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RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00556

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00556

Identity

Kingdom:
phage

Quality

56.0 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 6-70
PDB
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3n3fA01 3.40.1620.70 Alpha Beta › 3-Layer(aba) Sandwich › YefM-like fold › 0.85 52.0 6.27e-01 100.0% 95.3%
3hshE00 3.40.1620.70 Alpha Beta › 3-Layer(aba) Sandwich › YefM-like fold › 0.82 51.0 5.51e-01 100.0% 74.5%
1yu0A01 2.10.10.30 Mainly Beta › Ribbon › Seminal Fluid Protein PDC-109 (Domain B) › 0.81 49.0 5.47e-01 100.0% 78.4%
4oelB00 2.40.50.170 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Cysteine proteinases. Chain C 0.64 35.0 3.49e-01 72.3% 50.7%
2onlC01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.55 43.0 4.02e-01 89.2% 86.0%
1ywkC00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.54 45.0 3.15e-01 100.0% 98.4%
2znrA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.53 46.0 3.38e-01 98.5% 41.6%
1kj6A00 3.10.360.10 Alpha Beta › Roll › Antimicrobial Peptide, Beta-defensin 2; Chain A › Antimicrobial Peptide, Beta-defensin 2; Chain A 0.53 31.0 3.57e-01 90.8% 84.4%
4oj5B01 3.30.2020.50 Alpha Beta › 2-Layer Sandwich › NE0471 N-terminal domain-like › 0.51 44.0 4.18e-01 100.0% 80.5%
4feuF01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.99e-01 90.8% 100.0%
3lmmA03 3.30.565.60 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › 0.51 43.0 3.30e-01 100.0% 95.3%
3h09A03 3.30.160.280 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 41.0 3.75e-01 100.0% 67.0%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3528795 3761.1.1.0 beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related 0.87 50.0 5.98e-01 100.0% 84.4%
1505155 3761.1.1.2 beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Collagen_trimer 0.83 51.0 5.52e-01 100.0% 73.2%
1107990 3761.1.1.1 beta duplicates or obligate multimers › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Major tropism determinant (Mtd) trimerization domain-related › Mtd_N 0.81 49.0 5.51e-01 100.0% 80.0%
2512672 3856.1.2.1 beta sandwiches › Putative tailspike protein Orf210 N-terminal domain › Putative tailspike protein Orf210 N-terminal domain › tailspike protein Orf211 N-terminal domain › Phage_tail_beta 0.80 74.0 7.34e-01 100.0% 98.5%
3502260 214.1.1.9 a+b two layers › SH2 › SH2 › SH2 › DUF7063 0.63 45.0 3.63e-01 100.0% 39.2%
4421536 601.23.1.4 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.55 38.0 2.42e-01 72.3% 14.8%
4033230 2008.1.1.155 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › CoiA_nuc 0.54 44.0 3.44e-01 100.0% 41.4%
3449835 2492.1.1.2 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.52 45.0 3.35e-01 100.0% 42.9%
5053690 2492.1.1.2 a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › JAB 0.52 44.0 3.42e-01 100.0% 77.9%
3780553 2484.1.1.15 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › GDA1_CD39 0.51 36.0 2.53e-01 75.4% 85.4%
D2 high residues 76-152
PDB
CATH (28)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vsvA01 2.160.20.10 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › Single-stranded right-handed beta-helix, Pectin lyase-like 0.84 67.0 3.97e-01 92.2% 12.7%
6kqsA01 2.160.20.10 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › Single-stranded right-handed beta-helix, Pectin lyase-like 0.78 68.0 4.17e-01 94.8% 17.7%
4oj5C04 2.160.20.130 Mainly Beta › 3 Solenoid › Pectate Lyase C-like › 0.76 60.0 4.45e-01 93.5% 34.6%
4zyaB00 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.68 54.0 5.45e-01 84.4% 97.4%
5ntfA01 3.40.50.10590 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Zn-dependent exopeptidases 0.64 53.0 4.11e-01 93.5% 79.0%
2kqrA01 3.30.1910.20 Alpha Beta › 2-Layer Sandwich › so0334 like fold › asparaginyl-tRNA synthetase, N-terminal domain 0.63 46.0 4.69e-01 75.3% 89.2%
2xveA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.62 41.0 3.83e-01 100.0% 53.0%
1f8fA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 45.0 3.79e-01 100.0% 48.2%
3k2wB02 3.40.309.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 0.58 49.0 3.69e-01 94.8% 73.7%
1sz2B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 49.0 4.25e-01 94.8% 80.0%
3nhmA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 48.0 4.26e-01 93.5% 67.8%
2mwmA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.57 48.0 3.85e-01 100.0% 47.0%
4i3vA02 3.40.309.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 0.57 47.0 3.56e-01 93.5% 69.7%
3k5wA02 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.57 38.0 2.71e-01 100.0% 21.2%
3gc6A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 50.0 4.42e-01 98.7% 86.6%
2px7A00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.56 39.0 2.93e-01 96.1% 28.1%
3e0xA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 47.0 3.38e-01 97.4% 43.3%
1wcwA02 3.40.50.10090 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.54 45.0 3.99e-01 94.8% 85.7%
4c76A00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.54 45.0 3.51e-01 96.1% 60.4%
1nni100 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.54 44.0 3.53e-01 94.8% 60.0%
7tjhE01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 43.0 3.41e-01 92.2% 62.4%
4xjvA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 44.0 3.30e-01 94.8% 38.9%
3rjlA02 3.40.309.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 2 › Aldehyde Dehydrogenase; Chain A, domain 2 0.53 44.0 3.41e-01 96.1% 96.3%
