Back to structures

SRR1747035_scaffold_3_prodigal-single.1__X__X__00264

Bact-Vir

SRR1747035_scaffold_3_prodigal-single.1__X__X__00264

Identity

Kingdom:
phage

Quality

91.1 mean pLDDT

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 8-23_233-333
PDB
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2i53A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.60 42.0 4.30e-01 82.9% 75.7%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.58 40.0 4.55e-01 81.2% 98.8%
2w96A02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.57 39.0 4.03e-01 80.3% 73.5%
5ymrC00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.56 49.0 3.00e-01 97.4% 33.6%
1s7bA00 1.10.3730.20 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › 0.56 38.0 3.99e-01 70.9% 76.4%
4pcwC00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.56 33.0 3.64e-01 98.3% 73.6%
1zklA00 1.10.1300.10 Mainly Alpha › Orthogonal Bundle › Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b › 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain 0.55 43.0 3.24e-01 85.5% 67.8%
3vkgA09 1.20.920.30 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › 0.55 42.0 4.00e-01 83.8% 70.8%
4yibA01 1.10.530.10 Mainly Alpha › Orthogonal Bundle › Lysozyme › 0.54 41.0 3.73e-01 81.2% 90.5%
4xxiA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.52 38.0 3.60e-01 86.3% 61.9%
3k2jA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.51 41.0 4.06e-01 85.5% 95.0%
3go6A00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.51 41.0 3.17e-01 88.0% 97.2%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3877927 632.8.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.66 30.0 3.17e-01 86.3% 45.5%
2979253 632.21.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › EndoS_helical 0.61 33.0 4.21e-01 79.5% 88.6%
3951581 2003.6.1.1 a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › PfkB 0.60 42.0 3.12e-01 77.8% 28.0%
2845 101.1.10.17 alpha arrays › HTH › HTH › Cyclin-like › CycT2-like_C 0.60 42.0 4.31e-01 82.9% 76.4%
3411106 3345.1.1.1 alpha arrays › MRG domain › MRG domain › MRG domain › MRG 0.59 48.0 4.25e-01 86.3% 81.1%
3451722 3930.1.1.0 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.57 45.0 4.46e-01 85.5% 92.8%
3455585 198.1.1.0 alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.55 39.0 4.18e-01 96.6% 87.0%
4162402 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.55 40.0 3.84e-01 76.9% 90.7%
5061156 101.1.10.3 alpha arrays › HTH › HTH › Cyclin-like › TFIIB 0.54 39.0 3.90e-01 76.9% 73.3%
3859555 601.19.1.1 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Apolipoprotein 0.52 41.0 3.62e-01 85.5% 85.0%
3999064 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 31.0 2.80e-01 70.9% 39.4%
4451883 3281.1.1.1 alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.51 44.0 2.98e-01 100.0% 77.2%
3453526 3930.1.1.0 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.51 40.0 3.95e-01 85.5% 97.6%
3816427 101.1.2.386 alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.50 31.0 3.30e-01 80.3% 68.6%
D2 high residues 32-51_105-223
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06067.17 best DUF932 84.6 1.30e-23 89.9% 50.2%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3jv1A00 3.10.280.10 Alpha Beta › Roll › Mitochondrial Matrix Protein; Chain A › Mitochondrial glycoprotein 0.65 45.0 4.08e-01 98.6% 52.7%
2lnjA00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.58 37.0 3.53e-01 71.9% 52.9%
4r7kA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 41.0 3.92e-01 74.1% 80.4%
1wzvA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.57 44.0 4.29e-01 84.9% 74.0%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.56 41.0 4.22e-01 74.8% 98.5%
1gyvA00 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.55 33.0 3.54e-01 71.9% 67.5%
2imjD01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.54 37.0 3.77e-01 71.2% 81.7%
5e4bA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.53 39.0 3.60e-01 74.8% 83.0%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.52 34.0 3.64e-01 97.1% 74.6%
6gh3A01 2.70.98.40 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Glycoside hydrolase, family 65, N-terminal domain 0.52 47.0 3.59e-01 100.0% 81.2%
1gydB00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.52 46.0 3.55e-01 97.1% 75.2%
2g8sB00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.51 45.0 3.35e-01 96.4% 60.5%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3829563 897.1.1.0 a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.77 45.0 4.27e-01 91.4% 49.1%
3941745 241.15.1.4 a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › DUF932 0.70 62.0 6.19e-01 96.4% 99.3%
3574500 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 46.0 3.17e-01 87.8% 79.2%
3628522 5.1.4.489 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Prenyltrans 0.56 46.0 2.85e-01 87.8% 47.3%
3972573 3692.1.1.1 a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.55 36.0 3.91e-01 74.8% 78.3%
4059717 4099.1.1.0 a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.55 34.0 4.13e-01 72.7% 100.0%
3958869 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.55 40.0 3.47e-01 76.3% 99.1%
3736685 881.1.1.0 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.54 40.0 3.74e-01 76.3% 87.1%
3921815 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 41.0 3.31e-01 79.9% 54.5%
4951151 5.1.4.40 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PQQ_2 0.54 41.0 3.08e-01 79.9% 67.2%
3164281 5069.1.1.92 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › CcmF_C 0.53 35.0 4.06e-01 77.0% 93.0%
