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NC_048679.1__YP_009835535.1__HWB34_gp60__00060

Bact-Vir

Identity

Accession:: NC_048679 ↗
Kingdom:: phage

Quality

73.7 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nylescharonvirus› Leptospira_phage_LE4

TaxID: 2041383

Cluster

View cluster (3 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 12-66

PDB

Domain cluster: rep: IMGVR_UViG_3300029825_000506-3300029825-Ga0134835_100077716__D157-220

CATH (22)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3d9xA01	6.20.50.100	Special › Other non-globular › N-terminal domain of TfIIb ›	0.61	33.0	3.49e-01	74.5%	56.0%
3l7yA02	3.30.1240.10	Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 ›	0.57	41.0	3.30e-01	76.4%	65.1%
4r78A01	3.30.200.20	Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1	0.57	40.0	3.39e-01	76.4%	43.8%
5flmA02	3.30.1360.140	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 ›	0.57	43.0	3.26e-01	83.6%	49.3%
6qavC02	1.10.510.10	Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1	0.56	40.0	2.91e-01	80.0%	28.8%
3kxyJ00	3.30.1460.10	Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, ›	0.56	39.0	3.09e-01	76.4%	93.8%
5umbA02	3.90.640.10	Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › ATPase, substrate binding domain, subdomain 4	0.55	45.0	4.18e-01	96.4%	82.7%
4qmfB01	3.30.1370.10	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1	0.54	41.0	3.75e-01	89.1%	96.3%
3rh9A01	3.40.605.10	Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1	0.54	45.0	2.92e-01	98.2%	95.2%
1ecxB01	3.90.1150.10	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1	0.54	40.0	3.27e-01	83.6%	93.9%
6fjxA01	3.40.605.10	Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1	0.53	43.0	2.83e-01	94.5%	94.5%
5xnsC00	1.10.10.580	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E	0.53	34.0	3.22e-01	70.9%	51.4%
4jz6A01	3.40.605.10	Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1	0.53	39.0	2.57e-01	80.0%	81.0%
4k2mA02	3.90.1150.10	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1	0.53	41.0	3.12e-01	85.5%	93.1%
3aafA00	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	0.52	45.0	3.64e-01	98.2%	79.8%
1ku9B01	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	0.52	37.0	3.22e-01	76.4%	69.0%
2pulB01	3.30.200.20	Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1	0.52	33.0	2.87e-01	72.7%	38.0%
3l7wA00	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	0.52	44.0	3.64e-01	98.2%	62.9%
6qpqB00	1.10.10.580	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E	0.52	34.0	3.05e-01	72.7%	45.7%
3zcoA00	1.10.10.2450	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A ›	0.51	39.0	3.04e-01	83.6%	89.0%
2z3tA00	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.51	42.0	2.59e-01	98.2%	23.1%
5hs7B00	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	0.50	43.0	3.60e-01	98.2%	58.2%

