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NC_055055.1__YP_010084016.1__KMD55_gp13__00013

Bact-Vir

NC_055055.1__YP_010084016.1__KMD55_gp13__00013

Identity

Accession:
NC_055055 ↗
Kingdom:
phage

Quality

92.1 mean pLDDT

Taxonomy

Loebvirae› Hofneiviricota› Faserviricetes› Tubulavirales› Inoviridae› Xylivirus› Xanthomonas_phage_Xf409

TaxID: 1979540

Cluster

View cluster (13 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 high residues 2-55
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3v2uC02 3.30.70.3170 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.70 59.0 4.94e-01 96.3% 94.7%
3pvlA02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.67 52.0 4.43e-01 100.0% 50.0%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.64 55.0 3.94e-01 100.0% 47.9%
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.62 46.0 4.77e-01 100.0% 92.0%
7ufsA01 2.70.98.30 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4 0.62 42.0 2.69e-01 70.4% 29.9%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.61 53.0 4.43e-01 96.3% 89.1%
2pk0A00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.61 53.0 3.46e-01 100.0% 45.7%
4p4tA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.60 45.0 2.85e-01 100.0% 14.0%
4ehoB03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.59 41.0 2.91e-01 74.1% 40.2%
1uz5A04 2.40.340.10 Mainly Beta › Beta Barrel › Beta-clip › MoeA, C-terminal, domain IV 0.59 37.0 3.34e-01 100.0% 47.2%
3flkA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.59 43.0 2.66e-01 90.7% 11.7%
1vq8E02 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.58 49.0 4.11e-01 94.4% 100.0%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.57 48.0 4.41e-01 94.4% 90.1%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.57 42.0 4.05e-01 100.0% 69.7%
2cs4A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.57 40.0 3.52e-01 100.0% 44.2%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.57 49.0 4.15e-01 100.0% 89.4%
4tm5A01 3.30.470.10 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain 0.57 46.0 3.53e-01 90.7% 62.9%
2g9gA00 2.60.120.1020 Mainly Beta › Sandwich › Jelly Rolls › PAW domain 0.55 36.0 2.55e-01 100.0% 19.0%
1ujrA01 3.30.720.50 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.54 46.0 4.10e-01 100.0% 83.1%
2wadA02 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.54 38.0 2.93e-01 100.0% 28.4%
5t89Y06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 46.0 3.92e-01 100.0% 58.7%
2i44B00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.53 44.0 2.81e-01 100.0% 94.0%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 42.0 2.97e-01 87.0% 94.6%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 44.0 4.05e-01 100.0% 73.7%
2jjuA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 44.0 3.63e-01 100.0% 50.5%
4gj1A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.51 39.0 2.68e-01 87.0% 38.4%
1ekjA00 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.50 38.0 2.71e-01 90.7% 69.5%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.50 42.0 3.29e-01 98.1% 58.8%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.50 40.0 3.29e-01 98.1% 95.9%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3259532 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.73 47.0 3.41e-01 88.9% 24.0%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.70 61.0 5.61e-01 98.1% 100.0%
3620456 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.69 54.0 4.24e-01 100.0% 41.8%
3213931 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.68 47.0 3.60e-01 72.2% 61.5%
3786112 317.1.1.0 ↗ a+b two layers › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase › Translation initiation factor eIF4e and phosphothreonine lyase 0.68 48.0 3.48e-01 100.0% 24.8%
5031824 2004.1.1.220 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SWI2_SNF2 0.68 55.0 3.16e-01 90.7% 19.0%
3651007 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.67 47.0 2.62e-01 74.1% 6.4%
4967778 329.1.1.2 ↗ a+b two layers › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › Prokaryotic AspRS, insert domain › DUF4443 0.66 45.0 3.60e-01 72.2% 89.1%
4231372 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.63 54.0 5.05e-01 100.0% 100.0%
3802543 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.63 44.0 2.52e-01 74.1% 12.0%
4139791 304.41.1.1 ↗ a+b two layers › Alpha-beta plaits › Glutamyl tRNA-reductase catalytic, N-terminal domain › Glutamyl tRNA-reductase catalytic, N-terminal domain › GlutR_N 0.62 50.0 3.78e-01 100.0% 60.0%
3826384 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.61 44.0 2.64e-01 75.9% 16.8%
3419226 109.4.1.3173 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.61 45.0 2.76e-01 77.8% 21.2%
3622513 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.60 50.0 4.90e-01 100.0% 95.0%
5048876 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.60 41.0 3.96e-01 100.0% 61.5%
3377575 109.4.1.2064 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif, TPR_24 0.60 43.0 2.39e-01 75.9% 8.2%
3460821 2002.1.1.11 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PK 0.60 45.0 2.94e-01 81.5% 48.2%
3684103 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.60 44.0 2.55e-01 79.6% 12.0%
3356833 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.60 43.0 2.44e-01 75.9% 11.3%
3577630 2492.1.1.0 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.59 50.0 3.84e-01 100.0% 40.0%
3487190 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.59 40.0 3.39e-01 88.9% 41.1%
3825001 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.58 47.0 2.64e-01 88.9% 46.7%
3595003 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.58 46.0 4.52e-01 98.1% 83.3%
3335071 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.58 45.0 2.61e-01 87.0% 57.3%
3420651 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.58 48.0 3.02e-01 98.1% 27.4%
3646564 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.58 45.0 2.63e-01 87.0% 56.4%
3330921 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.58 45.0 2.71e-01 87.0% 79.0%
3743176 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.58 46.0 3.37e-01 87.0% 47.6%
3816405 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.57 45.0 2.56e-01 87.0% 52.8%
3443843 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.57 47.0 2.75e-01 98.1% 15.9%
None — 0.57 47.0 3.63e-01 98.1% 66.7%
3378740 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.57 45.0 2.50e-01 88.9% 34.4%
3439118 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.57 45.0 2.59e-01 88.9% 53.7%
3808939 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.57 47.0 3.62e-01 98.1% 72.6%
3434515 109.4.1.2925 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, PPR_long, E_motif 0.57 45.0 2.56e-01 88.9% 46.7%
3330581 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.56 45.0 2.47e-01 88.9% 5.5%
3429551 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.56 47.0 2.85e-01 98.1% 22.7%
3833836 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.56 47.0 3.59e-01 100.0% 87.8%
5014684 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.56 42.0 4.17e-01 100.0% 82.8%
3679857 109.4.1.2337 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif, TPR_24 0.56 46.0 2.87e-01 100.0% 31.9%
3187872 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.54 44.0 3.73e-01 96.3% 51.1%
3370073 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.53 43.0 2.60e-01 92.6% 13.3%
3375945 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.52 42.0 3.44e-01 96.3% 85.2%
3329353 3164.1.1.3 ↗ few secondary structure elements › Zinc-binding domain in Junin virus envelope glycoprotein › Zinc-binding domain in Junin virus envelope glycoprotein › Zinc-binding domain in Junin virus envelope glycoprotein › DYW_deaminase 0.52 42.0 3.27e-01 96.3% 87.4%
3452954 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.52 44.0 2.55e-01 98.1% 12.3%
3677917 109.3.1.320 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › DYW_deaminase 0.51 41.0 3.21e-01 96.3% 87.4%