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js4906-26-2_S25_scaffold_62_prodigal-single.1__X__X__00096

Bact-Vir

js4906-26-2_S25_scaffold_62_prodigal-single.1__X__X__00096

Identity

Kingdom:
phage

Quality

81.4 mean pLDDT

3D Structure

Domains

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

D1 medium residues 30-86
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 32.4 6.60e-08 93.0% 11.1%
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ivnA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.79 63.0 5.68e-01 100.0% 64.5%
4gyiA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.74 59.0 5.10e-01 100.0% 55.9%
1zarA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 59.0 5.15e-01 100.0% 78.7%
3dv8A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 54.0 4.97e-01 91.2% 80.8%
1t98A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 54.0 4.86e-01 94.7% 73.6%
3e3vA03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.66 52.0 5.27e-01 93.0% 91.1%
4ye6A02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.65 51.0 5.15e-01 91.2% 100.0%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.64 46.0 4.10e-01 75.4% 61.7%
3ol4A02 1.10.10.2390 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.64 51.0 5.12e-01 94.7% 91.7%
2np5D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.63 43.0 3.17e-01 70.2% 76.6%
3e3vA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.63 47.0 4.88e-01 93.0% 90.6%
4y0bA00 1.10.1780.10 Mainly Alpha › Orthogonal Bundle › Double Clp-N motif › Clp, N-terminal domain 0.61 45.0 3.50e-01 84.2% 76.4%
6fhpD00 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.60 44.0 4.37e-01 82.5% 85.5%
1zp2A01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.60 43.0 3.47e-01 100.0% 38.3%
1a41A02 1.20.120.380 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 0.60 47.0 4.16e-01 93.0% 88.3%
2ph5A02 3.30.360.30 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › homospermidine synthase like 0.59 49.0 3.17e-01 96.5% 84.1%
7crnA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.58 48.0 3.22e-01 98.2% 65.8%
1aisB02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.58 48.0 4.22e-01 100.0% 62.8%
3gziA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 45.0 3.20e-01 93.0% 57.6%
6b8hO01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.57 47.0 4.05e-01 96.5% 85.9%
1x42A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.57 45.0 4.14e-01 96.5% 96.4%
6eudA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 42.0 2.98e-01 93.0% 25.9%
1z21A00 1.10.10.1000 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Type III secretion system virulence factor YopR, core domain 0.57 45.0 3.98e-01 96.5% 61.5%
4k51B00 1.25.40.860 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 45.0 3.49e-01 100.0% 88.7%
2f76X00 1.10.150.490 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Retroviral GAG p10 protein 0.56 42.0 3.67e-01 87.7% 83.0%
2af6A02 6.10.140.450 Special › Helix non-globular › Helix Hairpins › 0.56 38.0 3.72e-01 70.2% 91.9%
2hwjA02 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.55 36.0 3.61e-01 70.2% 62.3%
1ze0A02 1.10.4070.10 Mainly Alpha › Orthogonal Bundle › putative redox-enzyme maturation protein fold › putative redox-enzyme maturation protein domain 0.55 38.0 3.53e-01 75.4% 82.1%
7qihA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 35.0 2.95e-01 94.7% 37.6%
2pkeA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 43.0 4.03e-01 98.2% 91.0%
3s64A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.53 43.0 3.99e-01 100.0% 77.8%
3k7dA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.53 40.0 3.24e-01 89.5% 61.9%
2j5vB01 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.53 41.0 2.83e-01 86.0% 72.7%
3umgA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 42.0 4.00e-01 94.7% 100.0%
1fc6A01 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.52 38.0 3.32e-01 84.2% 80.6%
