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SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00215

Bact-Vir

SR-VP_2-4_scaffold_141_5652861_prodigal-single.1__X__X__00215

Identity

Kingdom:
phage

Quality

89.8 mean pLDDT

3D Structure

Domains

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

D1 medium residues 14-126
PDB
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8an5A01 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.82 70.0 5.71e-01 89.4% 64.6%
2fclA00 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.79 70.0 6.22e-01 94.7% 82.1%
4o8sA01 3.10.450.620 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › JHP933, nucleotidyltransferase-like core domain 0.70 59.0 5.78e-01 91.2% 95.2%
1r89A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.67 54.0 5.21e-01 85.0% 92.2%
2w9mB03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.66 45.0 5.10e-01 80.5% 97.5%
4rt5A00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.65 33.0 3.50e-01 72.6% 54.5%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.64 45.0 4.61e-01 71.7% 88.9%
2bcqA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.64 50.0 4.86e-01 82.3% 95.1%
2o5aA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 44.0 4.61e-01 74.3% 93.1%
4s3nA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 48.0 4.41e-01 84.1% 87.1%
2rbbA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.61 46.0 4.38e-01 77.9% 97.7%
2id1A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 43.0 4.51e-01 73.5% 91.3%
3oguA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 52.0 5.06e-01 92.9% 99.2%
2ihmB03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.60 44.0 4.47e-01 78.8% 99.1%
3cskA03 3.30.70.2600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 39.0 4.56e-01 85.8% 100.0%
3ghjA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.58 41.0 4.09e-01 73.5% 95.7%
6iw6A02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 48.0 4.89e-01 94.7% 100.0%
6bu2A00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 41.0 3.69e-01 91.2% 58.0%
6ywnA01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.54 46.0 4.75e-01 93.8% 100.0%
1nkiA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 41.0 3.93e-01 82.3% 84.3%
3bqxA00 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.53 49.0 4.55e-01 100.0% 95.0%
1wmiA00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.51 31.0 3.47e-01 95.6% 77.3%
1cpyA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 43.0 3.17e-01 96.5% 63.6%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4959743 316.1.1.39 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF2204 0.82 68.0 5.57e-01 86.7% 58.9%
5050028 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 71.0 5.90e-01 92.0% 75.1%
4993673 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 69.0 5.77e-01 89.4% 65.8%
5039359 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 70.0 5.98e-01 90.3% 63.5%
5076537 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 69.0 5.68e-01 89.4% 63.7%
5069234 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 70.0 5.96e-01 91.2% 67.1%
4989039 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.81 66.0 5.83e-01 86.7% 81.9%
5074217 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.80 68.0 5.65e-01 90.3% 65.6%
5040839 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.79 69.0 5.87e-01 91.2% 67.1%
4993561 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.79 67.0 5.72e-01 90.3% 68.0%
6828 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.79 70.0 6.21e-01 94.7% 81.5%
5079184 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.79 69.0 5.63e-01 92.9% 66.7%
5040911 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.78 65.0 5.55e-01 87.6% 68.0%
5058624 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.78 64.0 5.91e-01 85.8% 82.9%
3197794 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.78 66.0 5.46e-01 90.3% 55.8%
5030984 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.77 66.0 5.49e-01 90.3% 64.3%
3633420 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.77 67.0 5.27e-01 92.9% 60.5%
4940185 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.76 57.0 5.46e-01 90.3% 68.5%
3726440 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.75 67.0 5.56e-01 94.7% 62.2%
3198176 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.75 65.0 5.41e-01 92.9% 56.8%
5021444 316.1.1.21 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Aminoglyc_resit 0.74 64.0 5.63e-01 91.2% 78.1%
5079837 316.2.1.0 a+b three layers › Nucleotidyltransferase-like › Rv2827c C-terminal domain-like › Rv2827c C-terminal domain-like 0.74 47.0 4.11e-01 89.4% 45.0%
4968276 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.74 63.0 5.10e-01 90.3% 52.0%
3721514 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.73 63.0 4.93e-01 92.0% 56.0%
4929446 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.72 64.0 5.75e-01 95.6% 70.3%
4969949 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.72 66.0 5.44e-01 99.1% 69.2%
