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polymerase_basic_1_protein
Euk-VirLake_Chad_virus
polymerase_basic_1_protein__YP_009987461__Lake_Chad_virus__688438
Identity
- Accession:
- YP_009987461 ↗
- Protein ID:
- polymerase_basic_1_protein
- Kingdom:
- euk
Quality
80.2
mean pLDDT
Cluster
View cluster (14 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 105-197_234-313_330-389_432-446
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00602.23 best | Flu_PB1 | 46.3 | 2.70e-12 | 58.5% | 12.7% |
| PF00602.23 | Flu_PB1 | 32.3 | 4.60e-08 | 41.9% | 11.5% |
CATH (6)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3kavA00 | 1.20.1270.360 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.61 | 22.0 | 3.26e-01 | 82.7% | 71.6% |
| 3ag7A00 | 1.10.287.110 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain | 0.59 | 26.0 | 3.77e-01 | 82.7% | 91.4% |
| 4dloB02 | 1.25.40.610 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.57 | 23.0 | 3.26e-01 | 93.5% | 75.2% |
| 1v9mA01 | 1.10.132.50 | Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › ATP synthase (C/AC39) subunit, domain 3 | 0.54 | 25.0 | 3.42e-01 | 88.7% | 87.0% |
| 1sumB01 | 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 | 0.53 | 24.0 | 3.57e-01 | 88.7% | 97.2% |
| 1rx0A03 | 1.20.140.10 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 | 0.50 | 26.0 | 3.20e-01 | 86.7% | 76.1% |
ECOD (14)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4859811 | 304.48.1.7 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flu_PB1 | 0.86 | 83.0 | 6.61e-01 | 100.0% | 65.0% |
| 1695458 | 304.48.1.7 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flu_PB1 | 0.85 | 83.0 | 6.45e-01 | 100.0% | 66.7% |
| 1411401 | 304.48.1.7 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flu_PB1 | 0.85 | 82.0 | 6.35e-01 | 100.0% | 67.7% |
| 4461237 | 4967.1.1.0 ↗ | alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases | 0.68 | 54.0 | 4.17e-01 | 94.0% | 39.4% |
| 223786 | 304.48.1.16 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 | 0.65 | 59.0 | 5.38e-01 | 100.0% | 74.0% |
| 3923013 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 53.0 | 4.73e-01 | 100.0% | 64.6% |
| 4434853 | 304.48.1.1 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 | 0.62 | 40.0 | 4.09e-01 | 93.5% | 65.8% |
| 3312196 | 650.1.1.0 ↗ | alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain | 0.59 | 25.0 | 3.74e-01 | 81.9% | 89.5% |
| 4968135 | 601.7.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN | 0.56 | 26.0 | 3.44e-01 | 86.3% | 78.5% |
| 4996239 | 601.7.1.2 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN | 0.55 | 24.0 | 3.12e-01 | 85.1% | 66.4% |
| 3807513 | 633.4.1.0 ↗ | alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor | 0.53 | 28.0 | 3.69e-01 | 81.9% | 91.1% |
| 3564576 | 106.1.1.8 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › HisK-N-like | 0.53 | 31.0 | 3.85e-01 | 94.8% | 93.3% |
| 3961693 | 106.1.1.11 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N | 0.52 | 31.0 | 3.76e-01 | 85.1% | 89.4% |
| 3504717 | 106.1.1.8 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › HisK-N-like | 0.51 | 29.0 | 3.70e-01 | 86.7% | 93.1% |
D2
medium
residues 48-104
Domain cluster:
representative
D3
medium
residues 575-609_623-699
Domain cluster:
representative
CATH (1)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3rhtA00 | 3.40.50.880 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain | 0.53 | 42.0 | 3.32e-01 | 88.4% | 94.4% |
D4
medium
residues 700-771
Domain cluster:
representative
CATH (31)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2zttA00 | 6.10.140.720 | Special › Helix non-globular › Helix Hairpins › | 0.77 | 68.0 | 6.80e-01 | 100.0% | 94.5% |
| 4gbjC02 | 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 | 0.63 | 43.0 | 3.52e-01 | 95.8% | 37.8% |
| 4dloB02 | 1.25.40.610 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › | 0.63 | 50.0 | 4.27e-01 | 87.5% | 67.5% |
| 1vq8V00 | 1.10.287.310 | Mainly Alpha › Orthogonal Bundle › Helix Hairpins › | 0.61 | 41.0 | 4.30e-01 | 93.1% | 76.9% |
