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NC_062753.1__YP_010357483.1__M1M31_gp41__00041
Bact-VirNC_062753.1__YP_010357483.1__M1M31_gp41__00041
Identity
- Accession:
- NC_062753 ↗
- Kingdom:
- phage
Quality
84.2
mean pLDDT
Taxonomy
Heunggongvirae›
Uroviricota›
Caudoviricetes›
Assiduviridae›
Nekkelsvirus›
Cellulophaga_phage_Nekkels_1
TaxID: 2745692
Cluster
View cluster (166 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 2-57_77-162_292-334
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03864.23 best | Phage_cap_E | 24.6 | 1.70e-05 | 54.0% | 24.7% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2qlzA02 | 6.10.250.2960 | Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › | 0.57 | 25.0 | 3.53e-01 | 72.4% | 84.9% |
| 1aqcB00 | 2.30.29.30 | Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) | 0.55 | 27.0 | 3.30e-01 | 77.3% | 70.5% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2443966 | 2485.3.1.1 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_cap_E | 0.72 | 59.0 | 4.42e-01 | 84.3% | 79.0% |
| 5041371 | 2485.3.1.0 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 | 0.65 | 57.0 | 4.73e-01 | 92.4% | 92.9% |
| 4241362 | 2485.3.1.0 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 | 0.61 | 56.0 | 4.77e-01 | 97.8% | 92.9% |
| 3583655 | 2485.3.1.5 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Gp23 | 0.61 | 50.0 | 4.08e-01 | 84.9% | 86.6% |
| 2989372 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.61 | 49.0 | 4.12e-01 | 84.9% | 83.2% |
| 4988094 | 2485.3.1.18 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 | 0.59 | 55.0 | 4.87e-01 | 97.8% | 92.2% |
| 3946670 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.59 | 54.0 | 4.71e-01 | 97.8% | 89.5% |
| 2989506 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.59 | 48.0 | 4.04e-01 | 84.9% | 87.1% |
| 3942344 | 2485.3.1.19 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › PF30928 | 0.58 | 47.0 | 3.97e-01 | 84.9% | 84.8% |
| 4884207 | 2485.3.1.7 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside | 0.58 | 49.0 | 4.16e-01 | 88.1% | 86.2% |
| 5081698 | 2485.3.1.18 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 | 0.58 | 52.0 | 4.42e-01 | 97.3% | 93.4% |
| 2989340 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.57 | 48.0 | 3.95e-01 | 87.6% | 82.5% |
| 4991535 | 2485.3.1.2 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 | 0.56 | 51.0 | 4.67e-01 | 98.9% | 92.7% |
| 4955362 | 2485.3.1.2 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 | 0.56 | 50.0 | 4.64e-01 | 95.7% | 92.3% |
| 4031028 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.56 | 52.0 | 4.46e-01 | 99.5% | 89.6% |
| 5011908 | 2485.3.1.2 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 | 0.52 | 47.0 | 4.30e-01 | 96.8% | 87.9% |
| 3944238 | 2485.3.1.7 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Major_capside | 0.52 | 43.0 | 3.72e-01 | 87.6% | 92.6% |
| 1389463 | 66.1.1.0 ↗ | beta sandwiches › ISP domain › ISP domain › ISP domain | 0.51 | 13.0 | 2.57e-01 | 98.9% | 85.7% |
D2
high
residues 369-423
Domain cluster:
representative
CATH (18)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2yukA00 | 1.10.30.10 | Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain | 0.67 | 54.0 | 4.60e-01 | 89.1% | 72.2% |
| 3veaA01 | 1.20.1270.380 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › MatP, N-terminal domain | 0.67 | 50.0 | 4.40e-01 | 85.5% | 79.8% |
| 3vdpA01 | 1.10.8.420 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › RecR Domain 1 | 0.66 | 45.0 | 4.67e-01 | 96.4% | 75.0% |
