Back to structures

SRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00528

Bact-Vir

SRR1747018_scaffold_2_1202_curated_prodigal-single.1__X__X__00528

Identity

Kingdom:
phage

Quality

92.4 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 3-36_133-198
PDB
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4hudA01 3.30.2000.40 Alpha Beta › 2-Layer Sandwich › STM4215-like › Myoviridae tail sheath stabiliser 0.61 49.0 3.91e-01 88.0% 81.0%
4c2mA09 3.30.70.2850 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 43.0 3.59e-01 73.0% 88.5%
1s2oA02 3.90.1070.10 Alpha Beta › Alpha-Beta Complex › Hypothetical Protein Ta0175; Chain: A, domain 2 › 0.60 39.0 4.47e-01 74.0% 93.0%
8gccA02 3.30.1360.40 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.59 39.0 4.22e-01 71.0% 79.1%
3ezjA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.59 32.0 3.71e-01 71.0% 75.0%
5mmiU01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 43.0 4.70e-01 77.0% 98.8%
3nwgA02 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.58 41.0 4.15e-01 74.0% 95.0%
3f44A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 41.0 3.31e-01 75.0% 75.2%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.58 43.0 4.42e-01 79.0% 90.5%
4qnyA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.57 45.0 4.29e-01 85.0% 84.9%
1o0vA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 41.0 3.98e-01 76.0% 94.5%
1kafA00 3.90.1150.20 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription regulator MotA, C-terminal domain 0.56 43.0 4.23e-01 81.0% 81.5%
4aqzA00 2.60.40.3470 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 41.0 3.69e-01 77.0% 56.5%
2rdeA02 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.56 50.0 4.86e-01 99.0% 94.6%
1lq9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 39.0 3.81e-01 75.0% 93.8%
2jgtA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 38.0 3.42e-01 81.0% 50.4%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.55 39.0 3.62e-01 76.0% 97.0%
3o4oC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 3.79e-01 74.0% 97.3%
1bwvA01 3.30.70.150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RuBisCO large subunit, N-terminal domain 0.54 39.0 3.63e-01 75.0% 93.0%
1vq8S00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 39.0 4.19e-01 76.0% 96.3%
2dbbA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.53 38.0 3.95e-01 75.0% 93.5%
4gaaA01 2.60.40.1730 Mainly Beta › Sandwich › Immunoglobulin-like › tricorn interacting facor f3 domain 0.53 40.0 3.25e-01 80.0% 99.0%
3hbxA03 3.90.1150.160 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.52 34.0 3.63e-01 70.0% 76.1%
2uvaG03 3.30.70.3320 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 34.0 3.33e-01 77.0% 59.3%
3qwuA03 3.30.70.2160 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 40.0 3.64e-01 84.0% 88.5%
4gf3A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 38.0 3.58e-01 92.0% 63.4%
4rmoA00 3.10.129.130 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › 0.51 43.0 3.82e-01 95.0% 98.1%
3gfhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.51 39.0 3.86e-01 83.0% 75.5%
5o5cB02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 36.0 3.42e-01 87.0% 58.6%
2mouA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.50 41.0 3.28e-01 92.0% 73.2%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3970545 310.3.1.2 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › T2SSM 0.64 47.0 5.21e-01 77.0% 98.7%
3618550 4955.1.1.0 a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.64 45.0 3.47e-01 73.0% 93.3%
3839205 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.64 46.0 4.33e-01 76.0% 62.5%
3246221 4955.1.1.0 a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.64 45.0 3.53e-01 73.0% 91.0%
3290652 306.2.1.0 a+b two layers › Glucose permease domain IIB-like › arginine repressor C terminal domain-related › C-terminal domain of arginine repressor 0.63 47.0 4.94e-01 77.0% 88.9%
3940163 4955.1.1.0 a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.63 44.0 3.42e-01 73.0% 92.4%
1211839 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.63 44.0 4.49e-01 72.0% 85.4%
3549861 4246.1.1.0 a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit 0.63 44.0 3.56e-01 72.0% 89.7%
4015743 4955.1.1.0 a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.62 44.0 3.45e-01 73.0% 91.0%
3777916 4956.1.1.0 a+b two layers › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit 0.62 44.0 3.43e-01 73.0% 91.6%
4992616 304.165.1.0 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 0.61 51.0 4.56e-01 93.0% 82.1%
4980724 304.165.1.4 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 › HVO_2525_N 0.61 51.0 4.60e-01 94.0% 81.4%
5052596 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.61 44.0 4.46e-01 77.0% 86.0%
3317802 304.8.1.45 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › bHLH-TF_ACT-like_plant 0.61 42.0 4.35e-01 72.0% 77.9%
3164985 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.60 43.0 3.72e-01 75.0% 47.5%
3415401 1.1.2.0 beta barrels › cradle loop barrel › RIFT-related › double psi 0.60 42.0 3.63e-01 72.0% 89.4%
4032883 1.1.13.3 beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Phage_H_T_join 0.60 49.0 4.83e-01 86.0% 100.0%
5025510 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.60 51.0 4.64e-01 95.0% 83.6%
3961122 3016.1.1.0 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.60 41.0 3.94e-01 80.0% 60.9%
4001363 220.1.1.1 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.60 49.0 4.48e-01 90.0% 77.8%
3957763 3016.1.1.1 a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_1_2 0.60 41.0 3.70e-01 80.0% 50.7%
4999898 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.59 41.0 4.25e-01 72.0% 82.2%
4185372 1075.1.2.1 alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.58 40.0 2.89e-01 70.0% 36.3%
4963322 304.165.1.2 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 › BAT 0.58 48.0 4.39e-01 93.0% 80.7%
