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OK040779.1__UDL14778.1__SEA_GRETCHEN_4__00004

Bact-Vir

OK040779.1__UDL14778.1__SEA_GRETCHEN_4__00004

Identity

Accession:
OK040779 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Microbacterium_phage_Gretchen

TaxID: 2885980

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 medium residues 1-163
PDB
Domain cluster: rep: OP434458.1__UYL87836.1__SEA_MALISHA_5__00005__D5-134
D2 medium residues 164-206_230-252
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25310.2 best VG15 47.7 3.30e-12 97.0% 21.2%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4n9jA02 3.30.1120.130 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.50 31.0 2.59e-01 87.9% 38.3%
1cw1A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.50 41.0 2.59e-01 95.5% 84.1%
D3 medium residues 207-229_253-339
PDB
Domain cluster: representative
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4mh6A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 61.0 5.29e-01 93.6% 73.0%
6t4hA03 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.55 32.0 2.77e-01 77.3% 36.6%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3741278 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.67 56.0 4.43e-01 87.3% 46.2%
3399224 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.65 56.0 4.66e-01 90.0% 56.1%
3886245 3562.1.1.1 ↗ alpha bundles › Calcium release-activated calcium channel protein 1 › Calcium release-activated calcium channel protein 1 › Calcium release-activated calcium channel protein 1 › Orai-1 0.60 56.0 4.33e-01 100.0% 77.3%
5048272 5073.1.1.11 ↗ alpha bundles › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain-related › Calcium ATPase transmembrane domain M › Cation_ATPase_C 0.57 44.0 2.89e-01 80.9% 57.2%
D4 medium residues 359-434
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.70 42.0 4.13e-01 97.4% 55.4%
2xheA03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.67 50.0 4.34e-01 100.0% 50.4%
1td6A01 1.20.1480.10 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › hypothetical protein mp506/mpn330, domain 1 0.66 55.0 5.05e-01 93.4% 80.4%
5c0yA02 1.10.150.80 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › HRDC domain 0.65 56.0 5.26e-01 96.1% 86.0%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.65 56.0 4.94e-01 98.7% 89.5%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.62 53.0 4.82e-01 100.0% 97.3%
5mdtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.61 45.0 3.59e-01 77.6% 45.4%
5m9dA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.60 41.0 3.45e-01 71.1% 76.1%
3f7cA00 1.20.1590.10 Mainly Alpha › Up-down Bundle › YP_001051499.1 fold like › YP_001051499.1 domain like 0.59 49.0 3.76e-01 96.1% 48.7%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.59 43.0 4.29e-01 77.6% 94.9%
6h5hA00 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.59 48.0 4.96e-01 90.8% 100.0%
2p5tA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.59 43.0 4.08e-01 78.9% 78.3%
1xwmA00 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 49.0 3.68e-01 100.0% 92.0%
1udyA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.58 39.0 3.47e-01 72.4% 53.3%
3bulA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.57 42.0 4.09e-01 80.3% 100.0%
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.57 39.0 3.03e-01 72.4% 85.1%
3frrA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.56 43.0 3.37e-01 88.2% 67.7%
7dfeA01 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.56 43.0 3.69e-01 85.5% 68.5%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.55 40.0 4.15e-01 97.4% 83.1%
2etjA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.55 45.0 3.29e-01 89.5% 89.0%
3bhgA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.55 42.0 3.72e-01 82.9% 76.5%
1svmA01 1.10.10.510 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Zinc finger, large T-antigen D1 domain 0.54 41.0 3.94e-01 97.4% 70.0%
1fx8A00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.54 40.0 2.81e-01 78.9% 67.7%
1b8dA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.53 44.0 3.63e-01 100.0% 59.1%
3zojA00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.53 39.0 2.81e-01 81.6% 55.9%
3td7A02 1.20.120.1250 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Sulfhydryl oxidase R596, ORFan domain 0.53 39.0 3.29e-01 80.3% 69.1%
