Back to structures

PH2015_10_scaffold_0_prodigal-single.1__X__X__00053

Bact-Vir

PH2015_10_scaffold_0_prodigal-single.1__X__X__00053

Identity

Kingdom:
phage

Quality

62.4 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 12-156
PDB
CATH (51)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3tfiA00 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.73 39.0 2.88e-01 100.0% 20.6%
1wosA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.70 37.0 4.67e-01 100.0% 86.0%
4paaA05 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.69 37.0 4.79e-01 99.3% 93.7%
1pj5A05 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.69 36.0 4.77e-01 99.3% 93.6%
1x31A02 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.68 40.0 2.89e-01 100.0% 21.2%
1v5vA03 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.68 36.0 4.77e-01 99.3% 97.3%
3girA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.66 35.0 4.59e-01 99.3% 94.9%
3b82A06 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 32.0 3.52e-01 100.0% 57.0%
2dgxA01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.62 35.0 4.47e-01 100.0% 97.5%
4pcqA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.62 33.0 4.20e-01 100.0% 89.3%
2djwA01 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.62 32.0 4.32e-01 100.0% 98.6%
3nwgA02 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.62 33.0 3.91e-01 100.0% 74.3%
2ia0B02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 34.0 3.94e-01 100.0% 75.8%
2vd3A03 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 30.0 4.01e-01 100.0% 89.2%
2dbbA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 33.0 4.03e-01 100.0% 80.6%
5fiiB00 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.61 33.0 4.33e-01 100.0% 97.4%
2gqqA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 33.0 4.17e-01 100.0% 89.4%
7ocxC01 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.61 33.0 4.33e-01 98.6% 100.0%
2apoA03 3.30.70.3190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 37.0 4.46e-01 100.0% 94.6%
2qz8A02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.61 32.0 4.09e-01 100.0% 88.9%
2ausC02 3.30.2350.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › Pseudouridine synthase 0.60 36.0 3.33e-01 100.0% 43.8%
2joqA01 3.30.70.260 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain 0.60 32.0 4.21e-01 100.0% 97.3%
2bj3D02 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.60 31.0 4.03e-01 100.0% 88.9%
2efpA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.60 32.0 3.76e-01 100.0% 74.5%
4h4kA01 3.30.70.2940 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 35.0 4.26e-01 100.0% 93.3%
4pg4B03 3.30.70.3100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 31.0 4.03e-01 100.0% 94.7%
2cyyA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.59 32.0 3.84e-01 100.0% 78.9%
2p5vA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.58 32.0 3.97e-01 100.0% 89.3%
2cfxA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.58 29.0 3.54e-01 100.0% 74.4%
2lxfA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 31.0 3.42e-01 100.0% 61.2%
1shyA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 34.0 3.91e-01 99.3% 80.4%
2kvoA01 2.40.30.220 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Photosystem II Psb28 0.57 30.0 3.39e-01 70.3% 65.4%
2od4B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 34.0 4.16e-01 100.0% 95.5%
2ypyA00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.57 33.0 3.45e-01 100.0% 61.2%
2l48A00 3.30.70.2030 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 28.0 3.53e-01 100.0% 77.6%
1bwvA01 3.30.70.150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RuBisCO large subunit, N-terminal domain 0.57 39.0 4.17e-01 100.0% 80.5%
3ttgA00 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.56 35.0 2.65e-01 100.0% 26.1%
2v9kA04 3.30.70.3190 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 39.0 4.44e-01 100.0% 97.2%
1reoA01 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.55 37.0 3.45e-01 99.3% 53.9%
2go8A01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 29.0 3.82e-01 100.0% 97.3%
4hl9A00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 34.0 4.03e-01 100.0% 95.7%
3m05B01 3.30.70.120 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.54 33.0 3.92e-01 100.0% 93.5%
2gffA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 33.0 3.93e-01 100.0% 93.8%
2ahoB03 3.30.70.1130 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › EIF_2_alpha 0.53 33.0 4.00e-01 96.6% 100.0%
6k2lA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.52 33.0 3.71e-01 86.2% 82.0%
1ywuA00 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.52 32.0 3.47e-01 95.9% 70.4%
1vdhA01 3.30.70.1030 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Apc35880; domain 1 0.52 34.0 3.65e-01 100.0% 76.9%
1iujA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 34.0 4.00e-01 100.0% 95.1%
2op5B01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.52 35.0 4.08e-01 100.0% 100.0%
5fm5P00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 29.0 3.32e-01 89.7% 76.5%
2y8yA02 3.30.70.1210 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 2 0.51 36.0 4.02e-01 100.0% 93.9%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3946833 1.1.16.2 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › Phage_GPO 0.80 71.0 7.34e-01 98.6% 100.0%
3165956 2007.2.4.10 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Phosphoinositide phosphatase › Mu-like_Pro 0.76 69.0 7.07e-01 95.2% 100.0%
3964948 1.1.16.4 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › Peptidase_S78 0.76 61.0 6.60e-01 98.6% 97.6%
5003309 50.1.1.0 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin 0.76 65.0 6.91e-01 97.9% 100.0%
