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SR-VP_2-4_scaffold_141_2548329_prodigal-single.1__X__X__00165
Bact-VirSR-VP_2-4_scaffold_141_2548329_prodigal-single.1__X__X__00165
Identity
- Kingdom:
- phage
Quality
87.0
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 8-78
Domain cluster:
representative
CATH (21)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3if8B02 | 1.20.58.730 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.69 | 62.0 | 5.50e-01 | 98.6% | 76.0% |
| 2hjmA01 | 1.20.120.460 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › protein pf1176 like | 0.69 | 52.0 | 4.94e-01 | 81.7% | 72.1% |
| 3ljbA00 | 1.20.120.1240 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Dynamin, middle domain | 0.68 | 52.0 | 3.73e-01 | 84.5% | 86.3% |
| 4bjmC00 | 1.20.58.1680 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.67 | 49.0 | 3.54e-01 | 81.7% | 26.0% |
| 2p11A02 | 1.10.286.50 | Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › | 0.66 | 51.0 | 5.06e-01 | 88.7% | 78.4% |
| 2mqaA00 | 1.10.274.60 | Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain | 0.66 | 53.0 | 4.50e-01 | 91.5% | 98.4% |
| 2xdoD00 | 3.50.50.60 | Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain | 0.64 | 52.0 | 3.32e-01 | 90.1% | 88.5% |
| 2zxqA06 | 1.20.1270.70 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle | 0.64 | 49.0 | 5.09e-01 | 84.5% | 93.9% |
| 1jkwA02 | 1.10.472.10 | Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like | 0.61 | 47.0 | 4.21e-01 | 83.1% | 70.3% |
| 4cqiA00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.61 | 47.0 | 4.00e-01 | 80.3% | 95.3% |
| 2lseA00 | 1.20.120.1360 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.60 | 49.0 | 4.43e-01 | 91.5% | 94.1% |
| 8sbeA01 | 1.20.1250.20 | Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains | 0.59 | 49.0 | 3.72e-01 | 98.6% | 52.6% |
| 1qsdA00 | 1.20.58.90 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.59 | 45.0 | 3.96e-01 | 81.7% | 100.0% |
| 1yq3C02 | 1.20.1300.10 | Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit | 0.58 | 44.0 | 3.93e-01 | 84.5% | 99.1% |
| 2wcjA00 | 1.10.238.20 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain | 0.56 | 46.0 | 3.68e-01 | 90.1% | 54.6% |
| 3c18A02 | 1.20.120.330 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 | 0.54 | 39.0 | 3.45e-01 | 80.3% | 56.8% |
| 5grqA00 | 1.10.8.810 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Daxx helical bundle domain | 0.54 | 44.0 | 4.19e-01 | 100.0% | 81.1% |
| 2rkkA01 | 1.25.40.270 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Vacuolar protein sorting-associated protein vta1 | 0.53 | 44.0 | 3.44e-01 | 93.0% | 76.3% |
| 2w0gA00 | 1.20.58.610 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Cdc37, Hsp90 binding domain | 0.52 | 41.0 | 3.46e-01 | 90.1% | 71.3% |
| 4fqnC00 | 1.20.1160.20 | Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › | 0.52 | 37.0 | 3.55e-01 | 85.9% | 64.7% |
| 3rh3A01 | 1.20.120.930 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF12889, N-terminal DUF3829 | 0.52 | 44.0 | 3.67e-01 | 98.6% | 64.7% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5071256 | 131.1.1.3 ↗ | alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD | 0.71 | 55.0 | 4.21e-01 | 84.5% | 79.4% |
| 3323416 | 3831.1.1.7 ↗ | alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › DUF842 | 0.71 | 55.0 | 4.84e-01 | 84.5% | 83.8% |
| 4585171 | 103.1.1.6 ↗ | alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C | 0.69 | 50.0 | 5.55e-01 | 95.8% | 100.0% |
| 3217103 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.68 | 59.0 | 4.09e-01 | 98.6% | 50.2% |
| 3965610 | 3831.1.1.1 ↗ | alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › LprI | 0.65 | 47.0 | 4.49e-01 | 77.5% | 88.2% |
| 4001581 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.65 | 46.0 | 3.50e-01 | 74.6% | 39.4% |
| 4927595 | 6049.1.1.0 ↗ | alpha bundles › PH0832-like › PH0832-like › PH0832-like | 0.64 | 51.0 | 4.90e-01 | 84.5% | 76.2% |
