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NC_023502.1__YP_009003286.1__CC53_gp129__00129

Bact-Vir

NC_023502.1__YP_009003286.1__CC53_gp129__00129

Identity

Accession:
NC_023502 ↗
Kingdom:
phage

Quality

72.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Rhizobium_phage_vB_RleS_L338C

TaxID: 1414737

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 5-63
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.97 69.0 7.80e-01 72.9% 93.5%
2pihA00 1.20.1500.10 Mainly Alpha › Up-down Bundle › YheA-like fold › YheA/YmcA-like 0.95 67.0 5.05e-01 72.9% 35.0%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.92 65.0 5.21e-01 72.9% 41.7%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.91 64.0 5.78e-01 72.9% 57.9%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.90 67.0 7.24e-01 79.7% 90.2%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.89 62.0 5.66e-01 72.9% 57.9%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.89 62.0 5.07e-01 72.9% 42.2%
4malA00 1.20.58.2200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.89 61.0 6.14e-01 74.6% 71.2%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.89 62.0 6.37e-01 72.9% 76.8%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.88 66.0 6.19e-01 78.0% 66.7%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.88 61.0 5.72e-01 72.9% 70.4%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.87 63.0 6.67e-01 74.6% 84.6%
2qvaA02 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.87 64.0 6.79e-01 79.7% 86.8%
2wwxB00 1.20.1260.70 Mainly Alpha › Up-down Bundle › Ferritin › 0.86 59.0 3.95e-01 71.2% 21.0%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.86 60.0 4.85e-01 72.9% 40.6%
2rklF00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.86 60.0 6.42e-01 72.9% 82.7%
1nfvA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.85 78.0 5.48e-01 100.0% 73.4%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 77.0 5.69e-01 98.3% 89.1%
4i9cA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.84 74.0 4.86e-01 100.0% 25.3%
1zs3A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.84 76.0 5.33e-01 98.3% 76.6%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.84 64.0 5.88e-01 79.7% 67.1%
1s3qG00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 76.0 5.41e-01 100.0% 76.7%
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.83 66.0 7.17e-01 83.1% 100.0%
7e9uA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.83 76.0 4.45e-01 100.0% 30.3%
2chpA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.83 75.0 5.52e-01 100.0% 89.2%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.83 57.0 6.31e-01 71.2% 100.0%
3iq1B00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.82 75.0 5.39e-01 100.0% 83.0%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.82 75.0 5.54e-01 100.0% 92.4%
3bvoA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.82 74.0 6.46e-01 100.0% 84.9%
2fbaA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.81 72.0 4.19e-01 100.0% 29.7%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 73.0 5.30e-01 100.0% 89.3%
2ondA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.79 71.0 4.42e-01 100.0% 21.4%
3craB01 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 62.0 5.43e-01 84.7% 58.1%
4g09A03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.78 51.0 5.33e-01 84.7% 72.7%
1kaeA03 1.20.5.1300 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.77 51.0 5.25e-01 89.8% 72.7%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.76 69.0 6.35e-01 98.3% 90.5%
8fnyA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.76 64.0 4.35e-01 93.2% 28.2%
3tdvA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.76 64.0 4.39e-01 94.9% 98.1%
2katA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.75 69.0 5.43e-01 100.0% 72.2%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.74 68.0 5.23e-01 100.0% 75.8%
4dmvA01 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 66.0 5.83e-01 100.0% 78.8%
1dd3A01 1.20.5.710 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Single helix bin 0.73 60.0 6.08e-01 100.0% 93.0%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.73 62.0 4.74e-01 94.9% 42.0%
2crbA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.72 61.0 5.30e-01 100.0% 69.1%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.70 62.0 4.62e-01 100.0% 51.7%
1t3dA01 1.10.3130.10 Mainly Alpha › Orthogonal Bundle › serine acetyltransferase, domain 1 › serine acetyltransferase, domain 1 0.70 58.0 4.35e-01 89.8% 68.6%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.70 51.0 4.87e-01 79.7% 70.4%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.70 50.0 5.35e-01 79.7% 95.8%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.69 59.0 4.75e-01 98.3% 57.0%
4gmnA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.68 59.0 3.44e-01 100.0% 20.9%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.65 52.0 4.72e-01 88.1% 93.8%