| 1zq3P00 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.63 | 40.0 | 3.82e-01 | 92.7% | 52.9% |
| 6bzrB01 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.62 | 53.0 | 3.50e-01 | 96.4% | 24.2% |
| 5t3wA00 | 1.20.120.1160 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.61 | 45.0 | 3.47e-01 | 81.8% | 65.7% |
| 2bduA02 | 1.10.150.340 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain | 0.61 | 44.0 | 4.04e-01 | 78.2% | 94.6% |
| 2d7lA01 | 1.10.30.10 | Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain | 0.59 | 46.0 | 4.70e-01 | 85.5% | 96.2% |
| 1j09A04 | 1.10.8.70 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutamate-tRNA synthetase, class I, anticodon-binding domain 1 | 0.56 | 38.0 | 4.02e-01 | 89.1% | 81.2% |
| 3f2eA00 | 1.20.58.800 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › | 0.55 | 41.0 | 3.58e-01 | 80.0% | 89.2% |
| 3by4A00 | 3.90.70.80 | Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › | 0.55 | 44.0 | 3.24e-01 | 96.4% | 41.3% |
| 1c0gA03 | 3.90.640.10 | Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4 | 0.54 | 39.0 | 3.56e-01 | 89.1% | 94.6% |
| 3nhiA01 | 1.10.238.20 | Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain | 0.54 | 43.0 | 3.34e-01 | 100.0% | 77.9% |
| 2zgdA00 | 1.25.40.20 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain | 0.53 | 36.0 | 3.05e-01 | 72.7% | 58.8% |
| 4heoA00 | 1.10.8.10 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain | 0.52 | 40.0 | 4.02e-01 | 87.3% | 92.7% |
| 4fcyB02 | 1.10.10.60 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like | 0.52 | 37.0 | 3.54e-01 | 83.6% | 64.6% |
| 4hwdD00 | 1.20.58.120 | Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain | 0.51 | 40.0 | 3.41e-01 | 85.5% | 86.7% |
| 1zv1A00 | 1.10.8.10 | Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain | 0.51 | 36.0 | 3.61e-01 | 83.6% | 72.9% |
ECOD (9)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3501989 | 4143.1.1.0 ↗ | a+b two layers › THUMP domain-like › THUMP domain-like › THUMP domain-like | 0.80 | 72.0 | 5.19e-01 | 100.0% | 66.7% |
| 3573927 | 3065.1.1.1 ↗ | alpha bundles › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › ANIS5_cation-bd | 0.66 | 48.0 | 3.68e-01 | 76.4% | 49.2% |
| 4019367 | 235.1.1.0 ↗ | a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like | 0.66 | 54.0 | 3.87e-01 | 94.5% | 48.8% |
| 4065433 | 2004.1.1.0 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases | 0.64 | 51.0 | 3.36e-01 | 96.4% | 24.6% |
| 5073312 | 2006.1.1.18 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 | 0.63 | 47.0 | 3.21e-01 | 85.5% | 28.7% |
| 3502247 | 101.1.1.63 ↗ | alpha arrays › HTH › HTH › Three-helical HTH › HTH_28 | 0.55 | 34.0 | 3.35e-01 | 92.7% | 55.0% |
| 5038858 | 184.1.1.1 ↗ | alpha arrays › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Nucleoside phosphorylase/phosphoribosyltransferase-N › Glycos_trans_3N | 0.54 | 37.0 | 3.52e-01 | 72.7% | 61.5% |
| 4036856 | 7.1.1.1 ↗ | beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ | 0.53 | 43.0 | 3.23e-01 | 92.7% | 45.5% |
| 3474593 | 216.1.1.0 ↗ | a+b two layers › UBC-like › UBC-like › UBC-like | 0.50 | 36.0 | 2.79e-01 | 83.6% | 83.7% |
D3
medium
residues 163-291_335-364
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF03864.23 best | Phage_cap_E | 29.2 | 6.90e-07 | 97.5% | 33.5% |
CATH (13)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2e0zC03 | 3.30.2320.10 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain | 0.78 | 47.0 | 6.02e-01 | 92.5% | 100.0% |
