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IMGVR_UViG_3300029581_000043-3300029581-Ga0244848_100114616

Arc-Vir

IMGVR_UViG_3300029581_000043-3300029581-Ga0244848_100114616

Quality

94.3 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 5-189
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 42.8 4.70e-11 64.9% 18.4%
CATH (8)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2py5A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.94 87.0 8.81e-01 100.0% 96.2%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.63 43.0 4.99e-01 98.9% 98.4%
4okeA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 51.0 5.48e-01 100.0% 99.4%
2bcqA03 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.55 35.0 4.18e-01 100.0% 95.1%
3mweB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 28.0 3.27e-01 99.5% 68.8%
4fxdA05 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.53 21.0 2.65e-01 92.4% 56.4%
2lc4A00 2.30.30.830 Mainly Beta › Roll › SH3 type barrels. › 0.52 25.0 3.18e-01 78.9% 75.7%
3m4uB00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.50 42.0 3.69e-01 90.8% 66.1%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
11150 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.94 87.0 8.83e-01 100.0% 96.7%
3506686 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.92 90.0 8.36e-01 100.0% 86.4%
4147965 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.83 80.0 7.04e-01 100.0% 82.8%
4261005 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.81 78.0 6.75e-01 100.0% 83.0%
5081301 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.79 71.0 5.42e-01 99.5% 44.6%
4486407 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.79 74.0 7.32e-01 100.0% 92.8%
3176263 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.66 53.0 5.15e-01 100.0% 75.1%
3172729 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.65 53.0 5.15e-01 100.0% 76.1%
3916593 2484.1.1.13 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RNase_T 0.65 54.0 5.03e-01 100.0% 71.8%
3951613 2484.1.1.73 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Rv2179c-like 0.61 51.0 5.41e-01 100.0% 97.0%
3950901 2484.1.1.73 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Rv2179c-like 0.60 51.0 5.30e-01 100.0% 95.9%
3962916 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 47.0 5.08e-01 98.9% 100.0%
3515806 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 37.0 4.27e-01 100.0% 85.9%
4939185 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 23.0 2.84e-01 70.8% 60.0%
4993093 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.52 42.0 3.50e-01 100.0% 48.5%
5065203 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.50 41.0 3.64e-01 100.0% 60.6%
D2 medium residues 190-246_394-441
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 30.6 2.40e-07 48.6% 9.4%
D3 medium residues 247-286_472-535
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 34.4 1.70e-08 77.9% 8.3%
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2py5A02 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.94 91.0 7.30e-01 100.0% 81.0%
1q8iA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.81 76.0 5.90e-01 100.0% 75.6%
2gv9B04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.79 70.0 5.52e-01 93.3% 99.5%
1s5jA03 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.76 69.0 5.92e-01 96.2% 98.7%
4fxdA05 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.70 60.0 5.80e-01 92.3% 95.7%
3pjxA01 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.61 51.0 4.26e-01 91.3% 77.9%
7vxrA01 3.40.800.10 Alpha Beta › 3-Layer(aba) Sandwich › Arginase; Chain A › Ureohydrolase domain 0.58 40.0 4.12e-01 70.2% 87.8%
1zpwX00 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 40.0 4.47e-01 80.8% 91.5%
1f08B00 3.40.1310.10 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.51 39.0 3.47e-01 80.8% 63.4%
6mfaA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 28.0 3.10e-01 74.0% 68.4%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3506687 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.95 92.0 5.80e-01 100.0% 71.2%
3582653 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.91 88.0 6.94e-01 100.0% 65.3%
4243736 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.91 88.0 7.28e-01 100.0% 74.5%
4629102 2484.1.1.36 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_2 0.89 85.0 5.32e-01 100.0% 28.0%
3383559 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.88 72.0 6.53e-01 83.7% 85.4%
3680878 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.88 84.0 5.72e-01 100.0% 78.1%
4365778 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.88 84.0 5.92e-01 100.0% 75.0%
4264107 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.87 83.0 5.75e-01 100.0% 72.7%
