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SR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00331
Bact-VirSR-VP_4-6_scaffold_141_4086954_prodigal-single.1__X__X__00331
Identity
- Kingdom:
- phage
Quality
85.4
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 3-70
Domain cluster:
representative
CATH (16)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4i98C01 | 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 | 0.71 | 36.0 | 3.53e-01 | 75.0% | 45.3% |
| 1t6sA01 | 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 | 0.70 | 35.0 | 3.25e-01 | 75.0% | 38.4% |
| 4lgcA00 | 3.40.50.12780 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain | 0.62 | 51.0 | 3.23e-01 | 94.1% | 72.0% |
| 2felA00 | 1.20.200.10 | Mainly Alpha › Up-down Bundle › Fumarase C; Chain A, domain 2 › Fumarase/aspartase (Central domain) | 0.61 | 51.0 | 3.33e-01 | 97.1% | 60.2% |
| 1xp8A02 | 3.30.250.10 | Alpha Beta › 2-Layer Sandwich › Rec A Protein; domain 2 › RecA protein, C-terminal domain | 0.57 | 44.0 | 4.62e-01 | 82.4% | 100.0% |
| 2j0nB00 | 1.20.1710.10 | Mainly Alpha › Up-down Bundle › IpaD-like › IpaD-like | 0.55 | 45.0 | 3.26e-01 | 88.2% | 64.2% |
| 3pe5A00 | 3.40.630.190 | Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein | 0.55 | 47.0 | 3.20e-01 | 100.0% | 84.1% |
| 1vyiA00 | 1.20.120.820 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Phosphoprotein, C-terminal domain | 0.54 | 44.0 | 3.87e-01 | 95.6% | 95.5% |
| 5tvoB00 | 3.30.360.50 | Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › S-adenosylmethionine decarboxylase | 0.53 | 28.0 | 3.00e-01 | 79.4% | 55.9% |
| 6ui4A01 | 1.20.120.720 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain | 0.53 | 40.0 | 3.71e-01 | 95.6% | 63.6% |
| 1hywA00 | 3.30.1580.10 | Alpha Beta › 2-Layer Sandwich › Head-to-tail joining protein W, gpW › Head-to-tail joining protein W | 0.52 | 34.0 | 3.59e-01 | 83.8% | 77.6% |
| 1qviA01 | 1.20.120.720 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Myosin VI head, motor domain, U50 subdomain | 0.52 | 44.0 | 3.68e-01 | 92.6% | 76.5% |
| 3bjoA00 | 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 | 0.52 | 37.0 | 3.39e-01 | 80.9% | 68.9% |
| 7x0fA01 | 3.30.559.10 | Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain | 0.51 | 38.0 | 3.03e-01 | 79.4% | 91.2% |
| 6guvA00 | 3.30.710.10 | Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A | 0.51 | 36.0 | 2.90e-01 | 73.5% | 72.4% |
| 2zxiA03 | 1.10.10.1800 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA | 0.51 | 35.0 | 3.20e-01 | 92.6% | 51.5% |
ECOD (26)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4204745 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.68 | 50.0 | 3.69e-01 | 79.4% | 45.0% |
| 5059636 | 7584.1.1.1 ↗ | a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding | 0.68 | 50.0 | 3.70e-01 | 79.4% | 45.6% |
| 5038509 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.66 | 48.0 | 3.67e-01 | 77.9% | 46.3% |
| 3394330 | 323.1.1.0 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases | 0.65 | 47.0 | 3.72e-01 | 75.0% | 57.8% |
| 3166357 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.65 | 48.0 | 3.55e-01 | 79.4% | 45.0% |
| 4021620 | 323.1.1.0 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases | 0.64 | 46.0 | 3.51e-01 | 75.0% | 49.4% |
| 3756698 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.64 | 51.0 | 3.46e-01 | 88.2% | 73.6% |
