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RTP_09252017_15_scaffold_29_prodigal-single.1__X__X__00008

Bact-Vir

RTP_09252017_15_scaffold_29_prodigal-single.1__X__X__00008

Identity

Kingdom:
phage

Quality

93.7 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 16-183_287-345
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02739.23 best 5_3_exonuc_N 85.1 6.30e-24 78.4% 95.1%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zdbA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.91 60.0 7.24e-01 74.0% 96.2%
1xo1A02 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.85 59.0 7.11e-01 80.6% 100.0%
1tfrA01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.79 69.0 7.21e-01 96.9% 99.5%
5v07Z01 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.68 50.0 5.26e-01 74.0% 87.4%
1z06A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.65 28.0 3.30e-01 80.6% 54.5%
2rbgA00 3.40.50.11100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 35.0 4.57e-01 70.0% 99.2%
1qfjA02 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.60 35.0 4.52e-01 74.0% 97.0%
3s40A01 3.40.50.10330 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Probable inorganic polyphosphate/atp-NAD kinase; domain 1 0.58 32.0 4.11e-01 74.0% 91.7%
1kjnA00 3.40.50.10160 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › MTH777-like 0.55 34.0 4.06e-01 92.1% 90.8%
3u7qB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 31.0 3.86e-01 83.7% 89.0%
2lciA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 27.0 3.53e-01 70.9% 85.8%
2yeqA02 3.60.21.70 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Alkaline phosphatase D (PhoD) 0.52 38.0 3.15e-01 74.0% 91.8%
3abiA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 33.0 3.73e-01 74.0% 83.7%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3387660 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.91 64.0 7.44e-01 74.0% 95.3%
3261281 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.90 63.0 7.41e-01 74.0% 96.4%
3969358 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.90 62.0 7.44e-01 73.1% 99.4%
3283240 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.89 65.0 7.06e-01 74.0% 92.8%
4031817 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.89 64.0 7.45e-01 74.0% 97.1%
4995752 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.89 63.0 7.47e-01 74.0% 99.4%
4040391 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.89 65.0 7.31e-01 74.0% 97.8%
4324598 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 67.0 7.47e-01 100.0% 94.6%
4238071 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 64.0 7.36e-01 73.6% 97.7%
4031881 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.88 64.0 7.34e-01 74.0% 96.6%
4125023 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 63.0 7.27e-01 74.0% 97.1%
4157264 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 64.0 7.19e-01 74.0% 96.1%
3942272 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 64.0 7.41e-01 74.0% 99.4%
4029535 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.87 64.0 7.17e-01 74.0% 97.8%
3838776 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 60.0 7.06e-01 74.0% 97.0%
3964138 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 67.0 7.54e-01 81.1% 100.0%
4299585 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 68.0 7.60e-01 99.6% 99.5%
3831671 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.86 62.0 6.78e-01 74.0% 97.4%
4165496 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.85 67.0 7.49e-01 99.1% 99.5%
4355422 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.84 64.0 7.25e-01 99.1% 99.4%
4322588 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.84 65.0 7.36e-01 80.2% 100.0%
3942445 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.82 65.0 7.23e-01 99.1% 98.9%
3329169 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.79 56.0 6.42e-01 74.0% 94.3%
4136793 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.77 67.0 6.98e-01 95.6% 96.7%
3838580 2006.1.4.4 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › 5_3_exonuc_N 0.75 56.0 6.27e-01 75.8% 96.1%
3683988 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.73 53.0 5.51e-01 74.0% 87.4%
5041646 2006.1.4.13 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN_9 0.71 42.0 5.37e-01 73.1% 98.5%
4947341 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.61 39.0 4.80e-01 70.0% 100.0%
3744314 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.60 54.0 5.03e-01 94.7% 91.6%
3281327 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.59 38.0 4.51e-01 70.0% 94.2%
3581443 2006.1.4.1 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_N,XPG_I 0.57 54.0 4.87e-01 100.0% 92.5%
3330038 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.57 38.0 4.25e-01 72.7% 86.3%
5071580 2006.1.4.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.56 37.0 4.27e-01 70.0% 88.8%
4988582 2005.1.1.3 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › Usp 0.56 38.0 4.45e-01 70.5% 97.5%
3645022 2005.1.1.43 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd 0.55 38.0 4.42e-01 70.0% 97.0%
4977784 2484.1.1.302 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.54 39.0 3.94e-01 74.0% 97.0%
