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js4906-29-5_S40_scaffold_9_prodigal-single.1__X__X__00027

Bact-Vir

js4906-29-5_S40_scaffold_9_prodigal-single.1__X__X__00027

Identity

Kingdom:
phage

Quality

76.5 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 51-117
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08666.18 best SAF 32.1 1.90e-07 97.0% 92.1%
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3frnA02 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.86 76.0 7.58e-01 100.0% 94.1%
1ameA00 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.85 72.0 7.31e-01 100.0% 92.4%
2wqpA02 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.84 72.0 7.03e-01 100.0% 84.9%
1wvoA00 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.83 71.0 6.66e-01 100.0% 77.2%
3g8rA02 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.80 69.0 6.42e-01 100.0% 76.5%
1vliA02 3.90.1210.10 Alpha Beta › Alpha-Beta Complex › Type Iii Antifreeze Protein Isoform Hplc 12 › Antifreeze-like/N-acetylneuraminic acid synthase C-terminal domain 0.78 67.0 6.82e-01 97.0% 95.4%
1hyoA02 3.90.850.10 Alpha Beta › Alpha-Beta Complex › Fumarylacetoacetate hydrolase; domain 2 › Fumarylacetoacetase-like, C-terminal domain 0.64 52.0 3.47e-01 92.5% 51.7%
6jvvB02 3.90.850.10 Alpha Beta › Alpha-Beta Complex › Fumarylacetoacetate hydrolase; domain 2 › Fumarylacetoacetase-like, C-terminal domain 0.61 51.0 3.71e-01 94.0% 56.7%
3pi7A01 3.90.180.10 Alpha Beta › Alpha-Beta Complex › Quinone Oxidoreductase; Chain A, domain 1 › Medium-chain alcohol dehydrogenases, catalytic domain 0.60 52.0 3.80e-01 100.0% 70.9%
1b33N01 3.30.1490.170 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Allophycocyanin linker chain (domain) 0.53 35.0 3.82e-01 100.0% 83.6%
2k5wA00 2.40.50.480 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Protein of unknown function DUF1093 0.50 39.0 3.35e-01 86.6% 74.8%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3962108 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.90 81.0 7.99e-01 100.0% 91.4%
3972515 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.89 75.0 7.95e-01 97.0% 100.0%
3386541 70.3.1.18 beta barrels › beta-clip › SET domain-like › SET domain-like › ChapFlgA 0.89 79.0 8.03e-01 100.0% 96.9%
3983417 70.3.1.0 beta barrels › beta-clip › SET domain-like › SET domain-like 0.89 78.0 7.91e-01 97.0% 95.4%
4046971 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.88 78.0 7.98e-01 100.0% 98.5%
1005319 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.88 76.0 7.76e-01 97.0% 95.4%
1395523 70.3.1.18 beta barrels › beta-clip › SET domain-like › SET domain-like › ChapFlgA 0.88 77.0 7.86e-01 98.5% 96.9%
3970891 70.3.1.18 beta barrels › beta-clip › SET domain-like › SET domain-like › ChapFlgA 0.87 77.0 7.89e-01 100.0% 98.5%
4588640 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.87 77.0 7.61e-01 100.0% 91.4%
3840012 70.3.1.18 beta barrels › beta-clip › SET domain-like › SET domain-like › ChapFlgA 0.87 72.0 7.63e-01 97.0% 100.0%
5032882 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.86 72.0 7.21e-01 100.0% 88.2%
185265 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.86 76.0 7.67e-01 100.0% 97.0%
5028485 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.85 72.0 7.36e-01 100.0% 92.3%
224541 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.85 73.0 7.27e-01 100.0% 89.7%
3587047 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.84 71.0 6.85e-01 100.0% 81.1%
5078504 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.84 71.0 7.22e-01 100.0% 92.3%
3388436 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.84 70.0 6.82e-01 100.0% 82.2%
4159528 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.84 70.0 6.92e-01 100.0% 85.7%
159366 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.83 71.0 6.66e-01 100.0% 77.2%
4409168 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.82 70.0 6.92e-01 98.5% 87.1%
4678813 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.82 68.0 7.20e-01 98.5% 100.0%
3393782 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.82 69.0 7.22e-01 98.5% 100.0%
