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SR-VP_0-2_scaffold_141_2071242_prodigal-single.1__X__X__00171

Bact-Vir

SR-VP_0-2_scaffold_141_2071242_prodigal-single.1__X__X__00171

Identity

Kingdom:
phage

Quality

86.1 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 21-162
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09709.16 best Cas_Csd1 43.8 2.10e-11 100.0% 26.6%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3186225 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.57 41.0 2.98e-01 74.6% 97.4%
3479996 109.4.1.328 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF2428 0.54 39.0 2.98e-01 73.9% 50.8%
3694135 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.53 39.0 3.02e-01 75.4% 84.9%
3742023 5081.1.1.4 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › DUF1751 0.51 37.0 3.20e-01 73.9% 93.5%
3694169 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 42.0 3.09e-01 87.3% 41.1%
D2 high residues 258-398
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4hkqA04 3.10.20.370 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.59 24.0 3.31e-01 70.2% 72.4%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4847868 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.61 23.0 3.66e-01 93.6% 92.3%
3212571 3937.1.1.2 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Innexin 0.54 40.0 2.92e-01 78.0% 42.5%
3917315 3937.1.1.1 ↗ alpha bundles › Connexin 26 › Connexin 26 › Connexin 26 › Connexin 0.51 37.0 3.25e-01 75.2% 80.5%
4087500 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.50 25.0 2.96e-01 89.4% 67.8%
D3 high residues 432-556
PDB
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xq9A02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.67 52.0 5.32e-01 81.6% 95.9%
2b0hA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.64 47.0 4.67e-01 75.2% 89.1%
1y4cA03 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.61 43.0 4.50e-01 72.0% 87.6%
2j0nB00 1.20.1710.10 Mainly Alpha › Up-down Bundle › IpaD-like › IpaD-like 0.60 49.0 4.36e-01 89.6% 80.7%
2kmfA01 1.20.58.810 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Photosystem II Pbs27 0.59 43.0 4.63e-01 74.4% 95.1%
6t0bc02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.59 46.0 3.99e-01 81.6% 87.4%
1fftC00 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.59 46.0 4.03e-01 81.6% 88.1%
2l10A00 1.20.1420.10 Mainly Alpha › Up-down Bundle › A middle domain of Talin 1 › Talin, central domain 0.59 45.0 4.20e-01 81.6% 86.7%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.58 41.0 3.42e-01 71.2% 77.3%
1hw1A02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.58 44.0 4.14e-01 80.0% 86.1%
2yevA03 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.58 44.0 3.93e-01 81.6% 89.1%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.57 45.0 4.45e-01 84.8% 91.8%
4k0dA00 1.20.120.1730 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.56 47.0 4.53e-01 90.4% 88.1%
2wdqC00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.55 39.0 3.97e-01 72.8% 94.2%
1sxjB03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.55 37.0 4.22e-01 78.4% 94.6%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.55 46.0 3.89e-01 90.4% 63.5%
4yjwA00 1.20.120.930 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF12889, N-terminal DUF3829 0.54 45.0 4.23e-01 89.6% 82.4%
1m56C02 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.54 43.0 3.75e-01 85.6% 90.8%
1qmgA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.54 44.0 3.40e-01 89.6% 78.2%
2zy9A03 1.10.357.20 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › SLC41 divalent cation transporters, integral membrane domain 0.53 40.0 3.62e-01 78.4% 77.0%
2np5D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 41.0 3.80e-01 80.8% 79.1%
8sbeA02 1.20.1250.20 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains 0.53 46.0 4.02e-01 95.2% 86.1%
8b70A01 1.20.1740.10 Mainly Alpha › Up-down Bundle › Amino acid/polyamine transporter I › Amino acid/polyamine transporter I 0.52 46.0 3.24e-01 97.6% 57.4%
1ezvC00 1.20.810.10 Mainly Alpha › Up-down Bundle › Cytochrome Bc1 Complex; Chain C › Cytochrome Bc1 Complex; Chain C 0.52 42.0 3.05e-01 87.2% 48.3%
4od4A01 1.10.357.140 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › UbiA prenyltransferase 0.52 41.0 3.85e-01 84.8% 89.1%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.51 38.0 3.80e-01 76.0% 88.8%
3fmsA02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.51 41.0 3.95e-01 85.6% 96.5%
6o7uc01 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.50 45.0 3.89e-01 99.2% 63.7%
4nqfA00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.50 39.0 3.78e-01 81.6% 92.4%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3209703 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.74 38.0 3.23e-01 92.0% 31.5%