5058173 316.1.1.39 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DUF2204 0.71 61.0 4.97e-01 92.9% 62.9%
3640051 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.70 65.0 5.12e-01 100.0% 66.7%
3636819 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.70 54.0 5.40e-01 80.5% 96.5%
1160872 211.1.1.1 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.66 34.0 4.22e-01 73.5% 80.0%
3197454 316.1.1.0 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.65 60.0 4.74e-01 100.0% 60.9%
4500383 316.1.1.26 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › SMODS 0.64 52.0 4.41e-01 87.6% 88.6%
3259379 316.1.1.5 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › RsfS 0.61 42.0 4.14e-01 71.7% 73.6%
4086362 211.1.1.1 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.61 33.0 4.38e-01 92.9% 100.0%
4030472 316.1.1.36 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › MTPAP-like_central 0.60 50.0 4.16e-01 89.4% 61.1%
3385505 316.1.1.5 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › RsfS 0.59 41.0 4.24e-01 70.8% 88.6%
4096725 316.1.1.5 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › RsfS 0.59 43.0 4.27e-01 74.3% 82.6%
3579770 316.1.1.28 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › TUTase 0.58 46.0 4.14e-01 85.0% 73.8%
4809709 211.1.1.33 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › RsfS 0.58 40.0 4.02e-01 71.7% 80.0%
3949523 316.1.1.5 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › RsfS 0.56 46.0 4.60e-01 90.3% 99.2%
4555762 316.1.1.1 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › PolyA_pol 0.54 48.0 4.54e-01 99.1% 91.1%
5031280 316.1.1.2 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.53 47.0 4.23e-01 98.2% 84.5%
None 0.53 45.0 3.16e-01 97.3% 92.7%
5028247 2003.1.5.81 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.53 41.0 3.38e-01 84.1% 98.6%
4932862 316.1.1.27 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.52 41.0 4.34e-01 94.7% 98.0%
D2 medium residues 127-184
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2b1eA01 1.20.58.1150 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 54.0 4.71e-01 91.4% 70.9%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 51.0 4.32e-01 91.4% 63.9%
1x9fD00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.62 48.0 3.82e-01 93.1% 56.4%
2o7tA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.61 52.0 3.74e-01 100.0% 62.7%
3k8pC01 1.20.58.1440 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 49.0 4.21e-01 100.0% 86.7%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 46.0 3.88e-01 86.2% 78.2%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.58 42.0 4.05e-01 79.3% 77.6%
1binA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 46.0 3.63e-01 98.3% 58.0%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.56 46.0 3.63e-01 93.1% 59.0%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.55 49.0 3.95e-01 100.0% 65.8%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.55 46.0 3.74e-01 91.4% 60.2%
4w8pA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.54 43.0 3.37e-01 87.9% 72.3%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.54 46.0 3.67e-01 100.0% 60.8%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 42.0 3.98e-01 89.7% 86.5%
2zueA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.53 42.0 3.50e-01 96.6% 73.9%
3l1nA02 1.20.1280.140 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.53 42.0 3.76e-01 91.4% 83.9%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.52 40.0 3.44e-01 84.5% 77.3%
1kt1A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 44.0 3.29e-01 100.0% 38.6%
2oifB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.50 37.0 2.92e-01 84.5% 50.3%
2mx8A01 1.10.274.70 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain 0.50 41.0 3.50e-01 100.0% 94.7%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
329329 3814.1.1.1 alpha bundles › Uncharacterized protein GSU0061 › Uncharacterized protein GSU0061 › Uncharacterized protein GSU0061 › DUF3232 0.67 45.0 3.52e-01 70.7% 71.9%
3706015 603.1.1.6 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin_2 0.65 58.0 3.93e-01 100.0% 69.3%
3248574 109.4.1.926 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FH3_FHOD1-3 0.63 55.0 3.57e-01 100.0% 26.3%
5031064 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.63 55.0 4.53e-01 94.8% 65.0%
3955107 106.1.1.11 alpha arrays › Globin-like › Globin-like › Globin-like › RsbRD_N 0.63 53.0 4.02e-01 100.0% 62.6%
3809489 574.1.1.1 alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp 0.60 41.0 3.15e-01 70.7% 48.9%
4247950 4994.1.1.1 alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.60 46.0 3.98e-01 86.2% 69.5%
3199608 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.55 43.0 3.64e-01 91.4% 86.4%
4197249 7014.1.1.1 alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA 0.55 43.0 3.33e-01 89.7% 71.2%
3578909 604.1.1.1 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.54 43.0 3.67e-01 91.4% 81.9%