←Back to structures

S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00404

Bact-Vir

S2_005_003_R2_scaffold_7_prodigal-single.1__X__X__00404

Identity

Kingdom:
phage

Quality

71.4 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 1-85
PDB
Domain cluster: representative
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2cpeA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.62 40.0 4.09e-01 97.6% 67.1%
2pmzK00 3.90.940.10 Alpha Beta › Alpha-Beta Complex › Eukaryotic RPB6 RNA polymerase subunit › RNA polymerase subunit, RPB6/omega 0.61 31.0 3.23e-01 100.0% 51.2%
1ru8A02 3.90.1490.10 Alpha Beta › Alpha-Beta Complex › putative n-type atp pyrophosphatase, domain 2 › putative n-type atp pyrophosphatase, domain 2 0.60 29.0 2.85e-01 74.1% 40.7%
4qu7A00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.57 32.0 3.29e-01 98.8% 55.6%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 38.0 3.64e-01 91.8% 61.9%
3cynB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 36.0 2.88e-01 98.8% 34.1%
1rkuA02 3.90.1470.10 Alpha Beta › Alpha-Beta Complex › thrh gene product, domain 2 › thrh gene product, domain 2 0.53 42.0 4.07e-01 100.0% 76.8%
2oo4A02 3.30.70.3310 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 35.0 3.26e-01 94.1% 53.2%
1p8jA01 3.40.50.200 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Peptidase S8/S53 domain 0.51 39.0 2.71e-01 83.5% 96.6%
4qu6A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 30.0 3.03e-01 98.8% 53.3%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3250907 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.58 35.0 3.41e-01 98.8% 52.6%
3172634 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.58 39.0 3.31e-01 100.0% 40.7%
3727976 320.1.1.0 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain 0.53 31.0 3.45e-01 100.0% 73.8%
D2 high residues 118-189
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05157.21 best MshEN 49.7 4.30e-13 100.0% 74.4%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2d27A02 3.30.300.160 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Type II secretion system, protein E, N-terminal domain 0.89 83.0 7.79e-01 98.6% 84.7%
2bh1X00 3.30.300.160 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Type II secretion system, protein E, N-terminal domain 0.77 66.0 6.84e-01 97.2% 100.0%
2xr1A02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.74 55.0 5.58e-01 79.2% 91.5%
1floA01 3.30.300.80 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › FLP Recombinase, lambda integrase-like, N-terminal domain (domain 1) 0.71 53.0 4.70e-01 80.6% 74.3%
6he0A01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.67 57.0 5.07e-01 97.2% 81.3%
4alzA01 3.30.1340.30 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › 0.65 48.0 5.09e-01 80.6% 98.4%
3dnsA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.64 47.0 3.87e-01 77.8% 76.3%
6juyC01 3.75.10.10 Alpha Beta › 5-stranded Propeller › L-arginine/glycine Amidinotransferase; Chain A › L-arginine/glycine Amidinotransferase; Chain A 0.61 54.0 3.71e-01 100.0% 98.9%
3dfuA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 43.0 3.60e-01 77.8% 89.1%
2vq3A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 46.0 3.48e-01 86.1% 90.6%
3dnpA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.59 44.0 3.81e-01 80.6% 94.7%
4om8A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 42.0 3.26e-01 80.6% 91.9%
4hujA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 46.0 3.41e-01 91.7% 85.8%
5bseA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 44.0 3.42e-01 87.5% 90.2%
3triA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 42.0 3.31e-01 86.1% 90.5%
1evyA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 45.0 3.39e-01 95.8% 91.9%
3mdqA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 40.0 3.43e-01 80.6% 77.2%
3fd3A02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.54 41.0 3.82e-01 87.5% 90.1%
2gerA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 41.0 3.27e-01 87.5% 93.0%
3k96A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 43.0 3.32e-01 97.2% 94.1%
6tm3A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 44.0 3.57e-01 100.0% 92.7%
2q5cA02 3.40.50.10660 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › PrpR receptor domain-like 0.51 41.0 3.80e-01 87.5% 100.0%
1vhnA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 39.0 2.83e-01 87.5% 56.4%
ECOD (60)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4041929 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.97 91.0 8.49e-01 100.0% 82.4%
4368029 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.96 87.0 8.39e-01 95.8% 86.3%
3971171 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.94 85.0 8.20e-01 98.6% 86.3%
2771393 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.91 83.0 7.63e-01 100.0% 78.7%
2390328 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.90 84.0 7.83e-01 98.6% 86.0%
1891393 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.90 83.0 7.78e-01 100.0% 83.3%
3971810 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.90 82.0 7.85e-01 100.0% 87.5%
1891419 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.89 81.0 7.73e-01 98.6% 85.4%
3165603 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.84 78.0 7.31e-01 100.0% 84.7%
4010786 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.83 73.0 7.10e-01 100.0% 87.5%