3933957 4051.1.1.1 a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.53 43.0 4.18e-01 88.5% 86.3%
5039596 331.3.1.52 a+b two layers › TBP-like › Bet v1-like › Bet v1-like › PF28469 0.53 38.0 3.72e-01 74.8% 94.2%
3173251 4051.1.1.1 a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.53 44.0 4.13e-01 90.6% 87.6%
3290197 222.1.1.0 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.52 43.0 3.78e-01 90.6% 84.1%
5052962 3692.1.1.1 a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.52 36.0 3.74e-01 77.0% 73.9%
3933455 3369.1.1.1 beta meanders › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › lysosome-associated membrane protein LAMP-3 › Lamp2-like_luminal 0.52 45.0 4.12e-01 95.7% 82.2%
3995515 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 46.0 3.57e-01 96.4% 84.1%
4629131 9.29.1.1 beta barrels › Lipocalins/Streptavidin › VirK › VirK › VirK 0.52 39.0 4.10e-01 78.4% 91.9%
4145032 12.3.1.69 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › DUF4861 0.50 41.0 3.34e-01 87.1% 92.6%
4064251 12.3.1.70 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › PF26374 0.50 44.0 3.22e-01 97.8% 90.1%
3924608 4059.1.1.0 a+b complex topology › Serpins › Serpins › Serpins 0.50 39.0 2.96e-01 81.3% 65.7%
3190582 5084.1.1.0 beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like 0.50 40.0 3.72e-01 90.6% 68.0%
4403418 12.3.1.6 beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Bgal_small_N 0.50 42.0 3.34e-01 91.4% 92.5%
D3 high residues 53-99
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ijcA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.77 43.0 2.49e-01 100.0% 7.0%
2z3zA01 2.140.10.30 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Dipeptidylpeptidase IV, N-terminal domain 0.67 42.0 2.48e-01 100.0% 7.5%
6xw5A01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.65 47.0 3.30e-01 83.0% 45.7%
2sliA03 2.40.220.10 Mainly Beta › Beta Barrel › Intramolecular trans-sialidase; domain 3 › Intramolecular Trans-sialidase; Domain 3 0.61 44.0 3.49e-01 89.4% 37.0%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.61 40.0 2.47e-01 72.3% 10.4%
2yxdA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 37.0 2.53e-01 76.6% 15.1%
4f0aB02 3.30.2460.20 Alpha Beta › 2-Layer Sandwich › Endo-n-acetylneuraminidase fold › Wnt (Wingless and Int-1), C-terminal domain 0.58 42.0 3.77e-01 93.6% 52.9%
1v1qA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 38.0 2.94e-01 70.2% 46.4%
4cvbA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.56 46.0 2.67e-01 95.7% 24.0%
2r61A02 2.40.50.110 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 33.0 2.87e-01 100.0% 34.2%
1kb0A01 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.56 46.0 2.62e-01 100.0% 11.8%
3k8aB00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.54 37.0 2.93e-01 70.2% 45.6%
2z13A00 2.30.29.170 Mainly Beta › Roll › PH-domain like › 0.53 40.0 3.10e-01 100.0% 34.2%
3kbgA02 2.40.50.740 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Ribosomal protein S4, central domain 0.53 47.0 4.54e-01 97.9% 98.1%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.53 41.0 2.93e-01 87.2% 30.3%
3bzwF00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.53 42.0 2.77e-01 95.7% 67.1%
3aonA00 1.10.287.3240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 36.0 2.63e-01 83.0% 26.6%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.51 40.0 2.89e-01 89.4% 67.1%
3ga8A00 3.10.20.860 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 35.0 3.30e-01 100.0% 56.7%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4223395 4967.1.1.25 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Intron_maturas2+MatK_N 0.64 46.0 2.72e-01 78.7% 20.5%
4551865 391.1.2.27 few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › Cys_knot 0.64 46.0 3.37e-01 83.0% 26.0%
4546371 220.1.1.219 beta barrels › PH domain-like › PH domain-like › PH domain-like › CheF-arch 0.63 53.0 3.93e-01 93.6% 48.3%
4666185 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.63 43.0 2.55e-01 74.5% 19.3%
3220090 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.62 45.0 2.61e-01 78.7% 14.4%
4635290 4967.1.1.25 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Intron_maturas2+MatK_N 0.62 42.0 2.46e-01 70.2% 10.2%
4351239 4967.1.1.6 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Intron_maturas2 0.61 43.0 3.23e-01 76.6% 62.3%
4361292 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.60 44.0 2.56e-01 80.9% 17.9%
2772633 71.1.1.15 beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › UCP033729 0.60 40.0 2.70e-01 100.0% 19.4%
4990821 7571.1.1.1 a/b three-layered sandwiches › Formyltransferase › Formyltransferase › Formyltransferase › Formyl_trans_N 0.60 41.0 2.66e-01 76.6% 24.0%
5049119 221.10.1.1 a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.60 49.0 4.04e-01 91.5% 88.2%
3582577 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 48.0 3.59e-01 95.7% 95.4%
3602563 2007.1.5.14 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › ATC-like › PF27247 0.57 39.0 3.00e-01 74.5% 33.6%
3717787 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 44.0 2.67e-01 100.0% 51.9%
4968312 2484.1.1.66 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DDE_3 0.55 45.0 3.04e-01 100.0% 25.2%
4396101 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.54 35.0 2.11e-01 70.2% 10.0%
3624119 2.3.1.2 beta barrels › OB-fold › TIMP-like › TIMP-like › NTR 0.51 39.0 3.03e-01 100.0% 75.2%
5019602 212.1.1.0 a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like 0.50 39.0 3.00e-01 91.5% 94.2%
3636832 222.1.1.4 a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT 0.50 38.0 2.77e-01 93.6% 55.4%