UHGV-0008359

Genome information

Genome length 41,360 bps

CDS count 60

Completeness 86.06% (medium-quality)

geNomad score 0.9695

Prediction confidence Confident

Genome information
Genome ID	UHGV-0008359
vOTU ID	vOTU-034192
vOTU representative	Yes
Source dataset	Hadza
Original genome ID	Hadza_PheChl_Fiber-Hadza-Nepal_E_16_1654__NODE_4_length_467688_cov_12.685929_1
BioSample	SAMEA11460265
Country	Tanzania
Virus prediction confidence	Confident

Quality assessment
CheckV method	AAI-based
CheckV completeness	86.06% (medium-quality)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	13
CheckV host markers	0
Recoded stop codon	No

Viral signal
geNomad score	0.9695
Virus hallmark genes (geNomad)	11
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	44.58
Jumbo phage	No

Genome content
Genome length	41,360 bps
GC content	60.64%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	60
CDS density	87.04%
Average CDS length	601.80 bps
tRNA count	2
Suppressor tRNA genes	0

Genome content

Select view: Genome viewer Functional annotation

Functional annotation

Gene ID	Reference	Reference ID	Information	Category
UHGV-0008359_1	PHROG	phrog_962	holin	lysis
UHGV-0008359_1	UniRef90	UniRef90_A0A410PWW8	Phage holin	NA
UHGV-0008359_1	eggNOG-mapper	887929.HMP0721_1251	Bacteriophage holin	NA
UHGV-0008359_1	Pfam	PF04531	Bacteriophage holin	Phage_holin_1
UHGV-0008359_1	NCBIFam	TIGR01598.1	phage holin	NA
UHGV-0008359_1	COG	COG5546	NA	NA
UHGV-0008359_1	Structural annotation	COG5546	NA	NA
UHGV-0008359_3	KOfam	K14059	int; integrase	NA
UHGV-0008359_3	PHROG	phrog_1	integrase	integration and excision
UHGV-0008359_3	UniRef90	UniRef90_A0A5K1IJD6	Prophage phiRv2 integrase	NA
UHGV-0008359_3	eggNOG-mapper	445975.COLSTE_01092	Belongs to the 'phage' integrase family	NA
UHGV-0008359_3	Pfam	PF14659	Phage integrase, N-terminal SAM-like domain	Phage_int_SAM_3
UHGV-0008359_3	Pfam	PF00589	Phage integrase family	Phage_integrase
UHGV-0008359_3	COG	COG0582	Integrase/recombinase, includes phage integrase	NA
UHGV-0008359_3	Structural annotation	PF00589, PF14659, MF_02055, NF001399, COG4974	NA	NA
UHGV-0008359_9	eggNOG-mapper	1121866.AUGK01000003_gene1445	NA	NA
UHGV-0008359_10	PHROG	phrog_6616	tail protein	tail
UHGV-0008359_10	UniRef90	UniRef90_UPI00085BC306	tail fiber domain-containing protein	NA
UHGV-0008359_10	eggNOG-mapper	1121866.AUGK01000003_gene1439	Phage minor structural protein	NA
UHGV-0008359_10	COG	COG4926	Phage-related protein	NA
UHGV-0008359_10	Structural annotation	PF05113, NF033848, COG4379	NA	NA
UHGV-0008359_11	PHROG	phrog_1194	NA	unknown function
UHGV-0008359_11	eggNOG-mapper	1121866.AUGK01000003_gene1438	NA	NA
UHGV-0008359_11	Pfam	PF20458	NA	DUF6711
UHGV-0008359_11	Structural annotation	PF20458, TIGR02126, COG3499	NA	NA
UHGV-0008359_12	PHROG	phrog_1535	tail length tape measure protein	tail
UHGV-0008359_12	eggNOG-mapper	1121866.AUGK01000003_gene1437	phage tail tape measure protein	NA
UHGV-0008359_12	COG	COG1280	Threonine/homoserine/homoserine lactone efflux protein	NA
UHGV-0008359_14	UniRef90	UniRef90_UPI001106B496	NA	NA
UHGV-0008359_15	PHROG	phrog_158	major tail protein	tail
UHGV-0008359_15	UniRef90	UniRef90_UPI001106E87B	phage tail protein	NA
UHGV-0008359_15	eggNOG-mapper	60520.HR47_13435	Phage tail tube protein, TTP	NA
UHGV-0008359_15	Pfam	PF08813	Phage tail tube protein, TTP	Phage_tail_3
UHGV-0008359_15	Structural annotation	PF16463, TIGR02241, COG5437	NA	NA
UHGV-0008359_16	Structural annotation	PF06141, TIGR02367, COG3167	NA	NA
UHGV-0008359_17	Structural annotation	PF17395, TIGR01725, COG5005	NA	NA
