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NC_048751.1__YP_009843750.1__HWC07_gp069__00069

Bact-Vir

NC_048751.1__YP_009843750.1__HWC07_gp069__00069

Identity

Accession:
NC_048751 ↗
Kingdom:
phage

Quality

89.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Lietduovirus› Pantoea_phage_vB_PagM_LIET2

TaxID: 2508071

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 medium residues 3-80
PDB
Domain cluster: rep: MW824434.1__QZI93307.1__SIPHO075v1_p0084__00084__D7-61
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4oddA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.66 40.0 3.21e-01 92.3% 31.5%
1e5pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.66 38.0 3.08e-01 89.7% 30.2%
3htyA00 2.40.128.280 Mainly Beta › Beta Barrel › Lipocalin › 0.63 38.0 3.58e-01 89.7% 48.9%
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.60 50.0 3.42e-01 94.9% 62.5%
1kczA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.59 50.0 4.08e-01 100.0% 85.3%
3ml4C01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 40.0 3.65e-01 100.0% 52.8%
4p2iA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.55 46.0 4.11e-01 97.4% 96.6%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.55 33.0 3.55e-01 97.4% 70.1%
2afsA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 43.0 2.94e-01 89.7% 66.6%
5oj2B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 39.0 3.68e-01 80.8% 84.4%
2vqeE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 36.0 3.81e-01 73.1% 98.4%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 36.0 3.69e-01 74.4% 95.8%
3ddmA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.51 43.0 3.82e-01 100.0% 88.8%
2xzmE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 36.0 3.21e-01 74.4% 56.0%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3632407 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.62 41.0 3.57e-01 92.3% 45.3%
3270408 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.59 41.0 2.85e-01 75.6% 83.3%
3485405 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.58 46.0 3.11e-01 88.5% 62.8%
4025547 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.57 41.0 4.20e-01 75.6% 90.7%
4023930 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.57 41.0 4.07e-01 75.6% 83.7%
3799677 7026.1.1.0 ↗ beta meanders › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 › N-terminal region of lipid transporter Vps13 0.57 46.0 3.25e-01 93.6% 47.1%
4069560 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 38.0 3.89e-01 93.6% 72.0%
3273105 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.55 36.0 3.33e-01 100.0% 50.5%
4453085 7579.1.1.137 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › FrsA-like, Abhydrolase_6 0.55 40.0 2.61e-01 80.8% 93.0%
4003790 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.54 40.0 3.65e-01 78.2% 79.0%
3707385 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.54 43.0 2.79e-01 89.7% 74.4%
4785124 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.54 37.0 3.87e-01 70.5% 94.1%
4171258 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.54 38.0 3.92e-01 75.6% 89.3%
4016319 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.54 39.0 3.62e-01 76.9% 67.0%
3830478 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.54 38.0 3.54e-01 75.6% 64.1%
3501684 2011.1.1.8 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Zn-dependent exopeptidases › Zn-dependent exopeptidases › Peptidase_M28 0.54 44.0 3.04e-01 93.6% 68.2%
5030556 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.54 38.0 3.79e-01 76.9% 76.5%
3261477 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.53 38.0 3.59e-01 75.6% 70.5%
4282507 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.53 38.0 3.41e-01 78.2% 58.3%
4254696 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.53 38.0 3.88e-01 76.9% 88.0%
5029482 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.53 37.0 3.76e-01 75.6% 82.5%
3742742 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.53 38.0 3.40e-01 76.9% 60.0%
4937992 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.53 38.0 3.82e-01 76.9% 98.8%
139759 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.53 44.0 4.03e-01 100.0% 81.4%
3798455 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.53 38.0 3.48e-01 78.2% 60.0%
4581369 4.1.1.166 ↗ beta barrels › SH3 › SH3 › SH3 › DUF2314 0.53 40.0 3.68e-01 100.0% 61.9%
3469530 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.53 38.0 3.19e-01 76.9% 47.1%
4622062 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 40.0 2.89e-01 100.0% 27.7%
3352266 9.2.1.3 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › FBO_C 0.52 46.0 3.48e-01 98.7% 61.4%
3445812 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 37.0 3.15e-01 100.0% 42.1%
4196939 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.52 38.0 3.80e-01 78.2% 98.8%
3345144 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.52 37.0 3.78e-01 75.6% 88.0%
3739782 9.2.1.3 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › FBO_C 0.52 44.0 3.63e-01 97.4% 67.1%
4932428 65.1.1.0 ↗ beta sandwiches › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases › Composite domain of metallo-dependent hydrolases 0.52 37.0 3.84e-01 79.5% 84.3%
4943159 330.1.1.21 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5_C 0.52 36.0 3.36e-01 73.1% 61.0%
3336892 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.52 37.0 3.26e-01 76.9% 53.6%
3298321 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.52 37.0 3.27e-01 76.9% 54.0%
5040200 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.52 37.0 3.74e-01 76.9% 85.0%
4886524 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.52 37.0 3.92e-01 76.9% 100.0%
4678825 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.52 36.0 3.52e-01 75.6% 74.4%
3768115 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.51 37.0 3.23e-01 78.2% 47.7%
4989491 3174.2.1.0 ↗ beta barrels › Ribosomal protein L14-like › Barrel domain in flagellar protein FlgA › Barrel domain in flagellar protein FlgA 0.51 33.0 3.45e-01 98.7% 72.9%
4347716 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.51 36.0 3.46e-01 75.6% 68.4%
3595183 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 37.0 3.79e-01 78.2% 88.0%
3788359 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.51 37.0 3.51e-01 79.5% 63.2%
3297534 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.51 37.0 2.98e-01 78.2% 40.0%
5053861 330.1.1.2 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Ribosomal_S5 0.51 37.0 3.61e-01 79.5% 85.6%
4838879 3274.1.1.1 ↗ extended segments › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › N-terminal region in 40S ribosomal protein rpS2 (S5p) › Ribosomal_S5 0.51 35.0 3.50e-01 70.5% 80.0%
4944869 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 34.0 3.00e-01 85.9% 42.3%
3313814 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.50 34.0 2.67e-01 93.6% 31.4%
D2 medium residues 92-148
PDB
Domain cluster: representative
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4027110 109.4.1.195 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_11 0.83 65.0 4.12e-01 82.5% 58.8%
3262220 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.82 61.0 3.84e-01 78.9% 47.5%
3623273 101.1.2.712 ↗ alpha arrays › HTH › HTH › winged helix domain › FNIP_C 0.70 61.0 3.91e-01 100.0% 20.4%
3319905 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.67 53.0 3.45e-01 86.0% 33.1%
3223496 568.1.1.7 ↗ few secondary structure elements › p8-MTCP1-related › p8-MTCP1-related › p8-MTCP1-related › Cmc1 0.65 55.0 4.96e-01 94.7% 70.0%