| 5041165 | 7584.1.1.1 ↗ | a/b three-layered sandwiches › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › Rossmann-like domain in Acetyl-CoA synthetase-like proteins › AMP-binding | 0.64 | 48.0 | 3.58e-01 | 80.9% | 47.4% |
| 5008330 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.64 | 48.0 | 3.69e-01 | 80.9% | 53.5% |
| 3957794 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.63 | 47.0 | 3.36e-01 | 79.4% | 40.2% |
| 3254190 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.63 | 48.0 | 3.42e-01 | 80.9% | 40.0% |
| 3931606 | 192.2.1.2 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin | 0.60 | 43.0 | 3.66e-01 | 76.5% | 47.0% |
| 3876065 | 323.1.1.3 ↗ | a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding | 0.59 | 47.0 | 3.40e-01 | 88.2% | 49.3% |
| 3810835 | 601.1.2.0 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) | 0.57 | 41.0 | 3.09e-01 | 75.0% | 48.4% |
| 4385210 | 633.21.1.18 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CASP_dom | 0.57 | 40.0 | 2.89e-01 | 73.5% | 57.3% |
| 5061627 | 5073.1.2.0 ↗ | alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Copper efflux ATPase transmembrane domain | 0.57 | 49.0 | 3.46e-01 | 100.0% | 48.7% |
| 3493963 | 192.2.1.1 ↗ | alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 | 0.56 | 40.0 | 3.58e-01 | 76.5% | 52.0% |
| 4086368 | 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 | 0.54 | 43.0 | 3.15e-01 | 88.2% | 49.5% |
| 3279916 | 633.21.1.34 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › DUF7144 | 0.54 | 43.0 | 3.70e-01 | 89.7% | 96.5% |
| 4022379 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.54 | 43.0 | 3.37e-01 | 88.2% | 83.3% |
| 4998665 | 604.39.1.0 ↗ | alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters | 0.53 | 47.0 | 3.34e-01 | 100.0% | 69.3% |
| 3946654 | 517.2.1.0 ↗ | beta barrels › CBF-like › TraF › TraF | 0.52 | 35.0 | 2.36e-01 | 70.6% | 17.8% |
| 5045781 | 604.39.1.0 ↗ | alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters | 0.52 | 45.0 | 3.40e-01 | 100.0% | 96.6% |
| 3297656 | 601.1.2.68 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › DUF1218 | 0.51 | 39.0 | 2.97e-01 | 83.8% | 60.6% |
| 4956226 | 304.120.1.6 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI › ThiI_fer | 0.51 | 38.0 | 3.69e-01 | 91.2% | 72.0% |
| 4978628 | 2498.1.1.0 ↗ | mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" | 0.50 | 44.0 | 2.59e-01 | 100.0% | 13.6% |
D2
high
residues 85-139
Domain cluster:
representative
CATH (18)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1h10A00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.63 | 42.0 | 3.38e-01 | 70.9% | 41.9% |
| 7oc3A01 | 2.30.30.140 | Mainly Beta › Roll › SH3 type barrels. › | 0.62 | 54.0 | 4.60e-01 | 100.0% | 79.3% |
| 1x1fA00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.61 | 41.0 | 3.08e-01 | 70.9% | 30.2% |
| 2vpzA01 | 2.20.25.90 | Mainly Beta › Single Sheet › N-terminal domain of TfIIb › ADC-like domains | 0.60 | 41.0 | 3.87e-01 | 70.9% | 76.1% |
| 3vmaA03 | 3.30.2060.10 | Alpha Beta › 2-Layer Sandwich › Penicillin-binding protein 1b fold › Penicillin-binding protein 1b domain | 0.59 | 46.0 | 4.00e-01 | 89.1% | 60.0% |
| 5b4wA00 | 2.130.10.10 | Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase | 0.58 | 44.0 | 2.69e-01 | 87.3% | 50.2% |
| 4hhvA00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.57 | 39.0 | 3.27e-01 | 72.7% | 44.7% |
| 4fdyA02 | 3.90.1720.10 | Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › endopeptidase domain like (from Nostoc punctiforme) | 0.56 | 46.0 | 3.62e-01 | 100.0% | 56.0% |
