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NC_054771.1__YP_010060364.1__KIP28_gp02__00002

Bact-Vir

NC_054771.1__YP_010060364.1__KIP28_gp02__00002

Identity

Accession:
NC_054771 ↗
Kingdom:
phage

Quality

85.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Veracruzvirus› Mycobacterium_phage_MA5

TaxID: 2725640

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 45-112
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF25673.2 best Terminase_7 79.4 3.60e-22 100.0% 48.9%
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3geeA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.74 55.0 4.14e-01 80.9% 93.5%
4kjmB01 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.71 53.0 5.50e-01 85.3% 87.3%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 49.0 4.79e-01 73.5% 80.3%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.69 49.0 3.95e-01 73.5% 75.6%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 50.0 4.83e-01 77.9% 76.9%
3rf7A02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.67 55.0 4.10e-01 89.7% 40.7%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.67 59.0 4.92e-01 98.5% 80.5%
3o39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.67 45.0 4.01e-01 77.9% 49.0%
2bl2A00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.67 52.0 4.03e-01 85.3% 87.8%
3craA02 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.67 47.0 3.83e-01 73.5% 43.0%
1s05A00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.66 56.0 4.67e-01 98.5% 67.4%
3kr9A02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 42.0 4.40e-01 75.0% 72.1%
2au5A00 1.20.120.590 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › EF2947-like 0.65 55.0 4.55e-01 97.1% 75.2%
3lysA00 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.65 53.0 4.63e-01 91.2% 74.3%
1xvhB00 1.20.120.1850 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Ebh helix bundles repeating unit (S and A modules) 0.64 49.0 4.17e-01 86.8% 49.2%
4m0mA04 1.20.1270.440 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.64 54.0 4.52e-01 94.1% 86.3%
2qytA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.64 54.0 4.81e-01 97.1% 94.1%
3kd3A02 1.10.150.210 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Phosphoserine phosphatase; domain 2 0.63 45.0 4.78e-01 91.2% 86.7%
1m62A00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.63 43.0 4.02e-01 72.1% 58.6%
4yjwA00 1.20.120.930 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF12889, N-terminal DUF3829 0.63 56.0 4.33e-01 100.0% 58.8%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 46.0 4.39e-01 76.5% 69.2%
2e9fB01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.62 52.0 4.69e-01 95.6% 78.1%
4pdyA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.62 52.0 3.72e-01 100.0% 74.2%
2v7kA02 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 41.0 2.92e-01 72.1% 22.9%
3a11B01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.59 43.0 3.55e-01 76.5% 75.2%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.59 41.0 3.87e-01 73.5% 72.9%
1ywmA02 1.20.1270.150 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Surface Active Protein 0.59 45.0 4.38e-01 85.3% 78.9%
2qguA02 1.10.10.640 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › phospholipid-binding protein 0.58 46.0 4.47e-01 97.1% 76.9%
2yfaB01 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.58 49.0 4.17e-01 100.0% 68.1%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.57 50.0 4.77e-01 100.0% 89.0%
1sqgA01 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.57 45.0 3.65e-01 89.7% 48.2%
3u9jA00 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.57 48.0 3.80e-01 100.0% 54.1%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.56 47.0 3.45e-01 100.0% 62.5%
1fouA01 1.10.246.30 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.56 47.0 4.63e-01 100.0% 97.3%
3f5cB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.56 46.0 3.52e-01 98.5% 61.2%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.56 43.0 3.59e-01 85.3% 79.2%
1tfkB00 1.20.120.650 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Colicin D 0.54 45.0 4.20e-01 94.1% 75.6%
5grqA00 1.10.8.810 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Daxx helical bundle domain 0.53 44.0 4.10e-01 95.6% 87.8%
3i2fA02 1.10.3020.10 Mainly Alpha › Orthogonal Bundle › alpha-amino acid ester hydrolase ( Helical cap domain) › alpha-amino acid ester hydrolase ( Helical cap domain) 0.53 40.0 3.73e-01 92.6% 62.1%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.53 40.0 4.13e-01 100.0% 90.9%
ECOD (57)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3769844 4.1.1.310 ↗ beta barrels › SH3 › SH3 › SH3 › PF26050 0.80 55.0 4.12e-01 72.1% 32.0%
3521328 192.10.1.5 ↗ alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain › Helical_CED_Drosha 0.80 54.0 5.77e-01 72.1% 80.0%
3486871 192.10.1.5 ↗ alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain › Helical_CED_Drosha 0.78 54.0 5.69e-01 72.1% 80.0%
4933354 3755.3.1.637 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF7121 0.75 51.0 3.40e-01 70.6% 82.9%
3717887 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.74 48.0 3.10e-01 73.5% 14.8%
3600361 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.74 50.0 4.43e-01 70.6% 61.1%
3227820 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 48.0 3.75e-01 70.6% 45.3%
3249236 4207.1.2.93 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › RNA12 0.70 48.0 3.30e-01 70.6% 22.0%
