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NC_062753.1__YP_010357503.1__M1M31_gp61__00061

Bact-Vir

NC_062753.1__YP_010357503.1__M1M31_gp61__00061

Identity

Accession:
NC_062753 ↗
Kingdom:
phage

Quality

93.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Assiduviridae› Nekkelsvirus› Cellulophaga_phage_Nekkels_1

TaxID: 2745692

Cluster

View cluster (6 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 1-99_160-176
PDB
Domain cluster: rep: NC_021789.1__YP_008240881.1__Phi19-3_gp096__00096__D1-92
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2pfdA03 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.73 59.0 4.84e-01 85.3% 92.1%
1ivhA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.72 54.0 5.05e-01 82.8% 63.8%
5zw7A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.72 53.0 4.85e-01 82.8% 59.2%
4x28C03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.71 52.0 4.86e-01 82.8% 62.2%
2wdqD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.70 55.0 5.81e-01 82.8% 98.1%
3p4tA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.70 53.0 4.86e-01 83.6% 61.3%
2jifA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.70 52.0 4.71e-01 82.8% 58.4%
2wbiB03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.69 52.0 4.68e-01 82.8% 58.2%
1r0dA00 1.20.1410.10 Mainly Alpha › Up-down Bundle › I/LWEQ domain › I/LWEQ domain 0.68 51.0 4.28e-01 85.3% 47.2%
2c0uA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.66 54.0 4.71e-01 85.3% 58.6%
3c1yA02 1.20.1260.110 Mainly Alpha › Up-down Bundle › Ferritin › DNA integrity scanning linker region 0.66 50.0 4.56e-01 100.0% 60.8%
1dbhA01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.65 51.0 4.16e-01 82.8% 93.4%
2or0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.64 51.0 4.35e-01 84.5% 62.9%
4i17A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.61 43.0 3.42e-01 80.2% 37.1%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.61 42.0 3.91e-01 70.7% 82.8%
2lquA01 1.20.1420.40 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Decorin-binding protein 0.61 49.0 4.44e-01 85.3% 94.2%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 43.0 4.31e-01 90.5% 72.0%
7xxiA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.60 55.0 4.08e-01 100.0% 85.5%
2rfqC03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.59 47.0 4.14e-01 85.3% 66.3%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.59 46.0 3.79e-01 83.6% 60.5%
1at9A00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.58 51.0 4.14e-01 100.0% 83.9%
4k5yA01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 52.0 4.03e-01 100.0% 85.9%
2qvaA01 1.20.58.190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 1 0.55 38.0 3.68e-01 90.5% 62.8%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.55 50.0 3.40e-01 100.0% 80.4%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.54 40.0 3.89e-01 100.0% 69.8%
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 0.54 39.0 4.08e-01 75.9% 83.2%
2yayA02 1.20.1670.10 Mainly Alpha › Up-down Bundle › all-alpha NTP pyrophosphatase › Type II deoxyuridine triphosphatase 0.54 41.0 3.98e-01 82.8% 99.3%
2r4rA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.54 45.0 3.73e-01 93.1% 80.1%
6fjxA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.53 43.0 3.31e-01 87.1% 66.4%
3i44A01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.53 43.0 3.23e-01 86.2% 62.8%
1xg2B00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.53 44.0 4.04e-01 88.8% 78.1%
2q58B00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.52 47.0 3.39e-01 99.1% 41.6%
5klkB01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.52 41.0 3.15e-01 87.1% 62.3%
2p1aB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.52 40.0 3.75e-01 100.0% 66.4%
1lk3A00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.51 45.0 4.31e-01 95.7% 100.0%
2v7kA02 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 41.0 3.34e-01 85.3% 97.7%
8agyA01 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.51 39.0 3.10e-01 81.0% 70.1%
4rfsS00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.50 35.0 3.04e-01 81.0% 45.5%
1bgcA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.50 45.0 4.10e-01 100.0% 95.6%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4273940 633.6.1.4 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_2 0.71 53.0 4.83e-01 83.6% 60.0%
4100508 3843.1.1.4 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.70 53.0 5.30e-01 84.5% 76.7%
4931893 3843.1.1.4 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › PhaG_MnhG_YufB 0.69 49.0 5.26e-01 85.3% 85.0%
4949399 601.7.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HepT-like 0.65 59.0 5.45e-01 100.0% 93.1%
5052139 601.7.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HepT-like 0.64 59.0 5.57e-01 100.0% 94.2%
4993628 601.7.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HepT-like 0.64 57.0 5.47e-01 97.4% 100.0%
