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NC_019405.1__YP_006987902.1__D865_gp006__00006

Bact-Vir

NC_019405.1__YP_006987902.1__D865_gp006__00006

Identity

Accession:
NC_019405 ↗
Kingdom:
phage

Quality

83.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Jeanschmidtviridae› Shapirovirus› Caulobacter_phage_phiCbK

TaxID: 2927985

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

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

D1 high residues 7-60
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4llgM00 3.10.20.510 Alpha Beta › Roll › Ubiquitin-like (UB roll) › RNA polymerase inhibitor 0.78 63.0 6.49e-01 94.4% 96.0%
3egrA00 3.10.20.520 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phenylacetic acid degradation B 0.75 64.0 6.12e-01 96.3% 84.1%
3nrnA02 3.90.660.50 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.75 61.0 4.24e-01 90.7% 47.7%
3k7mX02 3.90.660.10 Alpha Beta › Alpha-Beta Complex › Polyamine Oxidase; Chain A, domain 2 › 0.74 62.0 4.12e-01 92.6% 35.9%
3ir9A02 3.30.1330.30 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Ribosomal protein L30/S12 0.64 53.0 4.11e-01 96.3% 42.5%
5o60I00 3.30.70.1730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein L10, N-terminal RNA-binding domain 0.63 54.0 4.19e-01 100.0% 75.4%
7zxkB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 53.0 4.54e-01 100.0% 59.1%
5of3A00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.60 51.0 3.19e-01 100.0% 67.1%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.60 49.0 3.65e-01 100.0% 92.2%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.60 50.0 4.30e-01 100.0% 93.5%
1o07A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.59 40.0 2.46e-01 75.9% 10.7%
2aehA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 50.0 4.24e-01 100.0% 91.7%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.59 44.0 4.27e-01 94.4% 72.7%
2edyA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 48.0 3.95e-01 100.0% 49.5%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.58 47.0 4.85e-01 92.6% 98.0%
1n7vA02 2.60.330.10 Mainly Beta › Sandwich › receptor-binding protein prd1-p2, domain 2 › receptor-binding protein prd1-p2, domain 2 0.58 42.0 3.30e-01 77.8% 35.8%
1dgsA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.58 48.0 4.11e-01 100.0% 70.5%
5e50A01 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.57 42.0 3.55e-01 83.3% 100.0%
2k2dA00 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.56 38.0 3.98e-01 83.3% 80.9%
3hrzC01 2.20.210.20 Mainly Beta › Single Sheet › ubp-family deubiquitinating enzyme fold › 0.56 43.0 4.44e-01 90.7% 91.8%
2w7qB00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.56 43.0 3.13e-01 90.7% 75.6%
2q0oA01 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.55 39.0 2.80e-01 74.1% 26.8%
4qq1C03 2.40.128.240 Mainly Beta › Beta Barrel › Lipocalin › 0.54 43.0 3.82e-01 94.4% 93.2%
2r1fA03 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.54 32.0 3.51e-01 77.8% 79.5%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.53 43.0 3.75e-01 100.0% 67.7%
5e4eC02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 44.0 3.73e-01 100.0% 53.5%
2b39A10 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.53 43.0 3.44e-01 92.6% 57.8%
2npnA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.53 40.0 3.38e-01 92.6% 45.0%
1yuzA02 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.52 34.0 3.91e-01 81.5% 94.7%
2p4zA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.51 42.0 2.79e-01 98.1% 72.4%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4013514 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.75 63.0 5.04e-01 92.6% 54.3%
5067865 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.75 63.0 5.75e-01 92.6% 81.4%
5007155 304.163.1.0 ↗ a+b two layers › Alpha-beta plaits › ATP-binding protein TM_1403 insertion domain › ATP-binding protein TM_1403 insertion domain 0.75 54.0 5.79e-01 88.9% 93.3%
5068178 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.70 59.0 4.87e-01 92.6% 67.4%
1836327 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.70 58.0 5.52e-01 92.6% 95.4%
4151900 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.70 60.0 4.39e-01 96.3% 38.9%
3730441 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.68 59.0 3.63e-01 100.0% 41.7%
5077796 304.104.1.1 ↗ a+b two layers › Alpha-beta plaits › Sulfolobus fructose-1,6-bisphosphatase-like › Sulfolobus fructose-1,6-bisphosphatase-like › FBPase_3 0.68 57.0 3.52e-01 100.0% 60.0%
