UHGV-0040480

Genome information

Genome length 41,240 bps

CDS count 55

Completeness 99.90% (high-quality)

geNomad score 0.9689

Prediction confidence Confident

Genome information
Genome ID	UHGV-0040480
vOTU ID	vOTU-009390
vOTU representative	Yes
Source dataset	Hadza
Original genome ID	Hadza_PheChl_Fiber-Hadza-Nepal_E_14_1557__NODE_1742_length_41240_cov_13.028618
BioSample	SAMEA4765847
Country	Tanzania
Virus prediction confidence	Confident

Quality assessment
CheckV method	AAI-based
CheckV completeness	99.90% (high-quality)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	11
CheckV host markers	2
Recoded stop codon	No

Viral signal
geNomad score	0.9689
Virus hallmark genes (geNomad)	9
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	39.9
Jumbo phage	No

Genome content
Genome length	41,240 bps
GC content	53.27%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	55
CDS density	89.25%
Average CDS length	671.67 bps
tRNA count	1
Suppressor tRNA genes	0

Genome content

Select view: Genome viewer Functional annotation

Functional annotation

Gene ID	Reference	Reference ID	Information	Category
UHGV-0040480_1	eggNOG-mapper	1203606.HMPREF1526_02295	CRISPR-associated protein Cse2 (CRISPR_cse2)	NA
UHGV-0040480_5	eggNOG-mapper	999413.HMPREF1094_04343	NA	NA
UHGV-0040480_5	Structural annotation	PF18847	NA	NA
UHGV-0040480_10	Structural annotation	PF16677	NA	NA
UHGV-0040480_11	KOfam	K06909	xtmB; phage terminase large subunit	NA
UHGV-0040480_11	PHROG	phrog_979	terminase large subunit	head and packaging
UHGV-0040480_11	UniRef90	UniRef90_A0A1M5YHQ5	Phage terminase large subunit	NA
UHGV-0040480_11	eggNOG-mapper	693746.OBV_01690	phage Terminase large subunit	NA
UHGV-0040480_11	Pfam	PF04466	Phage terminase large subunit	Terminase_3
UHGV-0040480_11	COG	COG1783	Phage terminase large subunit	NA
UHGV-0040480_11	Structural annotation	PF04466, PF20454, MF_04148, TIGR01547, COG1783	NA	NA
UHGV-0040480_13	PHROG	phrog_156	portal protein	head and packaging
UHGV-0040480_13	eggNOG-mapper	693746.OBV_01670	NA	NA
UHGV-0040480_13	Structural annotation	PF16510, MF_04120, TIGR01538, COG5511	NA	NA
UHGV-0040480_14	PHROG	phrog_4105	NA	unknown function
UHGV-0040480_15	PHROG	phrog_443	holin	lysis
UHGV-0040480_15	UniRef90	UniRef90_R6MWB0	Conserved domain protein	NA
UHGV-0040480_15	eggNOG-mapper	411490.ANACAC_00704	Putative lactococcus lactis phage r1t holin	NA
UHGV-0040480_15	Pfam	PF16945	Putative lactococcus lactis phage r1t holin	Phage_r1t_holin
UHGV-0040480_15	Structural annotation	PF16945	NA	NA
UHGV-0040480_16	KOfam	K01447	xlyAB; N-acetylmuramoyl-L-alanine amidase [EC:3.5.1.28]	NA
UHGV-0040480_16	PHROG	phrog_20388	endolysin	lysis
UHGV-0040480_16	UniRef90	UniRef90_R5HQL6	N-acetylmuramoyl-L-alanine amidase domain-containing protein	NA