| 4966460 | 148.1.3.0 ↗ | alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain | 0.62 | 53.0 | 4.79e-01 | 98.6% | 75.0% |
| 3406162 | 4006.1.1.13 ↗ | alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › DUF842 | 0.61 | 48.0 | 4.09e-01 | 90.1% | 95.2% |
| 4007760 | 7014.1.1.2 ↗ | alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › TauE | 0.60 | 46.0 | 3.84e-01 | 81.7% | 72.5% |
| 3236352 | 4177.1.1.0 ↗ | alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like | 0.59 | 45.0 | 3.40e-01 | 84.5% | 87.6% |
| 4945388 | 5050.1.1.9 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 | 0.57 | 46.0 | 3.53e-01 | 98.6% | 44.5% |
| 3479515 | 603.1.1.0 ↗ | alpha bundles › STAT-like › t-snare proteins › t-snare proteins | 0.56 | 43.0 | 3.58e-01 | 83.1% | 77.6% |
| 3428082 | 509.1.1.0 ↗ | alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain | 0.56 | 42.0 | 4.13e-01 | 80.3% | 77.3% |
| 5042372 | 5054.1.1.8 ↗ | alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans_2 | 0.55 | 38.0 | 3.40e-01 | 73.2% | 62.5% |
| 4235797 | 563.1.1.1 ↗ | alpha bundles › ATPD N-terminal domain-like › N-terminal domain of the delta subunit of the F1F0-ATP synthase › N-terminal domain of the delta subunit of the F1F0-ATP synthase › OSCP | 0.53 | 44.0 | 3.33e-01 | 91.5% | 42.9% |
| 4097875 | 3712.1.1.2 ↗ | a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › DUF412 | 0.52 | 40.0 | 3.63e-01 | 83.1% | 98.0% |
| 3795605 | 4106.1.1.1 ↗ | few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC | 0.51 | 38.0 | 2.83e-01 | 93.0% | 31.1% |
| 4946345 | 3684.1.1.0 ↗ | alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like | 0.51 | 39.0 | 3.14e-01 | 81.7% | 77.1% |
D2
high
residues 81-178
Domain cluster:
representative
CATH (23)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2khmA01 | 1.10.10.1350 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Spidroin domain, C-terminal domain | 0.73 | 49.0 | 4.78e-01 | 78.6% | 62.0% |
| 2oerA00 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.66 | 52.0 | 4.32e-01 | 86.7% | 62.0% |
| 4uhiA01 | 1.10.630.10 | Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 | 0.66 | 53.0 | 3.45e-01 | 86.7% | 69.2% |
| 2lyiA01 | 1.10.274.60 | Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain | 0.65 | 55.0 | 4.81e-01 | 93.9% | 63.5% |
| 6opmD01 | 1.20.120.920 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain | 0.62 | 53.0 | 4.06e-01 | 95.9% | 60.9% |
| 8bypX01 | 3.90.1240.10 | Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" | 0.62 | 45.0 | 2.95e-01 | 100.0% | 18.0% |
| 2o7gA00 | 1.10.1740.10 | Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif | 0.62 | 44.0 | 4.62e-01 | 75.5% | 95.5% |
| 2eb1C00 | 1.10.1520.10 | Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain | 0.61 | 46.0 | 3.88e-01 | 79.6% | 92.3% |
| 1d2zB00 | 1.10.533.10 | Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas | 0.61 | 38.0 | 3.35e-01 | 84.7% | 40.7% |
| 4g12A02 | 1.10.357.10 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 | 0.59 | 48.0 | 4.25e-01 | 88.8% | 79.2% |
| 3hgtA00 | 3.40.50.12360 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › | 0.59 | 52.0 | 3.76e-01 | 98.0% | 87.8% |
| 5w1aB02 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.59 | 39.0 | 4.48e-01 | 79.6% | 100.0% |
| 5h5mA02 | 1.20.120.230 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like | 0.59 | 46.0 | 4.28e-01 | 86.7% | 97.7% |
| 1wdcC01 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.58 | 43.0 | 4.73e-01 | 94.9% | 100.0% |
| 2qvaA01 | 1.20.58.190 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 | 0.57 | 42.0 | 3.84e-01 | 77.6% | 63.6% |
| 4n06A02 | 1.20.120.920 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain | 0.56 | 48.0 | 3.62e-01 | 99.0% | 62.1% |
| 5n69G01 | 1.10.238.10 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand | 0.56 | 40.0 | 4.23e-01 | 93.9% | 86.2% |
| 1sr2A00 | 1.20.120.160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain | 0.55 | 43.0 | 4.07e-01 | 83.7% | 78.4% |