3387261 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.82 64.0 6.18e-01 94.0% 75.7%
4098701 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.79 70.0 6.82e-01 100.0% 87.7%
5029069 70.3.1.3 beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.79 71.0 6.79e-01 100.0% 86.7%
1005527 70.3.1.0 beta barrels › beta-clip › SET domain-like › SET domain-like 0.73 66.0 5.89e-01 100.0% 72.0%
2526359 70.4.1.2 beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_head_fibr 0.56 41.0 4.29e-01 95.5% 88.3%
2794904 807.1.1.1 a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › CpcD 0.52 34.0 3.52e-01 100.0% 69.7%
5057261 239.1.1.5 beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like › tRNA-synt_1c_C 0.52 31.0 2.93e-01 97.0% 45.9%
D2 high residues 128-237
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r5bA02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.76 50.0 5.48e-01 96.4% 82.0%
4he6A00 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.74 47.0 5.21e-01 87.3% 79.8%
3nziA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.70 37.0 3.77e-01 70.9% 51.9%
1whvA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.70 39.0 4.10e-01 83.6% 60.0%
2wssA01 2.40.30.20 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.70 38.0 4.13e-01 89.1% 62.4%
4rl1A02 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.69 38.0 4.66e-01 83.6% 84.5%
1nh8A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.68 38.0 4.74e-01 83.6% 89.6%
3bv8A00 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.68 32.0 3.59e-01 83.6% 56.5%
2vd3A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 38.0 4.54e-01 83.6% 82.4%
2e29A01 3.30.70.2280 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 40.0 4.68e-01 84.5% 88.2%
2mc2A00 2.80.10.50 Mainly Beta › Trefoil › Trefoil (Acidic Fibroblast Growth Factor, subunit A) › 0.64 46.0 3.72e-01 74.5% 100.0%
3mahA02 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 37.0 4.49e-01 84.5% 91.3%
1wf1A01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.63 36.0 3.98e-01 84.5% 68.9%
3b82A06 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.63 37.0 3.60e-01 84.5% 52.9%
3luyA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.63 40.0 4.44e-01 83.6% 80.9%
2cz4A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 41.0 4.29e-01 83.6% 74.7%
2qmwA03 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 39.0 4.53e-01 83.6% 92.2%
3ce8A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.60 37.0 4.10e-01 83.6% 77.5%
2htdB00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.59 40.0 3.89e-01 82.7% 61.3%
2d9oA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.59 39.0 4.07e-01 84.5% 73.0%
1vq8B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 44.0 4.14e-01 93.6% 64.2%
3wbiA04 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 52.0 4.73e-01 98.2% 85.5%
1jwwA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 34.0 3.93e-01 85.5% 80.0%
1o51A00 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 38.0 4.21e-01 83.6% 83.1%
1u0sA00 3.30.70.1110 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Histidine kinase CheA-like, P2 response regulator-binding domain 0.57 38.0 4.18e-01 85.5% 87.2%
4emeC02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.57 46.0 4.32e-01 88.2% 89.6%
2nyiA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 35.0 3.95e-01 83.6% 84.0%
2rqkA00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.56 37.0 3.76e-01 83.6% 67.9%
1a7gE00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.56 35.0 3.96e-01 83.6% 84.1%
2go8A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 31.0 3.68e-01 79.1% 81.1%
4n77A00 3.30.70.2660 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 48.0 3.99e-01 96.4% 87.7%
2ijzA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.54 43.0 4.39e-01 89.1% 87.9%
4lvnP00 3.30.70.2380 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 34.0 3.89e-01 83.6% 86.4%
2bopA00 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.54 35.0 3.87e-01 83.6% 84.7%
1cqmA00 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.54 39.0 4.12e-01 84.5% 84.7%
1x31C02 3.30.70.1520 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Heterotetrameric sarcosine oxidase 0.53 35.0 4.00e-01 83.6% 91.3%
