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NC_016165.1__YP_004934699.1__RcapMu56__00056

Bact-Vir

NC_016165.1__YP_004934699.1__RcapMu56__00056

Identity

Accession:
NC_016165 ↗
Kingdom:
phage

Quality

69.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhodobacter_phage_RcapMu

TaxID: 1105286

Cluster

Singleton — not in a non-trivial cluster

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 60-311
PDB
Domain cluster: rep: SR-VP_4-6_scaffold_141_2630357_prodigal-single.1__X__X__00142__D170-386
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03629.25 best SASA 43.4 4.70e-11 94.8% 86.3%
CATH (46)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zmbA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.85 76.0 7.67e-01 97.2% 92.7%
4rw0A00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.81 58.0 6.78e-01 95.6% 98.9%
4rshA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.81 55.0 6.64e-01 94.4% 99.4%
2aeaA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.80 73.0 7.46e-01 96.0% 97.1%
4s1pA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.80 57.0 6.64e-01 94.8% 98.9%
1yzfA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.79 58.0 6.62e-01 95.6% 96.4%
1bwpA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.79 55.0 5.97e-01 95.6% 83.5%
4h08A00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.78 55.0 6.11e-01 95.6% 88.5%
1ivnA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.78 54.0 6.36e-01 95.6% 98.3%
2vptA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.78 59.0 6.56e-01 95.6% 96.0%
4k7jA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.76 58.0 6.17e-01 96.0% 86.7%
7toiA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.75 59.0 6.37e-01 95.2% 94.9%
3skvA02 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.74 56.0 6.26e-01 96.4% 97.5%
4njmA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.74 41.0 5.45e-01 98.4% 99.3%
5a4aA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.73 53.0 5.87e-01 95.2% 89.4%
7tjbA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.71 55.0 6.07e-01 95.2% 97.1%
1tjyA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.71 38.0 4.78e-01 100.0% 83.7%
4jc8A01 3.40.50.2060 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Sec1/Munc18 (SM) protein, domain 1 0.70 33.0 4.47e-01 86.9% 82.4%
4m8kA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.70 56.0 6.06e-01 95.6% 96.2%
2hsjD00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.70 55.0 5.96e-01 81.7% 94.4%
1sulB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 46.0 5.13e-01 95.6% 86.7%
3pdiB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.64 34.0 4.32e-01 95.6% 85.5%
3u7qB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.63 34.0 4.30e-01 97.2% 87.7%
2fh5B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 46.0 5.24e-01 94.8% 100.0%
1yxmC00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.62 52.0 5.12e-01 100.0% 83.0%
4i8iA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.61 58.0 5.79e-01 100.0% 96.9%
5l3qA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 46.0 5.03e-01 100.0% 93.7%
3e8xA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 45.0 4.82e-01 97.2% 92.1%
1dinA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.57 45.0 4.64e-01 95.2% 86.7%
6qu3A02 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.57 42.0 4.75e-01 100.0% 98.4%
3lqkA00 3.40.50.1950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavin prenyltransferase-like 0.57 41.0 4.64e-01 97.2% 95.4%
1ebfA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 40.0 4.57e-01 95.6% 98.4%
6vlxA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 49.0 4.93e-01 99.6% 93.3%
3o8lA03 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.55 43.0 4.62e-01 99.2% 95.4%
4yheA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 50.0 4.34e-01 100.0% 97.2%
2yhaA02 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.53 36.0 3.73e-01 91.7% 71.6%
3fkqA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 45.0 4.69e-01 94.8% 97.0%
4v2xA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 47.0 4.29e-01 96.4% 88.0%
3vdhA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 46.0 4.24e-01 96.4% 92.6%
4rz2B00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 47.0 4.67e-01 95.2% 94.5%
5ly3A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 38.0 4.22e-01 99.6% 93.6%
4aibA02 3.20.20.10 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Alanine racemase 0.52 39.0 4.15e-01 84.9% 89.4%
