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SR-VP_4-6_scaffold_141_2630357_prodigal-single.1__X__X__00651

Bact-Vir

SR-VP_4-6_scaffold_141_2630357_prodigal-single.1__X__X__00651

Identity

Kingdom:
phage

Quality

76.7 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 high residues 5-58
PDB
Domain cluster: representative
CATH (55)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.91 70.0 7.50e-01 81.5% 95.7%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.85 68.0 5.80e-01 87.0% 60.0%
1nt2B02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.83 68.0 6.25e-01 87.0% 73.1%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.81 65.0 5.14e-01 87.0% 45.0%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.81 60.0 6.42e-01 81.5% 100.0%
4nqiD00 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 63.0 4.07e-01 85.2% 21.6%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.80 58.0 5.11e-01 77.8% 55.7%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.80 63.0 5.76e-01 87.0% 84.5%
3l0iA01 1.20.120.1520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.79 59.0 4.06e-01 79.6% 25.0%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 60.0 5.17e-01 83.3% 54.0%
2l3lA01 1.20.58.1250 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Tubulin Binding Cofactor C, N-terminal domain 0.79 65.0 5.17e-01 90.7% 47.2%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.79 60.0 6.11e-01 83.3% 90.2%
3qwwA03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.78 58.0 3.93e-01 79.6% 23.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 61.0 5.88e-01 87.0% 79.0%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.78 59.0 5.61e-01 83.3% 76.6%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.78 65.0 4.33e-01 92.6% 40.0%
1jxzC02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.78 56.0 5.40e-01 75.9% 68.3%
2hr2A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.77 59.0 4.24e-01 88.9% 28.8%
2qvaA02 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.77 58.0 5.90e-01 81.5% 84.9%
8alzB08 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.77 53.0 3.97e-01 72.2% 29.8%
5o5jT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.76 62.0 5.30e-01 90.7% 56.5%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.76 63.0 5.29e-01 92.6% 57.1%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.76 63.0 5.39e-01 92.6% 60.9%
2rklF00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.76 53.0 5.45e-01 75.9% 78.8%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.75 58.0 5.17e-01 83.3% 63.2%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 61.0 5.57e-01 92.6% 67.1%
4jvtA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.75 54.0 6.05e-01 75.9% 100.0%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.74 57.0 5.68e-01 83.3% 80.4%
4gouA01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.74 67.0 4.82e-01 100.0% 61.5%
3nkzA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.74 56.0 4.72e-01 85.2% 50.5%
1om2A00 1.20.960.10 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › Mitochondrial outer membrane translocase complex, subunit Tom20 domain 0.74 51.0 4.29e-01 74.1% 43.2%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 61.0 4.63e-01 100.0% 41.8%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 61.0 5.48e-01 98.1% 76.9%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.73 51.0 4.92e-01 77.8% 64.1%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.73 56.0 5.48e-01 87.0% 83.1%
3zc0D00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 61.0 4.25e-01 98.1% 29.4%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.73 55.0 4.89e-01 85.2% 56.1%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.72 58.0 5.65e-01 90.7% 88.3%
1z5zA02 1.20.120.850 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SWI2/SNF2 ATPases, N-terminal domain 0.71 50.0 4.55e-01 75.9% 57.9%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.71 49.0 5.16e-01 74.1% 85.1%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.71 60.0 4.98e-01 100.0% 63.7%
4jylA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.70 50.0 5.14e-01 75.9% 93.9%
1iipA02 1.10.150.160 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.70 52.0 4.60e-01 83.3% 54.1%
4jfcA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.70 56.0 5.57e-01 88.9% 100.0%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.70 61.0 5.26e-01 100.0% 94.1%
2wvxA04 1.20.1610.10 Mainly Alpha › Up-down Bundle › Glycosyl hydrolase family fold › alpha-1,2-mannosidases domains 0.69 57.0 4.16e-01 100.0% 78.6%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.68 50.0 4.82e-01 83.3% 69.7%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.68 55.0 4.81e-01 98.1% 61.5%
