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NC_028956.1__YP_009213800.1__AVV62_gp42__00042

Bact-Vir

NC_028956.1__YP_009213800.1__AVV62_gp42__00042

Identity

Accession:
NC_028956 ↗
Kingdom:
phage

Quality

91.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Mannheimia_phage_vB_MhS_1152AP2

TaxID: 1572747

Cluster

View cluster (3 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 6-79
PDB
Domain cluster: rep: ON146294.1__URG13002.1__B2_9__00009__D7-62
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF26890.1 best Phage_HP1_YO09 84.2 8.80e-24 100.0% 89.5%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2kgtA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.65 51.0 5.21e-01 93.2% 86.1%
1uebA01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.63 47.0 4.98e-01 100.0% 95.2%
4lduA03 2.30.30.1040 Mainly Beta › Roll › SH3 type barrels. › 0.61 51.0 5.29e-01 100.0% 100.0%
1tyeA00 2.130.10.130 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Integrin alpha, N-terminal 0.60 45.0 2.80e-01 81.1% 29.4%
3u1wA01 3.10.450.360 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 44.0 3.38e-01 81.1% 62.8%
1vw4I00 2.40.150.20 Mainly Beta › Beta Barrel › Ribosomal Protein L14 › Ribosomal protein L14/L23 0.59 47.0 4.02e-01 89.2% 96.8%
2iw3A05 2.40.50.990 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 41.0 3.64e-01 75.7% 61.5%
3fvzA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.57 43.0 2.82e-01 82.4% 24.3%
1f1uA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.55 35.0 2.81e-01 85.1% 31.8%
1mkeA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 45.0 3.70e-01 94.6% 56.2%
3sokB00 3.30.700.10 Alpha Beta › 2-Layer Sandwich › Glycoprotein, Type 4 Pilin › Glycoprotein, Type 4 Pilin 0.54 44.0 3.69e-01 93.2% 66.9%
2fp8B00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.54 45.0 3.12e-01 98.6% 70.6%
3bzcA03 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.54 40.0 3.38e-01 79.7% 68.0%
2fkcA01 3.40.1350.40 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.53 43.0 3.82e-01 90.5% 81.8%
6vilA01 2.30.30.490 Mainly Beta › Roll › SH3 type barrels. › Bromo adjacent homology (BAH) domain 0.53 41.0 3.33e-01 85.1% 64.8%
4fwwA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 42.0 2.69e-01 93.2% 50.7%
2ymuA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 41.0 2.81e-01 93.2% 23.1%
4ntqA00 3.10.380.20 Alpha Beta › Roll › Ribonuclease domain of colicin e3 (Residues 456-551) › Novel toxin 21 (CdiA), C-terminal domain 0.52 40.0 4.05e-01 83.8% 88.2%
1iwmA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.52 43.0 3.34e-01 94.6% 81.9%
2k5qA00 2.40.50.480 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Protein of unknown function DUF1093 0.52 39.0 3.56e-01 83.8% 70.5%
3eliA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.51 44.0 3.61e-01 98.6% 79.9%
3a9gA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.50 41.0 2.81e-01 98.6% 72.5%
4aq1A05 2.60.40.3460 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 38.0 3.39e-01 82.4% 90.0%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1945981 4.1.1.12 ↗ beta barrels › SH3 › SH3 › SH3 › PWWP 0.61 47.0 4.22e-01 100.0% 57.3%
2755517 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.60 36.0 3.58e-01 85.1% 55.6%
3732634 5.1.4.15 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › RPE65 0.60 45.0 2.73e-01 81.1% 33.7%
3802971 708.1.1.1 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › NAM 0.60 45.0 3.55e-01 79.7% 71.3%
3206928 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 47.0 3.10e-01 91.9% 26.9%
3530256 5.1.4.297 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40, NBCH_WD40 0.57 48.0 3.09e-01 95.9% 36.6%
3700528 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 46.0 4.04e-01 95.9% 68.8%
3728855 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.56 46.0 4.67e-01 100.0% 92.0%
3517945 5.1.3.128 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › TEN_NHL 0.56 43.0 2.72e-01 82.4% 22.4%
3368536 5.1.3.152 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Str_synth, SSL_N 0.55 44.0 2.93e-01 89.2% 29.8%
3609129 5.1.3.23 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › SGL 0.55 45.0 3.04e-01 93.2% 92.0%
4088247 5.1.5.4 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › DPPIV_N 0.55 43.0 2.71e-01 89.2% 42.8%
3508366 5.1.4.492 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR35_2nd, Beta-prop_WDR35_TULP_N 0.55 44.0 2.84e-01 93.2% 30.0%
3315951 220.1.1.86 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › ZGRF1-like_N 0.54 46.0 4.51e-01 94.6% 97.5%
4270966 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.54 37.0 3.74e-01 71.6% 94.7%
4307548 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.54 37.0 3.53e-01 70.3% 84.7%
3168539 109.4.1.69 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IKI3 0.54 43.0 2.98e-01 91.9% 57.0%
None — 0.54 43.0 2.91e-01 91.9% 39.4%
4360692 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.54 37.0 3.64e-01 71.6% 90.0%
3288624 5.1.3.132 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Phytase-like 0.54 42.0 2.83e-01 90.5% 53.8%
3643800 813.1.1.1 ↗ a+b two layers › Chalcone isomerase › Chalcone isomerase › Chalcone isomerase › Chalcone 0.53 43.0 3.21e-01 94.6% 93.3%