3581523 2003.1.5.4 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › PCMT 0.53 36.0 4.01e-01 74.0% 87.4%
3775314 2006.1.1.40 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › LNS2_PITM1-3 0.53 38.0 4.31e-01 100.0% 96.5%
3927366 2484.1.1.4 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.52 30.0 3.60e-01 99.1% 82.7%
3829770 2005.1.1.43 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › CHX17_2nd 0.52 36.0 4.09e-01 70.0% 93.7%
5036375 2007.6.1.5 a/b three-layered sandwiches › Flavodoxin-like › Ribosomal protein S2/SIS domain › Ribosomal protein S2/SIS domain › bact-PGI_C 0.52 31.0 3.62e-01 74.0% 82.5%
3916205 2003.1.2.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.52 38.0 3.68e-01 74.0% 84.8%
3736225 2484.1.1.4 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.51 28.0 3.40e-01 100.0% 80.7%
4309543 2484.1.1.4 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_H 0.51 27.0 3.33e-01 97.8% 80.0%
D2 high residues 184-281
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hmlA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.79 61.0 6.67e-01 100.0% 98.8%
4q4hA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.61 35.0 2.42e-01 92.9% 17.0%
3h7iA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.61 45.0 4.97e-01 95.9% 98.7%
3crvA02 1.10.275.30 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.58 41.0 3.96e-01 71.4% 88.9%
3u5nA02 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.57 46.0 4.31e-01 87.8% 96.7%
2jqqA00 1.20.58.1240 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 39.0 3.38e-01 73.5% 64.3%
1gnlA01 1.20.1270.20 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.54 43.0 3.82e-01 84.7% 83.5%
4gmqA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.54 40.0 4.10e-01 77.6% 92.4%
2x8xX02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.53 35.0 3.78e-01 92.9% 85.5%
2yqdA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.53 44.0 4.14e-01 90.8% 87.5%
3ckyA02 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 0.53 43.0 3.89e-01 87.8% 85.1%
3ccgA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.53 46.0 3.66e-01 93.9% 97.9%
3w6zA02 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 0.52 42.0 3.94e-01 85.7% 85.1%
1rx0A03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.52 39.0 3.43e-01 81.6% 90.3%
5kbwB00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.52 38.0 3.30e-01 81.6% 97.7%
4dllB02 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 0.51 42.0 3.85e-01 87.8% 81.5%
2jifA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.51 38.0 3.37e-01 80.6% 89.6%
2uyyA02 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 0.51 41.0 3.84e-01 86.7% 85.4%
1vpdA02 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 0.51 41.0 3.76e-01 87.8% 85.5%
6wimA02 3.10.20.310 Alpha Beta › Roll › Ubiquitin-like (UB roll) › membrane protein fhac 0.51 33.0 3.63e-01 92.9% 87.8%
2ctqA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.50 33.0 3.41e-01 71.4% 69.1%
3g0oA02 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 0.50 41.0 3.82e-01 86.7% 86.0%
3nrwA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.50 40.0 4.00e-01 91.8% 84.6%
5xfaA04 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.50 39.0 4.11e-01 82.7% 100.0%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4020083 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.62 46.0 4.09e-01 78.6% 86.4%
4997392 3930.1.1.3 alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase › RNA_helicase_helical 0.57 42.0 3.81e-01 81.6% 55.0%
3940107 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.57 50.0 4.22e-01 100.0% 58.8%
3676592 109.4.1.728 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 43.0 3.13e-01 87.8% 28.9%
3904284 601.1.3.15 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › A middle domain of Talin 1 › MNR 0.54 44.0 3.59e-01 86.7% 88.0%
3371228 109.4.1.1258 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2 0.53 36.0 2.37e-01 85.7% 15.0%
3735701 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.53 44.0 3.92e-01 87.8% 85.1%
4989807 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.53 43.0 3.98e-01 87.8% 85.6%
4033956 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.52 44.0 3.54e-01 90.8% 96.8%
4107395 3121.1.1.0 a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain 0.52 35.0 3.80e-01 92.9% 88.0%
4312076 3121.1.1.3 a+b duplicates or obligate multimers › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › Polypeptide transport-associated (POTRA) domain › POTRA_2 0.52 34.0 3.70e-01 92.9% 86.7%
3284057 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.51 42.0 3.81e-01 87.8% 87.7%
3681230 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.51 42.0 3.78e-01 87.8% 88.1%
3200818 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.51 44.0 3.96e-01 91.8% 89.2%
4988961 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.51 42.0 3.90e-01 87.8% 85.5%
3409854 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.51 42.0 3.80e-01 86.7% 80.0%
3164340 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.51 42.0 3.85e-01 87.8% 86.4%
3716300 102.1.1.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.51 43.0 3.62e-01 99.0% 54.3%
3972609 129.1.1.16 alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_11 0.50 41.0 3.87e-01 86.7% 89.0%