| 7mh2A01 | 3.30.2320.10 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain | 0.78 | 46.0 | 5.98e-01 | 88.1% | 100.0% |
| 2pk8A00 | 3.30.2320.10 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain | 0.78 | 46.0 | 5.93e-01 | 84.9% | 100.0% |
| 1ohgA02 | 3.30.2320.10 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain | 0.75 | 49.0 | 5.96e-01 | 93.7% | 100.0% |
| 3bjqA00 | 3.90.1690.10 | Alpha Beta › Alpha-Beta Complex › phage-related protein like fold › phage-related protein like domain | 0.73 | 66.0 | 5.26e-01 | 95.0% | 60.1% |
| 3bqwA02 | 3.30.1930.10 | Alpha Beta › 2-Layer Sandwich › capsid protein of prophage fold › capsid protein of prophage domain | 0.69 | 57.0 | 6.14e-01 | 93.1% | 100.0% |
| 1yueA03 | 3.30.2320.40 | Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › | 0.64 | 47.0 | 5.32e-01 | 93.1% | 98.3% |
| 2ux6A00 | 2.60.40.420 | Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins | 0.53 | 29.0 | 3.23e-01 | 94.3% | 66.4% |
| 2bx2L02 | 3.40.1260.20 | Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Ychn; Chain: A, › Ribonuclease E, catalytic domain | 0.53 | 33.0 | 3.83e-01 | 80.5% | 88.2% |
| 5jpoD01 | 3.40.30.10 | Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin | 0.52 | 23.0 | 3.10e-01 | 81.1% | 78.0% |
| 4jqfA02 | 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 | 0.51 | 22.0 | 3.05e-01 | 89.3% | 82.2% |
| 7kseA02 | 3.30.420.10 | Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H | 0.50 | 37.0 | 3.89e-01 | 98.7% | 84.2% |
| 1xexB00 | 3.40.50.300 | Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases | 0.50 | 27.0 | 2.70e-01 | 87.4% | 48.4% |
ECOD (15)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 11367 | 2485.3.1.6 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › ENCP4 | 0.78 | 46.0 | 5.93e-01 | 84.9% | 100.0% |
| 333200 | 2485.3.1.1 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_cap_E | 0.75 | 68.0 | 5.39e-01 | 95.0% | 60.7% |
| 2443966 | 2485.3.1.1 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_cap_E | 0.73 | 64.0 | 4.72e-01 | 94.3% | 56.0% |
| 4991535 | 2485.3.1.2 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Linocin_M18 | 0.64 | 53.0 | 4.51e-01 | 92.5% | 56.3% |
| 2989356 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.62 | 56.0 | 4.50e-01 | 96.2% | 56.1% |
| 2989363 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.62 | 55.0 | 4.35e-01 | 94.3% | 55.8% |
| 2639625 | 2485.3.1.18 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid_4 | 0.61 | 52.0 | 4.29e-01 | 95.0% | 52.1% |
| 5083777 | 2485.3.1.3 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › Phage_capsid | 0.60 | 54.0 | 4.32e-01 | 95.6% | 50.7% |
| 5002389 | 2485.3.1.0 ↗ | a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 | 0.60 | 53.0 | 4.37e-01 | 95.0% | 59.6% |
| 4121502 | 3008.1.1.0 ↗ | a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 0.60 | 31.0 | 4.00e-01 | 83.6% | 87.8% |
| 2074975 | 3779.1.1.0 ↗ | 0.59 | 29.0 | 3.40e-01 | 93.7% | 64.3% | |
| 3979724 | 298.3.1.1 ↗ | a+b two layers › FwdE/GAPDH domain-like › Serine dehydratase beta chain-like › Serine dehydratase beta chain-like › SDH_beta | 0.53 | 42.0 | 4.37e-01 | 88.7% | 90.0% |
| 4032230 | 298.3.1.1 ↗ | a+b two layers › FwdE/GAPDH domain-like › Serine dehydratase beta chain-like › Serine dehydratase beta chain-like › SDH_beta | 0.51 | 38.0 | 4.07e-01 | 89.3% | 87.9% |
| 4984125 | 2006.1.4.2 ↗ | a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN | 0.51 | 42.0 | 4.20e-01 | 92.5% | 87.3% |
| 2765405 | 2484.5.1.2 ↗ | mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH | 0.50 | 32.0 | 3.56e-01 | 98.7% | 79.5% |