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NC_070960.1__YP_010669391.1__PQC10_gp184__00129

Bact-Vir

NC_070960.1__YP_010669391.1__PQC10_gp184__00129

Identity

Accession:
NC_070960 ↗
Kingdom:
phage

Quality

94.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pantevenvirales› Kyanoviridae› Yushanluvirus› Synechococcus_phage_S-H9-2

TaxID: 2783669

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 7-78
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09568.18 best RE_MjaI 63.1 4.50e-17 98.6% 41.7%
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6tmfT00 1.10.60.20 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17 0.72 39.0 4.19e-01 97.2% 60.9%
1kxpD02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.66 52.0 4.89e-01 90.3% 71.6%
2pmsC00 6.10.140.920 Special › Helix non-globular › Helix Hairpins › 0.61 45.0 3.98e-01 80.6% 57.8%
4i0xG00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.61 44.0 4.52e-01 90.3% 80.9%
1ifwA00 1.10.1900.10 Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › c-terminal domain of poly(a) binding protein 0.60 40.0 3.71e-01 98.6% 53.3%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 43.0 3.50e-01 86.1% 41.2%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.59 48.0 4.57e-01 90.3% 79.3%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.59 44.0 4.50e-01 80.6% 85.3%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.58 48.0 4.37e-01 90.3% 76.0%
2dwkA00 1.20.58.900 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain 0.57 41.0 3.22e-01 76.4% 75.2%
3zbhA00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.56 46.0 4.30e-01 90.3% 77.8%
2lpbA00 1.10.287.2920 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.56 46.0 4.48e-01 100.0% 80.2%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.56 46.0 4.45e-01 90.3% 90.2%
2vs0A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.56 45.0 4.38e-01 90.3% 86.6%
3smtA02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.56 48.0 3.74e-01 98.6% 80.5%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.56 39.0 3.46e-01 75.0% 51.8%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.55 42.0 4.16e-01 90.3% 79.2%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.55 47.0 3.42e-01 97.2% 61.0%
2fji101 1.10.357.50 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.54 43.0 3.22e-01 91.7% 70.3%
4hhyC01 1.20.142.10 Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › Poly(ADP-ribose) polymerase, regulatory domain 0.54 44.0 3.58e-01 87.5% 76.3%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.54 36.0 3.43e-01 77.8% 57.6%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.53 40.0 4.03e-01 88.9% 82.4%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 39.0 3.40e-01 79.2% 56.1%
5svlA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.53 40.0 4.07e-01 83.3% 97.1%
3ok8A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 44.0 3.27e-01 98.6% 82.6%
3akjA02 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.53 44.0 3.19e-01 91.7% 76.6%
1hwyA03 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 45.0 3.01e-01 97.2% 59.7%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.52 41.0 3.86e-01 88.9% 71.1%
4nooB00 1.10.8.1160 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.52 43.0 3.96e-01 100.0% 68.4%
1vcsA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.52 38.0 3.48e-01 81.9% 56.9%
2xzmV01 1.10.60.20 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Ribosomal protein S17 0.52 34.0 3.59e-01 70.8% 78.7%
2h21A02 3.90.1420.10 Alpha Beta › Alpha-Beta Complex › set domain protein methyltransferase, domain 2 › Rubisco LSMT, substrate-binding domain 0.52 45.0 3.48e-01 98.6% 61.8%
4ivfA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 39.0 3.41e-01 83.3% 56.9%
4lunU00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.52 41.0 2.71e-01 87.5% 38.6%
3q1xA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.51 38.0 3.20e-01 84.7% 61.2%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.51 39.0 3.92e-01 97.2% 81.3%
4btfA01 1.20.930.20 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Adaptor protein Cbl, N-terminal domain 0.50 37.0 3.40e-01 80.6% 65.0%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3790887 174.1.1.32 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Transmemb_17 0.72 60.0 4.74e-01 90.3% 91.0%
3686641 551.1.1.0 ↗ alpha arrays › Hsp90 co-chaperone CDC37 middle domain › Hsp90 co-chaperone CDC37 middle domain › Hsp90 co-chaperone CDC37 middle domain 0.67 50.0 4.36e-01 100.0% 52.7%
4136906 5069.1.3.1 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › Sdh_cyt 0.66 51.0 4.43e-01 87.5% 52.5%
3468013 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 0.64 50.0 4.51e-01 84.7% 82.0%
5074535 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.61 48.0 4.10e-01 86.1% 95.0%
4562953 2004.1.1.43 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SRP54 0.61 42.0 2.80e-01 93.1% 17.9%
3885014 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.61 48.0 4.10e-01 86.1% 56.7%
4286197 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.61 47.0 4.62e-01 84.7% 78.8%
3904356 3755.3.1.9 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › SH3BP5 0.61 49.0 3.56e-01 88.9% 42.4%
3389690 174.1.1.29 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF4728 0.61 48.0 3.92e-01 86.1% 49.6%
3171100 603.1.1.100 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27017 0.60 47.0 4.26e-01 86.1% 63.0%
4944193 179.1.1.0 ↗ alpha bundles › CO dehydrogenase ISP C-domain like › CO dehydrogenase ISP C-domain like › CO dehydrogenase ISP C-domain like 0.60 37.0 3.74e-01 72.2% 61.4%
3810801 632.22.1.139 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › KIF21A_4th 0.60 47.0 3.73e-01 86.1% 86.0%
3517735 4177.1.1.2 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR 0.60 51.0 3.79e-01 98.6% 83.5%
