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MK509462.1__QBJ04408.1__MK13_00179__00175

Bact-Vir

MK509462.1__QBJ04408.1__MK13_00179__00175

Identity

Accession:
MK509462 ↗
Kingdom:
phage

Quality

71.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Ackermannviridae› Agtrevirus› Shigella_phage_MK-13

TaxID: 2530042

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 6-169
PDB
Domain cluster: rep: DGJ7_scaffold_2_2069_prodigal-single.1__X__X__00356__D1-122_262-302
D2 high residues 415-555
PDB
Domain cluster: rep: KR296692.1__AKJ73763.1__SP38_161__00161__D16-131
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6x1kA01 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.53 34.0 3.69e-01 85.1% 78.3%
3bgaA05 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.51 40.0 3.25e-01 82.3% 94.8%
3bbjA00 2.40.160.210 Mainly Beta › Beta Barrel › Porin › Acyl-CoA thioesterase, double hotdog domain 0.51 40.0 3.35e-01 86.5% 92.5%
1bt9A00 2.40.160.10 Mainly Beta › Beta Barrel › Porin › Porin 0.50 44.0 3.42e-01 98.6% 95.3%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5014272 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.66 34.0 4.63e-01 81.6% 100.0%
3593405 897.1.1.0 ↗ a+b two layers › Acidic mitochondrial matrix protein p32-like › Acidic mitochondrial matrix protein p32 › Acidic mitochondrial matrix protein p32 0.64 40.0 3.73e-01 76.6% 51.8%
3318685 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.58 36.0 4.09e-01 83.0% 81.9%
3206009 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.54 46.0 3.50e-01 91.5% 61.2%
3271908 210.2.1.0 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain 0.54 43.0 3.46e-01 84.4% 97.8%
3273105 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.53 28.0 3.13e-01 75.9% 64.8%
4968435 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 28.0 3.15e-01 73.8% 67.0%
3608636 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 41.0 2.67e-01 86.5% 39.1%
5009919 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.50 42.0 3.65e-01 87.9% 76.6%
5015593 3111.1.1.0 ↗ beta barrels › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain › STT3/PglB/AglB beta-barrel domain 0.50 35.0 3.77e-01 87.9% 83.3%
D3 high residues 562-680
PDB
Domain cluster: rep: MG973030.1__AVO22918.1__X__00078__D812-920
D4 medium residues 317-402
PDB
Domain cluster: rep: NC_042047.1__YP_009616088.1__FDI76_gp108__00178__D107-177
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ylxA00 3.30.70.1480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GK1464-like 0.66 48.0 4.61e-01 75.6% 72.7%
4h5bA00 3.30.1460.70 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.66 48.0 3.97e-01 76.7% 84.9%
2jobA00 3.30.160.320 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.64 42.0 4.00e-01 75.6% 56.9%
2opeA00 3.30.540.20 Alpha Beta › 2-Layer Sandwich › Fructose-1,6-Bisphosphatase; Chain A, domain 1 › 0.62 43.0 3.89e-01 73.3% 61.7%
1e69A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.61 46.0 3.25e-01 80.2% 46.0%
5dzeA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.60 45.0 3.47e-01 80.2% 91.5%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.60 43.0 3.67e-01 74.4% 73.3%
1h91A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.59 45.0 3.57e-01 81.4% 47.8%
1vkdA00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.59 48.0 3.31e-01 90.7% 79.1%
1qj8A00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.59 50.0 4.15e-01 91.9% 84.5%
1f2uA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 45.0 3.82e-01 83.7% 91.9%
3k1lA01 3.30.457.40 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.59 42.0 4.11e-01 74.4% 84.8%
6muwH00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.58 52.0 4.00e-01 100.0% 92.3%
2p4bB02 3.30.200.100 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › MucB/RseB, C-terminal domain 0.58 42.0 4.09e-01 77.9% 82.7%
1r0uA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 44.0 3.81e-01 83.7% 75.4%
3a7rA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.57 40.0 4.04e-01 74.4% 98.9%
2lexA00 2.20.25.80 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › WRKY domain 0.57 36.0 4.07e-01 74.4% 85.7%
4xmeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 50.0 3.90e-01 96.5% 82.6%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.56 39.0 3.37e-01 72.1% 73.3%
2e5aA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.55 42.0 4.15e-01 84.9% 98.9%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.54 30.0 3.27e-01 76.7% 62.0%
2g30A01 2.60.40.1150 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 40.0 3.68e-01 80.2% 98.3%
1u17A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.54 46.0 3.57e-01 93.0% 82.2%
4ca1B02 2.60.210.10 Mainly Beta › Sandwich › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A 0.54 43.0 3.73e-01 86.0% 86.4%
5hz7A01 3.30.700.50 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › 0.54 40.0 3.64e-01 91.9% 58.8%
6qp7A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 42.0 2.73e-01 91.9% 92.1%
4ao8A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 41.0 3.00e-01 84.9% 50.9%
2jqjA01 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 37.0 3.30e-01 76.7% 90.8%