UHGV-0008359_19	UniRef90	UniRef90_UPI001C9486FC	phage head-tail connector protein	NA
UHGV-0008359_19	Structural annotation	TIGR01560	NA	NA
UHGV-0008359_20	PHROG	phrog_247	major head protein	head and packaging
UHGV-0008359_20	UniRef90	UniRef90_UPI0009303115	major capsid protein	NA
UHGV-0008359_20	eggNOG-mapper	903814.ELI_3208	NA	NA
UHGV-0008359_20	Pfam	PF20036	Major capsid protein 13-like	Gp13-like
UHGV-0008359_20	Structural annotation	PF20036, MF_04113, TIGR04387, COG4653	NA	NA
UHGV-0008359_21	UniRef90	UniRef90_UPI001C9809E0	NA	NA
UHGV-0008359_21	Structural annotation	PF06810, MF_02110	NA	NA
UHGV-0008359_22	PHROG	phrog_64	portal protein	head and packaging
UHGV-0008359_22	UniRef90	UniRef90_A0A1H1L620	Phage portal protein, SPP1 family	NA
UHGV-0008359_22	eggNOG-mapper	1121866.AUGK01000003_gene1429	Phage portal protein, SPP1 Gp6-like	NA
UHGV-0008359_22	Pfam	PF05133	Phage portal protein, SPP1 Gp6-like	Phage_prot_Gp6
UHGV-0008359_22	Structural annotation	PF05133, MF_04120, TIGR01538, COG5511	NA	NA
UHGV-0008359_23	PHROG	phrog_38	terminase large subunit	head and packaging
UHGV-0008359_23	UniRef90	UniRef90_UPI001106681D	phage terminase large subunit	NA
UHGV-0008359_23	eggNOG-mapper	1121866.AUGK01000003_gene1428	chromosome segregation	NA
UHGV-0008359_23	NCBIFam	TIGR01630.1	phage terminase large subunit	NA
UHGV-0008359_23	COG	COG5410	NA	NA
UHGV-0008359_23	Structural annotation	PF17289, PF04466, MF_04147, NF033889, COG5410, COG5362	NA	NA
UHGV-0008359_25	KOfam	K14060	pinR; putative DNA-invertase from lambdoid prophage Rac	NA
UHGV-0008359_25	PHROG	phrog_125	DNA invertase	DNA, RNA and nucleotide metabolism
UHGV-0008359_25	UniRef90	UniRef90_UPI001BB21D57	recombinase family protein	NA
UHGV-0008359_25	eggNOG-mapper	1408423.JHYA01000001_gene988	Resolvase, N terminal domain	NA
UHGV-0008359_25	Pfam	PF00239	Resolvase, N terminal domain	Resolvase
UHGV-0008359_25	COG	COG1961	Site-specific DNA recombinase SpoIVCA/DNA invertase PinE	NA
UHGV-0008359_25	Structural annotation	PF00239, PF02796, MF_00489, NF009949, COG1961	NA	NA
UHGV-0008359_26	eggNOG-mapper	1232436.CAPF01000086_gene855	NA	NA
UHGV-0008359_27	PHROG	phrog_1373	transcriptional regulator	transcription regulation
UHGV-0008359_27	UniRef90	UniRef90_A0A1E8VUD2	HTH cro/C1-type domain-containing protein	NA
UHGV-0008359_27	Pfam	PF01381	Helix-turn-helix	HTH_3
UHGV-0008359_27	COG	COG3655	DNA-binding transcriptional regulator, XRE family	NA
UHGV-0008359_27	Structural annotation	PF20075, TIGR02612, COG1396	NA	NA
UHGV-0008359_32	Pfam	PF16677	DNA-packaging protein gp3	GP3_package
UHGV-0008359_34	PHROG	phrog_236	nucleotide kinase	other
UHGV-0008359_34	Pfam	PF11753	NA	DUF3310
UHGV-0008359_35	KOfam	K01520	dut, DUT; dUTP pyrophosphatase [EC:3.6.1.23]	NA
UHGV-0008359_35	PHROG	phrog_135	dUTPase	DNA, RNA and nucleotide metabolism
UHGV-0008359_35	UniRef90	UniRef90_UPI001E3E2DB2	dUTP diphosphatase	NA
UHGV-0008359_35	eggNOG-mapper	1121934.AUDX01000004_gene2520	This enzyme is involved in nucleotide metabolism it produces dUMP, the immediate precursor of thymidine nucleotides and it decreases the intracellular concentration of dUTP so that uracil cannot be incorporated into DNA	NA
UHGV-0008359_35	Pfam	PF00692	dUTPase	dUTPase
UHGV-0008359_35	NCBIFam	NF001862.0	dUTP diphosphatase	NA
UHGV-0008359_35	COG	COG0756	dUTP pyrophosphatase (dUTPase)	NA
UHGV-0008359_35	Structural annotation	PF00692, MF_00116, NF001862, COG0756	NA	NA
UHGV-0008359_36	Pfam	PF13560	Helix-turn-helix domain	HTH_31
UHGV-0008359_36	COG	COG1396	Transcriptional regulator, contains XRE-family HTH domain	NA
UHGV-0008359_37	Structural annotation	PF06530	NA	NA