5029357 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.58 43.0 4.12e-01 78.0% 78.3%
5027652 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.57 45.0 4.63e-01 84.0% 92.6%
3602142 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.57 43.0 4.29e-01 80.0% 85.7%
3444368 304.156.1.4 a+b two layers › Alpha-beta plaits › DNA translocase FtsK N-terminal domain › DNA translocase FtsK N-terminal domain › DUF2854 0.57 45.0 4.13e-01 84.0% 97.7%
4260084 1.1.5.25 beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ 0.57 51.0 4.80e-01 98.0% 88.3%
4078130 207.11.1.1 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.57 47.0 3.44e-01 89.0% 56.9%
4451235 207.11.1.1 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.57 46.0 3.42e-01 89.0% 69.1%
4961351 242.1.1.10 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › PF26411 0.56 41.0 4.08e-01 79.0% 91.8%
5065934 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 42.0 4.54e-01 80.0% 97.6%
5026235 304.165.1.5 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 › HVO_A0563_N 0.56 48.0 4.29e-01 96.0% 81.4%
5030027 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 43.0 3.96e-01 82.0% 78.5%
4993129 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 40.0 3.77e-01 76.0% 65.6%
3174832 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.56 47.0 2.87e-01 95.0% 16.8%
4993850 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.55 43.0 4.41e-01 83.0% 89.5%
3602910 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.55 41.0 4.35e-01 92.0% 90.0%
4562874 207.11.1.1 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.55 45.0 3.37e-01 90.0% 67.5%
3593122 304.109.1.0 a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e 0.54 40.0 3.83e-01 79.0% 70.0%
4998391 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.54 43.0 4.52e-01 86.0% 95.6%
4669669 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.53 41.0 3.97e-01 81.0% 76.4%
3603294 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.53 42.0 4.43e-01 86.0% 95.6%
5032322 242.1.1.2 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.53 43.0 4.35e-01 88.0% 88.0%
5027649 242.1.1.7 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.53 40.0 3.85e-01 82.0% 82.5%
4237289 207.11.1.1 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Urease accessory protein ureH › Urease accessory protein ureH › UreD 0.53 43.0 3.23e-01 90.0% 70.8%
3173046 304.162.1.2 a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › FLAD1_M 0.51 35.0 3.65e-01 71.0% 79.8%
D2 high residues 40-123
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s7hA02 3.30.70.930 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.69 45.0 4.56e-01 100.0% 67.1%
1sseB00 1.10.238.100 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › YAP1 redox domain. Chain B 0.63 32.0 3.24e-01 100.0% 45.3%
1ffvB04 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.59 40.0 2.99e-01 100.0% 29.8%
4id8A00 3.30.70.20 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 35.0 3.83e-01 94.0% 78.5%
6liuC02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.56 42.0 3.80e-01 91.7% 58.6%
6nd0A01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 47.0 4.44e-01 98.8% 77.6%
2eyqA07 3.90.1150.50 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription-repair-coupling factor, D7 domain 0.54 35.0 2.87e-01 100.0% 37.4%
2xxlA01 3.30.1640.30 Alpha Beta › 2-Layer Sandwich › mini-chromosome maintenance (MCM) complex, chain A, domain 1 › 0.52 36.0 3.76e-01 86.9% 79.5%
2xfvA00 3.10.260.30 Alpha Beta › Roll › Mlu1-box Binding Protein; DNA-binding Domain › 0.52 43.0 4.01e-01 96.4% 94.4%
3lszA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 35.0 3.14e-01 71.4% 92.0%
6zhhA01 3.40.1110.10 Alpha Beta › 3-Layer(aba) Sandwich › Calcium-transporting ATPase, cytoplasmic domain N › Calcium-transporting ATPase, cytoplasmic domain N 0.51 40.0 3.18e-01 85.7% 100.0%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3846390 2008.1.1.84 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Rab15_effector 0.65 43.0 3.14e-01 100.0% 26.5%
3889554 626.1.1.1 alpha complex topology › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › Formin homology 2 domain (FH2 domain) › FH2 0.59 43.0 2.96e-01 100.0% 21.7%
3981579 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.59 35.0 3.59e-01 94.0% 61.3%
3607656 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.58 44.0 4.25e-01 81.0% 95.8%
3868038 109.4.1.53 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IBN_N,Xpo1,Exportin-5 0.58 40.0 2.27e-01 73.8% 16.2%
3684974 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 0.56 48.0 2.92e-01 100.0% 22.6%
3369128 2004.1.1.615 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21, AAA_23, AAA_29 0.55 50.0 3.01e-01 100.0% 15.3%
5084006 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.54 27.0 2.95e-01 100.0% 53.8%
5040538 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.53 41.0 4.14e-01 84.5% 98.8%
3785380 5051.1.1.6 alpha complex topology › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Sodium:neurotransmitter symporter family (SNF)-like › Aa_trans 0.53 45.0 2.94e-01 97.6% 45.1%
3624832 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.52 39.0 3.65e-01 92.9% 62.7%
3921946 101.1.2.507 alpha arrays › HTH › HTH › winged helix domain › HTH_TANC1 0.52 42.0 3.52e-01 91.7% 84.5%
4436275 632.1.1.32 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › TMEM208_SND2 0.52 39.0 3.54e-01 81.0% 87.0%
3735604 601.19.1.0 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.52 45.0 2.64e-01 98.8% 98.8%
4016908 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.51 40.0 3.44e-01 89.3% 56.0%
4011979 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.51 39.0 3.55e-01 86.9% 60.8%
4641056 885.1.1.1 a+b complex topology › Transcription factor NusA, N-terminal domain › Transcription factor NusA, N-terminal domain › Transcription factor NusA, N-terminal domain › NusA_N 0.50 45.0 3.96e-01 100.0% 82.4%