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NC_021798.1__YP_008241619.1__Phi17-2_gp124__00124

Bact-Vir

NC_021798.1__YP_008241619.1__Phi17-2_gp124__00124

Identity

Accession:
NC_021798 ↗
Kingdom:
phage

Quality

87.8 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 10-69
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.76 52.0 4.96e-01 71.7% 70.4%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 52.0 5.15e-01 71.7% 85.5%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.75 51.0 5.59e-01 71.7% 95.8%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.75 50.0 4.77e-01 70.0% 64.8%
3ieeA02 1.20.58.820 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Uncharacterised protein PF12889, C-terminal DUF3829 0.73 64.0 5.39e-01 100.0% 85.4%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.73 50.0 5.17e-01 71.7% 76.8%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.72 44.0 5.07e-01 71.7% 94.7%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.72 51.0 4.49e-01 75.0% 74.4%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 49.0 5.04e-01 73.3% 75.9%
2db7A01 6.10.250.980 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 48.0 5.04e-01 70.0% 79.2%
3fxdC00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.71 49.0 5.21e-01 88.3% 86.0%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.70 51.0 3.89e-01 78.3% 40.0%
3nkzA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.70 48.0 4.11e-01 71.7% 45.4%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 48.0 4.70e-01 73.3% 71.9%
1hciA03 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 59.0 4.78e-01 100.0% 75.8%
1aueB00 1.20.120.150 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain 0.66 55.0 4.86e-01 98.3% 90.4%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.66 57.0 5.34e-01 100.0% 82.7%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.65 56.0 5.20e-01 100.0% 89.7%
1wrdA00 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 54.0 4.73e-01 100.0% 83.7%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.63 51.0 4.59e-01 100.0% 64.7%
1m4rB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 45.0 3.48e-01 76.7% 35.5%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.63 47.0 3.68e-01 85.0% 43.1%
4jvyB00 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.62 53.0 3.78e-01 98.3% 94.2%
5cegD00 3.30.2310.20 Alpha Beta › 2-Layer Sandwich › YaeB-like fold › RelE-like 0.61 45.0 3.83e-01 80.0% 75.2%
4nv0A02 1.10.150.340 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Pyrimidine 5'-nucleotidase (UMPH-1), N-terminal domain 0.61 48.0 4.37e-01 88.3% 65.9%
2ycdA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 51.0 4.23e-01 100.0% 65.0%
1xeqB00 1.10.287.10 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › S15/NS1, RNA-binding 0.60 51.0 4.62e-01 100.0% 76.5%
1bt3A00 1.10.1280.10 Mainly Alpha › Orthogonal Bundle › di-copper center containing domain from catechol oxidase › Di-copper center containing domain from catechol oxidase 0.53 43.0 2.71e-01 90.0% 19.6%
3dkqA02 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.53 38.0 3.99e-01 88.3% 100.0%
3zukA02 1.10.1380.10 Mainly Alpha › Orthogonal Bundle › Neutral endopeptidase; domain 2 › Neutral endopeptidase , domain2 0.52 46.0 2.84e-01 100.0% 30.4%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4373408 3757.1.1.0 extended segments › AF1503 pre-HAMP domain › AF1503 pre-HAMP domain › AF1503 pre-HAMP domain 0.80 47.0 5.36e-01 71.7% 80.0%
3265419 1128.1.1.0 alpha bundles › LYR protein › LYR protein › LYR protein 0.75 51.0 4.66e-01 71.7% 57.5%
3597591 1128.1.1.0 alpha bundles › LYR protein › LYR protein › LYR protein 0.74 51.0 4.89e-01 71.7% 61.4%
3484950 605.8.1.0 alpha duplicates or obligate multimers › ROP-like › BAS1536-like › BAS1536-like 0.74 50.0 5.59e-01 70.0% 100.0%
3989722 632.24.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › GBS CAMP factor C-terminal domain › GBS CAMP factor C-terminal domain 0.69 47.0 4.59e-01 70.0% 67.7%
3486248 6132.1.1.0 alpha bundles › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain › Nudix hydrolase N-terminal dimerization domain 0.68 57.0 5.62e-01 100.0% 86.2%
3227178 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 51.0 3.71e-01 100.0% 28.0%
3172138 3846.1.1.0 alpha bundles › IcmR › IcmR › IcmR 0.68 51.0 4.98e-01 81.7% 81.5%
5082509 101.1.2.31 alpha arrays › HTH › HTH › winged helix domain › TFIIE_alpha 0.67 56.0 4.28e-01 90.0% 41.5%
4187493 603.1.1.103 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF29732 0.67 56.0 4.38e-01 100.0% 52.4%
3258948 616.1.1.1 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.66 58.0 5.53e-01 100.0% 91.4%
3479913 616.1.1.0 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.66 57.0 5.51e-01 100.0% 91.4%
4501336 3390.1.1.0 extended segments › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT › Photosystem II reaction center protein T, PsbT 0.66 45.0 4.85e-01 71.7% 91.7%
3238747 5081.1.1.1 alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.65 53.0 3.79e-01 90.0% 32.2%
4932775 616.1.1.1 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.65 55.0 5.45e-01 98.3% 92.3%
3189035 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.63 43.0 4.11e-01 73.3% 62.7%
5044377 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 0.62 54.0 3.61e-01 100.0% 66.9%
