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NC_025470.1__YP_009104222.1__S140_224__00221

Bact-Vir

NC_025470.1__YP_009104222.1__S140_224__00221

Identity

Accession:
NC_025470 ↗
Kingdom:
phage

Quality

81.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shewanella_sp._phage_1/40

TaxID: 1458860

Cluster

View cluster (3 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 2-70
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ftxB01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.72 53.0 4.30e-01 78.3% 46.1%
4hbrA00 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.71 60.0 4.75e-01 92.8% 62.1%
7wa9A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.67 47.0 3.71e-01 72.5% 53.9%
3mx7A00 2.40.128.180 Mainly Beta › Beta Barrel › Lipocalin › 0.67 53.0 4.84e-01 85.5% 91.1%
4innA00 2.40.128.520 Mainly Beta › Beta Barrel › Lipocalin › 0.67 55.0 4.34e-01 91.3% 83.6%
3auxA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 56.0 3.57e-01 100.0% 81.9%
1qw2A00 3.30.1980.10 Alpha Beta › 2-Layer Sandwich › Hypothetical protein Ta1206 fold › Hypothetical protein YunC 0.62 46.0 4.06e-01 79.7% 88.2%
1xn5A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.62 42.0 3.39e-01 71.0% 58.0%
1ah5A03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.61 46.0 4.30e-01 81.2% 79.1%
1w0pA03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.61 53.0 3.96e-01 100.0% 61.5%
3kstA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.61 47.0 3.16e-01 85.5% 90.4%
2psbA00 3.50.90.10 Alpha Beta › 3-Layer(bba) Sandwich › YerB-like fold › YerB-like 0.60 54.0 3.55e-01 100.0% 81.4%
1imuA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.59 48.0 4.21e-01 89.9% 74.8%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 41.0 4.06e-01 71.0% 95.8%
2vszB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 44.0 3.77e-01 85.5% 83.8%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.57 43.0 3.84e-01 82.6% 82.4%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 45.0 4.47e-01 85.5% 95.8%
1ln1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 41.0 3.04e-01 79.7% 83.7%
1qyaB01 3.10.310.10 Alpha Beta › Roll › Diaminopimelate Epimerase; Chain A, domain 1 › Diaminopimelate Epimerase; Chain A, domain 1 0.55 38.0 2.98e-01 71.0% 51.4%
5vxzA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 47.0 3.42e-01 97.1% 57.0%
3ecqA01 2.60.120.870 Mainly Beta › Sandwich › Jelly Rolls › 0.54 47.0 3.56e-01 100.0% 83.6%
4iglB00 2.180.10.10 Mainly Beta › Shell › RHS repeat-associated core › RHS repeat-associated core 0.53 45.0 2.61e-01 94.2% 11.4%
3n6rA03 3.30.700.30 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.53 47.0 3.80e-01 97.1% 51.9%
4chmB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 42.0 3.60e-01 92.8% 75.8%
8b55A01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 47.0 3.45e-01 98.6% 75.4%
1su0B00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.53 38.0 3.16e-01 79.7% 75.7%
4m00A01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 44.0 3.11e-01 98.6% 88.2%
4cciA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 44.0 3.10e-01 100.0% 83.1%
7r97A02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 41.0 4.16e-01 92.8% 97.1%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.51 42.0 3.35e-01 92.8% 59.4%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3750819 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.72 64.0 5.12e-01 100.0% 65.7%
3400395 214.1.1.1 ↗ a+b two layers › SH2 › SH2 › SH2 › SH2 0.71 60.0 5.08e-01 94.2% 70.4%
3243569 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.68 60.0 4.17e-01 100.0% 36.1%
3391728 3459.1.1.1 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › FAIM1 0.68 53.0 5.02e-01 85.5% 95.2%
4940485 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.67 53.0 4.38e-01 85.5% 78.4%
3236870 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 59.0 4.83e-01 100.0% 58.5%
185415 3459.1.1.1 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › FAIM1 0.67 53.0 4.84e-01 85.5% 91.1%
None — 0.66 55.0 5.16e-01 92.8% 98.8%
3224967 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.66 57.0 3.92e-01 100.0% 30.6%
3232904 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.66 56.0 4.01e-01 100.0% 36.0%
