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JSantini_GMIN_scaffold_8_prodigal-single.1__X__X__00276

Bact-Vir

JSantini_GMIN_scaffold_8_prodigal-single.1__X__X__00276

Identity

Kingdom:
phage

Quality

92.3 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 9-80
PDB
Domain cluster: representative
CATH (57)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.75 54.0 5.85e-01 81.9% 90.2%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.74 61.0 4.81e-01 90.3% 64.1%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 52.0 5.68e-01 79.2% 91.5%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.72 58.0 5.47e-01 86.1% 83.5%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 53.0 5.60e-01 79.2% 100.0%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.70 59.0 5.89e-01 98.6% 90.5%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 53.0 5.67e-01 80.6% 93.7%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.70 51.0 5.35e-01 76.4% 90.9%
1vctA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.70 56.0 4.81e-01 86.1% 56.0%
1mhyG01 1.20.1280.10 Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 1 0.70 53.0 5.42e-01 98.6% 86.8%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.70 54.0 4.89e-01 81.9% 93.8%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 53.0 5.65e-01 79.2% 95.2%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.69 62.0 5.98e-01 100.0% 98.8%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 54.0 5.75e-01 91.7% 98.4%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 57.0 5.87e-01 90.3% 95.6%
4egwA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.69 62.0 5.22e-01 100.0% 80.7%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.68 61.0 5.57e-01 98.6% 83.9%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 52.0 5.60e-01 81.9% 98.3%
2pg0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.67 52.0 4.07e-01 81.9% 39.6%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.67 57.0 5.47e-01 100.0% 81.2%
4gouA03 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.66 51.0 3.73e-01 83.3% 36.0%
2rkhA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.66 53.0 5.28e-01 87.5% 93.4%
2uxwA01 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.66 50.0 3.74e-01 81.9% 32.3%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.66 53.0 5.20e-01 98.6% 81.8%
2xq0A03 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.65 55.0 4.28e-01 94.4% 90.4%
3lnnB03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.65 49.0 5.13e-01 81.9% 88.1%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 54.0 4.06e-01 100.0% 37.1%
2rpaA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.64 51.0 5.02e-01 94.4% 83.1%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 48.0 4.19e-01 81.9% 54.6%
1br0A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 53.0 4.60e-01 100.0% 85.0%
3pjxA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.62 45.0 3.34e-01 76.4% 60.2%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.62 43.0 4.70e-01 80.6% 89.7%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.62 45.0 4.89e-01 79.2% 100.0%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.62 46.0 4.65e-01 80.6% 81.7%
2zueA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.62 55.0 4.68e-01 100.0% 70.6%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 52.0 4.86e-01 98.6% 92.4%
6a6fA00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.61 52.0 4.21e-01 94.4% 52.2%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.61 45.0 3.59e-01 79.2% 51.0%
5zw7A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 51.0 4.12e-01 97.2% 86.8%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.61 54.0 4.63e-01 100.0% 88.8%
5jazA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.60 36.0 3.38e-01 73.6% 46.2%
1sumB01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.60 51.0 4.53e-01 98.6% 79.4%
5ojcA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 53.0 4.13e-01 100.0% 96.8%
2q5zB00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.59 51.0 4.71e-01 97.2% 74.5%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.59 50.0 3.83e-01 98.6% 98.9%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 52.0 4.59e-01 100.0% 84.9%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.58 43.0 4.31e-01 79.2% 75.7%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.58 50.0 4.56e-01 100.0% 85.7%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 49.0 4.50e-01 100.0% 86.1%
1lvlA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 39.0 2.76e-01 72.2% 59.9%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.56 48.0 4.31e-01 100.0% 100.0%