3s6bA01 3.90.230.10 Alpha Beta › Alpha-Beta Complex › Creatine Amidinohydrolase › Creatinase/methionine aminopeptidase superfamily 0.52 42.0 2.87e-01 100.0% 80.2%
1hnnA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 42.0 2.72e-01 91.2% 21.5%
2raeA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.50 40.0 3.17e-01 94.7% 60.6%
ECOD (70)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3768919 4016.1.1.1 alpha bundles › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › alpha-helical domain in type II DNA topoisomerase › DNA_topoisoIV 0.89 82.0 5.00e-01 100.0% 22.0%
4238706 101.1.2.9 alpha arrays › HTH › HTH › winged helix domain › DNA_topoisoIV 0.88 81.0 4.98e-01 100.0% 22.0%
1165372 101.1.2.9 alpha arrays › HTH › HTH › winged helix domain › DNA_topoisoIV 0.88 80.0 5.90e-01 100.0% 46.4%
3096548 101.1.2.9 alpha arrays › HTH › HTH › winged helix domain › DNA_topoisoIV 0.85 76.0 5.74e-01 100.0% 52.6%
5035624 101.1.2.54 alpha arrays › HTH › HTH › winged helix domain › Penicillinase_R 0.76 63.0 5.52e-01 94.7% 62.4%
4977226 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.74 65.0 5.99e-01 100.0% 76.0%
4339648 101.1.2.852 alpha arrays › HTH › HTH › winged helix domain › PF27213 0.73 60.0 5.07e-01 98.2% 54.7%
3234666 101.1.2.577 alpha arrays › HTH › HTH › winged helix domain › SPK 0.73 59.0 4.78e-01 94.7% 48.3%
3224387 101.1.7.2 alpha arrays › HTH › HTH › Methylated DNA-protein cysteine methyltransferase-C › SPK 0.73 60.0 4.79e-01 94.7% 65.0%
5056734 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.73 60.0 4.90e-01 100.0% 47.8%
3948523 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.72 56.0 5.35e-01 87.7% 77.1%
4954772 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.72 59.0 6.01e-01 96.5% 94.5%
5022936 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.72 57.0 4.66e-01 91.2% 46.4%
3230169 101.1.1.264 alpha arrays › HTH › HTH › Three-helical HTH › SPK 0.72 59.0 4.71e-01 93.0% 64.2%
5057164 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.72 61.0 5.16e-01 100.0% 56.0%
3233735 101.1.1.264 alpha arrays › HTH › HTH › Three-helical HTH › SPK 0.72 59.0 5.46e-01 100.0% 78.8%
3234078 101.1.7.2 alpha arrays › HTH › HTH › Methylated DNA-protein cysteine methyltransferase-C › SPK 0.72 59.0 4.75e-01 93.0% 67.8%
3239312 101.1.1.264 alpha arrays › HTH › HTH › Three-helical HTH › SPK 0.71 59.0 4.79e-01 93.0% 69.7%
4304583 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 58.0 5.63e-01 94.7% 98.5%
4175293 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.70 58.0 5.15e-01 94.7% 94.1%
3350998 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.70 57.0 5.62e-01 93.0% 88.3%
3492110 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.70 57.0 5.57e-01 94.7% 93.8%
3243067 101.1.2.577 alpha arrays › HTH › HTH › winged helix domain › SPK 0.70 58.0 4.78e-01 100.0% 70.4%
3227729 101.1.2.101 alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.69 59.0 4.91e-01 100.0% 59.0%
3174047 195.1.1.0 alpha complex topology › NusB-like › NusB-like › NusB-like 0.69 56.0 4.44e-01 93.0% 44.8%
3325314 101.1.2.10 alpha arrays › HTH › HTH › winged helix domain › Linker_histone 0.69 56.0 5.30e-01 93.0% 78.6%
3964745 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.69 53.0 4.78e-01 86.0% 61.3%
3431444 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.68 56.0 5.56e-01 94.7% 98.3%
3234731 101.1.1.21 alpha arrays › HTH › HTH › Three-helical HTH › HTH_Tnp_Tc5 0.68 58.0 5.61e-01 100.0% 95.4%
4665743 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.68 54.0 4.60e-01 94.7% 67.6%
4941477 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.68 57.0 4.83e-01 98.2% 62.0%
3436562 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.67 55.0 5.13e-01 94.7% 78.7%
3993206 101.1.2.352 alpha arrays › HTH › HTH › winged helix domain › HTH_Tnp_Tc5 0.67 55.0 5.19e-01 94.7% 100.0%