| 3l8rA00 | 1.20.58.80 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit | 0.60 | 41.0 | 3.71e-01 | 70.8% | 96.1% |
| 1khbA03 | 3.90.228.20 | Alpha Beta › Alpha-Beta Complex › Phosphoenolpyruvate Carboxykinase; domain 3 › | 0.60 | 46.0 | 3.21e-01 | 84.7% | 63.9% |
| 8fbnB01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.60 | 52.0 | 3.75e-01 | 100.0% | 55.0% |
| 1zeeA01 | 1.20.58.600 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 46.0 | 3.94e-01 | 84.7% | 96.6% |
| 3onjA00 | 1.20.58.400 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins | 0.59 | 40.0 | 3.64e-01 | 70.8% | 100.0% |
| 1j1jA02 | 1.20.58.200 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 | 0.59 | 41.0 | 3.89e-01 | 72.2% | 96.5% |
| 2c2lA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.59 | 48.0 | 3.90e-01 | 88.9% | 56.4% |
| 2ip6A00 | 1.20.1440.140 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.58 | 48.0 | 4.62e-01 | 95.8% | 100.0% |
| 1ashA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.58 | 44.0 | 3.59e-01 | 91.7% | 41.5% |
| 2w02B01 | 1.10.150.640 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle | 0.57 | 43.0 | 4.35e-01 | 93.1% | 79.7% |
| 1icrA00 | 3.40.109.10 | Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase | 0.56 | 42.0 | 2.99e-01 | 79.2% | 65.7% |
| 1b5lA00 | 1.20.1250.10 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › | 0.56 | 46.0 | 3.55e-01 | 88.9% | 71.7% |
| 2l3lA01 | 1.20.58.1250 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Tubulin Binding Cofactor C, N-terminal domain | 0.56 | 42.0 | 3.71e-01 | 87.5% | 54.7% |
| 3agtA00 | 1.20.120.50 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like | 0.56 | 47.0 | 3.90e-01 | 95.8% | 66.2% |
| 3nbxX03 | 1.20.58.1510 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.56 | 44.0 | 3.90e-01 | 84.7% | 72.3% |
| 4lvpA00 | 1.10.418.70 | Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Intraflagellar transport protein 81, N-terminal domain | 0.55 | 42.0 | 3.56e-01 | 95.8% | 47.6% |
| 2k19A00 | 1.20.1440.140 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.55 | 46.0 | 4.24e-01 | 95.8% | 88.8% |
| 6jpaE00 | 1.20.140.150 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › | 0.54 | 48.0 | 3.69e-01 | 100.0% | 79.9% |
| 6a7hA01 | 1.20.140.180 | Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › | 0.54 | 40.0 | 3.28e-01 | 77.8% | 59.1% |
| 3f4mA00 | 1.20.1440.160 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Tumor necrosis factor alpha-induced protein 8-like | 0.54 | 43.0 | 3.44e-01 | 88.9% | 98.1% |
| 2ds2D01 | 1.10.110.10 | Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins | 0.53 | 37.0 | 4.09e-01 | 88.9% | 94.7% |
| 1jt6A02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.52 | 39.0 | 3.20e-01 | 80.6% | 89.1% |
| 3fseB02 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.52 | 43.0 | 3.57e-01 | 98.6% | 72.9% |
| 4fpwB00 | 3.30.530.20 | Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain | 0.51 | 41.0 | 3.24e-01 | 88.9% | 94.4% |
| 5k3hA01 | 1.10.540.10 | Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain | 0.51 | 37.0 | 3.14e-01 | 77.8% | 45.5% |
| 1ugoA00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.51 | 39.0 | 3.58e-01 | 84.7% | 61.6% |
| 2n1rA00 | 1.10.150.90 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Immunodeficiency lentiviruses, gag gene matrix protein p17 | 0.50 | 42.0 | 3.56e-01 | 98.6% | 70.1% |
ECOD (35)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4861235 | 3078.1.1.1 ↗ | extended segments › RNA polymerase PB1 C-terminal fragment › RNA polymerase PB1 C-terminal fragment › RNA polymerase PB1 C-terminal fragment › Flu_PB1 | 0.81 | 60.0 | 6.71e-01 | 77.8% | 100.0% |
| 2617397 | 3078.1.1.1 ↗ | extended segments › RNA polymerase PB1 C-terminal fragment › RNA polymerase PB1 C-terminal fragment › RNA polymerase PB1 C-terminal fragment › Flu_PB1 | 0.80 | 73.0 | 6.77e-01 | 100.0% | 81.8% |
| 5076031 | 244.3.1.7 ↗ | a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU › DUF166 | 0.69 | 53.0 | 4.63e-01 | 83.3% | 56.2% |
| 3657582 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.66 | 46.0 | 3.60e-01 | 73.6% | 59.5% |
