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S2_005_003_R2_scaffold_22_prodigal-single.1__X__X__00053

Bact-Vir

S2_005_003_R2_scaffold_22_prodigal-single.1__X__X__00053

Identity

Kingdom:
phage

Quality

74.7 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 medium residues 61-211
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12699.14 best phiKZ_IP 57.9 1.70e-15 95.4% 35.0%
D2 medium residues 212-335
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6w08A01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.54 48.0 3.48e-01 97.6% 99.1%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.53 22.0 2.84e-01 93.5% 65.3%
1ewqA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.52 39.0 3.81e-01 79.0% 96.3%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3899940 331.4.1.9 a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › CPSF73-100_C 0.68 20.0 2.56e-01 90.3% 40.0%
5041857 192.2.1.2 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.54 40.0 3.92e-01 77.4% 100.0%
4967607 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.53 41.0 3.81e-01 79.8% 96.1%
3728487 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.52 41.0 3.55e-01 82.3% 92.6%
4002410 5001.1.1.1 alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.51 37.0 3.50e-01 75.8% 67.3%
3453075 3543.1.1.4 alpha complex topology › Acid-activated urea channel › Acid-activated urea channel › Acid-activated urea channel › DUF716 0.50 40.0 3.16e-01 85.5% 94.3%
4951445 601.23.1.1 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.50 38.0 2.86e-01 79.0% 43.9%
D3 medium residues 336-411
PDB
Domain cluster: representative
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
8fbnB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.84 64.0 4.48e-01 85.5% 27.5%
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.81 69.0 7.13e-01 96.1% 100.0%
2d1lA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.80 73.0 5.00e-01 100.0% 30.9%
4ijjB00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.79 60.0 5.01e-01 86.8% 47.7%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 61.0 6.09e-01 88.2% 84.4%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 62.0 6.15e-01 86.8% 85.9%
3etvA01 1.10.287.3290 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 56.0 5.43e-01 78.9% 70.2%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.76 55.0 4.26e-01 92.1% 35.6%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.76 56.0 5.69e-01 84.2% 81.1%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.74 67.0 4.63e-01 100.0% 31.8%
1i4dA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.73 65.0 4.88e-01 100.0% 62.2%
4cqiA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 52.0 4.61e-01 73.7% 81.3%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.73 54.0 5.77e-01 81.6% 95.3%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.73 58.0 5.25e-01 88.2% 64.1%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.72 57.0 5.11e-01 88.2% 61.3%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.72 62.0 5.01e-01 96.1% 49.7%
1vx7301 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 54.0 5.49e-01 93.4% 83.8%
2gtaA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.72 51.0 4.76e-01 76.3% 58.8%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.72 59.0 5.35e-01 93.4% 66.0%
1orjD00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.72 51.0 4.33e-01 82.9% 45.6%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 52.0 5.38e-01 77.6% 97.2%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.71 55.0 5.62e-01 97.4% 87.7%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.71 56.0 4.33e-01 86.8% 39.4%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 52.0 5.37e-01 80.3% 84.5%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 63.0 5.38e-01 100.0% 76.4%
1fs0G02 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.70 53.0 5.12e-01 82.9% 85.4%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.70 52.0 5.38e-01 86.8% 84.5%
3i2wA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.70 61.0 4.25e-01 100.0% 31.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 53.0 5.66e-01 81.6% 100.0%
1vq8V00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 47.0 5.04e-01 78.9% 81.5%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 54.0 5.34e-01 84.2% 91.4%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 50.0 5.33e-01 78.9% 90.6%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.69 55.0 4.89e-01 92.1% 59.8%
1ykeD00 6.10.280.10 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator complex, subunit Med21 0.69 60.0 5.24e-01 96.1% 67.3%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 59.0 5.91e-01 100.0% 96.2%
5y06A01 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 59.0 4.28e-01 98.7% 65.1%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 52.0 5.39e-01 81.6% 91.2%
6iknD01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.68 60.0 4.12e-01 100.0% 28.1%
2etnB01 1.10.287.180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain 0.68 52.0 5.29e-01 86.8% 84.2%
4gzrC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.67 45.0 4.87e-01 72.4% 85.2%
2bdeA03 1.20.58.1160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 50.0 5.05e-01 82.9% 80.5%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.66 51.0 5.23e-01 82.9% 88.7%
2ke4A00 6.10.140.470 Special › Helix non-globular › Helix Hairpins › 0.66 54.0 5.03e-01 93.4% 82.7%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 45.0 4.65e-01 85.5% 75.3%
1l8dA00 1.10.287.510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.64 55.0 5.07e-01 100.0% 79.6%