3781990 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.67 55.0 4.89e-01 94.7% 76.5%
3963007 2004.1.1.42 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.66 53.0 3.26e-01 93.0% 14.4%
4028933 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.66 54.0 5.10e-01 94.7% 81.4%
3286911 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.66 53.0 5.06e-01 94.7% 87.1%
4941699 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.66 55.0 5.12e-01 100.0% 74.7%
3509166 101.1.1.244 alpha arrays › HTH › HTH › Three-helical HTH › HTH_TIMELESS 0.66 51.0 4.86e-01 89.5% 74.3%
3969964 101.1.2.110 alpha arrays › HTH › HTH › winged helix domain › HTH_IclR 0.66 55.0 4.85e-01 94.7% 72.9%
3278769 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 56.0 4.92e-01 100.0% 65.6%
3738343 101.1.1.79 alpha arrays › HTH › HTH › Three-helical HTH › HTH_ABP1_N 0.65 53.0 5.25e-01 93.0% 86.7%
3933696 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 54.0 5.14e-01 100.0% 97.1%
4978899 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.65 53.0 4.78e-01 91.2% 90.0%
3255275 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.65 52.0 5.18e-01 93.0% 95.0%
3215919 101.1.1.264 alpha arrays › HTH › HTH › Three-helical HTH › SPK 0.64 54.0 4.36e-01 100.0% 47.5%
4014609 101.1.1.79 alpha arrays › HTH › HTH › Three-helical HTH › HTH_ABP1_N 0.64 51.0 4.96e-01 93.0% 80.0%
3220456 101.1.1.264 alpha arrays › HTH › HTH › Three-helical HTH › SPK 0.63 49.0 3.97e-01 93.0% 41.5%
3675688 101.1.3.0 alpha arrays › HTH › HTH › tetra-helical, LuxR-like 0.63 54.0 5.23e-01 100.0% 86.2%
4426191 101.1.3.26 alpha arrays › HTH › HTH › tetra-helical, LuxR-like › YcbB 0.63 53.0 3.97e-01 100.0% 91.3%
3609451 108.1.1.73 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.63 44.0 3.94e-01 75.4% 56.5%
3185107 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.63 54.0 5.11e-01 100.0% 82.9%
3333385 108.1.1.73 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.62 44.0 3.68e-01 77.2% 53.3%
5064744 610.3.1.1 alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › GatB_Yqey 0.61 52.0 3.81e-01 100.0% 41.8%
5055349 2006.1.1.18 a/b three-layered sandwiches › HAD domain-like › HAD domain-related › HAD-like › HAD_2 0.61 49.0 3.48e-01 94.7% 83.0%
3618842 101.1.1.244 alpha arrays › HTH › HTH › Three-helical HTH › HTH_TIMELESS 0.61 48.0 4.52e-01 89.5% 75.7%
4957643 247.1.1.1 a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B 0.60 51.0 3.38e-01 100.0% 50.2%
3769569 1091.1.1.0 alpha arrays › 60S acidic ribosomal protein P1/P2 › 60S acidic ribosomal protein P1/P2 › 60S acidic ribosomal protein P1/P2 0.59 47.0 4.59e-01 100.0% 83.1%
4013698 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.58 49.0 4.76e-01 100.0% 86.2%
5068621 101.7.1.0 alpha arrays › HTH › DEK-C › DEK-C 0.58 45.0 4.26e-01 93.0% 72.0%
3411117 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.56 42.0 3.84e-01 84.2% 75.0%
3617871 108.1.1.147 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_10 0.56 41.0 3.93e-01 86.0% 69.3%
3451874 108.1.1.153 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_5, EF-hand_8 0.55 46.0 4.30e-01 100.0% 88.0%
3716968 2004.1.1.17 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Myosin_head 0.54 45.0 2.57e-01 100.0% 44.1%
3570364 509.1.1.1 alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.54 41.0 3.68e-01 87.7% 70.0%
3598352 108.1.1.0 alpha arrays › EF-hand › EF-hand-related › EF-hand 0.53 42.0 3.84e-01 94.7% 81.2%
3445048 108.1.1.28 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_6,EF-hand_7 0.53 43.0 4.02e-01 98.2% 86.7%
3314108 108.1.1.73 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5+EF-hand_7 0.53 42.0 3.99e-01 96.5% 88.0%
4559285 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.50 41.0 3.63e-01 100.0% 61.1%
3670511 108.1.1.113 alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5, EF-hand_6 0.50 40.0 3.02e-01 100.0% 51.1%