UHGV-0040890

Genome information

Genome length 36,867 bps

CDS count 58

Completeness 100.00% (complete)

geNomad score 0.9799

Prediction confidence Confident

Genome information
Genome ID	UHGV-0040890
vOTU ID	vOTU-044854
vOTU representative	Yes
Source dataset	Hadza
Original genome ID	Nepal_MoBio_Fiber-Hadza-Nepal_D_19_CHE1008TZ__NODE_901_length_36912_cov_8.344944
BioSample	NA
Country	Nepal
Virus prediction confidence	Confident

Quality assessment
CheckV method	DTR
CheckV completeness	100.00% (complete)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	16
CheckV host markers	1
Recoded stop codon	No

Viral signal
geNomad score	0.9799
Virus hallmark genes (geNomad)	6
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	34.33
Jumbo phage	No

Genome content
Genome length	36,867 bps
GC content	46.37%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	58
CDS density	92.58%
Average CDS length	591.78 bps
tRNA count	0
Suppressor tRNA genes	0

Genome content

Select view: Genome viewer Functional annotation

Functional annotation

Gene ID	Reference	Reference ID	Information	Category
UHGV-0040890_2	PHROG	phrog_674	NA	unknown function
UHGV-0040890_2	UniRef90	UniRef90_A0A374N9T8	NA	NA
UHGV-0040890_2	eggNOG-mapper	665956.HMPREF1032_03103	NA	NA
UHGV-0040890_2	Pfam	PF07083	NA	DUF1351
UHGV-0040890_2	Structural annotation	PF07083	NA	NA
UHGV-0040890_3	PHROG	phrog_14970	NA	unknown function
UHGV-0040890_3	UniRef90	UniRef90_UPI00123F00F5	Rad52/Rad22 family DNA repair protein	NA
UHGV-0040890_3	eggNOG-mapper	411470.RUMGNA_02193	double-strand break repair protein	NA
UHGV-0040890_3	Pfam	PF04098	Rad52/22 family double-strand break repair protein	Rad52_Rad22
UHGV-0040890_3	COG	COG4712	Predicted ssDNA annealing protein, contains HHH motif, Rad42/Rad22/RecT/erf family	NA
UHGV-0040890_3	Structural annotation	PF04098, TIGR00607, COG4712	NA	NA
UHGV-0040890_4	PHROG	phrog_398	NA	unknown function
UHGV-0040890_4	UniRef90	UniRef90_UPI000489F9F0	putative HNHc nuclease	NA
UHGV-0040890_4	eggNOG-mapper	1485543.JMME01000021_gene802	Putative HNHc nuclease	NA
UHGV-0040890_4	Pfam	PF16784	Putative HNHc nuclease	HNHc_6
UHGV-0040890_4	Structural annotation	PF16784	NA	NA
UHGV-0040890_5	KOfam	K03111	ssb; single-strand DNA-binding protein	NA
UHGV-0040890_5	PHROG	phrog_44	single strand DNA binding protein	DNA, RNA and nucleotide metabolism
UHGV-0040890_5	UniRef90	UniRef90_A0A2V2G341	Single-stranded DNA-binding protein	NA
UHGV-0040890_5	eggNOG-mapper	1235835.C814_01372	Single-stranded DNA-binding protein	NA
UHGV-0040890_5	Pfam	PF00436	Single-strand binding protein family	SSB
UHGV-0040890_5	NCBIFam	TIGR00621.2	single-stranded DNA-binding protein	NA
UHGV-0040890_5	COG	COG0629	Single-stranded DNA-binding protein	NA
UHGV-0040890_5	HAMAP	MF_00984	Single-stranded DNA-binding protein	NA
UHGV-0040890_5	Structural annotation	PF00436, MF_00984, NF005241, COG0629	NA	NA
UHGV-0040890_6	PHROG	phrog_2514	DnaD-like helicase loader	DNA, RNA and nucleotide metabolism
