←Back to structures

ON287373.1__URC22559.1__KAMAJI_01310__00116

Bact-Vir

ON287373.1__URC22559.1__KAMAJI_01310__00116

Identity

Accession:
ON287373 ↗
Kingdom:
phage

Quality

66.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Demerecviridae› Serratia_phage_vB_SmaM-Kamaji

TaxID: 2943833

Cluster

Singleton — not in a non-trivial cluster

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 9-48
PDB
Domain cluster: representative
D2 high residues 76-133
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lvsA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.75 55.0 5.65e-01 96.6% 82.1%
2cfxA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.73 54.0 5.71e-01 100.0% 94.0%
5dukB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.71 53.0 5.15e-01 100.0% 71.6%
3vfzB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 50.0 4.96e-01 93.1% 74.6%
2ao9I01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.64 48.0 4.27e-01 96.6% 55.2%
1u8bA02 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.63 50.0 4.96e-01 100.0% 83.6%
1zq3P00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 47.0 4.48e-01 86.2% 75.0%
4mloA03 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 47.0 4.68e-01 100.0% 83.6%
2j5oA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 49.0 4.78e-01 100.0% 89.2%
2xcqA02 3.90.199.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase II; domain 5 › Topoisomerase II, domain 5 0.57 47.0 3.15e-01 100.0% 24.4%
2jrtA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 47.0 4.20e-01 100.0% 69.8%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.55 47.0 3.56e-01 100.0% 82.1%
2ktaA01 6.10.140.530 Special › Helix non-globular › Helix Hairpins › 0.52 42.0 4.25e-01 100.0% 100.0%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.50 35.0 3.28e-01 77.6% 56.8%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4944479 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.80 64.0 5.99e-01 86.2% 72.9%
5068679 101.1.2.30 ↗ alpha arrays › HTH › HTH › winged helix domain › TrmB 0.77 59.0 6.09e-01 100.0% 87.3%
3767621 101.1.1.24 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CENP-B_N 0.77 59.0 5.32e-01 86.2% 60.0%
5040079 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.77 58.0 5.37e-01 100.0% 64.0%
3873677 101.1.1.24 ↗ alpha arrays › HTH › HTH › Three-helical HTH › CENP-B_N 0.76 57.0 5.37e-01 86.2% 67.1%
4962128 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.75 57.0 5.37e-01 100.0% 68.6%
3286027 101.1.2.140 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_AsnC-type 0.74 57.0 5.67e-01 100.0% 81.7%
4945141 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.74 56.0 5.75e-01 100.0% 87.3%
5038325 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 55.0 5.81e-01 98.3% 95.9%
4998813 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.73 55.0 5.66e-01 96.6% 87.3%
3784774 101.1.1.35 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_psq 0.71 51.0 5.11e-01 77.6% 75.0%
4978146 101.1.1.62 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_24 0.67 51.0 4.88e-01 100.0% 70.0%
4034096 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 60.0 5.39e-01 100.0% 78.8%
3279456 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.67 52.0 5.53e-01 100.0% 100.0%
3281220 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.66 51.0 5.43e-01 98.3% 98.0%
4550738 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.66 53.0 5.13e-01 100.0% 78.5%
3969487 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 50.0 5.36e-01 96.6% 98.0%
4034103 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.66 51.0 5.21e-01 98.3% 89.1%
4319964 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.66 51.0 5.24e-01 100.0% 90.9%
4034245 101.1.1.2 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_AraC 0.66 52.0 5.06e-01 100.0% 78.5%
3984767 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.65 50.0 5.03e-01 100.0% 83.3%
4134806 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.65 51.0 4.95e-01 100.0% 78.5%
3970263 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.64 50.0 5.04e-01 100.0% 85.0%
3974443 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.64 50.0 4.98e-01 98.3% 83.3%
4007503 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.64 49.0 5.17e-01 98.3% 98.0%
3973678 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 50.0 5.11e-01 100.0% 92.7%
4465858 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.63 48.0 5.10e-01 100.0% 100.0%
4030908 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.62 49.0 4.52e-01 100.0% 68.0%
3943107 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.61 45.0 4.41e-01 81.0% 87.7%
5067396 101.1.2.141 ↗ alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.61 53.0 5.28e-01 100.0% 100.0%
5078923 101.1.2.66 ↗ alpha arrays › HTH › HTH › winged helix domain › Mga 0.61 51.0 4.36e-01 98.3% 95.0%
3946093 101.1.1.58 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_18 0.60 51.0 5.23e-01 100.0% 100.0%
5072470 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.56 48.0 4.37e-01 100.0% 76.2%
D3 high residues 137-192
PDB
Domain cluster: rep: ON526839.1__URG17631.1__GRN51_150__00015__D54-100