4947640 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.59 47.0 3.23e-01 90.3% 25.1%
3972755 601.1.2.99 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › DAGK_prokar 0.58 46.0 4.08e-01 95.8% 56.8%
3580281 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.58 46.0 4.09e-01 90.3% 60.0%
3601853 604.7.1.0 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.58 45.0 3.65e-01 87.5% 48.3%
3277724 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.57 47.0 4.33e-01 90.3% 68.4%
3503329 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.57 45.0 4.15e-01 87.5% 67.4%
3258488 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.57 49.0 4.46e-01 98.6% 94.0%
3839497 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.56 45.0 4.31e-01 88.9% 82.4%
3252622 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 44.0 4.08e-01 87.5% 66.3%
4247116 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.55 43.0 3.83e-01 87.5% 59.1%
4408647 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.55 43.0 3.89e-01 87.5% 61.0%
3313893 604.14.1.4 ↗ alpha bundles › Spectrin repeat-like › PPK N-terminal domain-like › PPK N-terminal domain-like › DUF4110 0.55 45.0 3.97e-01 88.9% 75.2%
3927738 632.8.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.54 44.0 4.10e-01 93.1% 94.7%
4097875 3712.1.1.2 ↗ a+b complex topology › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › Mediator of RNA polymerase II transcription subunit 11 › DUF412 0.54 41.0 3.81e-01 86.1% 91.0%
3382744 109.38.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Telomere length regulation protein TEL2 › Telomere length regulation protein TEL2 › Telomere_reg-2, TELO2_ARM 0.54 42.0 2.46e-01 86.1% 15.6%
3368750 192.8.1.263 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF7615 0.54 41.0 3.71e-01 86.1% 60.0%
3349325 5086.1.1.135 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › DUF7615 0.54 41.0 4.04e-01 86.1% 78.8%
3942983 101.1.4.8 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like › Phage_CP76 0.53 41.0 3.30e-01 86.1% 40.7%
3573038 4207.1.1.99 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › PF28139 0.52 43.0 3.97e-01 97.2% 71.1%
3589846 2006.1.1.18 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 0.52 46.0 3.25e-01 98.6% 48.6%
3444337 109.4.1.532 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4704 0.51 41.0 2.39e-01 90.3% 8.9%
D2 high residues 82-171
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF09568.18 best RE_MjaI 87.8 1.10e-24 100.0% 55.4%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4g6vA00 3.40.1350.120 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.65 53.0 4.74e-01 91.1% 87.9%
3ndhA00 3.40.600.30 Alpha Beta › 3-Layer(aba) Sandwich › ECO RV Endonuclease; Chain A › 0.62 53.0 3.98e-01 92.2% 47.2%
1xttB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 50.0 3.85e-01 93.3% 79.8%
3ftbA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.53 39.0 2.99e-01 77.8% 63.5%
2m9mA00 3.40.50.10130 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 40.0 3.47e-01 81.1% 71.2%
1d2iA00 3.40.91.20 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.53 42.0 3.30e-01 92.2% 65.3%
2rghA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 39.0 2.92e-01 81.1% 75.5%
3kbrA02 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 34.0 3.41e-01 70.0% 65.9%
3egoA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 40.0 3.30e-01 85.6% 78.9%
1tzbA02 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.51 39.0 3.45e-01 84.4% 61.9%
3l2oB02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 40.0 3.32e-01 88.9% 87.4%
5k1rA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.50 41.0 3.06e-01 90.0% 69.7%
1u6eA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.50 44.0 3.74e-01 98.9% 84.7%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5036000 2008.1.1.165 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_MjaI 0.90 75.0 7.72e-01 86.7% 92.9%
4676512 2008.1.1.165 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › RE_MjaI 0.87 72.0 7.12e-01 87.8% 88.4%
4971943 2008.1.1.77 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › NOV_C 0.70 56.0 5.53e-01 84.4% 85.3%
5049071 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.70 58.0 4.84e-01 92.2% 66.3%
4008063 2008.1.1.197 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › PF27347 0.67 51.0 4.90e-01 82.2% 80.0%
5024737 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.65 55.0 4.57e-01 93.3% 84.4%
4940209 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.64 54.0 5.32e-01 92.2% 95.8%
4966826 2008.1.1.16 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like › Mrr_cat 0.60 47.0 4.37e-01 85.6% 87.8%
4989979 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 45.0 4.27e-01 81.1% 91.4%
3673071 7516.1.1.16 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glyco_transf_43 0.56 41.0 3.03e-01 78.9% 72.5%
4502617 2007.1.4.3 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Phosphofructokinase N-terminal domain › NAD_kinase 0.55 40.0 3.93e-01 85.6% 70.0%
4614252 281.1.1.1 ↗ a+b three layers › AraD-like aldolase/epimerase › AraD-like aldolase/epimerase › AraD-like aldolase/epimerase › Aldolase_II 0.55 42.0 3.23e-01 82.2% 90.0%
5043935 7516.1.1.1 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › NTP_transferase 0.52 41.0 3.25e-01 91.1% 92.3%
5050028 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.52 40.0 3.20e-01 82.2% 52.4%
3233384 2003.1.10.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain › Biotin_carb_N 0.51 37.0 3.24e-01 75.6% 74.5%
4366927 281.1.1.1 ↗ a+b three layers › AraD-like aldolase/epimerase › AraD-like aldolase/epimerase › AraD-like aldolase/epimerase › Aldolase_II 0.51 37.0 2.96e-01 80.0% 91.7%
5053076 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.51 39.0 3.20e-01 83.3% 66.3%