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SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00011

Bact-Vir

SR-VP_0-2_scaffold_141_316084_prodigal-single.1__X__X__00011

Identity

Kingdom:
phage

Quality

78.6 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 99-160
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.64 40.0 3.99e-01 100.0% 60.0%
2mk5A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.64 56.0 4.43e-01 100.0% 47.3%
1uirA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.61 43.0 4.56e-01 100.0% 88.5%
1iy9A02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.60 42.0 4.52e-01 100.0% 88.5%
2e5wA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 42.0 4.36e-01 100.0% 83.9%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 42.0 4.20e-01 100.0% 73.4%
2cmgA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.59 41.0 4.42e-01 100.0% 90.2%
2o07A01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.58 42.0 4.35e-01 100.0% 83.1%
3o4fC01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.58 41.0 4.38e-01 100.0% 90.2%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 37.0 3.81e-01 100.0% 69.5%
6uzjA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.57 43.0 4.29e-01 100.0% 82.5%
3c6kA02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.57 40.0 4.16e-01 100.0% 83.9%
4epcA02 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.56 48.0 4.62e-01 100.0% 87.3%
7oc3A01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 41.0 3.64e-01 100.0% 54.3%
2dmoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 40.0 3.93e-01 100.0% 73.5%
1gcqB00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 40.0 4.09e-01 100.0% 87.7%
2b2cA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.55 41.0 4.15e-01 100.0% 81.2%
8cukB01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 45.0 2.89e-01 95.2% 98.8%
2f5kA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 36.0 3.86e-01 100.0% 86.0%
1eqtA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 38.0 3.78e-01 74.2% 68.7%
1nr4C00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.54 37.0 3.73e-01 75.8% 69.7%
2it1A03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 35.0 3.58e-01 93.5% 68.9%
1f9qD00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 35.0 3.54e-01 71.0% 72.7%
3nmzD00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.53 38.0 3.51e-01 100.0% 58.3%
3nhqA02 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.52 44.0 3.57e-01 95.2% 75.6%
3fm8D03 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 41.0 3.59e-01 98.4% 74.1%
1a15A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 34.0 3.35e-01 71.0% 70.1%
6uy8A01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.50 37.0 3.81e-01 100.0% 89.8%
5cbeE00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.50 34.0 3.39e-01 71.0% 76.6%
2ppqA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.50 36.0 3.23e-01 79.0% 93.6%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3929809 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.70 39.0 4.64e-01 100.0% 85.0%
3333339 4.8.1.34 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo_SEND1 0.65 38.0 3.79e-01 100.0% 55.4%
3289944 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.64 44.0 3.93e-01 100.0% 48.9%
3405538 219.1.1.111 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Transglut_core, Rad4 0.62 39.0 2.51e-01 98.4% 13.6%
4336845 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.61 43.0 4.37e-01 100.0% 76.7%
5023580 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 40.0 4.02e-01 100.0% 66.2%
3987332 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.60 43.0 4.48e-01 100.0% 85.5%
2897014 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.60 42.0 4.27e-01 100.0% 76.7%
5041849 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.60 42.0 4.39e-01 100.0% 83.6%
5013328 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.59 42.0 4.31e-01 100.0% 78.3%
4039507 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.59 43.0 4.47e-01 100.0% 87.3%
4114201 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.59 41.0 4.11e-01 100.0% 70.8%
3885696 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.59 44.0 4.34e-01 100.0% 76.9%
4163458 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.59 42.0 4.43e-01 100.0% 87.3%
4427420 4.1.1.436 ↗ beta barrels › SH3 › SH3 › SH3 › PF29249 0.59 49.0 4.58e-01 100.0% 76.2%
3328685 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.58 41.0 4.13e-01 100.0% 72.3%
4407054 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.58 42.0 4.29e-01 100.0% 80.0%
3939881 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 42.0 3.99e-01 80.6% 65.3%
3869065 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.58 49.0 4.24e-01 100.0% 61.0%
4076873 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.58 40.0 4.17e-01 98.4% 81.8%
4024737 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.57 34.0 3.64e-01 95.2% 70.0%
3286756 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.57 43.0 3.60e-01 83.9% 93.9%
3910933 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.57 40.0 4.10e-01 100.0% 78.3%
4971071 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.56 41.0 4.25e-01 100.0% 87.3%
5056181 3699.1.1.1 ↗ beta meanders › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermidine synthase tetramerisation domain › Spermine_synt_N 0.56 40.0 4.20e-01 98.4% 87.3%
5021724 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 48.0 4.39e-01 95.2% 73.8%
4358801 4.1.1.178 ↗ beta barrels › SH3 › SH3 › SH3 › ribosomal_L24 0.56 34.0 2.89e-01 100.0% 34.5%
