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NC_004689.1__NP_818540.1__Barnyardp002__00002

Bact-Vir

NC_004689.1__NP_818540.1__Barnyardp002__00002

Identity

Accession:
NC_004689 ↗
Kingdom:
phage

Quality

73.6 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 17-141
PDB
D2 high residues 356-425
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6aefA01 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.58 45.0 3.15e-01 87.1% 54.4%
6wcsA02 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.57 45.0 3.29e-01 87.1% 52.9%
1vwxB03 3.30.1430.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein L3; Chain: B; domain 2, › 0.55 39.0 3.30e-01 80.0% 43.1%
5ja2A01 3.30.559.30 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Nonribosomal peptide synthetase, condensation domain 0.53 40.0 2.87e-01 88.6% 37.9%
3wy7D01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.52 45.0 3.76e-01 97.1% 75.0%
2byfA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.51 39.0 3.52e-01 87.1% 67.3%
4qclA05 1.10.132.60 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › B family DNA polymerase, thumb domain 0.50 35.0 2.70e-01 72.9% 79.2%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3635318 101.21.1.1 alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › TP6A_N 0.65 49.0 4.02e-01 82.9% 84.4%
3585180 109.4.1.1316 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Suf, HAT_PRP39_N, HAT_PRP39_C 0.62 32.0 1.86e-01 80.0% 5.3%
3284004 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.58 45.0 3.10e-01 87.1% 53.6%
3963060 323.1.1.5 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.57 44.0 3.22e-01 85.7% 60.9%
4878479 323.1.1.5 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.57 40.0 3.63e-01 74.3% 61.0%
3961932 323.1.1.9 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › WS_DGAT_cat,WS_DGAT_C 0.57 38.0 2.70e-01 70.0% 23.9%
3974570 323.1.1.5 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.56 43.0 3.04e-01 87.1% 56.4%
2492379 323.1.1.5 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Condensation 0.55 43.0 3.03e-01 87.1% 51.6%
3570332 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 42.0 3.65e-01 85.7% 62.6%
3818400 59.1.1.6 beta complex topology › triple barrel › triple barrel › Rap30/74 interaction domains-like › TFIIIC_sub6 0.54 38.0 3.45e-01 74.3% 88.4%
3731333 101.21.1.1 alpha arrays › HTH › HTH domain in DNA topoisomerase IV alpha subunit › HTH domain in DNA topoisomerase IV alpha subunit › TP6A_N 0.53 39.0 3.28e-01 82.9% 85.0%
4178455 2005.1.1.7 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.53 42.0 2.90e-01 92.9% 36.1%
3869304 11.1.1.9 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.51 36.0 2.86e-01 75.7% 86.5%
3952989 323.1.1.9 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › WS_DGAT_cat,WS_DGAT_C 0.51 39.0 2.84e-01 88.6% 62.9%
3937781 2006.1.6.0 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like 0.50 38.0 2.83e-01 84.3% 46.3%
D3 medium residues 144-184
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wtmA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 38.0 2.39e-01 95.1% 12.0%
1v7wA03 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.55 40.0 2.47e-01 100.0% 36.4%
1gv4A02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 39.0 2.75e-01 95.1% 32.5%
2o7iA03 3.10.105.10 Alpha Beta › Roll › Dipeptide-binding Protein; domain 3 › Dipeptide-binding Protein; Domain 3 0.51 39.0 2.55e-01 100.0% 45.3%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3259157 2003.1.2.24 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.51 39.0 2.56e-01 95.1% 17.3%
D4 medium residues 185-236
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qsbA00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.83 59.0 4.94e-01 75.0% 47.1%
4tpsA00 3.30.310.250 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Sporulation inhibitor of replication protein SirA 0.79 54.0 3.86e-01 73.1% 26.4%
7ep1B01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.77 52.0 3.34e-01 71.2% 16.5%
2xppA00 1.20.930.10 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 0.75 63.0 4.55e-01 92.3% 95.6%
3uumA00 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 60.0 4.58e-01 92.3% 46.7%
3tufA00 1.10.287.4300 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Stage III sporulation protein AH-like 0.71 56.0 4.35e-01 86.5% 39.1%
2ao9I01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.71 57.0 4.90e-01 96.2% 55.2%
4egwA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.71 59.0 4.52e-01 94.2% 45.4%
2qyuA02 1.25.40.300 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein 0.70 47.0 3.21e-01 71.2% 35.4%
3ea5D00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.69 53.0 2.92e-01 84.6% 9.5%
4c0eA01 1.25.40.790 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.67 57.0 3.63e-01 100.0% 50.2%
3rk6A00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 54.0 3.66e-01 98.1% 41.9%
2vsoF01 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 56.0 3.70e-01 100.0% 59.3%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.65 52.0 4.06e-01 96.2% 69.5%
1hu3A00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 57.0 3.77e-01 98.1% 58.3%
2p6vA00 1.20.120.1110 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › TAFH/NHR1 domain 0.64 47.0 3.92e-01 80.8% 45.4%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.64 48.0 4.36e-01 84.6% 60.8%
2uyyA02 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 50.0 3.77e-01 90.4% 35.8%
2guzB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.63 45.0 4.24e-01 76.9% 66.2%
3hr0B01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.63 51.0 4.65e-01 100.0% 67.1%