3938179 5054.1.1.9 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › PKD_channel 0.66 42.0 2.97e-01 100.0% 22.9%
3743845 3745.1.1.1 ↗ alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex 0.66 51.0 3.69e-01 80.8% 81.1%
5071300 601.27.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › MW0975(SA0943)-like › MW0975(SA0943)-like 0.66 50.0 4.44e-01 80.0% 80.0%
1503807 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.65 45.0 4.69e-01 70.4% 93.9%
3803267 5059.1.1.38 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA, Mg_trans_NIPA 0.65 49.0 3.73e-01 79.2% 88.6%
3970498 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.63 48.0 4.05e-01 81.6% 90.0%
4970859 601.28.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › VPS28 C-terminal domain-like › VPS28 C-terminal domain-like 0.63 43.0 4.74e-01 73.6% 88.0%
3624840 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 44.0 3.36e-01 72.0% 57.5%
4946592 604.5.1.1 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU_div 0.62 46.0 3.92e-01 77.6% 99.5%
3239393 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.62 43.0 4.58e-01 72.0% 94.5%
3589541 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.62 45.0 3.95e-01 75.2% 84.7%
4929564 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.60 46.0 4.62e-01 80.0% 93.0%
4032683 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.59 46.0 3.94e-01 84.0% 91.2%
3239895 188.1.1.1 ↗ alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Hormone_recep 0.58 44.0 3.54e-01 78.4% 86.3%
3579241 192.29.1.50 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › PTPLA 0.58 40.0 4.12e-01 70.4% 93.9%
4227779 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.57 45.0 3.94e-01 87.2% 95.1%
3243786 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.57 40.0 4.10e-01 73.6% 85.6%
4013887 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.57 49.0 4.70e-01 92.0% 87.9%
4089352 5069.1.1.63 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › SirB 0.56 39.0 3.97e-01 72.0% 90.4%
3695964 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.56 52.0 4.18e-01 100.0% 79.1%
3180205 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.56 51.0 4.21e-01 100.0% 81.8%
4026297 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.56 38.0 3.79e-01 70.4% 85.2%
3964502 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.56 40.0 4.29e-01 75.2% 100.0%
3600846 611.4.1.0 ↗ alpha bundles › N-cbl like › PG0775 C-terminal domain-like › PG0775 C-terminal domain-like 0.55 37.0 3.84e-01 92.8% 72.5%
3724837 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.55 49.0 3.94e-01 97.6% 75.0%
4012296 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.54 48.0 3.94e-01 97.6% 77.0%
3687375 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 48.0 4.00e-01 97.6% 80.9%
5020411 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.54 46.0 4.34e-01 92.0% 82.7%
3736269 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 50.0 4.04e-01 100.0% 80.0%
4014181 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.54 47.0 3.67e-01 95.2% 64.1%
3729299 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.54 43.0 4.08e-01 87.2% 85.8%
3586969 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.53 45.0 3.83e-01 91.2% 82.0%
3788896 5082.1.1.0 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like 0.53 44.0 3.79e-01 88.8% 88.5%
3710097 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.53 41.0 4.03e-01 88.0% 75.0%
1118607 611.9.1.0 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain 0.53 41.0 4.36e-01 90.4% 92.0%
4020823 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 46.0 3.91e-01 95.2% 73.7%
3731084 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.53 47.0 3.77e-01 97.6% 73.9%
1148047 601.7.1.2 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN 0.52 43.0 4.06e-01 87.2% 92.7%
3987427 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 45.0 3.89e-01 93.6% 76.4%
3177532 5050.1.1.9 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1 0.52 47.0 3.90e-01 97.6% 80.5%
3714072 5050.1.1.4 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Nucleoside_tran 0.52 42.0 3.85e-01 87.2% 89.1%
3695328 5050.1.1.1 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr 0.51 45.0 3.78e-01 96.0% 80.5%
3968776 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.50 43.0 3.38e-01 94.4% 71.6%
D4 medium residues 1-20_164-257
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09709.16 best Cas_Csd1 63.3 2.60e-17 94.7% 14.6%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3624557 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.60 36.0 3.73e-01 77.2% 63.8%