6gn6A01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 42.0 3.89e-01 85.7% 85.2%
2p4hX00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 47.0 4.40e-01 100.0% 89.4%
1hjxA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 44.0 4.28e-01 95.2% 99.3%
1xx1A00 3.20.20.190 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphatidylinositol (PI) phosphodiesterase 0.50 45.0 4.33e-01 95.2% 96.8%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
10060 2007.5.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA 0.85 76.0 7.23e-01 97.2% 81.2%
3968788 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.82 61.0 6.43e-01 96.0% 84.0%
1492214 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.81 58.0 6.78e-01 95.6% 98.9%
1411712 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.81 55.0 6.64e-01 94.4% 99.4%
4624410 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.80 56.0 6.38e-01 95.6% 91.8%
3683753 2007.5.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA 0.80 74.0 7.48e-01 96.0% 96.0%
4319241 2007.5.1.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › SASA 0.80 74.0 7.41e-01 95.6% 97.3%
4999654 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.79 61.0 6.62e-01 95.6% 92.5%
3200837 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.79 60.0 6.46e-01 96.0% 88.6%
3288559 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.79 61.0 6.39e-01 96.0% 85.7%
3983672 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.78 54.0 6.25e-01 95.6% 93.6%
2429326 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.78 50.0 5.69e-01 86.9% 82.6%
4013308 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.78 61.0 6.60e-01 96.0% 91.8%
167873 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.78 59.0 6.56e-01 95.6% 96.0%
4478613 2007.5.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase 0.75 61.0 6.68e-01 95.6% 100.0%
3410655 2004.1.1.222 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RhoGAP_pG1_pG2 0.74 44.0 5.51e-01 95.6% 93.1%
3568978 2004.1.1.222 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RhoGAP_pG1_pG2 0.73 47.0 5.39e-01 95.6% 84.7%
1682152 2007.5.1.14 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › OSK 0.73 53.0 5.84e-01 95.2% 89.0%
3581937 2007.5.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase 0.69 50.0 5.78e-01 94.8% 98.9%
3921897 2007.5.1.21 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › NXPE4_C 0.68 53.0 4.91e-01 95.6% 64.3%
5048992 2004.1.1.119 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Gtr1_RagA 0.67 47.0 5.37e-01 95.6% 95.1%
3942294 7522.1.1.1 ↗ a/b three-layered sandwiches › TK C-terminal domain-like › TK C-terminal domain-like › TK C-terminal domain-like › Transketolase_C 0.67 35.0 4.63e-01 95.6% 92.5%
5074218 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.66 61.0 6.20e-01 96.0% 98.0%
5051236 2004.1.1.119 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Gtr1_RagA 0.65 46.0 5.27e-01 95.6% 97.3%
5042343 2003.1.6.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Tubulin nucleotide-binding domain-like › Tubulin 0.64 49.0 5.50e-01 94.8% 100.0%
4318837 2007.1.2.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ABC_sub_bind 0.62 33.0 4.30e-01 97.6% 89.7%
3180657 7542.1.1.4 ↗ a/b three-layered sandwiches › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Aconitase iron-sulfur domain › Peptidase_S66C 0.61 34.0 3.92e-01 87.3% 72.3%
3620417 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.58 44.0 4.74e-01 95.6% 91.9%
3195188 2003.1.1.3 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short 0.55 51.0 4.74e-01 100.0% 88.1%
2468538 2499.2.1.0 ↗ a/b three-layered sandwiches › Subtilisin-like › Domain III of tail sheath protein Gp18 › Domain III of tail sheath protein Gp18 0.55 48.0 4.79e-01 100.0% 91.4%
3216300 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.53 47.0 4.28e-01 94.8% 96.2%
None — 0.53 48.0 4.84e-01 95.2% 100.0%
4973846 2004.1.1.206 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_31 0.53 48.0 4.83e-01 95.2% 99.2%
4970484 2004.1.1.67 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › CbiA 0.53 47.0 4.76e-01 95.6% 98.4%
3661757 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.52 44.0 4.04e-01 87.7% 81.6%
3934317 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.52 46.0 4.29e-01 95.2% 95.8%
3375451 7512.1.1.3 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glycos_transf_1 0.50 36.0 3.64e-01 98.4% 72.0%
D2 high residues 319-398
PDB