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MN988539.1__QIG74597.1__EVC11_015__00015

Bact-Vir

MN988539.1__QIG74597.1__EVC11_015__00015

Identity

Accession:
MN988539 ↗
Kingdom:
phage

Quality

74.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Autographivirales› Morelosvirus› Rhizobium_phage_RHph_I20

TaxID: 2509730

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 36-100
PDB
Domain cluster: representative
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dt9A02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.66 52.0 4.38e-01 87.7% 54.5%
6mzoA01 3.40.50.11970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.65 54.0 4.45e-01 95.4% 83.3%
5jicA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 49.0 3.61e-01 84.6% 72.5%
1okjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.64 52.0 4.21e-01 90.8% 49.6%
2re2A00 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.63 49.0 4.11e-01 87.7% 56.8%
1mi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.62 43.0 3.77e-01 90.8% 45.7%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.61 46.0 3.88e-01 87.7% 71.9%
1sz2A02 3.40.367.20 Alpha Beta › 3-Layer(aba) Sandwich › Hexokinase; domain 1 › 0.61 48.0 3.55e-01 92.3% 68.5%
4a2bA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 49.0 4.37e-01 92.3% 69.5%
3htvA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 45.0 3.49e-01 87.7% 55.4%
2ywqA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.58 45.0 4.08e-01 84.6% 63.6%
2gupA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 44.0 3.30e-01 87.7% 60.7%
2dk1A00 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.58 34.0 3.79e-01 95.4% 76.0%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.58 45.0 3.50e-01 89.2% 65.6%
1zbsA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 37.0 3.36e-01 86.2% 44.8%
1xzpB00 3.30.1360.120 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › Probable tRNA modification gtpase trme; domain 1 0.57 46.0 3.83e-01 96.9% 84.0%
2a6aB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 43.0 3.64e-01 86.2% 49.6%
2dixA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 42.0 4.06e-01 84.6% 74.4%
3sreA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.56 44.0 2.84e-01 89.2% 33.1%
7vyjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 42.0 3.14e-01 86.2% 83.3%
3dcxA00 2.30.29.50 Mainly Beta › Roll › PH-domain like › Bacterial Pleckstrin homology domain 0.55 41.0 3.51e-01 93.8% 47.0%
3gvzA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.55 47.0 3.21e-01 100.0% 91.8%
3ttcA03 3.30.420.360 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.54 45.0 3.81e-01 98.5% 57.0%
2xqyA01 3.30.500.50 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › 0.54 43.0 3.25e-01 92.3% 87.1%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.54 42.0 4.13e-01 89.2% 83.1%
1o5zA01 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.54 41.0 2.76e-01 84.6% 84.2%
3lbfA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 37.0 2.68e-01 75.4% 63.3%
2gy5A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 41.0 3.67e-01 89.2% 93.9%
4qwoB00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.53 43.0 3.49e-01 92.3% 94.7%
2jaeA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 40.0 2.93e-01 83.1% 92.4%
4g1gA02 2.70.20.60 Mainly Beta › Distorted Sandwich › Topoisomerase I; domain 3 › Viral matrix protein, C-terminal domain 0.52 44.0 3.37e-01 100.0% 66.3%
3ewaA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 41.0 2.86e-01 90.8% 28.5%
2ltrA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.52 40.0 3.52e-01 87.7% 59.0%
4nhxA02 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.52 40.0 2.88e-01 90.8% 70.6%
8f5dA05 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.52 40.0 2.87e-01 89.2% 50.7%
1p9rA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.52 43.0 3.76e-01 100.0% 79.3%
7d27A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 40.0 2.83e-01 89.2% 37.8%
4fflA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.51 40.0 2.73e-01 87.7% 64.1%
1lfoA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 41.0 3.52e-01 100.0% 81.1%
1fr3A00 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 33.0 3.34e-01 100.0% 65.7%
4qdiA02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 38.0 2.71e-01 83.1% 88.6%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.51 39.0 2.80e-01 89.2% 33.6%
4c12A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.50 39.0 2.71e-01 87.7% 90.8%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4341865 4325.1.1.1 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.75 52.0 5.56e-01 80.0% 85.5%
3218019 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.71 39.0 3.55e-01 73.8% 40.0%
3923801 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 50.0 4.50e-01 100.0% 60.0%
4054263 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 49.0 3.40e-01 86.2% 77.9%
3615642 512.1.1.0 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) 0.62 45.0 4.52e-01 86.2% 78.5%