2y3vD00 2.170.210.20 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › Spindle assembly abnormal protein 6, N-terminal domain 0.50 35.0 2.96e-01 73.3% 74.7%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4956725 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.66 55.0 4.30e-01 91.9% 90.8%
222386 241.1.1.6 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › YbjN 0.66 48.0 3.97e-01 76.7% 84.9%
3856809 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.65 45.0 4.52e-01 77.9% 70.0%
3265309 4026.1.1.0 ↗ a+b three layers › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) › a+b domain in Rap/Ran-GAP (Pfam 02145) 0.64 44.0 3.74e-01 72.1% 60.4%
3495405 3131.1.1.1 ↗ a+b two layers › FYR domain › FYR domain › FYR domain › FYRN,FYRC 0.64 56.0 4.63e-01 95.3% 88.0%
5027940 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.64 54.0 4.38e-01 95.3% 91.2%
3802306 284.1.2.0 ↗ a+b two layers › FKBP-like › FKBP-like › Conserved carboxy-terminal domain of oxidative-stress-responsive kinase 1-like kinases 0.64 51.0 5.02e-01 88.4% 100.0%
4984958 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.63 49.0 3.28e-01 83.7% 82.0%
3242315 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.63 39.0 4.80e-01 81.4% 98.2%
5054228 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.63 53.0 4.30e-01 95.3% 92.4%
3318685 284.1.3.2 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain › OSR1_C 0.62 49.0 4.61e-01 87.2% 99.0%
5048803 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.61 47.0 3.14e-01 83.7% 80.5%
4999447 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.60 47.0 3.34e-01 86.0% 66.8%
3614108 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.60 45.0 2.92e-01 81.4% 69.9%
4940099 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.58 44.0 2.94e-01 82.6% 35.8%
5012521 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.58 46.0 3.39e-01 86.0% 43.4%
3683807 708.1.1.2 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › WRKY 0.57 36.0 3.54e-01 74.4% 57.9%
5028909 2004.1.1.198 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_23 0.57 43.0 2.75e-01 82.6% 28.2%
5057328 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.57 43.0 2.82e-01 82.6% 29.2%
3214007 145.1.1.1 ↗ alpha arrays › F-box domain › F-box domain › F-box domain › F-box 0.57 44.0 3.85e-01 81.4% 59.2%
3487199 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.56 44.0 4.14e-01 84.9% 80.6%
3748494 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.56 40.0 3.17e-01 75.6% 65.8%
4229031 2004.1.1.433 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_23 0.56 43.0 2.85e-01 82.6% 32.3%
3290610 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.56 42.0 2.98e-01 83.7% 49.5%
3667729 5084.5.1.3 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin › Porin_3 0.55 44.0 3.04e-01 83.7% 80.7%
4350765 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.55 42.0 2.81e-01 82.6% 31.1%
4999435 2007.1.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Class I glutamine amidotransferase-like 0.55 40.0 3.01e-01 76.7% 31.9%
3722183 868.1.1.0 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related 0.55 44.0 3.21e-01 89.5% 66.5%
4018596 4.1.1.320 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_CYT4 0.55 33.0 3.19e-01 79.1% 52.0%
3952629 2004.1.1.293 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_15 0.54 41.0 2.93e-01 82.6% 46.0%
3936392 101.1.12.3 ↗ alpha arrays › HTH › HTH › HTH motif inserted in other structures › SAS-6_N 0.54 38.0 3.17e-01 73.3% 80.0%
3594594 3794.1.1.0 ↗ a+b two layers › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Methylcrotonyl-CoA carboxylase alpha-subunit BT domain-related › Barrel domain in methylcrotonyl-CoA carboxylase alpha-subunit 0.54 41.0 3.62e-01 82.6% 75.4%
5035253 12.3.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich 0.54 48.0 3.35e-01 98.8% 42.5%
3981106 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.54 40.0 3.48e-01 83.7% 70.7%
3486812 101.1.12.3 ↗ alpha arrays › HTH › HTH › HTH motif inserted in other structures › SAS-6_N 0.53 37.0 3.11e-01 73.3% 69.7%
3300051 4.1.1.141 ↗ beta barrels › SH3 › SH3 › SH3 › PTM_DIR17_Tudor 0.53 35.0 3.71e-01 72.1% 76.0%
4001680 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 37.0 3.72e-01 81.4% 70.5%
3577440 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.53 39.0 3.56e-01 77.9% 60.9%
3233389 5.1.4.139 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40_2 0.53 41.0 2.67e-01 82.6% 27.2%
4029737 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.52 40.0 2.39e-01 82.6% 28.8%
3544943 9.3.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like 0.52 39.0 3.76e-01 81.4% 86.0%
5040016 331.3.1.0 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.52 40.0 3.43e-01 86.0% 73.5%
3784315 868.1.1.3 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › Med20 0.52 43.0 3.16e-01 90.7% 64.3%
4303165 5087.1.1.0 ↗ beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-2 › Lipovitellin LV-2 0.52 42.0 3.23e-01 88.4% 61.5%
3268196 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.51 38.0 3.33e-01 83.7% 73.3%
3965583 331.3.1.5 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Polyketide_cyc 0.51 39.0 3.43e-01 86.0% 75.7%
3352682 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.51 37.0 4.02e-01 89.5% 95.7%