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NC_041976.1__YP_009606475.1__FDI01_gp048__00048

Bact-Vir

NC_041976.1__YP_009606475.1__FDI01_gp048__00048

Identity

Accession:
NC_041976 ↗
Kingdom:
phage

Quality

70.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Jimmervirus› Brevibacillus_phage_Jimmer2

TaxID: 1296658

Cluster

View cluster (12 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 33-112
PDB
Domain cluster: rep: ON210835.1__URO01824.1__268TH002_29__00029__D38-107
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08863.16 best YolD 35.7 1.00e-08 100.0% 79.8%
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ej9A02 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.86 52.0 6.50e-01 76.2% 100.0%
1kq1H00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.84 60.0 6.55e-01 86.3% 89.4%
4x9cD00 2.30.30.100 Mainly Beta › Roll › SH3 type barrels. › 0.83 55.0 6.29e-01 86.3% 91.7%
7afrX02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.78 54.0 6.10e-01 82.5% 96.7%
1zq1A01 2.30.30.520 Mainly Beta › Roll › SH3 type barrels. › 0.75 59.0 6.07e-01 91.3% 87.0%
2f5tX02 2.30.30.690 Mainly Beta › Roll › SH3 type barrels. › 0.68 58.0 5.58e-01 93.8% 91.1%
6my0A02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.66 44.0 4.74e-01 75.0% 83.1%
2jngA00 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.66 55.0 5.58e-01 96.2% 94.8%
6o5cA02 2.30.30.90 Mainly Beta › Roll › SH3 type barrels. › Ferrous iron transport protein A (FeoA) 0.64 51.0 5.23e-01 85.0% 92.1%
2btwA00 3.90.70.30 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Phytochelatin synthase, N-terminal domain 0.64 54.0 4.00e-01 93.8% 43.8%
7u32F02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.64 40.0 4.67e-01 75.0% 100.0%
1zvfB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 41.0 3.26e-01 96.2% 32.3%
2lccA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.62 43.0 4.46e-01 77.5% 77.6%
2qsdA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.61 41.0 4.45e-01 71.2% 82.1%
3agjF01 2.30.30.870 Mainly Beta › Roll › SH3 type barrels. › Pelota, domain A 0.61 52.0 4.53e-01 96.2% 71.7%
2egeA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.60 41.0 4.27e-01 71.2% 90.7%
1cv8A00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.60 47.0 3.79e-01 88.7% 49.7%
3fm2A00 3.40.1570.10 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › HemS/ChuS/ChuX like domains 0.59 48.0 4.09e-01 90.0% 73.7%
4qqgG00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 46.0 4.83e-01 88.7% 97.2%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.58 36.0 4.23e-01 71.2% 92.5%
3pp2A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.57 41.0 3.75e-01 77.5% 83.9%
1s3rA04 2.60.40.1430 Mainly Beta › Sandwich › Immunoglobulin-like › Perfringolysin, domain 4 0.55 41.0 3.69e-01 87.5% 56.8%
3cp7B02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.55 39.0 3.64e-01 85.0% 57.1%
1upqA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 38.0 3.56e-01 73.8% 82.2%
2i0nA01 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.55 37.0 4.21e-01 75.0% 98.2%
4emeC02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.54 43.0 3.73e-01 90.0% 92.6%
2imlA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.53 41.0 3.69e-01 85.0% 59.3%
2gtlM02 2.40.128.620 Mainly Beta › Beta Barrel › Lipocalin › 0.53 46.0 3.68e-01 100.0% 85.5%
2gtlN02 2.40.128.620 Mainly Beta › Beta Barrel › Lipocalin › 0.52 46.0 3.64e-01 100.0% 83.5%
1vwxS02 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 36.0 3.73e-01 72.5% 76.3%
1awoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.52 35.0 3.92e-01 76.2% 98.2%
6euaA01 3.90.215.10 Alpha Beta › Alpha-Beta Complex › Gamma Fibrinogen; Chain A, domain 1 › Gamma Fibrinogen, chain A, domain 1 0.52 44.0 3.73e-01 97.5% 64.7%
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.51 43.0 3.91e-01 95.0% 75.4%
5chtB00 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.51 45.0 3.09e-01 100.0% 70.0%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.51 40.0 3.07e-01 87.5% 74.0%
4qmaA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.51 35.0 3.02e-01 97.5% 41.3%