1djxA03 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.51 35.0 3.35e-01 90.0% 58.8%
1m0wA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.50 32.0 3.28e-01 86.4% 64.8%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3972500 1.1.7.53 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › RcpC 0.79 67.0 6.53e-01 89.1% 89.2%
3954857 1.1.8.0 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.76 60.0 6.32e-01 88.2% 91.8%
3957568 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.73 60.0 6.36e-01 88.2% 97.0%
3496071 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.70 40.0 4.43e-01 83.6% 70.0%
4047241 1.1.7.17 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.69 38.0 4.05e-01 89.1% 61.1%
4854958 1.1.7.17 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.69 38.0 4.07e-01 89.1% 61.5%
4204303 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.68 38.0 4.12e-01 88.2% 64.4%
3973553 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.67 38.0 4.48e-01 88.2% 84.3%
4971582 1.1.7.19 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › GTP_EFTU_D2 0.64 52.0 5.19e-01 100.0% 82.6%
4105022 304.5.1.7 a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.63 37.0 4.11e-01 82.7% 71.1%
4297401 304.110.1.0 a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like 0.63 37.0 4.23e-01 82.7% 80.0%
3962952 304.8.1.1 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Thr_dehydrat_C 0.62 40.0 4.18e-01 83.6% 71.0%
3169767 1.1.7.49 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Ski7_2nd 0.61 55.0 5.08e-01 100.0% 77.1%
3661726 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 41.0 4.30e-01 83.6% 75.0%
4648413 304.4.1.20 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg2 0.60 36.0 3.72e-01 83.6% 63.0%
4964447 304.4.1.20 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg2 0.59 36.0 3.96e-01 83.6% 76.5%
3972053 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.58 34.0 3.76e-01 83.6% 70.0%
1756829 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 46.0 4.35e-01 85.5% 80.3%
3974593 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.58 34.0 3.76e-01 83.6% 74.1%
4674170 4.1.1.17 beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.57 40.0 3.88e-01 82.7% 65.8%
4946218 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.56 37.0 3.78e-01 83.6% 68.6%
4928686 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.56 38.0 4.21e-01 83.6% 85.6%
5062932 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.56 34.0 3.91e-01 83.6% 83.7%
3196006 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 45.0 4.18e-01 90.0% 80.7%
4578112 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.55 33.0 3.57e-01 83.6% 71.1%
3496352 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 45.0 4.43e-01 90.9% 83.3%
2066826 304.107.1.0 a+b two layers › Alpha-beta plaits › Aminomethyltransferase folate-binding domain › Aminomethyltransferase folate-binding domain 0.53 36.0 3.91e-01 83.6% 83.9%
5052337 304.165.1.0 a+b two layers › Alpha-beta plaits › Uncharacterized protein Ta1207 › Uncharacterized protein Ta1207 0.53 41.0 3.83e-01 83.6% 94.3%
3289257 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.52 31.0 3.47e-01 85.5% 75.3%
3391377 11.1.1.37 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › E1_DerP2_DerF2 0.52 39.0 3.68e-01 90.0% 64.3%
4270536 1.1.7.96 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FIST_C 0.52 38.0 3.99e-01 89.1% 86.0%
3672819 302.1.1.0 a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain 0.52 40.0 3.57e-01 87.3% 57.5%
4401417 304.7.1.2 a+b two layers › Alpha-beta plaits › Protease propeptides/inhibitors › Protease propeptides/inhibitors › Inhibitor_I9 0.51 35.0 3.64e-01 84.5% 76.0%
4524153 304.22.1.1 a+b two layers › Alpha-beta plaits › Urease metallochaperone UreE, C-terminal domain › Urease metallochaperone UreE, C-terminal domain › UreE_C 0.51 35.0 3.90e-01 93.6% 92.9%
4400596 4.1.1.17 beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.50 39.0 3.50e-01 83.6% 70.0%
3414240 11.1.1.37 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › E1_DerP2_DerF2 0.50 38.0 3.58e-01 89.1% 65.2%