ECOD (23)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3638956	101.1.2.309 ↗	alpha arrays › HTH › HTH › winged helix domain › GPAT_C	0.64	49.0	3.66e-01	85.5%	98.7%
3722159	5001.1.1.10 ↗	alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Ceramidase	0.64	55.0	3.46e-01	100.0%	45.7%
1548765	225.1.1.0 ↗	a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	0.63	44.0	3.60e-01	72.7%	48.0%
3183587	101.1.2.281 ↗	alpha arrays › HTH › HTH › winged helix domain › Tfb2	0.62	46.0	3.06e-01	80.0%	97.3%
4581259	1112.1.1.0 ↗	alpha arrays › MshE c-di-GMP-binding domain › MshE c-di-GMP-binding domain › MshE c-di-GMP-binding domain	0.61	44.0	4.29e-01	92.7%	70.0%
5049534	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.58	38.0	3.25e-01	76.4%	42.4%
3658810	304.109.1.4 ↗	a+b two layers › Alpha-beta plaits › Ribosomal proteins S24e, L23 and L15e › Ribosomal proteins S24e, L23 and L15e › Ribosomal_S24e	0.57	39.0	3.54e-01	74.5%	50.0%
4600617	101.1.2.25 ↗	alpha arrays › HTH › HTH › winged helix domain › FUR	0.56	42.0	3.13e-01	100.0%	30.7%
3179796	4291.1.1.1 ↗	beta barrels › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol_BP	0.56	40.0	2.36e-01	74.5%	65.7%
3579195	101.1.2.65 ↗	alpha arrays › HTH › HTH › winged helix domain › Rad21_Rec8	0.56	39.0	3.64e-01	74.5%	90.0%
3734793	222.1.1.15 ↗	a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT_3C	0.56	47.0	3.25e-01	96.4%	78.5%
4937013	101.1.2.39 ↗	alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA	0.55	39.0	3.50e-01	74.5%	84.0%
4817079	327.11.2.5 ↗	a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_8	0.55	44.0	3.96e-01	94.5%	82.9%
5071858	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.54	35.0	3.40e-01	72.7%	56.9%
1901867	7524.1.1.1 ↗	a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh	0.54	39.0	2.64e-01	78.2%	68.4%
1903283	7524.1.1.1 ↗	a/b three-layered sandwiches › ALDH-like › ALDH-like › ALDH-like › Aldedh	0.53	43.0	2.82e-01	90.9%	94.5%
3568995	101.1.2.65 ↗	alpha arrays › HTH › HTH › winged helix domain › Rad21_Rec8	0.53	34.0	3.25e-01	72.7%	52.9%
5040871	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.53	46.0	4.06e-01	98.2%	71.2%
3890261	101.1.2.65 ↗	alpha arrays › HTH › HTH › winged helix domain › Rad21_Rec8	0.51	33.0	3.17e-01	72.7%	53.6%
2081642	101.1.2.39 ↗	alpha arrays › HTH › HTH › winged helix domain › SMC_ScpA	0.51	32.0	3.12e-01	72.7%	51.5%
3486431	304.48.1.0 ↗	a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like	0.51	44.0	2.74e-01	98.2%	20.3%
3167163	101.1.2.65 ↗	alpha arrays › HTH › HTH › winged helix domain › Rad21_Rec8	0.50	33.0	2.84e-01	72.7%	38.9%
3785110	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.50	39.0	2.93e-01	83.6%	66.7%

D2 high residues 80-197

PDB

Domain cluster: rep: MK448940.1__QBX28202.1__Javan444_0040__00013__D85-185

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03837.20 best	RecT	38.9	9.70e-10	97.5%	36.5%

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1ah5A03	3.30.160.40	Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain	0.69	36.0	4.14e-01	96.6%	67.4%
4htgA03	3.30.160.40	Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain	0.61	32.0	3.70e-01	95.8%	69.6%
2rrfA00	2.30.29.160	Mainly Beta › Roll › PH-domain like › Zinc finger FYVE domain-containing protein 21, C-terminal	0.57	32.0	3.02e-01	84.7%	44.7%
3s98A01	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.55	31.0	3.62e-01	79.7%	79.3%
1v1cA00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.50	20.0	2.52e-01	88.1%	52.9%

ECOD (9)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3982792	330.1.1.14 ↗	a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › RecT	0.89	56.0	5.13e-01	100.0%	50.7%
5004275	330.1.1.14 ↗	a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › RecT	0.84	61.0	6.52e-01	100.0%	83.8%
4423403	330.1.1.14 ↗	a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › RecT	0.70	59.0	5.53e-01	100.0%	73.1%
5072832	2484.1.1.0 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like	0.62	35.0	3.18e-01	98.3%	39.4%
3517035	330.1.1.0 ↗	a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like	0.61	40.0	4.49e-01	97.5%	84.2%
3844858	220.1.1.39 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like › ZFYVE21_C	0.56	32.0	2.95e-01	88.1%	42.9%
3663326	292.2.1.1 ↗	a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › POLO_box	0.55	25.0	2.63e-01	83.1%	45.7%
4363805	292.2.1.9 ↗	a+b two layers › RIP/Polo-box domain › Polo-box domain › Polo-box domain › Polo_box_4	0.52	28.0	3.18e-01	81.4%	67.8%
3992964	11.1.1.1 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Cadherin	0.50	31.0	3.55e-01	97.5%	85.9%