4xriA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.63 49.0 2.75e-01 96.2% 15.3%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.63 50.0 4.61e-01 96.2% 75.3%
3vhlA02 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.62 49.0 3.95e-01 96.2% 45.0%
2kwhA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 40.0 3.97e-01 71.2% 62.5%
4ielA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 45.0 3.64e-01 86.5% 89.7%
3fmcC01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.60 44.0 2.81e-01 80.8% 14.8%
3i7aA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.59 43.0 2.83e-01 94.2% 15.8%
2pmsC00 6.10.140.920 Special › Helix non-globular › Helix Hairpins › 0.58 47.0 3.91e-01 100.0% 47.7%
1di1A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 42.0 2.80e-01 96.2% 24.1%
4mk3A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 40.0 3.32e-01 94.2% 41.7%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 41.0 3.39e-01 94.2% 65.1%
ECOD (44)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3711093 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.79 55.0 3.29e-01 75.0% 11.5%
3679700 601.33.1.0 alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.78 62.0 4.73e-01 90.4% 39.1%
4318541 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.76 64.0 5.05e-01 92.3% 45.7%
5082352 109.3.1.0 alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.76 54.0 3.92e-01 76.9% 28.3%
2028819 377.1.1.2 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_S14 0.75 58.0 4.31e-01 80.8% 49.6%
3364607 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.75 60.0 5.10e-01 88.5% 95.3%
3595768 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.75 53.0 2.96e-01 75.0% 6.7%
4682501 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.74 59.0 4.71e-01 86.5% 46.0%
4100012 327.13.1.5 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif I in type III secretion system › Ring-building motif I in type III secretion system › SpoIIIAH 0.73 54.0 4.13e-01 78.8% 37.3%
3438255 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.73 59.0 5.23e-01 88.5% 86.7%
4003558 109.4.1.1953 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_EDRF1, EDRF1_N 0.73 62.0 3.55e-01 100.0% 33.3%
3678601 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 0.72 56.0 4.02e-01 90.4% 29.3%
4129436 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.71 55.0 4.44e-01 86.5% 43.8%
3707093 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 54.0 3.66e-01 84.6% 43.5%
4928483 101.1.3.36 alpha arrays › HTH › HTH › tetra-helical, LuxR-like › HTH_23 0.71 54.0 4.34e-01 86.5% 41.7%
4293733 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.70 58.0 4.62e-01 92.3% 46.7%
4232718 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.70 58.0 4.69e-01 92.3% 49.0%
4634395 4006.1.1.1 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.70 52.0 4.17e-01 80.8% 41.9%
3369732 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.69 58.0 3.50e-01 96.2% 49.9%
3225544 4006.1.1.0 alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain 0.69 54.0 4.39e-01 86.5% 45.0%
5056432 607.1.1.0 alpha arrays › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain 0.68 56.0 4.32e-01 94.2% 59.2%
3631582 604.7.1.0 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.68 57.0 4.72e-01 100.0% 52.0%
3200160 604.7.1.0 alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A 0.68 56.0 4.57e-01 100.0% 50.0%
3821024 109.4.1.1720 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IBN_N, TPR_IMB1, TPR_IPO5 0.67 54.0 2.98e-01 90.4% 10.7%
4970557 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.67 50.0 4.64e-01 84.6% 62.9%
4663650 605.1.1.108 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › GrpE 0.67 47.0 4.69e-01 75.0% 70.9%
5011233 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.66 51.0 3.87e-01 84.6% 80.0%
4883406 622.4.1.1 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Blo-t-5 0.66 51.0 4.05e-01 88.5% 51.7%
4029016 109.4.1.1 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › 14-3-3 0.65 54.0 3.55e-01 100.0% 29.2%
3518386 192.1.1.0 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.65 50.0 4.55e-01 86.5% 62.7%
3880244 603.2.1.24 alpha bundles › STAT-like › STAT › STAT › TBCA_PH 0.65 49.0 3.64e-01 88.5% 73.5%
3651732 2484.1.1.157 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF4371 0.64 56.0 3.55e-01 98.1% 38.1%
3993061 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 54.0 3.71e-01 98.1% 81.0%
3402630 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 54.0 3.94e-01 96.2% 95.3%
3707108 109.4.1.1720 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › IBN_N, TPR_IMB1, TPR_IPO5 0.64 52.0 2.88e-01 98.1% 14.7%
5056995 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 50.0 3.63e-01 90.4% 50.0%
4873022 601.51.1.1 alpha bundles › Four-helical up-and-down bundle › alpha-helical domain in phase 1 flagellin › alpha-helical domain in phase 1 flagellin › Flagellin_N 0.62 45.0 3.22e-01 78.8% 24.6%
4300897 5094.1.1.1 a+b duplicates or obligate multimers › OmpH-like › OmpH-like › OmpH-like › OmpH 0.62 47.0 3.62e-01 86.5% 35.4%
3783600 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 0.60 48.0 4.02e-01 100.0% 80.0%
3381605 109.4.1.146 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cohesin_load 0.57 46.0 2.65e-01 100.0% 88.1%
4259224 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.56 45.0 3.40e-01 100.0% 33.5%
3934904 109.4.1.106 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CPL 0.56 47.0 2.73e-01 100.0% 25.9%
2979138 377.1.1.2 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › Ribosomal_S14 0.54 38.0 3.22e-01 82.7% 41.2%
3408508 3712.1.1.1 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 › Med11 0.53 41.0 3.77e-01 96.2% 65.0%