5039158 50.1.1.3 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Peptidase_S78 0.74 66.0 6.37e-01 93.8% 94.4%
3166306 50.1.1.4 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › DUF2213 0.73 68.0 6.69e-01 98.6% 97.4%
3945977 50.1.1.4 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › DUF2213 0.71 67.0 6.41e-01 100.0% 97.6%
4101729 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.70 37.0 4.85e-01 100.0% 92.5%
3993911 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.70 38.0 4.85e-01 100.0% 90.6%
4995675 50.1.1.0 beta barrels › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin › Herpes virus serine proteinase, assemblin 0.70 61.0 5.82e-01 91.7% 84.2%
4078993 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.69 40.0 4.99e-01 100.0% 92.2%
5047459 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.69 37.0 4.63e-01 100.0% 87.1%
3997269 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.68 41.0 4.74e-01 100.0% 82.5%
3394046 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.68 39.0 4.70e-01 100.0% 85.3%
3789121 1.1.8.0 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.68 40.0 4.01e-01 100.0% 56.4%
3952346 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.68 43.0 4.37e-01 100.0% 64.1%
4011585 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.67 36.0 3.60e-01 86.2% 49.0%
3568840 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.67 38.0 4.64e-01 100.0% 85.3%
3952336 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.67 43.0 4.25e-01 100.0% 61.3%
4623083 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.67 35.0 4.27e-01 100.0% 78.9%
4960055 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.67 61.0 6.23e-01 95.9% 100.0%
3960853 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.67 42.0 4.29e-01 100.0% 64.1%
134079 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.66 36.0 4.44e-01 100.0% 86.2%
4024066 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.65 37.0 4.60e-01 100.0% 92.9%
3439532 304.3.1.1 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.65 34.0 4.57e-01 100.0% 98.7%
3169216 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.65 40.0 4.23e-01 100.0% 68.2%
4006501 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.65 41.0 4.09e-01 100.0% 61.7%
3761477 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.64 40.0 4.49e-01 100.0% 79.1%
3286392 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.64 42.0 4.44e-01 97.9% 73.8%
5030786 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 36.0 4.53e-01 100.0% 98.8%
3970471 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.63 42.0 4.29e-01 97.9% 68.3%
3386025 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.63 41.0 4.20e-01 98.6% 66.9%
3593122 304.109.1.0 a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e 0.63 30.0 3.26e-01 98.6% 52.5%
5067982 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.61 32.0 3.93e-01 100.0% 80.0%
3236827 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.61 41.0 4.39e-01 100.0% 79.2%
4961367 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.61 33.0 3.76e-01 100.0% 70.5%
4019320 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.61 39.0 4.57e-01 100.0% 94.0%
3404823 304.9.1.81 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RBD_AKAP-17A 0.61 38.0 4.16e-01 100.0% 77.4%
3515518 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.60 41.0 4.39e-01 100.0% 80.0%
3291834 304.3.1.0 a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain 0.60 30.0 4.08e-01 100.0% 97.1%
5001314 304.102.1.4 a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › TruB_N 0.60 40.0 3.41e-01 100.0% 40.0%
3219903 304.9.1.81 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RBD_AKAP-17A 0.60 37.0 4.45e-01 100.0% 94.7%
3474805 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.60 36.0 3.71e-01 100.0% 60.8%
3965235 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.60 41.0 4.60e-01 97.2% 88.7%
5043890 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.60 31.0 3.94e-01 100.0% 84.7%
3986531 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.60 41.0 4.20e-01 97.9% 72.1%
3748998 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.60 39.0 3.70e-01 100.0% 55.6%
4989811 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.59 36.0 4.12e-01 100.0% 81.9%
4029023 1.1.8.3 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › GCV_T_C 0.59 38.0 4.42e-01 100.0% 90.5%
3628325 327.11.2.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.58 28.0 3.86e-01 92.4% 96.9%
4983446 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.58 36.0 4.08e-01 100.0% 82.9%
5034098 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.58 34.0 3.87e-01 100.0% 77.1%
3936663 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 39.0 4.22e-01 86.2% 80.8%
3163706 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.57 41.0 4.67e-01 93.1% 98.2%
4889080 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.56 40.0 4.17e-01 99.3% 79.5%
4913415 1.1.16.0 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain 0.56 40.0 4.17e-01 99.3% 79.5%
3739289 1.1.8.18 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › POP1_C 0.56 40.0 3.84e-01 100.0% 63.5%
4246888 304.102.1.3 a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › PseudoU_synth_1 0.55 44.0 3.66e-01 100.0% 48.8%
5055839 1.1.8.0 beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.54 39.0 4.40e-01 98.6% 98.2%
3965226 1.1.16.1 beta barrels › cradle loop barrel › RIFT-related › Mammalian cell entry (MCE) domain › MlaD 0.53 42.0 4.49e-01 93.1% 95.2%
5160 304.4.1.4 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › ABM 0.52 34.0 4.00e-01 100.0% 95.1%