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RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00028

Bact-Vir

RifSed_csp2_10ft_3_scaffold_6_prodigal-single.1__X__X__00028

Identity

Kingdom:
phage

Quality

87.4 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 3-56
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2p84A02 2.30.30.290 Mainly Beta › Roll › SH3 type barrels. › YopX-like domains 0.77 70.0 6.28e-01 100.0% 76.7%
4o5vA03 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.75 65.0 5.80e-01 98.1% 96.1%
4innA00 2.40.128.520 Mainly Beta › Beta Barrel › Lipocalin › 0.74 59.0 4.32e-01 88.9% 83.6%
2yk0A03 1.20.58.1930 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 57.0 3.76e-01 85.2% 55.5%
2zkmX01 2.30.29.240 Mainly Beta › Roll › PH-domain like › 0.70 56.0 3.78e-01 87.0% 50.5%
3zx7A02 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.70 52.0 3.93e-01 81.5% 97.1%
3gd0A02 3.30.920.50 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Beta-1,3-glucanase, C-terminal domain 0.70 55.0 4.42e-01 88.9% 81.2%
3oyyA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.69 60.0 5.64e-01 98.1% 95.5%
3n6rA03 3.30.700.30 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.68 57.0 4.35e-01 96.3% 82.7%
2yf0A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 51.0 4.45e-01 83.3% 83.9%
1k07A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.67 50.0 3.21e-01 81.5% 57.3%
4usoA00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.66 51.0 3.94e-01 88.9% 100.0%
1qmyA00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.66 52.0 3.84e-01 98.1% 31.4%
3ge2A00 2.40.128.50 Mainly Beta › Beta Barrel › Lipocalin › 0.66 52.0 4.51e-01 90.7% 95.5%
3gceA00 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.65 49.0 4.05e-01 83.3% 94.2%
4hwmA00 2.40.128.500 Mainly Beta › Beta Barrel › Lipocalin › YedD-like protein 0.65 57.0 4.49e-01 100.0% 85.5%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.65 56.0 5.41e-01 98.1% 100.0%
6s8zA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.65 57.0 5.46e-01 98.1% 100.0%
3c12A01 2.30.30.910 Mainly Beta › Roll › SH3 type barrels. › 0.65 50.0 5.14e-01 87.0% 96.1%
4r3dA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.65 53.0 4.13e-01 100.0% 39.4%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.64 45.0 4.31e-01 75.9% 89.2%
4aghA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.63 43.0 3.84e-01 72.2% 68.8%
2dk3A00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.61 51.0 4.50e-01 98.1% 84.9%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.61 51.0 4.80e-01 98.1% 94.2%
1xdiA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.61 45.0 3.51e-01 79.6% 97.5%
4pq0A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.61 44.0 3.85e-01 83.3% 74.2%
1yzbA01 3.90.70.40 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › 0.60 49.0 3.95e-01 100.0% 58.1%
7dpyB01 2.40.128.200 Mainly Beta › Beta Barrel › Lipocalin › C-type lysozyme inhibitor 0.60 46.0 4.17e-01 90.7% 95.2%
1v73A00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.59 43.0 2.69e-01 79.6% 23.0%
5w7zA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.58 42.0 3.44e-01 79.6% 83.2%
1bm8A00 3.10.260.10 Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › Transcription regulator HTH, APSES-type DNA-binding domain 0.58 42.0 3.58e-01 81.5% 93.9%
3cpfA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.57 46.0 4.41e-01 98.1% 95.4%
2qc5A00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 40.0 2.61e-01 83.3% 26.2%
3ci0J01 3.10.610.10 Alpha Beta › Roll › Pili subunits › GSPII I/J protein-like 0.54 39.0 3.35e-01 83.3% 66.3%
2v3aA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 44.0 3.40e-01 94.4% 94.8%
1vx7200 3.30.390.110 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.54 40.0 3.32e-01 81.5% 59.6%
3o0hB02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 44.0 3.52e-01 94.4% 100.0%
1npeA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.54 39.0 2.65e-01 85.2% 83.7%
2r9zA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 45.0 3.50e-01 94.4% 100.0%
1gv4A02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 43.0 3.10e-01 90.7% 80.1%
2aq5A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 42.0 2.62e-01 90.7% 93.0%
4d6wA03 2.30.29.130 Mainly Beta › Roll › PH-domain like › 0.53 46.0 3.83e-01 100.0% 61.1%
1db3A02 3.90.25.10 Alpha Beta › Alpha-Beta Complex › UDP-galactose 4-epimerase; domain 1 › UDP-galactose 4-epimerase, domain 1 0.52 42.0 3.29e-01 88.9% 82.8%
2wjsA03 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 41.0 3.09e-01 98.1% 93.8%
1y13A00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.50 40.0 2.89e-01 92.6% 28.8%
ECOD (64)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4990212 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 61.0 6.08e-01 88.9% 94.5%
4966534 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.75 61.0 6.36e-01 90.7% 100.0%
3436173 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.73 63.0 3.96e-01 100.0% 25.9%
4946165 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.73 60.0 6.05e-01 90.7% 96.4%
4930179 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 59.0 5.89e-01 90.7% 94.5%
5002449 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 60.0 5.97e-01 90.7% 92.7%
5025079 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 60.0 6.01e-01 92.6% 98.2%
3495619 220.1.1.22 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C 0.72 55.0 4.35e-01 83.3% 65.5%
4982334 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.72 60.0 5.98e-01 90.7% 90.9%
3396951 4.1.1.330 ↗ beta barrels › SH3 › SH3 › SH3 › SH3-B_UBE2O, SH3-C_UBE2O 0.71 58.0 3.46e-01 90.7% 17.0%
