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MZ516527.1__QXN68744.1__X__00022

Bact-Vir

MZ516527.1__QXN68744.1__X__00022

Identity

Accession:
MZ516527 ↗
Kingdom:
phage

Quality

83.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Hafnia_phage_yong2

TaxID: 2859519

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 6-133
PDB
Domain cluster: rep: ON615601.1__UTS51982.1__X__00034__D5-121
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12571.14 best Phage_tail_fib 113.4 1.40e-32 100.0% 88.0%
D2 high residues 269-339
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3otlA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.69 55.0 4.26e-01 85.9% 49.0%
1lj5A02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.68 56.0 4.41e-01 91.5% 98.1%
3rd6A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.68 55.0 4.39e-01 88.7% 52.8%
3q63F00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.67 54.0 4.37e-01 88.7% 51.8%
2rkcA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.65 54.0 3.42e-01 94.4% 79.7%
6v04A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.65 52.0 4.37e-01 90.1% 55.1%
8gn6A01 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.64 51.0 3.32e-01 88.7% 83.7%
4hrzB00 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 42.0 3.56e-01 71.8% 49.6%
3fyfA00 2.40.128.410 Mainly Beta › Beta Barrel › Lipocalin › 0.60 47.0 3.73e-01 84.5% 71.8%
8aimG01 3.10.450.20 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor 0.60 47.0 4.57e-01 85.9% 84.0%
4mnrA02 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.60 47.0 3.08e-01 85.9% 48.4%
2opeA00 3.30.540.20 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › 0.60 48.0 4.04e-01 87.3% 100.0%
2w38A01 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.59 44.0 2.87e-01 78.9% 17.8%
2jiiA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.59 42.0 3.69e-01 76.1% 90.9%
1jsgA00 2.40.15.10 Mainly Beta › Beta Barrel › Proto-oncogene - Oncogene Product P14tcl1 › TCL1/MTCP1 0.59 44.0 3.77e-01 78.9% 73.0%
2ebmA00 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.59 41.0 3.47e-01 74.6% 50.8%
6kd0A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.59 50.0 3.34e-01 98.6% 71.2%
1ohfA03 2.60.270.70 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › 0.58 48.0 3.87e-01 93.0% 84.4%
2eqjA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.57 34.0 3.54e-01 70.4% 63.6%
4g56D00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.57 46.0 3.04e-01 88.7% 85.8%
3k1lA01 3.30.457.40 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.57 44.0 4.08e-01 84.5% 94.6%
2e5aA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.56 39.0 3.66e-01 74.6% 67.7%
4jf6A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.56 42.0 3.06e-01 85.9% 81.2%
2xlgA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 45.0 3.21e-01 91.5% 40.6%
6nhsA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.55 42.0 3.05e-01 85.9% 82.0%
1lqvB00 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.55 43.0 3.31e-01 87.3% 76.3%
1b34B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.54 35.0 3.49e-01 70.4% 62.2%
1w1wA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 40.0 2.76e-01 84.5% 36.5%
5zwzA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.53 36.0 3.67e-01 70.4% 75.7%
4c92B00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.50 34.0 3.10e-01 71.8% 52.4%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4929655 331.3.1.9 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › AHSA1 0.69 58.0 4.36e-01 90.1% 45.5%
3949576 331.3.1.11 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc2 0.67 56.0 4.26e-01 90.1% 46.9%
3960453 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.67 56.0 4.39e-01 90.1% 50.3%
3510918 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.65 47.0 3.83e-01 77.5% 44.4%
3589805 243.8.1.0 ↗ a+b two layers › Cystatin-like › Uracil-DNA glycosylase inhibitor protein › Uracil-DNA glycosylase inhibitor protein 0.64 55.0 5.03e-01 95.8% 85.3%
3245468 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.63 47.0 3.98e-01 80.3% 47.5%
3792511 206.1.1.72 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Pkinase_fungal 0.63 45.0 2.88e-01 76.1% 31.5%
3991944 206.1.1.20 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PK_Tyr_Ser-Thr 0.62 45.0 3.09e-01 77.5% 41.9%
3476478 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 35.0 3.23e-01 70.4% 42.1%
5027940 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.61 49.0 3.82e-01 91.5% 52.4%
4469310 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.61 51.0 3.75e-01 94.4% 50.0%
4295817 274.1.1.0 ↗ a+b two layers › Pili subunits › Pili subunits › Pili subunits 0.61 47.0 3.86e-01 83.1% 50.8%
3272573 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.61 42.0 4.16e-01 71.8% 68.0%
3445705 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.60 41.0 4.17e-01 80.3% 71.4%
3246581 207.1.1.81 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › FTH 0.60 45.0 2.96e-01 80.3% 28.5%
3532358 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 43.0 2.79e-01 76.1% 33.0%
3592763 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.60 49.0 3.63e-01 91.5% 46.8%
4028525 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.60 46.0 3.51e-01 88.7% 47.4%
3962436 222.1.1.0 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase 0.59 46.0 3.87e-01 85.9% 92.8%