4962459 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.62 45.0 4.17e-01 95.4% 59.1%
3219961 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 49.0 3.97e-01 96.9% 43.7%
5023577 2484.1.1.80 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C 0.62 48.0 4.00e-01 87.7% 53.3%
3743110 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.61 46.0 4.01e-01 98.5% 51.4%
3386900 2484.1.1.80 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C 0.60 46.0 3.99e-01 86.2% 54.5%
3592742 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.60 48.0 4.41e-01 92.3% 74.4%
4961801 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.60 46.0 3.43e-01 90.8% 93.7%
4012540 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 45.0 4.36e-01 84.6% 74.7%
4018089 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.59 45.0 3.81e-01 86.2% 73.3%
3925738 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.59 47.0 4.02e-01 89.2% 52.7%
3719189 5.1.5.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed 0.58 43.0 2.96e-01 80.0% 27.5%
5026433 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 48.0 4.25e-01 95.4% 67.0%
4485741 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.58 47.0 2.67e-01 89.2% 12.9%
3648118 3270.1.1.0 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase 0.58 45.0 4.13e-01 87.7% 71.1%
4979039 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.58 47.0 3.43e-01 96.9% 95.7%
3549045 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 43.0 3.73e-01 84.6% 52.7%
3633647 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.57 42.0 4.22e-01 93.8% 83.1%
3822364 3270.1.1.1 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase › DUF2470 0.57 46.0 4.23e-01 90.8% 74.1%
3330227 3270.1.1.0 ↗ a+b two layers › a+b domain in heme oxygenase › a+b domain in heme oxygenase › a+b domain in heme oxygenase 0.57 45.0 4.15e-01 90.8% 70.0%
3623534 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 41.0 3.76e-01 95.4% 57.8%
4113552 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 39.0 3.70e-01 86.2% 60.0%
3797523 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.56 42.0 3.47e-01 84.6% 44.6%
3955489 2484.1.1.211 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605, Cas12f1-like_TNB 0.55 47.0 3.35e-01 98.5% 48.6%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.55 43.0 3.98e-01 89.2% 85.6%
5047554 241.1.1.5 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › DUF2299 0.55 42.0 3.28e-01 84.6% 66.0%
146717 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.55 38.0 3.40e-01 89.2% 49.0%
3244701 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.55 36.0 2.65e-01 76.9% 24.4%
3401966 2.1.1.350 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF30298 0.55 42.0 3.24e-01 90.8% 92.8%
3657336 206.1.1.74 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, PK_Tyr_Ser-Thr 0.55 45.0 2.99e-01 95.4% 62.3%
5017438 2484.1.1.80 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HypF_C 0.54 47.0 3.88e-01 98.5% 71.7%
3934739 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 42.0 3.76e-01 89.2% 70.0%
1387073 227.1.1.6 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › PCNA_C 0.54 34.0 3.10e-01 70.8% 42.9%
3216768 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 44.0 3.78e-01 90.8% 65.7%
3209694 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 42.0 3.75e-01 89.2% 68.0%
3974797 206.1.1.9 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › RIO1 0.54 44.0 3.05e-01 100.0% 38.9%
3175837 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 42.0 3.27e-01 87.7% 38.0%
9790 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.54 41.0 2.76e-01 84.6% 84.2%
5074419 512.1.1.1 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_1st 0.54 37.0 3.77e-01 84.6% 73.8%
4022280 2011.2.1.3 ↗ a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › Pept_tRNA_hydro 0.53 42.0 3.07e-01 90.8% 48.5%
None — 0.53 45.0 2.82e-01 100.0% 22.2%
4652221 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.53 40.0 2.89e-01 86.2% 27.0%
3721374 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.53 42.0 3.78e-01 96.9% 61.0%
3479661 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 41.0 3.54e-01 89.2% 63.6%
None — 0.52 44.0 2.87e-01 100.0% 27.9%
4276713 2004.1.1.159 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Mur_ligase_M 0.51 39.0 2.74e-01 89.2% 34.9%
4370678 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 43.0 2.80e-01 100.0% 27.1%
4011254 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.51 39.0 2.62e-01 87.7% 92.3%
3865191 220.1.1.61 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › FERM_C_FAK1 0.51 41.0 3.64e-01 100.0% 58.2%
3620293 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 43.0 3.54e-01 100.0% 64.6%
3991383 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.51 38.0 3.49e-01 83.1% 61.1%
4842242 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 42.0 2.76e-01 100.0% 28.7%
3388100 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 42.0 2.70e-01 100.0% 23.6%
4955536 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.51 42.0 3.01e-01 98.5% 51.4%