5030430 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 59.0 5.60e-01 92.6% 84.6%
3603357 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 59.0 5.94e-01 92.6% 98.2%
5056706 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 58.0 6.01e-01 90.7% 100.0%
4950396 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.71 59.0 5.86e-01 90.7% 89.1%
5060760 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.71 60.0 5.64e-01 94.4% 92.3%
5017214 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 57.0 5.72e-01 90.7% 94.5%
4995677 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 56.0 5.63e-01 88.9% 98.2%
4935681 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 58.0 5.80e-01 92.6% 96.4%
5033075 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 58.0 5.78e-01 92.6% 94.5%
5023740 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 57.0 5.85e-01 90.7% 98.0%
3961546 4.1.1.13 ↗ beta barrels › SH3 › SH3 › SH3 › MS_channel_2nd 0.69 56.0 5.32e-01 92.6% 86.2%
4938404 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.69 57.0 5.67e-01 90.7% 89.1%
3507373 391.1.1.7 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2 0.69 47.0 4.24e-01 72.2% 85.3%
3364875 239.3.1.1 ↗ beta barrels › Ribosomal protein L25-like › FAS1 domain › FAS1 domain › Fasciclin 0.69 51.0 3.91e-01 83.3% 45.2%
3101373 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.68 57.0 4.27e-01 96.3% 78.0%
4113514 304.51.1.6 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cmr3 0.68 59.0 4.03e-01 100.0% 80.0%
1124180 3794.1.1.1 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit › PCC_BT 0.68 57.0 4.33e-01 96.3% 81.5%
3306779 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.68 60.0 5.68e-01 98.1% 96.9%
3273079 9.4.1.0 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains 0.68 54.0 4.65e-01 90.7% 97.8%
3079243 9.4.1.0 ↗ beta barrels › Lipocalins/Streptavidin › D-aminopeptidase, middle and C-terminal domains › D-aminopeptidase, middle and C-terminal domains 0.67 52.0 4.61e-01 88.9% 88.2%
3282992 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.67 52.0 4.16e-01 85.2% 57.4%
3463325 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.67 53.0 3.49e-01 90.7% 32.9%
3586827 274.1.1.25 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits › ComGF 0.67 48.0 3.81e-01 77.8% 42.6%
3824503 5.1.4.550 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Kelch_FKB95 0.66 51.0 3.20e-01 83.3% 45.0%
185792 9.17.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipoprotein YedD › Lipoprotein YedD › YedD 0.65 57.0 4.49e-01 100.0% 85.5%
3989333 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.65 47.0 4.57e-01 77.8% 73.3%
4133709 2004.1.1.19 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.65 53.0 3.60e-01 90.7% 24.4%
3938829 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.65 51.0 3.02e-01 85.2% 81.7%
4957409 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.65 52.0 5.37e-01 90.7% 96.0%
4063575 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.65 48.0 3.85e-01 83.3% 67.8%
4077367 4.1.1.57 ↗ beta barrels › SH3 › SH3 › SH3 › EFP_N 0.64 56.0 5.28e-01 98.1% 100.0%
4020598 2003.1.5.19 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › TRM 0.64 53.0 3.09e-01 92.6% 26.3%
4453958 274.1.1.23 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits › DUF5374 0.63 45.0 4.38e-01 75.9% 75.0%
3339163 4.1.1.302 ↗ beta barrels › SH3 › SH3 › SH3 › tSH3-B_UBE2O 0.62 51.0 4.39e-01 90.7% 96.5%
4027218 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 54.0 4.77e-01 100.0% 91.3%
3602276 881.4.1.2 ↗ a+b three layers › Mog1p/PsbP-like › C-terminal domain in sigma-E factor regulatory protein rseB › C-terminal domain in sigma-E factor regulatory protein rseB › DUF4367 0.61 44.0 3.35e-01 75.9% 36.3%
3591534 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.61 42.0 3.34e-01 74.1% 38.4%
4987649 3110.1.1.0 ↗ a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain 0.61 46.0 3.13e-01 87.0% 40.9%
3469461 109.4.1.1256 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.59 43.0 2.72e-01 79.6% 85.5%
3787920 5.1.4.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CNH 0.59 45.0 2.76e-01 85.2% 75.5%
3413140 6129.1.1.1 ↗ beta barrels › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › VWD 0.58 43.0 3.04e-01 83.3% 32.6%
4052154 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.57 46.0 3.37e-01 94.4% 82.4%
3227619 6129.1.1.1 ↗ beta barrels › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › Repulsive guidance molecule (RGM) family › VWD 0.57 44.0 3.16e-01 88.9% 71.9%
3933890 101.1.1.76 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 0.57 43.0 3.57e-01 83.3% 72.0%
3244902 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.57 48.0 3.50e-01 100.0% 53.7%
3640328 4.1.1.411 ↗ beta barrels › SH3 › SH3 › SH3 › Pkinase_fungal 0.56 40.0 3.81e-01 79.6% 87.1%
4072037 2003.1.2.15 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_3 0.54 45.0 2.94e-01 94.4% 56.9%
3227881 2484.1.1.200 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FTH 0.53 44.0 3.25e-01 100.0% 42.4%
4681650 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.53 43.0 3.12e-01 96.3% 81.1%
4031750 274.1.1.25 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits › ComGF 0.53 43.0 3.60e-01 92.6% 72.7%
3228484 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.52 43.0 2.90e-01 100.0% 27.5%
5039096 274.1.1.67 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits › DUF7289 0.52 37.0 3.04e-01 77.8% 71.3%
3244243 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.51 43.0 3.05e-01 100.0% 33.3%
3218627 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.51 42.0 2.93e-01 100.0% 30.2%