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.80 67.0 6.34e-01 100.0% 77.9%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.71 45.0 4.56e-01 96.4% 64.9%
2pwyA01 3.10.330.20 Alpha Beta › Roll › Vcp-like ATPase; Chain A, domain 2 › 0.64 53.0 5.28e-01 96.4% 100.0%
3kjxD01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.63 43.0 4.26e-01 73.2% 78.7%
4pytA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.63 43.0 3.36e-01 100.0% 32.0%
1w1oA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.62 43.0 3.38e-01 100.0% 32.3%
4b9kE00 3.30.710.10 Alpha Beta › 2-Layer Sandwich › Potassium Channel Kv1.1; Chain A › Potassium Channel Kv1.1; Chain A 0.62 42.0 3.69e-01 85.7% 46.5%
3waiA02 2.60.40.3390 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 46.0 3.87e-01 100.0% 50.5%
2cyjA00 3.40.1230.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Mth938; Chain: A, › MTH938-like 0.58 48.0 3.86e-01 96.4% 83.8%
2jz6A01 2.30.170.40 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L28/L24 0.57 35.0 3.67e-01 100.0% 68.0%
3oouA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.55 43.0 4.42e-01 92.9% 89.1%
4nlcA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.55 41.0 2.68e-01 82.1% 56.5%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.53 39.0 3.88e-01 98.2% 75.4%
2yzhA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 45.0 3.26e-01 100.0% 53.5%
1gg3A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 44.0 4.02e-01 98.2% 91.0%
3ewlB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 44.0 3.42e-01 100.0% 70.8%
2fb7A00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.51 45.0 4.01e-01 100.0% 87.5%
1wdjA00 3.90.1570.10 Alpha Beta › Alpha-Beta Complex › tt1808, chain A › tt1808, chain A 0.51 41.0 3.03e-01 100.0% 74.7%
2iciA01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.50 38.0 2.95e-01 89.3% 79.9%
3bh1A03 3.40.140.40 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Domain of unknown function (DUF1846), C-terminal subdomain 0.50 42.0 3.19e-01 100.0% 71.9%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.80 67.0 6.31e-01 100.0% 76.8%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.72 58.0 5.13e-01 100.0% 61.2%
3698670 101.15.1.1 ↗ alpha arrays › HTH › LysM domain › LysM domain › LysM 0.68 47.0 4.66e-01 73.2% 83.3%
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.67 55.0 5.22e-01 100.0% 76.8%
3171408 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.67 53.0 5.57e-01 96.4% 100.0%
4430398 284.1.1.5 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › Gcd10p 0.64 50.0 3.62e-01 89.3% 95.3%
3022172 375.12.1.0 ↗ few secondary structure elements › Rubredoxin-like › Nicotinate phosphoribosyltransferase C-terminal domain-related › Nicotinate phosphoribosyltransferase C-terminal domain-related 0.64 37.0 3.62e-01 98.2% 50.8%
5002807 11.14.1.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Ig-like domains in STT3 › Ig-like domains in STT3 › AglB_L1 0.61 49.0 4.08e-01 100.0% 52.1%
3805835 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.60 52.0 3.38e-01 100.0% 27.2%
3262469 375.1.1.94 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › ZnF_RZ-type 0.60 47.0 4.90e-01 92.9% 100.0%
3296049 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.58 47.0 3.27e-01 96.4% 33.5%
3368299 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.58 49.0 3.19e-01 100.0% 27.1%
4964418 2485.1.1.4 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › AhpC-TSA 0.57 49.0 3.59e-01 100.0% 55.2%
3670391 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.57 47.0 3.05e-01 98.2% 25.2%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.57 43.0 3.77e-01 100.0% 53.3%
3324543 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.56 45.0 3.05e-01 98.2% 28.4%
5064213 314.1.1.2 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_2b 0.56 44.0 2.84e-01 94.6% 76.4%
3595361 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 37.0 3.20e-01 100.0% 42.1%
3266341 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.55 45.0 3.08e-01 98.2% 30.4%
3599528 2485.1.1.0 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like 0.54 45.0 3.19e-01 100.0% 48.7%
3606454 4357.1.1.0 ↗ beta barrels › WWE domain › WWE domain › WWE domain 0.52 43.0 4.19e-01 98.2% 98.5%
1096061 3375.1.1.1 ↗ beta barrels › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › Single-stranded DNA-binding protein DdrB › DdrB 0.52 40.0 3.12e-01 83.9% 60.2%
4943773 297.1.1.2 ↗ a+b complex topology › YrdC/RibB › YrdC/RibB › YrdC/RibB › Sua5_yciO_yrdC 0.52 41.0 2.92e-01 96.4% 83.3%
4019840 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.52 41.0 3.36e-01 92.9% 100.0%
3969773 7523.1.1.15 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › LysR_substrate 0.52 43.0 3.52e-01 92.9% 63.8%
3523591 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.51 39.0 3.31e-01 85.7% 90.0%
11035 2008.1.1.20 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Uma2 0.51 41.0 3.03e-01 100.0% 74.7%
3581875 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.51 41.0 2.55e-01 94.6% 55.5%
4226244 304.24.1.1 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_C 0.51 44.0 3.45e-01 96.4% 93.9%
3992794 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.50 41.0 2.73e-01 98.2% 30.4%