1sqsA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.53 45.0 3.31e-01 100.0% 35.1%
2q9uA02 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.52 42.0 3.58e-01 94.8% 69.0%
4g1vA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.52 43.0 3.68e-01 96.1% 86.0%
2fzvA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.51 42.0 3.14e-01 97.4% 64.7%
4yrbA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 43.0 3.26e-01 100.0% 43.2%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1841000 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.84 67.0 6.78e-01 92.2% 86.7%
3263728 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.80 69.0 4.79e-01 93.5% 30.2%
2831959 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.80 69.0 4.05e-01 94.8% 13.7%
4211588 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.79 70.0 4.25e-01 100.0% 15.9%
2831960 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.79 70.0 4.13e-01 96.1% 13.7%
5046331 207.2.1.33 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Pel9A-like_beta_helix 0.79 66.0 4.09e-01 96.1% 16.7%
4969946 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.78 57.0 3.53e-01 93.5% 14.2%
4969480 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.78 58.0 3.84e-01 90.9% 21.1%
5035023 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.78 57.0 3.84e-01 93.5% 21.1%
4969266 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.78 58.0 3.22e-01 96.1% 6.3%
4954461 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.77 67.0 4.41e-01 94.8% 23.5%
3256985 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.76 63.0 3.81e-01 94.8% 14.4%
5032868 207.2.1.13 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › NosD 0.75 57.0 4.15e-01 94.8% 30.2%
5034990 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.74 57.0 3.60e-01 96.1% 16.6%
5034599 207.2.1.22 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › Beta_helix 0.74 54.0 3.42e-01 90.9% 15.9%
4954462 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.74 63.0 3.91e-01 98.7% 17.3%
4970380 207.2.1.13 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › NosD 0.70 58.0 3.79e-01 94.8% 21.6%
4466879 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.70 63.0 3.96e-01 100.0% 36.5%
3804366 207.1.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.69 54.0 3.39e-01 100.0% 16.4%
3896831 1089.1.1.0 a+b two layers › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain 0.68 49.0 3.53e-01 76.6% 32.1%
3221312 1089.1.1.1 a+b two layers › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain › AsnRS_N 0.66 48.0 4.91e-01 76.6% 89.3%
3800826 1089.1.1.0 a+b two layers › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain › Asparaginal-tRNA synthetase N-terminal domain 0.66 48.0 5.01e-01 75.3% 94.3%
4970042 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.65 59.0 3.41e-01 100.0% 18.6%
4948247 7512.1.1.54 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Alg14 0.65 40.0 3.24e-01 90.9% 31.2%
4059017 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.62 42.0 3.81e-01 100.0% 51.4%
4012888 129.1.1.0 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.61 41.0 3.38e-01 100.0% 37.2%
4989876 3979.1.1.0 a+b four layers › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain 0.59 45.0 4.74e-01 94.8% 91.4%
138284 2007.15.1.1 a/b three-layered sandwiches › Flavodoxin-like › N-deoxyribosyltransferase › N-deoxyribosyltransferase › Rib_hydrolayse 0.59 53.0 3.70e-01 100.0% 33.9%
3681732 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.58 49.0 3.35e-01 94.8% 35.4%
3630555 207.1.1.79 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › F-box 0.57 48.0 3.29e-01 98.7% 30.3%
3257549 3979.1.1.0 a+b four layers › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain 0.57 44.0 4.57e-01 96.1% 92.9%
3436764 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.56 47.0 3.53e-01 94.8% 41.5%
4207588 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.56 44.0 3.43e-01 100.0% 38.3%
4950046 2007.2.1.3 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › FMN_red 0.55 45.0 3.57e-01 96.1% 65.9%
3544111 207.1.1.63 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6,LRR_8 0.55 47.0 3.50e-01 100.0% 36.9%
4950691 2007.2.5.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Rhodanese/Cell cycle control phosphatase › Rhodanese 0.55 46.0 3.74e-01 94.8% 65.2%
4030114 7579.1.1.0 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases 0.55 48.0 3.38e-01 100.0% 58.8%
3726364 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.54 46.0 3.60e-01 94.8% 81.8%
3447945 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.54 45.0 3.30e-01 97.4% 35.8%
3672662 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 44.0 3.27e-01 94.8% 32.9%
3430363 2004.1.1.56 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › NB-ARC 0.53 44.0 3.33e-01 94.8% 47.3%
3278267 2007.2.1.6 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › Flavodoxin_5 0.53 46.0 3.72e-01 100.0% 50.3%
4011103 2003.1.1.5 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › ADH_zinc_N 0.52 43.0 3.46e-01 98.7% 58.3%
4295393 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.52 43.0 3.32e-01 94.8% 53.2%
5048729 2007.2.1.3 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › FMN_red 0.51 44.0 3.63e-01 100.0% 52.4%
4023150 2003.1.7.2 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NagB/RpiA/CoA transferase-like › IF-2B 0.51 41.0 3.13e-01 100.0% 35.9%
4969980 207.2.1.0 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.50 42.0 2.58e-01 100.0% 15.6%
D3 high residues 249-449
PDB