| 4qunA00 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.55 | 48.0 | 3.04e-01 | 98.2% | 39.2% |
| 1vkdA00 | 2.115.10.20 | Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 | 0.54 | 41.0 | 2.63e-01 | 87.3% | 85.9% |
| 6xw5A01 | 2.40.510.10 | Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses | 0.54 | 37.0 | 2.67e-01 | 72.7% | 23.7% |
| 3e07A00 | 2.10.90.10 | Mainly Beta › Ribbon › Cystine Knot Cytokines, subunit B › Cystine-knot cytokines | 0.53 | 38.0 | 3.30e-01 | 76.4% | 86.7% |
| 4fbcA01 | 3.40.420.10 | Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 | 0.53 | 39.0 | 2.93e-01 | 85.5% | 93.7% |
| 2kcjA00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.52 | 36.0 | 3.05e-01 | 76.4% | 48.1% |
| 1w1hD00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.52 | 38.0 | 3.02e-01 | 83.6% | 58.4% |
| 6iikB00 | 3.90.70.10 | Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases | 0.52 | 42.0 | 2.72e-01 | 100.0% | 89.2% |
| 2odxA00 | 2.60.260.40 | Mainly Beta › Sandwich › HSP40/DNAj peptide-binding domain › q5lls5 like domains | 0.52 | 36.0 | 3.69e-01 | 80.0% | 77.8% |
| 1srzA00 | 2.10.70.10 | Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 | 0.51 | 36.0 | 3.46e-01 | 87.3% | 64.7% |
ECOD (17)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3881117 | 4.1.1.9 ↗ | beta barrels › SH3 › SH3 › SH3 › TUDOR | 0.66 | 57.0 | 4.75e-01 | 100.0% | 60.0% |
| 3919719 | 206.1.1.1 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase | 0.63 | 45.0 | 2.98e-01 | 76.4% | 56.3% |
| 3796759 | 4.1.1.287 ↗ | beta barrels › SH3 › SH3 › SH3 › DUF5641 | 0.63 | 52.0 | 4.37e-01 | 92.7% | 75.8% |
| 5006906 | 1001.1.1.1 ↗ | a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Molybdop_Fe4S4 | 0.61 | 42.0 | 4.05e-01 | 72.7% | 78.5% |
| 3630702 | 206.1.1.20 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr | 0.61 | 44.0 | 2.77e-01 | 76.4% | 47.0% |
| 4951973 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.60 | 42.0 | 4.22e-01 | 72.7% | 76.4% |
| 4024732 | 295.1.1.40 ↗ | a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › Microp_apicomplexa_10 | 0.57 | 40.0 | 3.57e-01 | 74.5% | 60.0% |
| 4319097 | 4.1.1.0 ↗ | beta barrels › SH3 › SH3 › SH3 | 0.56 | 38.0 | 3.81e-01 | 72.7% | 82.8% |
| 5031647 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.56 | 38.0 | 3.56e-01 | 70.9% | 57.1% |
| 3602976 | 375.1.1.0 ↗ | few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related | 0.55 | 38.0 | 3.85e-01 | 72.7% | 76.4% |
| 3293131 | 5084.5.1.3 ↗ | beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Porin_3 | 0.54 | 40.0 | 2.76e-01 | 85.5% | 25.3% |
| 3241718 | 5.1.4.0 ↗ | beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed | 0.53 | 36.0 | 2.42e-01 | 74.5% | 34.4% |
| 2967043 | 216.1.1.32 ↗ | a+b two layers › UBC-like › UBC-like › UBC-like › PF29693 | 0.51 | 38.0 | 3.02e-01 | 85.5% | 49.6% |
| 3579531 | 11.2.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain | 0.51 | 37.0 | 3.39e-01 | 83.6% | 96.5% |
| 3608028 | 206.1.1.70 ↗ | a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, ABC1 | 0.51 | 41.0 | 2.66e-01 | 94.5% | 45.1% |
| 3267419 | 601.51.1.7 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › DUF4460 | 0.51 | 40.0 | 3.01e-01 | 94.5% | 67.9% |
| 3953070 | 243.1.1.80 ↗ | a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF26580 | 0.50 | 34.0 | 2.87e-01 | 70.9% | 80.0% |