4943252 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.68 58.0 4.25e-01 96.3% 39.3%
5747 4007.1.1.1 ↗ a+b two layers › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › a+b domain in YebC-like proteins › Transcrip_reg 0.67 51.0 5.16e-01 87.0% 85.2%
3395675 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.67 43.0 3.16e-01 74.1% 23.2%
5027350 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.67 56.0 4.16e-01 94.4% 37.7%
3994984 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.67 54.0 5.11e-01 92.6% 86.2%
5049794 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.66 55.0 4.11e-01 96.3% 39.3%
3504586 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.65 56.0 4.04e-01 96.3% 34.2%
5034902 301.1.1.2 ↗ a+b three layers › Bacillus chorismate mutase-like › L30e-like › L30e-like › eRF1_3 0.65 55.0 4.04e-01 94.4% 35.9%
3216210 3115.1.1.0 ↗ a+b two layers › GP2-like › RplX-like › RplX-like 0.65 51.0 5.22e-01 90.7% 96.0%
3917143 304.100.1.0 ↗ a+b two layers › Alpha-beta plaits › PurS-like › PurS-like 0.65 50.0 4.96e-01 90.7% 96.7%
3389022 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.65 45.0 4.62e-01 94.4% 80.0%
4152762 2492.1.1.20 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › APOBEC3 0.65 54.0 3.81e-01 100.0% 55.3%
3974655 223.3.1.3 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Transpeptidase 0.64 45.0 3.35e-01 74.1% 32.9%
3177995 5050.1.1.32 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Acatn 0.64 45.0 2.59e-01 92.6% 7.5%
4231372 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.64 49.0 4.66e-01 90.7% 100.0%
4625721 302.1.1.1 ↗ a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C 0.63 50.0 4.04e-01 92.6% 45.8%
5059354 2492.1.1.61 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › MOFRL 0.63 52.0 4.10e-01 100.0% 85.4%
3789334 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.63 53.0 4.25e-01 92.6% 52.4%
3278973 375.1.1.185 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Zn_ribbon_8 0.63 44.0 4.90e-01 81.5% 100.0%
3179826 11.1.1.642 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig-like_Pom152_1 0.63 53.0 4.15e-01 100.0% 58.4%
4448678 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.62 49.0 4.53e-01 94.4% 100.0%
4147528 4.1.1.307 ↗ beta barrels › SH3 › SH3 › SH3 › PF26132 0.61 47.0 4.43e-01 88.9% 100.0%
5018298 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.61 45.0 3.61e-01 81.5% 60.0%
4011483 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 49.0 4.03e-01 100.0% 61.7%
5047755 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.59 50.0 3.80e-01 100.0% 62.1%
3603767 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.59 49.0 3.96e-01 92.6% 53.3%
3193216 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.59 40.0 3.30e-01 75.9% 37.9%
4968352 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.58 48.0 4.16e-01 92.6% 64.7%
3637444 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.58 49.0 3.22e-01 98.1% 67.1%
3250180 223.3.1.6 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins › Peptidase_S13 0.58 40.0 2.91e-01 75.9% 30.0%
3239839 221.1.1.19 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › DCX 0.57 47.0 4.09e-01 98.1% 77.8%
3928714 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 46.0 4.00e-01 100.0% 55.8%
3187671 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.57 47.0 4.55e-01 92.6% 91.7%
3998576 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.57 42.0 3.03e-01 92.6% 25.7%
185296 862.1.1.4 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.57 46.0 3.28e-01 100.0% 62.3%
3704667 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.56 48.0 3.00e-01 100.0% 48.1%
3628791 3680.1.1.1 ↗ a+b complex topology › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › Zinc finger FYVE domain-containing protein 9 C-terminal domain › SARA_C 0.56 38.0 2.91e-01 75.9% 37.4%
3490257 11.1.4.75 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › NOMO_3rd 0.55 44.0 3.61e-01 100.0% 84.2%
3286547 223.3.1.0 ↗ a+b three layers › Profilin-like › a+b domain in beta-lactamase/transpeptidase-like proteins › a+b domain in beta-lactamase/transpeptidase-like proteins 0.54 38.0 2.82e-01 77.8% 82.5%
3260724 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.52 40.0 3.10e-01 100.0% 36.4%
4974400 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.51 44.0 2.86e-01 100.0% 55.6%