4962251 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.55 46.0 3.66e-01 96.8% 65.2%
3883586 1170.1.1.1 ↗ beta barrels › IL8-related › IL8-related › IL8 › IL8 0.55 37.0 3.61e-01 74.2% 68.0%
3544595 5.1.3.9 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › OLF 0.54 45.0 2.94e-01 96.8% 80.6%
4093535 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.54 45.0 3.65e-01 96.8% 55.4%
3799100 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 44.0 2.79e-01 93.5% 99.1%
3848483 4.1.1.248 ↗ beta barrels › SH3 › SH3 › SH3 › CABIT 0.53 45.0 3.97e-01 100.0% 67.3%
4093354 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.52 41.0 4.06e-01 100.0% 82.9%
5023617 4111.1.1.2 ↗ a+b two layers › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › AF0104/ALDC/Ptd012-like › PCC 0.51 40.0 3.25e-01 100.0% 42.2%
3552969 4.8.1.1 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › Chromo 0.51 42.0 3.84e-01 96.8% 69.4%
D2 medium residues 1-92
PDB
Domain cluster: representative
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.62 35.0 4.08e-01 79.3% 78.5%
1m9sA04 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.61 44.0 4.56e-01 77.2% 82.6%
1r77A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.59 45.0 4.44e-01 81.5% 100.0%
1aqcB00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 41.0 3.80e-01 73.9% 85.2%
2mk5A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.58 44.0 3.92e-01 79.3% 62.6%
2f5kA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 33.0 4.06e-01 78.3% 100.0%
4epcA02 2.30.30.170 Mainly Beta › Roll › SH3 type barrels. › 0.57 39.0 4.30e-01 77.2% 93.0%
5kcoA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.56 34.0 4.02e-01 80.4% 93.2%
5umsA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 41.0 3.97e-01 78.3% 86.3%
3c6kA02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.55 31.0 3.72e-01 91.3% 89.3%
2e5wA01 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.53 30.0 3.55e-01 88.0% 87.5%
1inlC02 2.30.140.10 Mainly Beta › Roll › Spermidine Synthase; Chain: A, domain 2 › Spermidine synthase, tetramerisation domain 0.53 30.0 3.39e-01 88.0% 76.6%
2grgA01 3.40.1840.10 Alpha Beta › 3-Layer(aba) Sandwich › Profilin-like › YNR034W-A-like 0.53 38.0 3.97e-01 75.0% 97.6%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 36.0 3.73e-01 73.9% 94.3%
4rs6A01 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.51 39.0 3.61e-01 81.5% 77.1%
3u12A00 2.30.29.180 Mainly Beta › Roll › PH-domain like › Ubiquitin carboxyl-terminal hydrolase 26/29/37, pleckstrin homology-like domain 0.50 37.0 3.60e-01 78.3% 96.2%
4huzA02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.50 39.0 3.35e-01 84.8% 80.8%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3929809 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.72 34.0 4.75e-01 72.8% 100.0%
4616207 4.1.1.448 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5372 0.69 37.0 4.74e-01 73.9% 94.0%
3933293 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.69 33.0 4.08e-01 71.7% 72.4%
3687350 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 35.0 4.34e-01 77.2% 87.3%
2727964 4.1.1.105 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5604 0.59 36.0 4.24e-01 80.4% 93.2%
3917372 4.1.1.101 ↗ beta barrels › SH3 › SH3 › SH3 › Tudor_2 0.58 40.0 4.39e-01 87.0% 88.0%
3664734 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 43.0 3.52e-01 78.3% 73.5%
4161673 4.1.1.105 ↗ beta barrels › SH3 › SH3 › SH3 › DUF5604 0.58 35.0 3.65e-01 80.4% 64.7%
3702154 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.57 36.0 3.89e-01 80.4% 76.0%
3258100 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.57 40.0 2.55e-01 72.8% 90.8%
4284709 4.1.1.111 ↗ beta barrels › SH3 › SH3 › SH3 › Tudor_RapA 0.57 32.0 3.92e-01 81.5% 90.9%
3176175 5.1.4.250 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF2415 0.56 40.0 2.67e-01 73.9% 97.1%
4950324 207.7.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Alpha subunit of glutamate synthase-C › Alpha subunit of glutamate synthase-C 0.56 40.0 2.89e-01 75.0% 31.4%
3921576 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.55 39.0 3.42e-01 73.9% 72.1%
3245838 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 43.0 2.46e-01 88.0% 28.1%
4335022 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 38.0 3.78e-01 77.2% 69.5%
3950193 4.1.1.137 ↗ beta barrels › SH3 › SH3 › SH3 › PcrA_UvrD_tudor 0.54 31.0 3.83e-01 80.4% 96.2%
4093535 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.54 38.0 3.44e-01 73.9% 66.2%
3493294 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 38.0 3.38e-01 75.0% 62.8%
3781119 5.1.4.97 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Rrn6_beta-prop 0.53 37.0 2.43e-01 71.7% 84.8%
4195627 4.6.1.6 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC_RimM 0.53 35.0 3.98e-01 90.2% 93.8%
5021724 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 37.0 3.94e-01 73.9% 88.7%
3243549 2484.1.1.162 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › F-box 0.52 42.0 3.45e-01 85.9% 81.8%
3413733 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 36.0 2.50e-01 70.7% 92.9%
3165957 3454.1.1.0 ↗ beta barrels › GspC HR domain/PilP-like › GspC HR domain/PilP-like › GspC HR domain/PilP-like 0.52 35.0 3.84e-01 75.0% 85.3%
3385654 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 38.0 3.55e-01 80.4% 95.8%
4186983 4.6.1.2 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC 0.51 35.0 3.84e-01 91.3% 88.0%
3396958 719.2.1.1 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like › GBBH-like_N 0.51 37.0 3.69e-01 80.4% 73.0%
4072405 4.6.1.2 ↗ beta barrels › SH3 › PRC-barrel domain › PRC-barrel domain › PRC 0.50 35.0 3.79e-01 91.3% 88.0%