3756433 604.1.1.262 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PLU-1 0.70 51.0 4.77e-01 77.9% 77.6%
4364347 632.21.1.2 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › FIVAR 0.70 52.0 5.57e-01 83.8% 94.8%
3970792 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.70 57.0 4.77e-01 91.2% 70.8%
4988178 633.29.1.0 ↗ alpha bundles › Bromodomain-like › Putative uncharacterized protein PAV1-137 › Putative uncharacterized protein PAV1-137 0.69 60.0 5.33e-01 95.6% 87.4%
3841109 192.29.1.293 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › SHCBP_N 0.68 56.0 4.89e-01 88.2% 90.0%
4972788 601.2.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes 0.68 58.0 4.96e-01 100.0% 58.2%
3497441 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.68 57.0 3.86e-01 92.6% 72.4%
5078788 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.67 47.0 4.30e-01 73.5% 68.9%
4374012 6091.1.1.1 ↗ alpha bundles › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › Helical bundle domain in Endo-alpha-N-acetylgalactosaminidase › FIVAR 0.67 51.0 5.40e-01 85.3% 94.9%
3662351 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.67 55.0 4.53e-01 91.2% 80.0%
3634546 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.66 57.0 5.55e-01 100.0% 86.7%
3594727 192.10.1.0 ↗ alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain 0.66 59.0 5.13e-01 100.0% 77.1%
5001960 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.66 56.0 5.44e-01 94.1% 90.7%
5079439 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.66 59.0 5.07e-01 98.5% 68.6%
4440860 632.21.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › DUF7917 0.66 51.0 4.50e-01 83.8% 60.0%
1505665 192.27.1.1 ↗ alpha bundles › Long alpha-hairpin › Helical hairpin in putative tRNA methyltransferase › Helical hairpin in putative tRNA methyltransferase › TrmK 0.66 42.0 4.38e-01 75.0% 71.0%
3711337 632.24.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › GBS CAMP factor C-terminal domain › GBS CAMP factor C-terminal domain 0.66 53.0 5.40e-01 94.1% 92.3%
4041623 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.66 52.0 5.03e-01 86.8% 77.3%
4567993 632.21.1.2 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › FIVAR 0.65 51.0 5.19e-01 85.3% 90.8%
5019504 601.14.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Hemerythrin › Hemerythrin › Hemerythrin 0.64 58.0 4.48e-01 100.0% 52.7%
3226726 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.64 55.0 4.72e-01 98.5% 60.9%
4463205 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.64 47.0 2.80e-01 76.5% 10.8%
4142332 4177.1.1.66 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › ATG17_like 0.64 56.0 3.58e-01 100.0% 71.1%
4968618 611.6.1.0 ↗ alpha bundles › N-cbl like › PT26-6P helical domain › PT26-6P helical domain 0.64 55.0 4.90e-01 95.6% 76.5%
3398779 5001.1.1.0 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like 0.64 57.0 4.01e-01 100.0% 62.9%
2979253 632.21.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › EndoS_helical 0.64 49.0 4.93e-01 94.1% 84.3%
1548122 601.43.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Biofilm formation modulator YmoB › Biofilm formation modulator YmoB › YbaJ 0.64 56.0 4.59e-01 97.1% 54.9%
3501998 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.63 52.0 4.81e-01 89.7% 82.4%
5048205 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.63 54.0 4.14e-01 95.6% 92.9%
3978379 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.63 55.0 4.10e-01 98.5% 62.9%
4408647 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.62 49.0 4.32e-01 88.2% 95.2%
4027655 5069.1.3.23 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DAD 0.62 48.0 4.28e-01 85.3% 78.0%
3249529 601.1.2.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) 0.61 52.0 4.26e-01 100.0% 65.2%
4288630 603.1.1.153 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › DGCcoil 0.61 45.0 3.93e-01 100.0% 49.6%
5033439 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.60 50.0 5.01e-01 95.6% 94.3%
4979567 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.59 47.0 3.87e-01 91.2% 80.0%
3935661 109.4.1.375 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TRC8_N 0.59 50.0 3.33e-01 100.0% 47.7%
3693560 5059.1.1.3 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › TPT 0.59 49.0 3.29e-01 100.0% 67.3%
3967501 632.18.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 › DUF4398 0.58 47.0 4.30e-01 94.1% 66.3%
3782787 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.58 44.0 4.38e-01 88.2% 89.3%
4376239 150.5.1.50 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › EspA_EspE 0.58 49.0 3.50e-01 100.0% 94.0%
4473372 150.8.1.5 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE › EspA_EspE 0.58 49.0 3.58e-01 100.0% 94.8%
3215515 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.58 48.0 4.50e-01 98.5% 82.2%
3220649 109.4.1.375 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TRC8_N 0.57 49.0 3.23e-01 98.5% 61.0%
3965811 3711.1.1.0 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein 0.56 45.0 3.96e-01 91.2% 91.7%
3973390 632.18.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 › DUF4398 0.56 46.0 4.65e-01 98.5% 95.7%
3779360 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.55 47.0 3.68e-01 98.5% 75.0%
4242973 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.53 37.0 2.89e-01 75.0% 33.8%
3447427 616.1.1.1 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Ribosomal_S15 0.51 34.0 2.82e-01 70.6% 50.0%