1hx8A02 1.20.58.150 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › ANTH domain 0.63 46.0 4.05e-01 78.9% 53.0%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 48.0 4.99e-01 86.8% 94.2%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.62 53.0 4.60e-01 100.0% 80.8%
1f45B00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.61 44.0 3.77e-01 78.9% 67.7%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.59 44.0 4.44e-01 81.6% 83.3%
2pbiA02 1.10.1240.60 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.57 40.0 3.72e-01 75.0% 91.1%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5062668 3755.1.1.0 alpha bundles › YscO-like › Putative type III secretion protein YscO-related › Putative type III secretion protein YscO-related 0.80 73.0 6.16e-01 100.0% 71.2%
3240634 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.77 70.0 5.46e-01 100.0% 57.4%
3908132 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.77 69.0 4.73e-01 100.0% 30.7%
3913300 3755.3.1.303 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF21A_4th 0.76 66.0 5.26e-01 97.4% 48.7%
3248423 109.42.1.1 alpha superhelices › Repetitive alpha hairpins › E3 ubiquitin-protein ligase SHPRH first helical domain › E3 ubiquitin-protein ligase SHPRH first helical domain › SHPRH_helical-1st 0.75 56.0 4.06e-01 78.9% 31.2%
3970019 3755.4.1.0 alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.75 67.0 4.72e-01 100.0% 50.9%
5057549 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.74 55.0 4.75e-01 78.9% 58.5%
3741801 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.74 64.0 5.53e-01 100.0% 62.4%
4257759 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 63.0 6.05e-01 98.7% 86.7%
3565534 4177.1.1.2 alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.73 66.0 4.57e-01 100.0% 47.8%
3997950 5069.1.3.56 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › GOST_TM 0.73 56.0 5.29e-01 81.6% 72.2%
3810801 632.22.1.139 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › KIF21A_4th 0.73 64.0 5.15e-01 100.0% 61.3%
3176480 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 61.0 5.80e-01 94.7% 79.8%
3961296 150.5.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.72 64.0 5.99e-01 100.0% 86.2%
3889547 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.72 63.0 4.75e-01 100.0% 41.1%
3611632 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.71 63.0 5.73e-01 97.4% 74.0%
3620725 5041.1.1.17 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › Periphilin_C 0.71 61.0 5.53e-01 96.1% 74.3%
2572867 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 58.0 5.13e-01 92.1% 61.3%
4156473 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.71 53.0 4.96e-01 84.2% 64.2%
3361164 3860.1.1.0 alpha bundles › Myosin VI lever arm › Myosin VI lever arm › Myosin VI lever arm 0.71 61.0 4.56e-01 100.0% 97.1%
4022925 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.70 61.0 4.52e-01 100.0% 49.0%
3393794 3922.1.1.211 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › DRC7_C 0.70 60.0 5.02e-01 100.0% 54.8%
3655688 3755.3.1.303 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › KIF21A_4th 0.70 60.0 4.71e-01 100.0% 44.6%
4474737 3711.1.1.44 alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › Med11 0.70 58.0 5.55e-01 96.1% 77.8%
3569625 604.12.1.4 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 0.70 57.0 4.72e-01 97.4% 49.0%
3318812 192.8.1.248 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › KIF21A_4th 0.70 60.0 4.91e-01 100.0% 52.0%
3471023 164.1.1.15 alpha bundles › Chorismate mutase II › Chorismate mutase II › Chorismate mutase II › PPPI_inhib 0.70 56.0 4.45e-01 89.5% 50.6%
4303085 3755.3.1.467 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DRC7_C 0.69 60.0 5.15e-01 96.1% 61.7%
3337008 192.2.1.60 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › KIF21A_4th 0.69 60.0 4.97e-01 100.0% 55.7%
3485546 109.4.1.123 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U3_assoc_6 0.69 60.0 3.88e-01 100.0% 38.4%
3207548 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.69 53.0 4.30e-01 81.6% 82.1%
4652719 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.68 59.0 5.53e-01 97.4% 78.9%
1032114 150.5.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.67 45.0 4.87e-01 72.4% 85.2%
4465072 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.67 55.0 4.92e-01 96.1% 62.6%
3754639 150.5.1.106 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › LIN9_C 0.67 49.0 4.81e-01 97.4% 71.8%
3168929 4323.1.1.1 alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.67 58.0 4.50e-01 100.0% 42.9%
3598025 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.67 59.0 4.55e-01 100.0% 44.1%
4051951 605.2.1.0 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 0.67 58.0 5.48e-01 97.4% 83.3%
3641527 192.8.1.353 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Med10 0.66 48.0 4.79e-01 78.9% 73.8%
3477418 4992.1.1.12 extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.65 53.0 5.00e-01 92.1% 77.9%
4129922 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.65 51.0 4.73e-01 88.2% 66.0%
3840952 601.19.1.39 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › LIN9_C 0.65 52.0 5.26e-01 92.1% 89.3%
3965698 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 0.64 55.0 3.29e-01 100.0% 14.8%
4177674 4992.1.1.23 extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N 0.63 50.0 4.54e-01 92.1% 62.7%
3839497 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.62 50.0 4.92e-01 92.1% 83.5%
3746558 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.61 52.0 3.89e-01 100.0% 52.4%