UHGV-0008359_38	Pfam	PF20037	NA	DUF6440
UHGV-0008359_41	PHROG	phrog_1313	DNA helicase	DNA, RNA and nucleotide metabolism
UHGV-0008359_41	UniRef90	UniRef90_UPI0012DD8630	bifunctional DNA primase/polymerase	NA
UHGV-0008359_41	eggNOG-mapper	1232453.BAIF02000110_gene773	AAA domain	NA
UHGV-0008359_41	Pfam	PF09250	Bifunctional DNA primase/polymerase, N-terminal	Prim-Pol
UHGV-0008359_41	Pfam	PF08708	Primase C terminal 1 (PriCT-1)	PriCT_1
UHGV-0008359_41	Pfam	PF05272	Virulence-associated protein E-like domain	VapE-like_dom
UHGV-0008359_41	COG	COG3598	RecA-family ATPase	NA
UHGV-0008359_41	Structural annotation	PF05272, PF09250, PF08708, MF_00016, NF011296, COG5545	NA	NA
UHGV-0008359_42	PHROG	phrog_3490	ERCC4-type nuclease	DNA, RNA and nucleotide metabolism
UHGV-0008359_42	UniRef90	UniRef90_A0A1Q9J756	ERCC4 domain-containing protein	NA
UHGV-0008359_42	eggNOG-mapper	742742.HMPREF9452_00432	NA	NA
UHGV-0008359_42	Structural annotation	PF03834, NF040956, COG1948	NA	NA
UHGV-0008359_43	PHROG	phrog_18107	NA	unknown function
UHGV-0008359_43	eggNOG-mapper	742742.HMPREF9452_00433	NA	NA
UHGV-0008359_43	Structural annotation	PF05037	NA	NA
UHGV-0008359_44	PHROG	phrog_2872	Sak4-like ssDNA annealing protein	DNA, RNA and nucleotide metabolism
UHGV-0008359_44	UniRef90	UniRef90_UPI0012E4046A	AAA family ATPase	NA
UHGV-0008359_44	eggNOG-mapper	1304866.K413DRAFT_0827	AAA domain	NA
UHGV-0008359_44	Pfam	PF13479	AAA domain	AAA_24
UHGV-0008359_44	Structural annotation	PF13479, MF_00350, TIGR01618, COG0468	NA	NA
UHGV-0008359_46	KOfam	K03465	thyX, thy1; thymidylate synthase (FAD) [EC:2.1.1.148]	NA
UHGV-0008359_46	PHROG	phrog_85	thymidylate synthase	DNA, RNA and nucleotide metabolism
UHGV-0008359_46	UniRef90	UniRef90_A0A415UW88	Flavin-dependent thymidylate synthase	NA
UHGV-0008359_46	eggNOG-mapper	665956.HMPREF1032_03153	Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor, and NADPH and FADH(2) as the reductant	NA
UHGV-0008359_46	Pfam	PF02511	Thymidylate synthase complementing protein	Thy1
UHGV-0008359_46	NCBIFam	TIGR02170.1	FAD-dependent thymidylate synthase	NA
UHGV-0008359_46	COG	COG1351	Thymidylate synthase ThyX, FAD-dependent family	NA
UHGV-0008359_46	HAMAP	MF_01408	Flavin-dependent thymidylate synthase [thyX]	NA
UHGV-0008359_46	Structural annotation	PF02511, MF_01408, TIGR02170, COG1351	NA	NA
UHGV-0008359_48	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-0008359_49	PHROG	phrog_21525	NA	unknown function
UHGV-0008359_51	Structural annotation	PF18195, NF041655	NA	NA
UHGV-0008359_58	PHROG	phrog_4583	transcriptional repressor	transcription regulation
UHGV-0008359_58	eggNOG-mapper	521003.COLINT_02305	NA	NA
UHGV-0008359_58	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-0008359_58	Structural annotation	PF08667, NF041951, COG3655	NA	NA
UHGV-0008359_59	eggNOG-mapper	700015.Corgl_1280	IMG reference gene	NA
UHGV-0008359_59	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-0008359_59	Structural annotation	PF13560, NF041677, COG1396	NA	NA
UHGV-0008359_60	KOfam	K06400	spoIVCA; site-specific DNA recombinase	NA
UHGV-0008359_60	PHROG	phrog_95	integrase	integration and excision
UHGV-0008359_60	UniRef90	UniRef90_A0A3G9KAD9	Site-specific DNA recombinase	NA
UHGV-0008359_60	eggNOG-mapper	1203606.HMPREF1526_01314	Resolvase, N terminal domain	NA
UHGV-0008359_60	Pfam	PF00239	Resolvase, N terminal domain	Resolvase
UHGV-0008359_60	Pfam	PF07508	Recombinase	Recombinase
UHGV-0008359_60	COG	COG1961	Site-specific DNA recombinase SpoIVCA/DNA invertase PinE	NA
UHGV-0008359_60	Structural annotation	PF00239, PF07508, NF041201, COG1961	NA	NA