| 1urvA00 | 1.10.490.10 | Mainly Alpha › Orthogonal Bundle › Globin-like › Globins | 0.55 | 39.0 | 3.43e-01 | 75.5% | 89.6% |
| 1f8uA00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.54 | 46.0 | 2.98e-01 | 100.0% | 71.0% |
| 2yfaB01 | 1.20.1440.210 | Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › | 0.53 | 43.0 | 4.08e-01 | 90.8% | 97.5% |
| 3kxpA00 | 3.40.50.1820 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain | 0.53 | 48.0 | 3.48e-01 | 100.0% | 48.9% |
| 2fsjA02 | 3.30.420.40 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain | 0.52 | 45.0 | 4.06e-01 | 94.9% | 78.3% |
ECOD (26)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3335926 | 7023.1.1.2 ↗ | alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › Pex2_Pex12 | 0.67 | 49.0 | 4.78e-01 | 77.6% | 90.0% |
| 3557007 | 3470.1.1.51 ↗ | extended segments › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › Glycophorin-A transmembrane domain › EMC6 | 0.67 | 50.0 | 5.12e-01 | 79.6% | 84.2% |
| 5011925 | 3896.1.1.0 ↗ | alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase | 0.66 | 56.0 | 4.40e-01 | 92.9% | 45.9% |
| 53398 | 4273.1.1.0 ↗ | alpha arrays › PTPA-like › PTPA-like › PTPA-like | 0.66 | 57.0 | 4.11e-01 | 95.9% | 82.5% |
| 3224983 | 106.1.1.1 ↗ | alpha arrays › Globin-like › Globin-like › Globin-like › Globin | 0.65 | 47.0 | 3.80e-01 | 74.5% | 78.9% |
| 3701326 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.65 | 50.0 | 5.15e-01 | 96.9% | 85.3% |
| 3841868 | 3826.1.1.37 ↗ | alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › NUCB1_N | 0.65 | 45.0 | 4.28e-01 | 72.4% | 95.8% |
| 3411117 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.63 | 46.0 | 5.03e-01 | 90.8% | 95.0% |
| 3749766 | 7023.1.1.2 ↗ | alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › Pex2_Pex12 | 0.63 | 45.0 | 4.33e-01 | 73.5% | 89.1% |
| 3864752 | 376.1.1.113 ↗ | few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › Pex2_Pex12 | 0.62 | 44.0 | 4.34e-01 | 74.5% | 94.3% |
| 5061118 | 601.7.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain | 0.61 | 50.0 | 4.65e-01 | 88.8% | 93.5% |
| 3284782 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.61 | 49.0 | 4.78e-01 | 88.8% | 93.6% |
| 3843360 | 108.1.1.29 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 | 0.61 | 45.0 | 3.91e-01 | 93.9% | 48.8% |
| 3396759 | 632.3.1.26 ↗ | alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain › Pex2_Pex12 | 0.60 | 52.0 | 4.03e-01 | 93.9% | 76.2% |
| 3523825 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.60 | 45.0 | 4.02e-01 | 93.9% | 54.5% |
| 5068160 | 601.3.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain | 0.59 | 44.0 | 4.17e-01 | 77.6% | 86.1% |
| 4518770 | 7023.1.1.2 ↗ | alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › Pex2_Pex12 | 0.59 | 51.0 | 4.84e-01 | 94.9% | 96.5% |
| 4985813 | 3563.1.1.1 ↗ | alpha bundles › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › TatC | 0.59 | 44.0 | 3.36e-01 | 78.6% | 34.6% |
| 3211172 | 2004.1.1.0 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases | 0.59 | 45.0 | 3.18e-01 | 80.6% | 46.9% |
| 3266394 | 108.1.1.28 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 | 0.57 | 41.0 | 4.55e-01 | 91.8% | 100.0% |
| 3963102 | 191.1.1.0 ↗ | alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain | 0.57 | 48.0 | 4.36e-01 | 96.9% | 79.3% |
| 4235542 | 2004.1.1.87 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N | 0.56 | 44.0 | 3.03e-01 | 86.7% | 44.1% |
| 3845296 | 108.1.1.29 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_7 | 0.55 | 45.0 | 4.57e-01 | 95.9% | 89.0% |
| 4945585 | 2004.1.1.0 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases | 0.53 | 43.0 | 3.28e-01 | 90.8% | 89.8% |
| 3599899 | 5050.1.1.0 ↗ | alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter | 0.52 | 46.0 | 2.88e-01 | 100.0% | 91.4% |
| 3709136 | 108.1.1.0 ↗ | alpha arrays › EF-hand › EF-hand-related › EF-hand | 0.51 | 43.0 | 4.09e-01 | 94.9% | 97.4% |