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DNA_packaging_terminase_subunit_1

Euk-Vir

Macacine_alphaherpesvirus_1

DNA_packaging_terminase_subunit_1__NP_851874__Macacine_alphaherpesvirus_1__10325

Identity

Accession:
NP_851874 ↗
Protein ID:
DNA_packaging_terminase_subunit_1
Kingdom:
euk

Quality

70.1 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Simplexvirus› Macacine_alphaherpesvirus_1

TaxID: 10325

Cluster

View cluster (63 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 34-148
PDB
D2 high residues 479-727
PDB
Domain cluster: rep: rifcsphigho2-12_scaffold_combined_curated_prodigal-single.1__X__X__00331__D317-603
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02499.23 best DNA_pack_C 317.1 2.10e-94 100.0% 68.4%
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3n4pC00 3.30.420.320 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › DNA-packaging terminase, C-terminal nuclease domain 0.96 81.0 8.74e-01 100.0% 98.2%
3obwA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.83 39.0 5.78e-01 91.6% 97.5%
3c6aA00 3.30.420.240 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.78 58.0 6.49e-01 99.6% 94.9%
3wuhB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.73 45.0 5.28e-01 92.0% 86.3%
4af1A02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.72 38.0 5.29e-01 89.6% 100.0%
2vgnA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.70 37.0 5.07e-01 91.2% 99.2%
6feaB01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.69 37.0 4.80e-01 92.0% 88.4%
4ep4A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.68 45.0 5.50e-01 91.6% 100.0%
1z05A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.67 41.0 5.15e-01 92.0% 97.4%
4kreA04 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.63 45.0 4.53e-01 73.1% 98.1%
1jceA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 37.0 4.65e-01 90.4% 100.0%
1asuA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.57 34.0 4.11e-01 86.3% 87.7%
1wn9A00 3.40.1530.10 Alpha Beta › 3-Layer(aba) Sandwich › hypothetical protein tt1805 › TTHA1528-like 0.54 28.0 3.77e-01 98.0% 95.2%
7rheA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 35.0 4.14e-01 85.5% 93.7%
4c6sA00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.53 31.0 3.90e-01 92.0% 97.2%
6d92A01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.51 44.0 4.53e-01 91.2% 96.3%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1311096 2484.1.1.28 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pack_C 0.98 80.0 8.62e-01 97.6% 94.1%
4974990 2484.1.1.77 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Terminase_6C 0.85 59.0 7.06e-01 98.4% 100.0%
4975080 2484.1.1.77 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Terminase_6C 0.84 58.0 6.72e-01 98.4% 93.5%
5012088 2484.1.1.38 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 0.84 38.0 5.84e-01 90.0% 100.0%
4314343 2484.1.1.38 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 0.77 39.0 5.37e-01 92.4% 93.1%
4939492 2484.1.1.38 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › eRF1_2 0.75 37.0 5.22e-01 92.4% 95.2%
4296237 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.73 46.0 5.79e-01 88.0% 100.0%
3310760 2484.1.1.7 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_S11 0.73 36.0 4.90e-01 78.3% 90.0%
4543638 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.72 46.0 5.62e-01 89.6% 96.4%
4202129 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.72 46.0 5.73e-01 89.2% 100.0%
4484979 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.71 46.0 5.53e-01 90.4% 94.6%
1096260 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.71 45.0 5.59e-01 92.0% 100.0%
4529580 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.71 46.0 5.66e-01 90.4% 100.0%
4123278 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.71 46.0 5.56e-01 91.2% 95.9%
4162179 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.70 44.0 5.54e-01 88.4% 100.0%
4292358 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.70 44.0 5.40e-01 89.2% 95.2%