UHGV-0040890_6	eggNOG-mapper	1384066.JAGT01000001_gene334	DnaD domain protein	NA
UHGV-0040890_6	Pfam	PF07261	Replication initiation and membrane attachment	DnaB_2
UHGV-0040890_6	NCBIFam	TIGR01446.1	DnaD domain protein	NA
UHGV-0040890_6	COG	COG3935	DNA replication protein DnaD	NA
UHGV-0040890_7	PHROG	phrog_757	DNA methyltransferase	other
UHGV-0040890_7	UniRef90	UniRef90_A0A355KVL2	DNA cytosine methyltransferase	NA
UHGV-0040890_7	eggNOG-mapper	748224.HMPREF9436_03069	DNA (cytosine-5-)-methyltransferase activity	NA
UHGV-0040890_7	COG	COG0270	DNA-cytosine methylase	NA
UHGV-0040890_7	Structural annotation	PF00145, MF_01872, TIGR00675, COG0270	NA	NA
UHGV-0040890_9	KOfam	K01160	rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]	NA
UHGV-0040890_9	PHROG	phrog_1682	RusA-like Holliday junction resolvase	DNA, RNA and nucleotide metabolism
UHGV-0040890_9	UniRef90	UniRef90_A0A6S6XJK5	Crossover junction endodeoxyribonuclease RusA	NA
UHGV-0040890_9	eggNOG-mapper	428125.CLOLEP_01819	Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC	NA
UHGV-0040890_9	COG	COG4570	Holliday junction resolvase RusA (prophage-encoded endonuclease)	NA
UHGV-0040890_9	Structural annotation	PF19595, NF007305, COG4570	NA	NA
UHGV-0040890_11	Structural annotation	PF09871, COG4014	NA	NA
UHGV-0040890_12	PHROG	phrog_478	site-specific recombination directionality factor RDF	integration and excision
UHGV-0040890_12	UniRef90	UniRef90_R6E548	Prophage pi1 protein 29	NA
UHGV-0040890_12	eggNOG-mapper	1111121.HMPREF1247_0834	NA	NA
UHGV-0040890_13	PHROG	phrog_801	endolysin; inhibits RNA polymerase	lysis
UHGV-0040890_13	UniRef90	UniRef90_A0A1M5RJM8	NA	NA
UHGV-0040890_13	eggNOG-mapper	1244856.K4PY83_9CAUD	Cytidine and deoxycytidylate deaminase zinc-binding region	NA
UHGV-0040890_13	Pfam	PF18909	dATP/dGTP diphosphohydrolase, N-terminal	dGTP_diPhyd_N
UHGV-0040890_17	AcrCatalog	cluster_47924	NA	NA
UHGV-0040890_18	eggNOG-mapper	1226322.HMPREF1545_00288	NA	NA
UHGV-0040890_19	PHROG	phrog_21498	NA	unknown function
UHGV-0040890_19	UniRef90	UniRef90_C7MM70	ParB-like nuclease	NA
UHGV-0040890_19	eggNOG-mapper	469378.Ccur_02830	DNA binding	NA
UHGV-0040890_19	COG	COG1475	Chromosome segregation protein Spo0J, contains ParB-like nuclease domain	NA
UHGV-0040890_19	Structural annotation	PF05869, TIGR01712	NA	NA
UHGV-0040890_21	KOfam	K06909	xtmB; phage terminase large subunit	NA
UHGV-0040890_21	PHROG	phrog_2	terminase large subunit	head and packaging
UHGV-0040890_21	UniRef90	UniRef90_UPI00137A4D1F	PBSX family phage terminase large subunit	NA
UHGV-0040890_21	eggNOG-mapper	411902.CLOBOL_00139	Phage terminase, large subunit, PBSX family	NA
UHGV-0040890_21	COG	COG1783	Phage terminase large subunit	NA
UHGV-0040890_21	Structural annotation	PF04466, PF20441, MF_04148, TIGR01547, COG1783	NA	NA
UHGV-0040890_22	PHROG	phrog_533	portal protein	head and packaging
UHGV-0040890_22	UniRef90	UniRef90_A0A136WBU7	Phage portal protein, SPP1 Gp6-like	NA