3e0jB00 3.90.1030.20 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › DNA polymerase delta, p66 (Cdc27) subunit, wHTH domain 0.50 44.0 3.63e-01 96.2% 56.6%
3dnhA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.50 40.0 3.36e-01 90.0% 88.7%
ECOD (79)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5004476 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.89 57.0 6.25e-01 81.2% 80.0%
4662294 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.88 58.0 6.92e-01 82.5% 98.2%
3289944 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.87 69.0 6.61e-01 85.0% 73.3%
3424637 4.1.1.313 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7912 0.86 69.0 6.51e-01 85.0% 93.7%
4975764 4.1.1.485 ↗ beta barrels › SH3 › SH3 › SH3 › DUF6897 0.86 60.0 6.44e-01 90.0% 82.9%
5024227 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.86 62.0 6.90e-01 81.2% 95.2%
5077969 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.86 73.0 7.37e-01 95.0% 90.0%
3587259 4.7.1.0 ↗ beta barrels › SH3 › RNase P subunit p29 › RNase P subunit p29 0.85 77.0 7.37e-01 95.0% 86.7%
4034320 4.1.1.398 ↗ beta barrels › SH3 › SH3 › SH3 › YolD 0.85 66.0 7.14e-01 85.0% 95.6%
5033892 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.85 63.0 6.90e-01 85.0% 95.4%
5063433 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.85 48.0 6.02e-01 71.2% 92.0%
3290160 4.1.1.323 ↗ beta barrels › SH3 › SH3 › SH3 › WYL 0.85 72.0 7.30e-01 96.2% 91.3%
4208040 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.84 63.0 6.59e-01 85.0% 84.9%
3286662 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.84 68.0 6.24e-01 92.5% 68.0%
4574546 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.84 63.0 6.93e-01 85.0% 95.4%
4122525 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.83 62.0 6.40e-01 85.0% 82.7%
4185009 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.83 60.0 6.60e-01 85.0% 92.3%
3519122 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.83 72.0 6.90e-01 92.5% 84.4%
3281271 4.31.1.1 ↗ beta barrels › SH3 › Central WYL domain of RspWYL1 › Central WYL domain of RspWYL1 › WYL 0.81 67.0 6.40e-01 91.3% 77.8%
4625654 4.1.1.445 ↗ beta barrels › SH3 › SH3 › SH3 › Spore_GerQ 0.80 63.0 6.56e-01 91.3% 89.3%
4118552 4.1.1.97 ↗ beta barrels › SH3 › SH3 › SH3 › DUF150_C 0.80 61.0 6.34e-01 86.3% 85.3%
4336500 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.78 49.0 5.69e-01 87.5% 92.7%
4252943 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.76 47.0 5.69e-01 82.5% 100.0%
5012604 219.1.1.51 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C39_2 0.76 63.0 4.60e-01 90.0% 35.7%
4585317 4.1.1.175 ↗ beta barrels › SH3 › SH3 › SH3 › MSSS 0.75 49.0 5.72e-01 93.8% 96.4%
3590784 4.1.1.297 ↗ beta barrels › SH3 › SH3 › SH3 › YajC 0.74 51.0 5.54e-01 93.8% 89.2%
5041801 4.15.1.0 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like 0.73 61.0 5.98e-01 90.0% 85.9%
4961940 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.73 60.0 5.52e-01 90.0% 86.7%
150293 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.73 60.0 5.67e-01 90.0% 84.4%
3967527 4216.1.1.1 ↗ a+b duplicates or obligate multimers › Heme iron utilization protein-like › Heme iron utilization protein-like › Heme iron utilization protein-like › HemS 0.70 58.0 4.51e-01 90.0% 55.6%
5025498 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.69 56.0 5.40e-01 88.7% 87.8%
5010832 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.69 58.0 5.67e-01 93.8% 93.3%
4400596 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.69 58.0 4.67e-01 93.8% 47.5%
5046498 219.1.1.51 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C39_2 0.68 54.0 4.24e-01 85.0% 45.5%
5026284 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.68 58.0 5.47e-01 93.8% 84.2%
4209798 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.68 57.0 5.65e-01 93.8% 91.8%
4581369 4.1.1.166 ↗ beta barrels › SH3 › SH3 › SH3 › DUF2314 0.67 58.0 5.31e-01 96.2% 86.7%
3759446 4.1.1.73 ↗ beta barrels › SH3 › SH3 › SH3 › Cul7 0.67 54.0 5.27e-01 96.2% 78.9%
4607738 4.1.1.17 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L19 0.66 55.0 5.00e-01 92.5% 69.1%
2978978 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.65 49.0 5.09e-01 81.2% 90.7%