4669382 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.69 46.0 5.53e-01 92.0% 100.0%
4615831 2484.1.1.48 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.69 38.0 4.60e-01 90.8% 80.0%
4252006 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.69 45.0 5.56e-01 90.0% 100.0%
4162427 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.68 44.0 5.36e-01 89.2% 100.0%
4942159 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.67 34.0 4.31e-01 91.6% 79.3%
4631411 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.67 43.0 5.25e-01 90.0% 99.4%
4522962 2484.1.1.25 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RuvC 0.66 42.0 4.94e-01 91.6% 89.1%
3933761 2484.5.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase 0.66 35.0 4.82e-01 88.8% 100.0%
3924791 2484.5.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › RNaseH-like domain in reverse transcriptase › RNaseH-like domain in reverse transcriptase › RT_RNaseH 0.65 35.0 4.78e-01 90.0% 100.0%
5035771 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.65 34.0 4.67e-01 83.5% 96.9%
3255559 2484.1.1.26 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Piwi 0.65 46.0 4.62e-01 72.7% 93.1%
3696411 2484.1.1.26 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Piwi 0.64 45.0 4.23e-01 71.5% 97.4%
4010765 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.64 34.0 4.62e-01 81.5% 100.0%
3436324 2484.1.1.48 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MutS_II 0.64 42.0 4.50e-01 90.8% 75.8%
3934190 2484.1.1.212 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RT_RNaseH 0.64 33.0 4.62e-01 87.6% 100.0%
5003367 2484.1.1.23 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydantoinase_A 0.63 38.0 4.82e-01 81.5% 98.0%
3923414 2484.1.1.26 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Piwi 0.63 45.0 4.30e-01 73.1% 93.2%
3452376 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.62 34.0 4.38e-01 91.2% 91.0%
4264240 2002.1.1.53 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Ala_racemase_N 0.62 29.0 3.12e-01 96.4% 49.1%
1866051 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 44.0 4.37e-01 73.5% 98.5%
3226291 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 30.0 4.17e-01 94.8% 95.2%
4381671 2484.1.1.55 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.60 35.0 4.26e-01 84.7% 86.7%
4182115 2484.1.1.55 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.59 35.0 4.33e-01 83.5% 90.6%
3411385 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 43.0 4.84e-01 94.8% 98.9%
4371406 2484.1.1.55 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.59 38.0 4.40e-01 81.9% 89.7%
4553664 7590.1.1.7 ↗ a/b three-layered sandwiches › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › Middle domain in Argonaute homologs › MID_MedPIWI 0.57 40.0 3.89e-01 92.0% 63.9%
4531223 2484.1.1.55 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH_dom 0.56 40.0 4.45e-01 83.1% 90.8%
None — 0.56 35.0 3.88e-01 99.6% 76.5%
4976437 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.55 39.0 4.47e-01 71.1% 100.0%
4152191 2484.1.1.43 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Endonuclease_5 0.55 39.0 3.96e-01 71.5% 88.6%
3647053 2484.1.1.26 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Piwi 0.54 41.0 4.54e-01 80.7% 99.0%
4158833 2484.1.1.12 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Acetate_kinase 0.51 36.0 3.97e-01 72.3% 90.5%
3192419 2484.1.1.114 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Med13_C 0.51 44.0 4.51e-01 91.6% 92.6%
D3 medium residues 151-178_199-248
PDB
Domain cluster: rep: DNA_packaging_terminase_subunit_1__NP_944422__Psittacid_alphaherpesvirus_1__50294__D199-219_264-310
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02500.23 best DNA_pack_N 85.6 6.70e-24 100.0% 28.8%
D4 medium residues 249-414
PDB
Domain cluster: rep: KX578043.1__AOT27930.1__X__00015__D87-267
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF03237.22 best Terminase_6N 22.6 1.00e-04 90.4% 65.1%
PF02500.23 DNA_pack_N 172.9 1.60e-50 59.0% 36.5%
PF02499.23 DNA_pack_C 66.1 4.20e-18 25.9% 12.2%
D5 medium residues 415-472
PDB