UHGV-0040890_22	eggNOG-mapper	641112.ACOK01000073_gene2889	NA	NA
UHGV-0040890_22	Structural annotation	PF05133, MF_04120, TIGR01542, COG5511	NA	NA
UHGV-0040890_23	PHROG	phrog_581	minor head protein	head and packaging
UHGV-0040890_23	UniRef90	UniRef90_A0A1C6B625	Phage minor capsid protein 2	NA
UHGV-0040890_23	eggNOG-mapper	693746.OBV_18050	Phage minor capsid protein 2	NA
UHGV-0040890_23	Pfam	PF06152	Phage minor capsid protein 2	Phage_min_cap2
UHGV-0040890_23	COG	COG2369	NA	NA
UHGV-0040890_23	Structural annotation	PF06152	NA	NA
UHGV-0040890_24	PHROG	phrog_194	head scaffolding protein	head and packaging
UHGV-0040890_24	UniRef90	UniRef90_A0A7T3RDX5	Phage scaffolding protein	NA
UHGV-0040890_24	eggNOG-mapper	536233.CLO_0885	Phage minor structural protein GP20	NA
UHGV-0040890_24	Pfam	PF06810	Phage minor structural protein GP20	Phage_GP20
UHGV-0040890_25	PHROG	phrog_422	major head protein	head and packaging
UHGV-0040890_25	UniRef90	UniRef90_A0A345MKD0	Main capsid protein	NA
UHGV-0040890_25	eggNOG-mapper	1160721.RBI_II00538	NA	NA
UHGV-0040890_25	Structural annotation	PF21703, MF_04119, TIGR04387, COG4834	NA	NA
UHGV-0040890_27	PHROG	phrog_541	head-tail adaptor	connector
UHGV-0040890_28	PHROG	phrog_3366	NA	unknown function
UHGV-0040890_28	Structural annotation	PF20536	NA	NA
UHGV-0040890_29	PHROG	phrog_556	minor head protein	head and packaging
UHGV-0040890_29	eggNOG-mapper	411461.DORFOR_01170	Minor capsid protein	NA
UHGV-0040890_29	Pfam	PF11114	Minor capsid protein	Minor_capsid_2
UHGV-0040890_29	Structural annotation	PF11114	NA	NA
UHGV-0040890_30	PHROG	phrog_3266	tail completion	connector
UHGV-0040890_30	Structural annotation	PF12691	NA	NA
UHGV-0040890_31	PHROG	phrog_3099	NA	unknown function
UHGV-0040890_31	eggNOG-mapper	1232443.BAIA02000078_gene23	NA	NA
UHGV-0040890_31	Structural annotation	PF10772, TIGR02126, COG3499	NA	NA
UHGV-0040890_32	PHROG	phrog_11299	NA	unknown function
UHGV-0040890_33	PHROG	phrog_706	NA	unknown function
UHGV-0040890_33	UniRef90	UniRef90_A0A2U1BEN4	Bacteriophage Gp15 protein	NA
UHGV-0040890_33	eggNOG-mapper	665956.HMPREF1032_03058	Bacteriophage Gp15 protein	NA
UHGV-0040890_33	Pfam	PF06854	Bacteriophage Gp15 protein	Phage_Gp15
UHGV-0040890_33	Structural annotation	PF06854	NA	NA
UHGV-0040890_34	PHROG	phrog_1535	tail length tape measure protein	tail
UHGV-0040890_34	UniRef90	UniRef90_S9TWQ7	Phage-like protein	NA
UHGV-0040890_34	eggNOG-mapper	1117108.PAALTS15_13517	minor tail protein	NA
UHGV-0040890_34	COG	COG1511	NA	NA
UHGV-0040890_34	Structural annotation	PF20155, TIGR01760, COG3941	NA	NA
UHGV-0040890_35	PHROG	phrog_1194	NA	unknown function
UHGV-0040890_35	eggNOG-mapper	1120998.AUFC01000030_gene2246	NA	NA
UHGV-0040890_35	Structural annotation	PF20458, TIGR01633, COG3499	NA	NA
UHGV-0040890_37	KOfam	K05996	cpt; carboxypeptidase T [EC:3.4.17.18]	NA
UHGV-0040890_37	PHROG	phrog_4722	zinc carboxypeptidase	other
UHGV-0040890_37	eggNOG-mapper	1540091.A0A0A0RV50_9CAUD	metallocarboxypeptidase activity	NA