3233815 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.65 54.0 3.71e-01 98.6% 26.0%
4658924 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.64 57.0 3.59e-01 100.0% 91.9%
4998236 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.64 56.0 3.41e-01 98.6% 85.9%
4139338 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.63 54.0 3.33e-01 100.0% 92.0%
1764974 2004.1.1.514 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23, AAA_29, SbcC_Walker_B 0.63 56.0 4.13e-01 100.0% 72.2%
3226259 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.63 53.0 4.11e-01 100.0% 44.7%
1390452 2004.1.1.748 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15, AAA_23, SbcC_Walker_B 0.62 55.0 4.08e-01 100.0% 71.4%
3609905 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.62 48.0 4.41e-01 84.1% 83.3%
3737620 5.1.5.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DPPIV_N 0.62 49.0 2.96e-01 87.0% 25.9%
4163583 330.4.1.0 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain 0.62 47.0 4.54e-01 82.6% 86.3%
4400687 2004.1.1.782 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23, AAA_29, SbcC_Walker_B 0.62 53.0 3.28e-01 97.1% 86.6%
5009130 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.62 53.0 3.42e-01 97.1% 82.9%
4558929 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.61 47.0 4.53e-01 85.5% 90.0%
4460237 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.61 45.0 4.45e-01 81.2% 94.7%
4031638 7089.1.1.1 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › DUF1108 0.60 45.0 4.26e-01 81.2% 72.9%
5054272 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.60 51.0 3.02e-01 97.1% 89.3%
4024649 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.60 45.0 4.14e-01 81.2% 78.9%
3700289 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 47.0 3.88e-01 87.0% 56.2%
4157358 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.59 45.0 4.35e-01 82.6% 88.5%
3515207 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.59 48.0 4.43e-01 91.3% 86.7%
3951937 330.8.1.1 ↗ a+b two layers › dsRBD-like › Rv2632c-like › Rv2632c-like › Rv2632c-like 0.58 40.0 3.72e-01 72.5% 92.1%
4950969 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 0.57 49.0 3.04e-01 100.0% 93.6%
3687101 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.57 48.0 3.20e-01 97.1% 88.0%
5032886 2004.1.1.293 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.57 49.0 2.88e-01 100.0% 95.3%
3420092 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 43.0 4.18e-01 92.8% 72.5%
4365325 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.57 46.0 4.31e-01 88.4% 81.2%
4994698 4041.1.1.0 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase 0.57 49.0 3.59e-01 98.6% 98.5%
4982005 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 49.0 3.05e-01 100.0% 93.0%
2410435 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.57 47.0 3.01e-01 95.7% 61.6%
4000877 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.56 46.0 3.69e-01 97.1% 80.0%
3780194 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.55 45.0 3.11e-01 91.3% 33.1%
3822567 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.55 45.0 2.98e-01 94.2% 70.3%
4609498 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.55 44.0 4.28e-01 91.3% 95.0%
4048220 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.54 44.0 4.23e-01 89.9% 87.5%
3519032 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 46.0 4.11e-01 95.7% 72.0%
3497120 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 46.0 4.14e-01 95.7% 85.3%
4965501 330.4.1.1 ↗ a+b two layers › dsRBD-like › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain › Porphobil_deamC 0.54 41.0 3.82e-01 84.1% 81.1%
3543416 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.54 45.0 3.64e-01 97.1% 76.6%
1124180 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.53 47.0 3.78e-01 97.1% 51.1%
3910727 4.1.1.353 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_TNRC18 0.53 44.0 4.52e-01 94.2% 100.0%
3512363 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.53 46.0 3.64e-01 97.1% 49.0%
3289254 220.1.1.82 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_6 0.50 42.0 3.83e-01 100.0% 68.4%
3389900 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.50 43.0 3.23e-01 100.0% 70.5%