4321860 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.84 79.0 6.32e-01 100.0% 64.2%
3349591 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.84 77.0 5.41e-01 97.1% 80.0%
3466667 2484.1.1.161 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.83 77.0 4.61e-01 98.1% 34.6%
4956224 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.83 79.0 5.85e-01 100.0% 93.6%
4982660 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.83 78.0 5.98e-01 100.0% 94.0%
4942685 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.82 77.0 4.81e-01 99.0% 46.4%
3968795 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.82 78.0 5.55e-01 100.0% 88.9%
5017083 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.82 76.0 5.44e-01 98.1% 87.0%
3993981 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.82 76.0 5.72e-01 98.1% 100.0%
3484036 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 0.82 75.0 5.38e-01 98.1% 100.0%
3597965 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 0.81 76.0 5.61e-01 99.0% 100.0%
5019480 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 77.0 4.51e-01 100.0% 37.0%
3784383 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 76.0 5.02e-01 99.0% 71.6%
4276636 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 77.0 5.21e-01 100.0% 78.2%
5025209 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 76.0 5.69e-01 100.0% 97.0%
3801150 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 76.0 5.33e-01 100.0% 83.4%
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 0.81 75.0 4.49e-01 99.0% 39.7%
4981193 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 0.81 77.0 5.56e-01 100.0% 87.8%
5005286 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 75.0 5.19e-01 98.1% 89.5%
3705562 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 0.81 76.0 4.52e-01 100.0% 42.1%
3615419 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.81 76.0 5.16e-01 100.0% 87.9%
None 0.81 74.0 4.45e-01 98.1% 38.7%
4958554 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.80 76.0 5.67e-01 100.0% 98.3%
4601946 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 0.80 75.0 5.34e-01 100.0% 79.6%
3480546 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 0.80 75.0 5.43e-01 100.0% 99.2%
4029141 304.48.1.3 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.80 75.0 5.44e-01 100.0% 93.8%
None 0.80 75.0 4.50e-01 100.0% 39.7%
4022366 2484.1.1.161 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.80 74.0 4.44e-01 99.0% 39.4%
4282509 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.79 74.0 4.51e-01 100.0% 32.4%
4972474 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.76 71.0 4.21e-01 100.0% 35.1%
4100823 4970.1.1.1 alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.72 67.0 4.93e-01 100.0% 85.6%
3185294 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.60 45.0 4.10e-01 78.8% 97.9%
4826592 2498.2.1.0 mixed a+b and a/b › Zincin-like › beta-N-acetylhexosaminidase-like domain › beta-N-acetylhexosaminidase-like domain 0.58 40.0 4.09e-01 70.2% 86.0%
2798012 304.56.1.2 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.56 42.0 4.36e-01 80.8% 85.3%
3954020 304.56.1.2 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.56 39.0 4.15e-01 80.8% 81.7%
3729695 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.53 44.0 4.24e-01 90.4% 97.5%
2723051 304.56.1.2 a+b two layers › Alpha-beta plaits › CRISPR associated protein Cas2-like › CRISPR associated protein Cas2-like › CRISPR_Cas2 0.51 38.0 4.00e-01 80.8% 86.5%
D4 medium residues 287-393_442-471
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03175.19 best DNA_pol_B_2 32.9 4.70e-08 81.8% 23.1%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2py5A03 3.30.1770.10 Alpha Beta › 2-Layer Sandwich › TPR 1 domain of DNA polymerase › TPR 1 domain of DNA polymerase 0.96 62.0 7.72e-01 70.1% 98.9%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3506687 304.48.1.17 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B_2 0.93 91.0 6.07e-01 100.0% 42.3%
3489385 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.57 36.0 3.78e-01 88.3% 68.8%
3321071 101.1.2.115 alpha arrays › HTH › HTH › winged helix domain › CDC27 0.55 36.0 3.66e-01 89.1% 65.7%
4024947 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.55 36.0 3.96e-01 88.3% 80.0%
3949369 10.32.1.0 beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.55 39.0 3.58e-01 74.5% 96.8%
3894181 101.1.2.115 alpha arrays › HTH › HTH › winged helix domain › CDC27 0.52 36.0 3.34e-01 89.8% 56.0%
3740598 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.51 37.0 3.58e-01 88.3% 66.5%
3378796 207.1.1.1 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_1 0.51 35.0 2.38e-01 70.8% 29.9%