UHGV-0040890_37	Pfam	PF00246	Zinc carboxypeptidase	Peptidase_M14
UHGV-0040890_40	PHROG	phrog_4105	NA	unknown function
UHGV-0040890_40	eggNOG-mapper	397288.C806_00056	NA	NA
UHGV-0040890_42	eggNOG-mapper	642492.Clole_0840	NA	NA
UHGV-0040890_43	KOfam	K19304	mepM; murein DD-endopeptidase [EC:3.4.24.-]	NA
UHGV-0040890_43	PHROG	phrog_7767	metallo-endopeptidase	other
UHGV-0040890_43	UniRef90	UniRef90_A0A2V2G827	SLH domain-containing protein	NA
UHGV-0040890_43	eggNOG-mapper	665956.HMPREF1032_00102	heme binding	NA
UHGV-0040890_43	Pfam	PF01551	Peptidase family M23	Peptidase_M23
UHGV-0040890_43	COG	COG0739	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain	NA
UHGV-0040890_44	UniRef90	UniRef90_A0A843IZ65	Sigma70_r4 domain-containing protein	NA
UHGV-0040890_44	Structural annotation	PF04545, MF_00245, NF001074, COG2739	NA	NA
UHGV-0040890_46	PHROG	phrog_16490	NA	unknown function
UHGV-0040890_46	eggNOG-mapper	641112.ACOK01000103_gene525	NA	NA
UHGV-0040890_47	Structural annotation	PF18573, NF033147	NA	NA
UHGV-0040890_48	Structural annotation	PF02255, TIGR00823, COG1447	NA	NA
UHGV-0040890_49	KOfam	K14059	int; integrase	NA
UHGV-0040890_49	PHROG	phrog_1	integrase	integration and excision
UHGV-0040890_49	UniRef90	UniRef90_A0A353J242	Site-specific integrase	NA
UHGV-0040890_49	eggNOG-mapper	742738.HMPREF9460_01344	Phage integrase family	NA
UHGV-0040890_49	Pfam	PF14659	Phage integrase, N-terminal SAM-like domain	Phage_int_SAM_3
UHGV-0040890_49	Pfam	PF00589	Phage integrase family	Phage_integrase
UHGV-0040890_49	COG	COG0582	Integrase/recombinase, includes phage integrase	NA
UHGV-0040890_49	Structural annotation	PF00589, PF12167, MF_02055, NF040815, COG4974	NA	NA
UHGV-0040890_50	PHROG	phrog_8545	superinfection exclusion Sie-like	moron, auxiliary metabolic gene and host takeover
UHGV-0040890_50	UniRef90	UniRef90_A0A7U9PG50	tRNA_anti	NA
UHGV-0040890_50	eggNOG-mapper	1203606.HMPREF1526_01637	tRNA_anti-like	NA
UHGV-0040890_50	Pfam	PF12869	tRNA_anti-like	tRNA_anti-like
UHGV-0040890_50	Structural annotation	PF12869, PF10571, MF_01959, TIGR03943, COG5235	NA	NA
UHGV-0040890_51	KOfam	K22300	dicA; HTH-type transcriptional regulator, cell division transcriptional repressor	NA
UHGV-0040890_51	PHROG	phrog_8	transcriptional regulator	transcription regulation
UHGV-0040890_51	UniRef90	UniRef90_A0A5D0CYS7	Helix-turn-helix transcriptional regulator	NA
UHGV-0040890_51	eggNOG-mapper	546270.GEMHA0001_0625	Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair	NA
UHGV-0040890_51	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-0040890_51	COG	COG1974	SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase)	NA
UHGV-0040890_51	Structural annotation	PF12844, NF041951, COG1476	NA	NA
UHGV-0040890_56	eggNOG-mapper	1403313.AXBR01000018_gene3548	Cell division suppressor protein YneA	NA
UHGV-0040890_56	COG	COG1388	LysM repeat	NA
UHGV-0040890_58	eggNOG-mapper	1235802.C823_04724	NA	NA