5nl6A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 54.0 4.49e-01 100.0% 80.6%
6a2aA01 1.50.10.130 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Terpene synthase, N-terminal domain 0.58 47.0 3.33e-01 93.2% 69.7%
2nsaA00 1.10.3120.10 Mainly Alpha › Orthogonal Bundle › Trigger factor, domain 2 › Trigger factor, C-terminal domain 0.55 45.0 3.23e-01 86.4% 31.1%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4958554 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.96 68.0 4.31e-01 72.9% 18.3%
3561468 192.17.1.1 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.96 67.0 6.50e-01 72.9% 66.2%
3240245 192.17.1.1 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.96 67.0 7.33e-01 72.9% 86.0%
3560750 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.95 67.0 6.22e-01 72.9% 61.4%
5068187 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.95 65.0 5.93e-01 71.2% 56.8%
4530141 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 69.0 7.55e-01 79.7% 92.0%
2100231 604.12.1.7 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1_C 0.91 60.0 6.28e-01 71.2% 74.1%
3262528 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.91 64.0 5.66e-01 72.9% 53.8%
4642864 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.91 66.0 7.22e-01 79.7% 90.0%
5044069 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.91 63.0 5.63e-01 72.9% 55.0%
3967220 632.11.1.13 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › PF27144 0.89 63.0 6.09e-01 72.9% 67.2%
None — 0.89 69.0 3.94e-01 83.1% 9.3%
3275782 109.4.1.244 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RPN6_N 0.88 76.0 4.81e-01 98.3% 20.8%
5068968 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.86 59.0 5.56e-01 71.2% 60.0%
5051215 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.86 74.0 6.79e-01 98.3% 73.3%
4469597 192.17.1.11 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.86 74.0 7.69e-01 96.6% 98.2%
4966860 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.86 79.0 5.99e-01 100.0% 94.6%
4965788 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.85 79.0 5.81e-01 100.0% 94.3%
5071867 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.85 79.0 5.71e-01 100.0% 82.6%
4937924 632.18.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 0.85 59.0 5.28e-01 72.9% 53.8%
4947470 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.84 78.0 5.81e-01 100.0% 91.1%
165192 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.84 77.0 5.68e-01 98.3% 88.5%
3473214 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.84 76.0 5.31e-01 100.0% 72.8%
4508405 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.83 72.0 7.43e-01 98.3% 100.0%
4432094 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.83 64.0 7.14e-01 86.4% 100.0%
3885169 109.4.1.218 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SNAP 0.83 75.0 4.64e-01 98.3% 20.0%
3768113 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.82 70.0 6.34e-01 93.2% 70.7%
3397519 109.4.1.386 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Rapsyn_N 0.82 73.0 4.34e-01 98.3% 22.4%
2825526 109.4.1.1300 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_16, TPR_19 0.81 68.0 6.18e-01 94.9% 68.8%
3511431 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.81 73.0 4.50e-01 98.3% 19.4%
3412599 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.81 73.0 4.51e-01 98.3% 21.0%
3274862 109.4.1.218 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SNAP 0.81 73.0 4.52e-01 98.3% 20.3%
4582542 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.80 69.0 6.80e-01 93.2% 92.1%
1910276 109.4.1.1499 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_2, TPR_6, TPR_19 0.79 66.0 6.05e-01 93.2% 70.7%
4050574 192.17.1.11 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.79 66.0 6.06e-01 91.5% 70.7%
3598017 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 69.0 4.36e-01 100.0% 30.9%
5023512 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.77 71.0 4.23e-01 100.0% 15.7%
3999236 622.1.1.1 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › HSCB_C 0.76 70.0 5.59e-01 96.6% 67.6%
4468502 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.76 67.0 6.70e-01 96.6% 95.0%
169780 109.4.1.210 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_19 0.75 67.0 5.38e-01 96.6% 75.7%
2095496 109.4.1.1304 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_10, TPR_12 0.75 66.0 4.28e-01 98.3% 22.4%
3448742 109.7.1.4 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E › SNAP 0.75 67.0 6.33e-01 100.0% 95.7%
4218735 109.4.1.2787 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Suf, TPR_6, HAT_Syf1_CNRKL1_N 0.75 62.0 3.91e-01 98.3% 18.3%
3224 515.1.1.1 ↗ alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › STAT_int 0.74 68.0 5.23e-01 100.0% 75.8%
3999931 192.17.1.1 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.72 69.0 6.62e-01 100.0% 96.9%
3870409 109.4.1.2292 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_6, HAT_PRP39_N, HAT_PRP39_C 0.70 55.0 3.45e-01 94.9% 17.2%