5049807 4009.1.1.0 alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.61 41.0 4.07e-01 75.0% 66.2%
4019167 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 52.0 3.65e-01 100.0% 33.7%
3254822 616.1.1.0 alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.59 51.0 4.61e-01 100.0% 82.4%
5022532 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.58 43.0 4.03e-01 95.0% 64.0%
3704554 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.58 43.0 3.79e-01 78.3% 58.0%
4150540 101.11.1.1 alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › PNPase 0.58 51.0 4.57e-01 100.0% 71.8%
5040510 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 0.57 47.0 3.16e-01 93.3% 61.2%
5004670 2498.1.1.0 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.55 44.0 3.01e-01 96.7% 25.1%
D2 high residues 78-158
PDB
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5dx9A01 3.30.70.1020 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trehalose-6-phosphate phosphatase related protein; domain 2 0.73 50.0 5.25e-01 70.4% 91.7%
2dvkA00 3.30.1960.10 Alpha Beta › 2-Layer Sandwich › SSo0622-like fold › tRNA wybutosine-synthesizing-like 0.65 44.0 3.53e-01 71.6% 63.9%
1weyA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.61 40.0 3.69e-01 80.2% 52.9%
5xyiY00 3.30.70.3370 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 42.0 3.89e-01 79.0% 77.1%
3p96A02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.55 37.0 3.65e-01 80.2% 66.7%
3njfA00 2.60.40.420 Mainly Beta › Sandwich › Immunoglobulin-like › Cupredoxins - blue copper proteins 0.53 36.0 3.26e-01 70.4% 71.4%
3gr5A02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.53 37.0 3.92e-01 88.9% 86.8%
1j6wA00 3.30.1360.80 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › S-ribosylhomocysteinase (LuxS) 0.52 42.0 3.42e-01 90.1% 89.4%
4mt1A03 3.30.70.1320 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain like 0.51 41.0 3.85e-01 86.4% 95.9%
1x4dA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.51 35.0 3.32e-01 88.9% 56.9%
4lvnP00 3.30.70.2380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 38.0 3.88e-01 81.5% 97.5%
2cpqA01 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.51 37.0 4.01e-01 88.9% 98.4%
1mwyA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.51 36.0 3.83e-01 76.5% 97.3%
2cg4A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.50 38.0 3.82e-01 81.5% 85.7%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2652201 2006.1.1.3 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › Trehalose_PPase 0.69 51.0 3.65e-01 80.2% 34.6%
3189865 310.2.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF › RRF 0.67 46.0 3.41e-01 72.8% 29.2%
3333353 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.61 35.0 3.65e-01 82.7% 60.0%
3800450 2003.1.5.13 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Spermine_synth 0.61 45.0 2.97e-01 80.2% 28.1%
5057050 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 46.0 4.03e-01 84.0% 92.8%
3826053 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.59 40.0 3.95e-01 70.4% 95.6%
4116365 880.1.1.1 a+b duplicates or obligate multimers › ADC synthase › ADC synthase › ADC synthase › Chorismate_bind 0.58 53.0 3.19e-01 100.0% 33.7%
4266108 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.58 39.0 3.72e-01 82.7% 58.9%
3280548 306.6.1.0 a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.58 44.0 4.43e-01 98.8% 82.5%
4640123 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.55 40.0 3.68e-01 82.7% 59.0%
3224075 304.9.1.1 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.55 42.0 3.02e-01 91.4% 27.3%
3806470 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.54 37.0 4.12e-01 88.9% 95.0%
3218849 390.1.1.1 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like › PAN_1 0.52 36.0 3.49e-01 72.8% 68.4%
3927505 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.52 41.0 4.12e-01 85.2% 98.8%
3599082 5104.1.1.0 a+b three layers › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases › C-terminal domain in DHH phosphoesterases 0.52 41.0 3.55e-01 92.6% 95.9%
4563109 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.52 37.0 3.63e-01 76.5% 96.7%
3309238 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.51 37.0 3.74e-01 79.0% 94.1%
3496351 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 41.0 3.68e-01 90.1% 62.6%
3265361 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.51 39.0 3.90e-01 84.0% 94.1%
4881297 304.8.1.1 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Thr_dehydrat_C 0.51 39.0 3.88e-01 93.8% 78.4%
4958990 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.51 36.0 3.97e-01 88.9% 95.4%
3284390 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 38.0 3.58e-01 82.7% 78.1%
3971965 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.50 36.0 3.86e-01 76.5% 98.6%
4991338 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.50 36.0 3.78e-01 77.8% 93.3%
4932737 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 0.50 35.0 3.78e-01 87.7% 90.8%
5013605 304.165.1.0 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 0.50 43.0 3.66e-01 100.0% 64.8%
4498088 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.50 42.0 4.19e-01 93.8% 91.8%
3963332 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.50 36.0 3.87e-01 88.9% 93.8%