D3 high residues 270-338

PDB

Domain cluster: representative

CATH (19)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4fymF00	3.40.50.2020	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold ›	0.87	71.0	4.93e-01	87.0%	38.3%
3t46A00	1.20.1270.10	Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 ›	0.82	55.0	5.41e-01	71.0%	64.0%
4u1cA01	4.10.860.10	Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain	0.81	58.0	6.53e-01	84.1%	100.0%
1konA01	1.10.10.200	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Integrase, N-terminal zinc-binding domain	0.79	57.0	5.83e-01	92.8%	76.5%
3nymA00	6.10.290.10	Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.78	57.0	4.69e-01	78.3%	78.2%
3craB01	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.77	58.0	5.30e-01	78.3%	72.1%
1vmgA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.76	55.0	5.17e-01	75.4%	64.6%
2yxhA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.76	54.0	4.52e-01	73.9%	54.9%
1luwA01	1.10.287.990	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain	0.75	56.0	5.84e-01	82.6%	85.9%
1wcrA00	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.74	65.0	5.74e-01	100.0%	94.2%
1grjA01	1.10.287.180	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Transcription elongation factor, GreA/GreB, N-terminal domain	0.74	55.0	5.45e-01	79.7%	82.4%
1yvwA00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.73	54.0	4.91e-01	78.3%	63.0%
3gonA02	3.30.70.890	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain	0.72	59.0	4.63e-01	87.0%	77.6%
3r6nA02	1.20.58.1060	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.70	62.0	4.81e-01	100.0%	55.5%
4h63K00	1.10.287.3490	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.68	51.0	4.56e-01	79.7%	58.2%
1e52A00	4.10.860.10	Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain	0.68	50.0	5.41e-01	81.2%	98.2%
3we0A03	1.10.405.40	Mainly Alpha › Orthogonal Bundle › Guanine Nucleotide Dissociation Inhibitor; domain 1 ›	0.63	47.0	3.78e-01	81.2%	65.7%
1tu9A00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.56	45.0	3.66e-01	88.4%	63.4%
1n69B00	1.10.225.10	Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like	0.51	36.0	3.45e-01	73.9%	72.5%

ECOD (23)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3470426	4274.1.1.0 ↗	extended segments › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region	0.91	68.0	6.29e-01	78.3%	63.5%
3481620	622.4.1.27 ↗	alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › TB2_DP1_HVA22	0.89	67.0	6.18e-01	78.3%	63.5%
3296414	192.29.1.168 ↗	alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF641	0.89	69.0	6.93e-01	81.2%	98.6%
3542527	5020.1.1.8 ↗	extended segments › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › Subunit VIII of photosystem I reaction centre, PsaI › TB2_DP1_HVA22	0.88	64.0	5.95e-01	76.8%	63.5%
3906647	5043.1.1.12 ↗	extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › TB2_DP1_HVA22	0.87	64.0	5.93e-01	76.8%	63.5%
4981305	3843.1.1.0 ↗	alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K	0.87	60.0	5.82e-01	71.0%	66.7%
3240245	192.17.1.1 ↗	alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn	0.86	60.0	6.94e-01	75.4%	100.0%
3971809	192.8.1.424 ↗	alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › H-kinase_dim	0.85	64.0	7.08e-01	79.7%	98.2%
5013251	3291.1.1.195 ↗	alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › H-kinase_dim	0.84	64.0	4.91e-01	81.2%	38.5%
4930198	605.1.1.2 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim	0.83	62.0	6.64e-01	79.7%	90.0%
4668964	604.9.1.0 ↗	alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20	0.83	75.0	7.00e-01	100.0%	87.1%
3513338	3877.1.1.0 ↗	alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC	0.82	55.0	3.74e-01	76.8%	21.3%
4995146	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	0.81	62.0	5.61e-01	81.2%	82.2%
3802185	192.8.1.359 ↗	alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF641	0.81	61.0	6.10e-01	81.2%	78.6%
5024703	3877.1.1.0 ↗	alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC	0.80	63.0	4.44e-01	82.6%	30.0%
4025810	3877.1.1.1 ↗	alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC › 60KD_IMP	0.79	53.0	3.53e-01	75.4%	18.5%
3738041	192.5.1.1 ↗	alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1	0.78	60.0	5.57e-01	82.6%	65.9%
5053329	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.78	57.0	4.63e-01	76.8%	43.3%
3980912	601.4.1.0 ↗	alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains	0.78	64.0	5.41e-01	91.3%	63.5%
4973347	515.1.1.4 ↗	alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › EMC3_TMCO1	0.77	60.0	4.40e-01	82.6%	33.5%
4127	159.1.2.2 ↗	alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › MazG-related › MazG	0.76	55.0	5.14e-01	75.4%	63.9%
4831662	5043.1.1.1 ↗	extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › Htr2	0.76	56.0	5.74e-01	78.3%	87.9%
3213282	616.1.1.21 ↗	alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › DUF4473	0.72	55.0	5.33e-01	81.2%	88.0%