3963826 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.82 74.0 7.15e-01 100.0% 88.7%
3969775 327.8.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › GSPE_N1E 0.79 66.0 6.92e-01 95.8% 100.0%
4560829 327.8.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › GSPE_N1E 0.78 69.0 6.81e-01 100.0% 93.3%
5903 327.8.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › GSPE_N1E 0.77 66.0 6.84e-01 97.2% 100.0%
3968611 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.75 67.0 6.21e-01 100.0% 82.2%
3979017 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.71 58.0 5.75e-01 90.3% 93.3%
3838454 327.10.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related 0.70 51.0 4.94e-01 77.8% 100.0%
5012868 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.69 57.0 4.87e-01 91.7% 86.7%
4008987 327.8.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like › MshEN 0.69 59.0 5.98e-01 98.6% 98.6%
4956343 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.68 48.0 5.37e-01 75.0% 96.4%
4994354 327.6.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Fe-S cluster assembly (FSCA) domain-like › Fe-S cluster assembly (FSCA) domain-like 0.67 51.0 4.85e-01 83.3% 90.6%
4007515 327.8.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GSPII protein E N-terminal domain-like › GSPII protein E N-terminal domain-like 0.66 51.0 5.30e-01 93.1% 95.4%
5029313 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.66 56.0 5.05e-01 95.8% 99.0%
5031013 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.64 52.0 4.55e-01 93.1% 85.2%
4976070 327.7.1.17 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › EFG_C 0.63 48.0 5.07e-01 81.9% 100.0%
4967162 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.63 52.0 4.77e-01 94.4% 100.0%
5007070 327.5.1.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C_2 0.63 53.0 5.15e-01 98.6% 95.2%
4960117 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.62 51.0 4.75e-01 88.9% 98.9%
4937865 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.62 51.0 4.58e-01 93.1% 96.2%
4955408 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.61 50.0 4.25e-01 90.3% 72.5%
5031901 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.61 51.0 4.29e-01 95.8% 75.4%
4993097 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.61 51.0 4.54e-01 97.2% 94.5%
5081837 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.61 46.0 4.14e-01 81.9% 80.6%
4081891 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.61 46.0 3.48e-01 83.3% 94.1%
5039191 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.61 49.0 4.35e-01 91.7% 100.0%
4938037 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.61 49.0 4.43e-01 93.1% 97.1%
3164036 7523.1.1.30 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_11 0.60 41.0 3.43e-01 70.8% 70.4%
4993307 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.60 49.0 4.42e-01 95.8% 97.2%
3281079 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.60 48.0 3.42e-01 87.5% 78.7%
5076343 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.60 49.0 4.05e-01 91.7% 78.5%
4411713 327.1.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › Pro_Al_protease 0.60 49.0 4.95e-01 94.4% 92.9%
4993544 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.60 49.0 4.44e-01 95.8% 94.3%
3282897 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.60 48.0 3.51e-01 91.7% 83.1%
5080097 316.2.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Rv2827c C-terminal domain-like › Rv2827c C-terminal domain-like 0.59 49.0 3.90e-01 97.2% 45.6%
5054232 316.1.1.2 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › NTP_transf_2 0.58 48.0 4.39e-01 94.4% 97.0%
5013484 2003.1.1.27 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › PDH_N 0.58 46.0 3.56e-01 86.1% 88.5%
3365085 2003.1.1.36 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 3HCDH_N 0.58 43.0 3.52e-01 81.9% 90.0%
3686708 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.58 45.0 3.48e-01 87.5% 89.4%
4400635 327.1.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › Pro_Al_protease 0.58 43.0 4.44e-01 80.6% 93.8%
3728402 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.57 42.0 3.54e-01 81.9% 77.0%
3984450 327.13.1.3 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system › PrgH 0.57 38.0 4.18e-01 70.8% 100.0%
154421 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.57 46.0 3.44e-01 91.7% 88.4%
3739067 2003.1.1.42 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › NAD_binding_2 0.57 44.0 3.25e-01 87.5% 76.2%
4934717 316.1.1.27 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › Polbeta 0.56 44.0 3.85e-01 90.3% 82.5%
5081764 300.1.1.7 ↗ a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease › PP_kinase_C 0.56 39.0 3.11e-01 83.3% 33.1%
3281138 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.56 46.0 3.19e-01 94.4% 82.6%
4937601 2003.1.1.27 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › PDH_N 0.54 42.0 3.17e-01 87.5% 73.7%
4609005 2003.1.1.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › F420_oxidored 0.54 43.0 3.41e-01 91.7% 94.1%
2455583 327.5.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C 0.54 44.0 4.25e-01 97.2% 83.0%
4009715 7523.1.1.3 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › SBP_bac_5 0.50 43.0 3.15e-01 100.0% 90.9%
D3 medium residues 207-223_240-285
PDB