1zhcA00 6.10.280.50 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.56 40.0 4.02e-01 77.8% 73.7%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 42.0 4.12e-01 81.9% 82.1%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 43.0 3.74e-01 83.3% 53.6%
3swhA01 1.10.357.50 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.56 47.0 3.74e-01 100.0% 55.2%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.55 45.0 4.04e-01 97.2% 94.5%
4nxtA01 1.10.1410.40 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 0.55 44.0 3.54e-01 88.9% 82.1%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4184330 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.76 51.0 4.57e-01 79.2% 50.0%
3399433 3826.1.1.39 alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › WHEP-TRS 0.75 51.0 5.25e-01 79.2% 72.9%
4175087 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 58.0 4.98e-01 81.9% 60.0%
4043484 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.75 58.0 4.97e-01 81.9% 60.0%
3487250 3930.1.1.0 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.73 65.0 5.10e-01 98.6% 80.7%
4147453 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 57.0 4.94e-01 83.3% 60.9%
1276361 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 57.0 4.83e-01 83.3% 58.6%
4555586 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.72 57.0 4.97e-01 83.3% 63.8%
4359654 605.2.1.3 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.72 56.0 4.82e-01 81.9% 60.0%
3531423 5106.1.1.14 extended segments › PetG subunit of the cytochrome b6f complex › PetG subunit of the cytochrome b6f complex › PetG subunit of the cytochrome b6f complex › TMEM174 0.72 50.0 5.52e-01 81.9% 94.5%
4045132 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.72 55.0 4.76e-01 81.9% 57.3%
4983442 604.5.1.2 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.70 55.0 4.98e-01 93.1% 63.2%
3597066 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.68 62.0 5.27e-01 100.0% 74.8%
4489485 11.1.1.2 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.68 52.0 3.79e-01 81.9% 31.8%
3833109 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.67 58.0 4.45e-01 97.2% 68.2%
5023244 604.5.1.2 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.67 57.0 4.90e-01 97.2% 60.0%
3603648 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.67 61.0 5.66e-01 100.0% 93.2%
3965571 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 0.66 48.0 4.66e-01 79.2% 68.8%
4075707 3711.1.1.0 alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.66 47.0 4.29e-01 75.0% 74.7%
3577232 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 51.0 4.33e-01 86.1% 60.8%
3934928 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 57.0 5.23e-01 97.2% 84.2%
3588519 101.1.2.49 alpha arrays › HTH › HTH › winged helix domain › PadR,Vir_act_alpha_C 0.65 59.0 4.46e-01 100.0% 82.4%
4009520 1.1.7.98 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25876 0.65 50.0 4.94e-01 81.9% 78.7%
4973175 159.1.2.33 alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › dUTPase_2 0.65 56.0 4.78e-01 95.8% 74.8%
3245731 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.64 54.0 5.27e-01 97.2% 85.0%
5072045 604.10.1.0 alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac 0.64 52.0 4.60e-01 90.3% 71.4%
5065894 4995.1.1.1 alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.63 53.0 5.13e-01 100.0% 83.5%
3585791 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.63 47.0 4.67e-01 81.9% 80.0%
4605223 375.1.9.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.62 54.0 5.01e-01 94.4% 77.8%
5049171 633.6.1.1 alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA_dh_1 0.61 52.0 3.67e-01 100.0% 71.6%
3909706 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.61 46.0 4.31e-01 79.2% 74.1%
3622515 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.61 50.0 4.80e-01 98.6% 78.8%
4587769 192.7.1.4 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.60 47.0 4.89e-01 86.1% 95.4%
3442151 5076.2.1.10 alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › PF29520 0.60 45.0 3.06e-01 80.6% 23.1%
3381499 314.1.1.1 a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2 0.59 44.0 2.78e-01 86.1% 13.7%
4505595 605.6.1.0 alpha duplicates or obligate multimers › ROP-like › HP1531-like › HP1531-like 0.59 43.0 3.84e-01 76.4% 92.0%
4805048 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.59 51.0 4.57e-01 98.6% 71.6%
3402740 102.1.3.8 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain › Mab-21_C 0.56 47.0 3.80e-01 91.7% 72.9%
3833888 3846.1.1.0 alpha bundles › IcmR › IcmR › IcmR 0.56 43.0 3.74e-01 81.9% 87.3%