3390463 708.1.1.4 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › FLYWCH 0.58 42.0 4.41e-01 77.5% 86.2%
3807532 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 45.0 2.77e-01 87.3% 53.2%
3657386 1.1.1.10 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_N 0.57 42.0 3.38e-01 80.3% 61.4%
3789126 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.56 43.0 2.76e-01 85.9% 44.6%
4992060 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.55 42.0 3.24e-01 85.9% 40.0%
3468880 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 43.0 2.79e-01 88.7% 46.9%
3732505 241.15.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 0.54 44.0 3.79e-01 91.5% 55.0%
3666858 9.1.1.9 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › CpeT 0.54 38.0 2.88e-01 77.5% 30.5%
4937517 247.1.1.11 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B_2 0.53 45.0 3.15e-01 100.0% 77.8%
3577440 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.53 38.0 3.37e-01 78.9% 88.7%
3234110 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.53 44.0 3.37e-01 100.0% 78.5%
3928985 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.53 36.0 3.40e-01 71.8% 70.0%
3593222 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 38.0 3.71e-01 80.3% 74.4%
3686225 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 40.0 3.07e-01 87.3% 70.8%
3285675 7579.1.1.102 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S9, Hydrolase_4 0.51 42.0 2.74e-01 95.8% 80.0%
D3 high residues 341-436
PDB
Domain cluster: rep: KP202970.1__AJD82855.1__JWAP_00022__00022__D143-223
D4 high residues 523-594
PDB
Domain cluster: rep: OM471789.1__UMM62452.1__X__00001__D31-84
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3girA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.65 45.0 4.45e-01 100.0% 66.7%
1wosA04 2.40.30.110 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Aminomethyltransferase beta-barrel domains 0.62 42.0 4.04e-01 100.0% 59.3%
3wndA03 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 45.0 4.21e-01 97.2% 67.0%
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 0.57 42.0 4.20e-01 81.9% 78.1%
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 0.55 40.0 3.95e-01 81.9% 75.3%
2nysA00 2.30.30.220 Mainly Beta › Roll › SH3 type barrels. › SspB-like 0.53 38.0 3.34e-01 77.8% 61.5%
1x31A02 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.52 46.0 2.91e-01 100.0% 22.5%
3psiA06 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 40.0 3.66e-01 98.6% 62.0%
1k8mA00 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.51 45.0 4.23e-01 98.6% 92.0%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4358094 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.60 43.0 4.80e-01 100.0% 98.2%
5083817 70.4.1.0 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) 0.59 48.0 5.05e-01 87.5% 100.0%
3981035 1.1.8.23 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › T6SS_TssF 0.58 48.0 4.32e-01 100.0% 65.0%
3389361 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.58 42.0 3.82e-01 95.8% 57.9%
3948566 1.16.1.4 ↗ beta barrels › cradle loop barrel › Baseplate wedge protein gp6 domain I › Baseplate wedge protein gp6 domain I › T6SS_TssF 0.57 46.0 4.29e-01 100.0% 70.0%
4409168 70.3.1.3 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › SAF 0.56 41.0 4.15e-01 81.9% 81.4%
3168193 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.56 39.0 3.99e-01 98.6% 75.7%
3970891 70.3.1.18 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like › ChapFlgA 0.55 42.0 4.43e-01 83.3% 93.8%
3960359 1.1.8.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.54 47.0 4.03e-01 98.6% 59.2%
3595828 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.54 42.0 3.23e-01 84.7% 92.3%
5017556 1.1.9.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.53 37.0 3.55e-01 100.0% 63.5%
4369338 2.1.1.21 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Methyltrn_RNA_3 0.51 36.0 3.64e-01 100.0% 74.3%
4932859 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.51 41.0 3.63e-01 97.2% 60.0%
4629157 2.1.1.7 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › S1 0.51 40.0 3.47e-01 98.6% 53.9%
3798375 304.102.1.0 ↗ a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase 0.51 39.0 2.66e-01 95.8% 21.4%
3173783 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.50 35.0 2.84e-01 73.6% 51.0%
D5 medium residues 159-209
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03406.19 best Phage_fiber_2 68.0 5.80e-19 72.5% 85.7%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1h6wA01 2.10.280.10 Mainly Beta › Ribbon › heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 1 › heat- and protease-stable fragment of the bacteriophage t4 short fibre, domain 1 0.68 51.0 5.55e-01 86.3% 100.0%
3l5lA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.54 43.0 2.67e-01 96.1% 25.6%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3975357 1083.1.1.3 ↗ a+b duplicates or obligate multimers › Phage T4 gp12 N-terminal repeating units › Phage T4 gp12 N-terminal repeating units › Phage T4 gp12 N-terminal repeating units › Phage_fiber_2 0.95 71.0 8.01e-01 78.4% 100.0%
1839946 1083.1.1.2 ↗ a+b duplicates or obligate multimers › Phage T4 gp12 N-terminal repeating units › Phage T4 gp12 N-terminal repeating units › Phage T4 gp12 N-terminal repeating units › Phage_fiber_rpt 0.86 63.0 6.88e-01 80.4% 100.0%
D6 medium residues 213-250
PDB
Domain cluster: representative