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NC_054952.1__YP_010077844.1__KMC40_gp107__00099

Bact-Vir

NC_054952.1__YP_010077844.1__KMC40_gp107__00099

Identity

Accession:
NC_054952 ↗
Kingdom:
phage

Quality

73.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Menderavirus› Stenotrophomonas_phage_IME-SM1

TaxID: 1654717

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 11-64
PDB
Domain cluster: representative
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4lfhD02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 52.0 4.60e-01 100.0% 63.5%
4h4nA00 2.60.40.3750 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 45.0 4.42e-01 87.0% 80.6%
2vo8A00 2.60.40.680 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 44.0 3.44e-01 83.3% 57.0%
2rikA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 51.0 4.39e-01 100.0% 60.9%
1iamA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 46.0 4.06e-01 100.0% 59.0%
7k0xA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 46.0 4.29e-01 100.0% 71.8%
1f35A00 2.60.120.390 Mainly Beta › Sandwich › Jelly Rolls › Olfactory marker 0.57 43.0 3.24e-01 88.9% 60.5%
8bxrA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 47.0 4.06e-01 100.0% 58.9%
4bfeA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 45.0 4.11e-01 100.0% 65.4%
3b43A06 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 48.0 4.06e-01 100.0% 61.1%
5uv6A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 47.0 4.11e-01 100.0% 64.0%
2wp3O00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 47.0 3.97e-01 100.0% 57.7%
4yg6B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 38.0 2.86e-01 81.5% 25.8%
3x1lB03 2.60.40.4350 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 43.0 3.69e-01 100.0% 79.0%
1j4sA00 2.100.10.30 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › Jacalin-like lectin domain 0.54 41.0 3.18e-01 90.7% 33.6%
3df7A02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.53 45.0 3.44e-01 100.0% 62.0%
2ws9100 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.53 42.0 2.93e-01 100.0% 44.7%
5gm0A02 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.52 40.0 3.33e-01 100.0% 76.9%
4u7mA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 44.0 3.76e-01 100.0% 58.5%
3ap9A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.50 39.0 3.10e-01 100.0% 70.2%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4882848 11.1.1.119 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Cyc-maltodext_N 0.67 56.0 4.75e-01 100.0% 55.9%
3265945 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.67 56.0 4.82e-01 100.0% 58.9%
4954333 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.63 51.0 4.49e-01 100.0% 60.0%
3996793 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.63 47.0 4.63e-01 85.2% 80.0%
3224993 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.62 52.0 4.27e-01 100.0% 56.4%
5070093 11.1.1.249 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Big_9 0.59 46.0 3.98e-01 100.0% 52.6%
5040305 11.1.1.249 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Big_9 0.58 48.0 4.08e-01 100.0% 54.7%
3245905 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.57 49.0 3.92e-01 100.0% 65.2%
3263951 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 47.0 4.14e-01 100.0% 63.5%
3581426 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.56 47.0 4.57e-01 100.0% 95.0%
3295963 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.55 34.0 3.37e-01 70.4% 54.2%
3501948 2007.1.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like 0.54 42.0 2.89e-01 85.2% 23.6%
3602123 1.1.8.4 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain › eIF2_C 0.54 46.0 4.17e-01 100.0% 69.2%
5060453 11.1.1.244 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Cadherin_5 0.54 39.0 3.56e-01 85.2% 68.2%
3895754 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.54 40.0 3.28e-01 100.0% 40.0%
5061945 245.1.1.0 ↗ a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 0.54 41.0 3.89e-01 85.2% 80.0%
4923380 304.51.1.6 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas_Cmr3 0.54 42.0 3.79e-01 100.0% 88.0%
5016579 1.1.8.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Aminomethyltransferase beta-barrel domain 0.53 45.0 4.06e-01 100.0% 68.4%
5056154 4081.1.1.0 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related 0.52 43.0 3.22e-01 100.0% 82.6%
3214327 10.1.1.4 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Gal-bind_lectin 0.51 39.0 3.23e-01 100.0% 73.3%
4219813 3747.1.1.2 ↗ a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod,Flg_bbr_C 0.51 40.0 3.21e-01 88.9% 72.7%
D2 medium residues 75-177
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2x41A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.66 40.0 3.87e-01 95.1% 52.9%
2q3zA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.65 38.0 3.93e-01 100.0% 60.4%
2f1eA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.61 40.0 3.91e-01 97.1% 59.5%
5dstA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.61 44.0 3.73e-01 100.0% 44.6%
1xvsA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.60 41.0 3.92e-01 99.0% 59.3%
1k12A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 36.0 3.11e-01 92.2% 38.6%
1qgwA00 3.90.510.10 Alpha Beta › Alpha-Beta Complex › Cryptophytan Phycoerythrin (Alpha-1 Chain); Chain A › Phycoerythrin alpha chain 0.58 26.0 3.01e-01 98.1% 53.9%
1xf1A03 2.60.40.1710 Mainly Beta › Sandwich › Immunoglobulin-like › Subtilisin-like superfamily 0.57 37.0 3.46e-01 96.1% 51.9%
3x0dA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.56 43.0 3.68e-01 100.0% 48.9%
4liqE05 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 35.0 3.55e-01 95.1% 63.0%
5hdwA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.56 38.0 3.57e-01 100.0% 55.7%
2rttA00 2.60.40.290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 37.0 3.69e-01 97.1% 69.5%
2ztbA02 2.60.40.4280 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 30.0 3.05e-01 100.0% 54.5%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.52 35.0 3.48e-01 100.0% 66.1%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4955277 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 44.0 4.24e-01 100.0% 60.9%
3839282 11.1.1.449 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF2393 0.64 44.0 4.47e-01 96.1% 72.7%
4970162 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.63 37.0 3.15e-01 94.2% 35.2%
3254117 11.1.1.67 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF525 0.63 43.0 4.06e-01 100.0% 60.0%
4229796 11.1.1.67 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF525 0.62 42.0 3.94e-01 100.0% 56.8%
5021919 10.1.2.194 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) › Lectin_like 0.61 37.0 3.18e-01 94.2% 35.9%
4526825 11.1.1.67 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF525 0.60 42.0 3.92e-01 99.0% 58.4%
3266273 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.60 44.0 3.71e-01 95.1% 44.4%
3771545 11.1.1.67 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF525 0.60 42.0 3.73e-01 100.0% 50.0%
2392680 222.1.1.17 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › PKS_DH_N 0.59 44.0 4.28e-01 95.1% 69.2%
4939973 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 41.0 3.90e-01 100.0% 61.6%
4454726 12.1.1.112 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › PF28665 0.56 41.0 4.22e-01 100.0% 79.0%
3581667 11.1.4.7 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › TTR-52 0.53 33.0 3.14e-01 93.2% 50.4%
3719717 11.1.1.41 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_C 0.50 43.0 3.70e-01 94.2% 62.4%
4970000 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 38.0 2.86e-01 100.0% 31.8%