| 3965046 | 604.12.1.76 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › IspA | 0.65 | 50.0 | 5.08e-01 | 83.3% | 82.9% |
| 3607111 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.65 | 56.0 | 4.16e-01 | 98.6% | 71.6% |
| 4796295 | 6102.1.1.1 ↗ | alpha arrays › N-terminal domain of segregation and condensation protein A, ScpA › N-terminal domain of segregation and condensation protein A, ScpA › N-terminal domain of segregation and condensation protein A, ScpA › SMC_ScpA | 0.65 | 47.0 | 4.80e-01 | 83.3% | 79.7% |
| 3992989 | 5054.1.1.8 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 | 0.64 | 47.0 | 3.75e-01 | 79.2% | 70.7% |
| 3198009 | 604.3.1.0 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain | 0.63 | 44.0 | 4.18e-01 | 72.2% | 94.1% |
| 4007848 | 3355.1.1.21 ↗ | alpha complex topology › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › dicarboxylate/sodium symporter › Na_sulph_symp, CitMHS | 0.63 | 47.0 | 2.89e-01 | 80.6% | 13.2% |
| 3187484 | 101.1.1.0 ↗ | alpha arrays › HTH › HTH › Three-helical HTH | 0.63 | 47.0 | 3.26e-01 | 80.6% | 63.6% |
| 3471595 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.62 | 52.0 | 3.65e-01 | 90.3% | 37.2% |
| 1157315 | 4983.1.1.2 ↗ | alpha superhelices › Indoleamine 2,3-dioxygenase N-terminal subdomain › Indoleamine 2,3-dioxygenase N-terminal subdomain › Indoleamine 2,3-dioxygenase N-terminal subdomain › PrnB | 0.62 | 48.0 | 4.12e-01 | 84.7% | 97.5% |
| 3841191 | 604.3.1.22 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › PF31030 | 0.60 | 47.0 | 4.42e-01 | 84.7% | 74.4% |
| 3815026 | 604.1.1.148 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › TBCC_N | 0.59 | 46.0 | 4.40e-01 | 84.7% | 77.6% |
| 3309583 | 604.12.1.65 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT_ATG1 | 0.59 | 44.0 | 4.30e-01 | 80.6% | 86.3% |
| 3502644 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.58 | 49.0 | 3.79e-01 | 98.6% | 62.2% |
| 4024831 | 5054.1.1.59 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans, Ion_trans_2 | 0.58 | 44.0 | 3.02e-01 | 81.9% | 40.4% |
| 5072726 | 6155.1.1.0 ↗ | alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter | 0.58 | 43.0 | 4.25e-01 | 87.5% | 76.0% |
| 3276672 | 604.3.1.1 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG | 0.57 | 51.0 | 4.19e-01 | 100.0% | 87.7% |
| 3939274 | 604.3.1.11 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › DUF155 | 0.57 | 45.0 | 3.54e-01 | 84.7% | 60.7% |
| 3222805 | 5054.1.1.8 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 | 0.57 | 39.0 | 2.76e-01 | 73.6% | 86.7% |
| 3577300 | 101.1.2.352 ↗ | alpha arrays › HTH › HTH › winged helix domain › HTH_Tnp_Tc5 | 0.57 | 42.0 | 4.24e-01 | 81.9% | 82.7% |
| 3409714 | 604.3.1.1 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG | 0.55 | 42.0 | 3.81e-01 | 83.3% | 67.0% |
| 3479953 | 604.3.1.1 ↗ | alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG | 0.55 | 42.0 | 4.01e-01 | 83.3% | 78.8% |
| 1145703 | 604.5.1.3 ↗ | alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › ArAE_1_C | 0.54 | 44.0 | 4.03e-01 | 88.9% | 77.7% |
| 3718268 | 192.10.1.0 ↗ | alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain | 0.53 | 43.0 | 4.19e-01 | 88.9% | 92.5% |
| 3995656 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.53 | 40.0 | 3.13e-01 | 79.2% | 80.6% |
| 2409305 | 375.1.1.26 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 | 0.53 | 41.0 | 3.42e-01 | 84.7% | 57.0% |
| 3513623 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.52 | 38.0 | 3.01e-01 | 79.2% | 78.8% |
| 3626530 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.52 | 42.0 | 3.84e-01 | 88.9% | 70.5% |
| 3693297 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.52 | 40.0 | 4.07e-01 | 83.3% | 91.4% |
| 4412725 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.51 | 44.0 | 3.34e-01 | 100.0% | 54.2% |
| 3382792 | 2004.1.1.24 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SNF2-rel_dom,Helicase_C | 0.51 | 41.0 | 2.44e-01 | 87.5% | 10.5% |
| 4972154 | 604.12.1.135 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Oxidored_q2 | 0.51 | 38.0 | 3.48e-01 | 81.9% | 64.0% |