3437523 4.1.1.303 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_retrovirus 0.65 47.0 4.93e-01 86.3% 87.1%
3615365 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.64 53.0 3.80e-01 90.0% 39.6%
3713334 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.64 45.0 4.98e-01 83.7% 100.0%
3704395 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.63 47.0 5.06e-01 90.0% 100.0%
3692073 4.1.1.92 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_9 0.63 42.0 4.47e-01 70.0% 84.3%
3275615 4.1.1.42 ↗ beta barrels › SH3 › SH3 › SH3 › Agenet 0.63 45.0 3.92e-01 86.3% 48.1%
3924619 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 54.0 4.77e-01 100.0% 67.5%
4020558 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 41.0 4.47e-01 70.0% 92.3%
3575959 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.61 50.0 4.55e-01 100.0% 66.4%
3714156 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 52.0 5.14e-01 97.5% 92.9%
3790897 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 51.0 4.74e-01 100.0% 75.0%
1758949 4216.1.1.1 ↗ a+b duplicates or obligate multimers › Heme iron utilization protein-like › Heme iron utilization protein-like › Heme iron utilization protein-like › HemS 0.60 50.0 4.16e-01 90.0% 68.4%
3712451 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 51.0 4.50e-01 97.5% 63.2%
3691622 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.60 49.0 5.10e-01 91.3% 97.3%
3244430 4.1.1.9 ↗ beta barrels › SH3 › SH3 › SH3 › TUDOR 0.60 49.0 4.51e-01 100.0% 68.6%
3485667 4.1.1.99 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_10 0.60 46.0 4.79e-01 85.0% 97.3%
3490689 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.59 45.0 4.78e-01 90.0% 94.3%
3523046 4.1.1.1 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_1 0.58 40.0 3.95e-01 71.2% 68.2%
169967 4216.1.1.2 ↗ a+b duplicates or obligate multimers › Heme iron utilization protein-like › Heme iron utilization protein-like › Heme iron utilization protein-like › ChuX_HutX 0.58 47.0 4.04e-01 90.0% 73.1%
4487949 220.1.1.69 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Meiotic_rec114 0.57 40.0 3.54e-01 73.8% 80.0%
3608562 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.57 49.0 3.97e-01 97.5% 70.4%
3778124 4.1.1.54 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_2 0.57 39.0 4.19e-01 71.2% 87.7%
1545880 4.1.1.278 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_YKFC_2nd 0.57 38.0 3.86e-01 70.0% 78.8%
3520654 4.1.1.187 ↗ beta barrels › SH3 › SH3 › SH3 › DIRP 0.56 49.0 4.05e-01 100.0% 76.7%
3489525 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.54 37.0 2.64e-01 71.2% 67.5%
3260733 220.1.1.158 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_LRR1 0.54 38.0 3.45e-01 73.8% 78.2%
4939745 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.53 46.0 3.44e-01 100.0% 72.3%
170199 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.52 45.0 3.40e-01 100.0% 75.9%
3907134 1.1.17.1 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 › Trypsin 0.52 45.0 3.35e-01 100.0% 72.7%
3836393 9.2.1.2 ↗ beta barrels › Lipocalins/Streptavidin › Avidin/Streptavidin › Avidin/Streptavidin › Vac_ImportDeg 0.52 38.0 3.02e-01 81.2% 87.8%
3501448 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.52 35.0 3.68e-01 71.2% 80.0%
4986859 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.52 45.0 3.08e-01 98.8% 31.5%
55 1.1.5.31 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_ox_2 0.51 40.0 3.11e-01 87.5% 77.8%
3632407 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.51 42.0 3.77e-01 92.5% 82.1%
4960009 862.1.1.5 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › LigD_Prim-Pol 0.51 44.0 3.04e-01 98.8% 33.7%
3180837 1.1.5.30 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_oxase_2 0.51 39.0 2.85e-01 86.3% 37.2%
3251320 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.50 34.0 2.47e-01 71.2% 52.2%
4625374 1.1.5.33 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Trypsin_2 0.50 43.0 3.19e-01 100.0% 70.0%
3636807 1.1.5.30 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › Pyridox_oxase_2 0.50 41.0 2.86e-01 92.5% 84.2%