3pvuA02 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.53 37.0 3.73e-01 76.3% 71.2%
1te2A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 38.0 3.95e-01 100.0% 86.1%
3r0xA02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 41.0 3.57e-01 86.8% 100.0%
3n2oA03 1.20.58.930 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 44.0 4.06e-01 97.4% 75.0%
6vbkB02 1.20.58.1480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.50 40.0 4.03e-01 90.8% 87.0%
2a6cA00 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.50 41.0 4.16e-01 100.0% 92.1%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1392345 4995.1.1.2 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › AppA_4HB 0.74 43.0 3.95e-01 98.7% 45.0%
3306390 604.9.1.1 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Ribosomal_S20p 0.71 49.0 4.43e-01 72.4% 77.1%
5038613 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.67 48.0 4.53e-01 76.3% 84.2%
3672 4270.1.1.1 ↗ alpha bundles › N-terminal domain of Hypothetical protein MPN330 › N-terminal domain of Hypothetical protein MPN330 › N-terminal domain of Hypothetical protein MPN330 › DUF3196 0.66 55.0 5.05e-01 93.4% 80.4%
4011264 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 44.0 3.60e-01 71.1% 73.6%
3980198 5069.1.1.26 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › NrfD 0.63 44.0 3.71e-01 75.0% 60.7%
3937526 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.63 50.0 4.14e-01 88.2% 81.4%
3269130 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 43.0 3.15e-01 72.4% 56.3%
3245015 3831.1.1.0 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 0.62 38.0 3.83e-01 98.7% 58.7%
3598594 4995.1.1.1 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like › B12-binding_2 0.61 40.0 3.49e-01 100.0% 44.3%
3941457 1203.1.2.3 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › YiaAB 0.61 53.0 4.61e-01 100.0% 81.7%
4942761 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.61 43.0 4.24e-01 76.3% 90.6%
352936 3813.1.1.1 ↗ alpha bundles › DUF416 › DUF416 › DUF416 › DUF416 0.59 49.0 3.76e-01 96.1% 48.7%
3743739 2485.1.1.49 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › Thioredoxin_12 0.59 47.0 3.55e-01 98.7% 37.1%
3736557 3718.1.1.0 ↗ alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT 0.59 42.0 4.18e-01 76.3% 85.0%
3514217 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.58 44.0 4.11e-01 81.6% 82.1%
5044067 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.58 42.0 4.00e-01 76.3% 72.2%
3599682 4156.1.1.0 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.57 48.0 3.89e-01 100.0% 58.7%
3614560 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.56 48.0 4.76e-01 98.7% 100.0%
3222373 605.4.1.18 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein › PF29357 0.56 41.0 4.03e-01 80.3% 85.9%
4224489 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.55 49.0 3.06e-01 100.0% 18.8%
3987813 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.55 44.0 4.51e-01 94.7% 98.7%
4570259 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.55 48.0 3.76e-01 100.0% 49.4%
3401715 4156.1.1.0 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like 0.54 47.0 3.45e-01 100.0% 37.8%
4239374 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.54 46.0 3.76e-01 100.0% 54.2%
3562784 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.53 45.0 3.78e-01 100.0% 69.7%
4543174 4156.1.1.4 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › HA2_C 0.52 43.0 3.51e-01 100.0% 54.1%
4053440 3455.1.1.0 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors 0.51 43.0 4.41e-01 100.0% 100.0%
5078867 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.51 32.0 3.07e-01 96.1% 52.2%
D5 medium residues 473-548
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4xsgB00 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.86 74.0 5.28e-01 92.1% 36.1%
2j3vA02 3.90.176.10 Alpha Beta › Alpha-Beta Complex › Toxin ADP-ribosyltransferase; Chain A, domain 1 › Toxin ADP-ribosyltransferase; Chain A, domain 1 0.79 66.0 4.66e-01 89.5% 33.5%
3s0aA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.51 34.0 3.00e-01 86.8% 43.7%
D6 medium residues 549-671
PDB
Domain cluster: rep: KR063281.1__AKJ72552.1__GMA2_14__00014__D100-243
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03496.21 best ADPrib_exo_Tox 55.3 7.80e-15 92.7% 55.4%