5052980 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 39.0 3.46e-01 79.7% 98.2%
3165405 4246.1.1.0 ↗ a+b complex topology › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit › N-terminal domain in RNA-polymerase beta-prime subunit 0.53 36.0 3.47e-01 70.3% 82.4%
3996653 5.1.4.377 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_WDR35_TULP_N 0.53 43.0 2.87e-01 93.2% 43.5%
5004589 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.53 43.0 3.84e-01 93.2% 96.4%
4036893 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.52 36.0 3.56e-01 71.6% 91.3%
3273170 9.15.1.1 ↗ beta barrels › Lipocalins/Streptavidin › TLDC domain of oxidation resistance protein 2 › TLDC domain of oxidation resistance protein 2 › TLD 0.52 43.0 3.50e-01 100.0% 71.2%
3512466 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.52 38.0 3.29e-01 81.1% 72.8%
4383797 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.51 39.0 3.55e-01 81.1% 85.0%
4949536 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 43.0 2.86e-01 98.6% 44.1%
3735753 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.51 41.0 2.34e-01 90.5% 23.2%
3648728 5.1.3.144 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.51 42.0 2.82e-01 97.3% 48.3%
3365419 5.3.1.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II › S_locus_glycop 0.50 42.0 3.47e-01 94.6% 77.9%
3846390 2008.1.1.84 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Rab15_effector 0.50 43.0 3.16e-01 98.6% 79.5%
4031998 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.50 39.0 3.94e-01 90.5% 86.7%
3167568 101.46.1.0 ↗ alpha arrays › HTH › Parafibromin N-terminal domain › Parafibromin N-terminal domain 0.50 39.0 3.35e-01 85.1% 57.5%
D2 high residues 102-148
PDB
Domain cluster: representative
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3zg9A00 6.20.370.110 Special › Other non-globular › Rhinovirus 14, subunit 4 › 0.68 26.0 2.85e-01 97.9% 41.5%
2kswA01 3.30.1490.260 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.61 44.0 4.44e-01 78.7% 82.6%
1wh2A01 3.30.1490.40 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › GYF domain 0.61 46.0 4.30e-01 85.1% 68.9%
2yfvC00 6.10.250.2010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.60 36.0 3.39e-01 70.2% 45.0%
2xnjA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.60 40.0 3.19e-01 70.2% 59.6%
1vx7000 2.30.170.20 Mainly Beta › Roll › Ribosomal Protein L24e; Chain: T; › Ribosomal protein L24 0.57 35.0 3.20e-01 93.6% 43.5%
1l6rA01 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.56 44.0 3.11e-01 87.2% 40.1%
7c2fB01 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.55 45.0 3.72e-01 91.5% 66.3%
2jiiA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.55 42.0 2.92e-01 93.6% 88.5%
8be0A01 3.40.91.90 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain 0.53 42.0 2.88e-01 91.5% 34.6%
4dqnA01 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 0.53 45.0 3.15e-01 95.7% 34.2%
3vz9B00 3.30.457.50 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Chromosome segregation protein Spc25 0.53 41.0 3.24e-01 87.2% 48.5%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.52 45.0 3.13e-01 100.0% 90.3%
1pmtA01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 41.0 3.40e-01 93.6% 84.0%
1yx1A00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.50 41.0 2.63e-01 93.6% 97.2%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3957374 1.1.5.8 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Putative_PNPOx 0.70 47.0 4.16e-01 70.2% 68.6%
3271984 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.66 44.0 3.17e-01 70.2% 90.3%
4813923 4967.1.1.14 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › Flavi_NS5_thumb 0.63 35.0 3.32e-01 89.4% 48.1%
3211717 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 39.0 4.30e-01 70.2% 82.9%
3574069 604.12.1.62 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › DuoxA 0.61 32.0 2.34e-01 100.0% 18.4%
4887990 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.60 38.0 2.63e-01 100.0% 18.6%
5057952 375.1.1.325 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › OapC 0.59 46.0 4.35e-01 100.0% 75.4%
4669972 304.24.1.0 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.56 40.0 3.16e-01 78.7% 98.2%
4158495 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.53 45.0 3.68e-01 97.9% 74.4%
3921046 3674.1.1.0 ↗ a+b duplicates or obligate multimers › Borealin C-terminal dimerization domain › Borealin C-terminal dimerization domain › Borealin C-terminal dimerization domain 0.52 36.0 3.67e-01 100.0% 75.6%
4037529 4180.1.1.1 ↗ a+b two layers › SpoVG-like › SpoVG-like › SpoVG-like › SpoVG 0.52 41.0 3.32e-01 89.4% 45.3%
3227416 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.51 37.0 2.66e-01 83.0% 26.5%
4886572 3326.1.1.1 ↗ alpha arrays › DNA-binding domain in UvrA › DNA-binding domain in UvrA › DNA-binding domain in UvrA › UvrA_DNA-bind 0.51 41.0 3.13e-01 91.5% 68.3%
3262387 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.50 32.0 2.61e-01 93.6% 35.2%
4294089 190.1.1.7 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › MATalpha_HMGbox 0.50 37.0 2.76e-01 85.1% 77.9%
4681348 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.50 38.0 2.99e-01 83.0% 83.0%