73e-01 | 100.0% | 60.0% |
| 4034005 | 1137.1.1.0 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain | 0.57 | 40.0 | 3.46e-01 | 100.0% | 45.7% |
| 3660684 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.57 | 49.0 | 4.39e-01 | 96.9% | 71.1% |
| 4946118 | 11.1.1.182 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Fn3-like | 0.57 | 47.0 | 3.88e-01 | 93.8% | 85.8% |
| 3220699 | 282.1.1.1 ↗ | a+b duplicates or obligate multimers › CBS-domain › CBS-domain › CBS-domain › CBS | 0.57 | 41.0 | 3.21e-01 | 78.1% | 38.0% |
| 4280213 | 1137.1.1.0 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain | 0.57 | 40.0 | 3.40e-01 | 100.0% | 43.6% |
| 3668241 | 3346.1.1.1 ↗ | a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › UfSP2_N | 0.57 | 49.0 | 3.37e-01 | 100.0% | 34.0% |
| 3625788 | 1.1.2.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › double psi | 0.56 | 44.0 | 4.30e-01 | 100.0% | 81.4% |
| 3898196 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.56 | 43.0 | 4.51e-01 | 90.6% | 100.0% |
| 4950008 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.55 | 46.0 | 3.87e-01 | 100.0% | 52.8% |
| 5052958 | 821.1.1.0 ↗ | a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease | 0.55 | 37.0 | 3.50e-01 | 100.0% | 56.2% |
| 3713085 | 206.1.3.12 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL | 0.55 | 44.0 | 2.77e-01 | 100.0% | 14.4% |
| 4107956 | 1137.1.1.0 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain | 0.55 | 39.0 | 3.29e-01 | 100.0% | 41.7% |
| 2768244 | 309.1.1.2 ↗ | a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16,Peptidase_M16_C | 0.54 | 43.0 | 2.92e-01 | 92.2% | 69.0% |
| 3896681 | 206.1.3.12 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › TTL | 0.54 | 47.0 | 3.00e-01 | 100.0% | 20.6% |
| 1937462 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.53 | 40.0 | 3.22e-01 | 100.0% | 39.3% |
| 4197453 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.53 | 40.0 | 3.23e-01 | 100.0% | 40.8% |
| 4489065 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.53 | 39.0 | 3.24e-01 | 100.0% | 42.4% |
| 3576143 | 221.1.1.113 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_3 | 0.53 | 44.0 | 3.80e-01 | 100.0% | 67.3% |
| 3433812 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.53 | 39.0 | 3.16e-01 | 100.0% | 39.3% |
| 3640841 | 4121.1.1.0 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like | 0.52 | 43.0 | 2.73e-01 | 96.9% | 15.7% |
| 3737833 | 10.32.1.175 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Rax2_3 | 0.52 | 44.0 | 3.47e-01 | 100.0% | 42.7% |
| 3251743 | 4357.1.1.1 ↗ | beta barrels › WWE domain › WWE domain › WWE domain › WWE | 0.52 | 41.0 | 3.82e-01 | 92.2% | 92.9% |
| 3837973 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.52 | 37.0 | 3.02e-01 | 100.0% | 39.2% |
| 4962686 | 4176.1.1.2 ↗ | a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N | 0.52 | 41.0 | 2.95e-01 | 100.0% | 27.0% |
| 4478414 | 103.15.1.2 ↗ | alpha arrays › RuvA-C › Mitoribosomal protein mS23 › Mitoribosomal protein mS23 › MRP-S25 | 0.52 | 38.0 | 3.13e-01 | 84.4% | 60.6% |
| 4961361 | 1137.1.1.1 ↗ | a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain › TP_methylase | 0.51 | 39.0 | 3.20e-01 | 100.0% | 44.2% |
| 2172926 | 11.1.1.182 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Fn3-like | 0.50 | 42.0 | 3.49e-01 | 100.0% | 63.0% |