4950924 601.7.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HepT-like 0.63 57.0 5.30e-01 100.0% 91.7%
3728798 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.63 57.0 4.99e-01 100.0% 87.4%
4926828 633.6.1.1 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.63 48.0 4.22e-01 81.9% 65.7%
4991477 5069.1.2.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Respiratory nitrate reductase 1 gamma chain 0.62 55.0 4.41e-01 95.7% 64.4%
3939799 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.62 50.0 4.69e-01 85.3% 75.7%
3701003 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.62 49.0 4.57e-01 85.3% 66.9%
3328086 3922.1.1.71 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Exo70_N 0.61 48.0 4.74e-01 85.3% 86.4%
3775826 4016.1.1.0 ↗ alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase 0.61 49.0 4.50e-01 84.5% 77.2%
3657913 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.60 44.0 3.79e-01 85.3% 48.3%
5035107 3922.1.1.358 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › PF26119 0.60 44.0 4.49e-01 76.7% 99.1%
3786110 5069.1.1.4 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Ferric_reduct 0.60 52.0 4.22e-01 96.6% 58.7%
3849157 192.29.1.11 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › FerA 0.59 53.0 5.18e-01 99.1% 93.6%
4942916 601.12.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Nickel-containing superoxide dismutase, NiSOD › Nickel-containing superoxide dismutase, NiSOD › Sod_Ni 0.59 52.0 4.80e-01 100.0% 81.3%
4092649 5050.1.1.32 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Acatn 0.58 54.0 4.45e-01 100.0% 61.0%
3413227 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 51.0 3.90e-01 96.6% 45.8%
3470317 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.58 51.0 3.78e-01 98.3% 42.3%
3489921 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.58 51.0 3.83e-01 98.3% 43.1%
3509926 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.57 49.0 3.70e-01 98.3% 37.9%
4317199 603.5.1.1 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like › FlgN 0.57 42.0 4.16e-01 92.2% 72.0%
3610620 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 39.0 4.01e-01 94.0% 73.0%
3336125 603.1.1.99 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27021 0.56 44.0 3.83e-01 81.9% 87.6%
4192699 603.5.1.1 ↗ alpha bundles › STAT-like › FlgN-like › FlgN-like › FlgN 0.56 43.0 4.10e-01 93.1% 70.0%
3735230 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.56 43.0 3.99e-01 85.3% 63.2%
4457335 3558.1.1.1 ↗ alpha arrays › HSDR subunit helical domain › HSDR subunit helical domain › HSDR subunit helical domain › EcoR124_C 0.56 40.0 4.06e-01 85.3% 75.7%
3449219 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.55 43.0 4.11e-01 81.9% 73.3%
4038790 150.3.1.6 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › IL10 0.55 50.0 4.55e-01 100.0% 98.7%
4958744 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.55 43.0 4.41e-01 84.5% 87.3%
4403727 620.1.1.6 ↗ alpha bundles › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › YfiT-like putative metal-dependent hydrolases › DinB_2 0.54 47.0 4.29e-01 100.0% 70.6%
3441715 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.54 41.0 4.24e-01 91.4% 82.7%
4264893 150.3.1.6 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › 4-helical cytokines › 4-helical cytokine › IL10 0.54 49.0 4.43e-01 100.0% 93.8%
3492486 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.54 43.0 3.47e-01 85.3% 55.7%
5046222 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.54 48.0 3.82e-01 98.3% 84.7%
3212086 109.4.1.431 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ERK-JNK_inhib 0.54 47.0 4.27e-01 93.1% 72.7%
3581305 604.12.1.92 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Meckelin 0.53 42.0 3.52e-01 84.5% 52.2%
3205192 4177.1.1.27 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_4 0.53 41.0 2.97e-01 80.2% 74.2%
4030289 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 40.0 2.53e-01 78.4% 33.5%
3579069 109.4.1.213 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FancD2 0.53 43.0 2.75e-01 85.3% 32.8%
3742785 5069.1.3.59 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › PF27892 0.52 43.0 4.35e-01 87.9% 92.2%
4577909 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.52 40.0 3.40e-01 81.9% 66.8%
3384195 603.2.1.0 ↗ alpha bundles › STAT-like › STAT › STAT 0.51 41.0 3.68e-01 85.3% 68.8%
3935671 109.4.1.431 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ERK-JNK_inhib 0.51 45.0 3.71e-01 94.0% 56.9%
3227347 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.50 44.0 3.95e-01 100.0% 91.2%
3172862 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.50 40.0 3.10e-01 85.3% 56.2%
D2 medium residues 100-159
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2keyA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.63 40.0 3.32e-01 71.7% 34.8%