2hw5A02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.66 52.0 5.15e-01 88.9% 100.0%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.66 47.0 4.84e-01 79.6% 93.8%
4l9aA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.65 51.0 3.25e-01 85.2% 60.8%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.65 54.0 4.29e-01 96.3% 69.0%
2vx2G02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.62 49.0 4.91e-01 92.6% 100.0%
1dd3A01 1.20.5.710 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Single helix bin 0.61 46.0 4.60e-01 92.6% 82.5%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 44.0 3.77e-01 87.0% 55.6%
ECOD (37)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1030831 5094.1.1.1 ↗ a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.93 76.0 5.16e-01 85.2% 29.9%
4369209 4146.1.1.0 ↗ alpha bundles › YqgQ-like › YqgQ-like › YqgQ-like 0.92 70.0 7.75e-01 79.6% 100.0%
3656585 3939.1.1.0 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain 0.91 73.0 6.15e-01 85.2% 57.6%
3429182 3826.1.1.48 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › DUF4220 0.91 73.0 5.89e-01 85.2% 51.6%
3784740 3712.1.1.1 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Med11 0.90 73.0 6.46e-01 87.0% 66.7%
3473413 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.89 72.0 6.04e-01 85.2% 60.0%
3528598 3826.1.1.0 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) 0.88 70.0 5.79e-01 85.2% 56.7%
3577228 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.87 78.0 5.93e-01 96.3% 63.5%
4999041 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.87 68.0 5.85e-01 83.3% 56.2%
3164951 5094.1.1.1 ↗ a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.87 70.0 4.81e-01 87.0% 30.0%
3824114 604.6.1.24 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › DUF6857 0.86 75.0 5.46e-01 96.3% 38.5%
3841270 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.86 68.0 5.79e-01 85.2% 58.8%
4943532 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.84 66.0 6.05e-01 85.2% 74.3%
3932626 3826.1.1.47 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › 7TM_GPCR_Str 0.83 66.0 4.99e-01 85.2% 41.7%
3448294 3826.1.1.33 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › eIF-4B 0.81 63.0 5.46e-01 85.2% 57.6%
3242683 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.81 64.0 5.37e-01 85.2% 53.3%
3511170 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.81 63.0 5.67e-01 85.2% 64.0%
3527434 6006.1.1.6 ↗ extended segments › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › Voltage gated calcium channel IQ domain › PF27661 0.80 74.0 5.18e-01 100.0% 51.6%
2841849 3710.1.1.0 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain 0.80 62.0 5.98e-01 85.2% 78.7%
3797638 3456.1.1.0 ↗ extended segments › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A › NADH-quinone oxidoreductase subunit A 0.80 66.0 5.16e-01 92.6% 45.2%
4934784 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.78 62.0 5.34e-01 87.0% 62.4%
3973171 607.1.1.1 ↗ alpha arrays › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › PEP-utilisers_N 0.78 59.0 4.51e-01 83.3% 38.4%
4877881 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 54.0 6.03e-01 74.1% 100.0%
4650373 604.1.1.169 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Med14 0.77 61.0 4.91e-01 87.0% 48.6%
3166880 906.1.1.0 ↗ few secondary structure elements › CCCH zinc finger › CCCH zinc finger › CCCH zinc finger 0.77 64.0 5.87e-01 92.6% 75.7%
5029773 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.76 57.0 5.16e-01 81.5% 59.5%
3628140 3826.1.1.43 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Med14 0.76 60.0 4.79e-01 87.0% 46.4%
3280086 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.75 62.0 4.29e-01 92.6% 28.9%
5055566 3922.1.1.0 ↗ 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 0.75 67.0 5.20e-01 100.0% 65.2%
3506234 5043.1.1.15 ↗ extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › Med14 0.75 59.0 4.80e-01 87.0% 48.6%
3915818 4207.1.1.35 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › Med14 0.75 61.0 5.02e-01 90.7% 53.0%
3927285 1008.1.1.51 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › Med14 0.75 61.0 4.81e-01 90.7% 46.1%
4968652 3922.1.1.0 ↗ 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 0.75 62.0 5.08e-01 92.6% 52.0%
3484742 3922.1.1.197 ↗ 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 › BBS2_hp 0.75 61.0 5.30e-01 92.6% 61.2%
3782334 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.75 61.0 5.00e-01 92.6% 52.0%
3548646 604.6.1.52 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › Med14 0.73 60.0 4.91e-01 90.7% 53.0%
3760483 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 63.0 4.31e-01 100.0% 81.1%