UHGV-0040480_16	eggNOG-mapper	1226322.HMPREF1545_04024	N-acetylmuramoyl-L-alanine amidase	NA
UHGV-0040480_16	Pfam	PF01510	N-acetylmuramoyl-L-alanine amidase	Amidase_2
UHGV-0040480_16	COG	COG3023	N-acetyl-anhydromuramyl-L-alanine amidase AmpD	NA
UHGV-0040480_16	Structural annotation	PF01510, MF_04111, NF008758, COG5632	NA	NA
UHGV-0040480_17	PHROG	phrog_14606	NA	unknown function
UHGV-0040480_18	PHROG	phrog_422	major head protein	head and packaging
UHGV-0040480_18	UniRef90	UniRef90_A0A8J6JH37	Chitobiase/beta-hexosaminidase C-terminal domain-containing protein	NA
UHGV-0040480_18	eggNOG-mapper	755731.Clo1100_2434	NA	NA
UHGV-0040480_18	Structural annotation	PF19821, MF_04119, TIGR04387, COG4653	NA	NA
UHGV-0040480_19	eggNOG-mapper	1519439.JPJG01000011_gene57	NA	NA
UHGV-0040480_19	Structural annotation	PF11650	NA	NA
UHGV-0040480_20	UniRef90	UniRef90_A0A4D7ASB8	NA	NA
UHGV-0040480_20	eggNOG-mapper	693746.OBV_01680	NA	NA
UHGV-0040480_20	Structural annotation	PF11134, MF_03027, NF010237, TIGR03511, COG2319	NA	NA
UHGV-0040480_21	KOfam	K19721	COL5AS; collagen type V/XI/XXIV/XXVII, alpha	NA
UHGV-0040480_21	PHROG	phrog_819	tail protein	tail
UHGV-0040480_21	UniRef90	UniRef90_UPI001F4CFECE	collagen-like protein	NA
UHGV-0040480_21	Pfam	PF01391	Collagen triple helix repeat (20 copies)	Collagen
UHGV-0040480_23	PHROG	phrog_30034	NA	unknown function
UHGV-0040480_23	UniRef90	UniRef90_A0A8D9UHK2	Chitin oligosaccharide deacetylase	NA
UHGV-0040480_23	eggNOG-mapper	552398.HMPREF0866_04507	NA	NA
UHGV-0040480_23	Pfam	PF02839	Carbohydrate-binding module family 5/12	CBM_5_12
UHGV-0040480_23	Structural annotation	PF14600	NA	NA
UHGV-0040480_24	UniRef90	UniRef90_A0A1Y3RJS2	Sigma70_r4_2 domain-containing protein	NA
UHGV-0040480_27	PHROG	phrog_21483	NA	unknown function
UHGV-0040480_27	eggNOG-mapper	693746.OBV_01600	NA	NA
UHGV-0040480_28	UniRef90	UniRef90_A0A318L9Z0	MuF_C domain-containing protein	NA
UHGV-0040480_28	eggNOG-mapper	1408437.JNJN01000060_gene452	heme binding	NA
UHGV-0040480_28	Pfam	PF18798	Large polyvalent protein-associated domain 3	LPD3
UHGV-0040480_28	COG	COG0503	Adenine/guanine phosphoribosyltransferase or related PRPP-binding protein	NA
UHGV-0040480_30	PHROG	phrog_6721	NA	unknown function
UHGV-0040480_30	eggNOG-mapper	665956.HMPREF1032_00655	NA	NA
UHGV-0040480_30	Structural annotation	PF02511, MF_01408, TIGR02170, COG1351	NA	NA
UHGV-0040480_31	UniRef90	UniRef90_UPI0019572D92	NA	NA
UHGV-0040480_31	eggNOG-mapper	397290.C810_05229	NA	NA
UHGV-0040480_31	Structural annotation	PF14359, MF_03036, TIGR03646, COG3613	NA	NA
UHGV-0040480_32	PHROG	phrog_474	phosphofructokinase	other
UHGV-0040480_32	UniRef90	UniRef90_A0A1Y4SQK6	NA	NA
UHGV-0040480_32	eggNOG-mapper	1123247.AUIJ01000002_gene2234	NA	NA
UHGV-0040480_32	Pfam	PF19905	NA	DUF6378
UHGV-0040480_32	Structural annotation	PF19905	NA	NA
UHGV-0040480_35	Pfam	PF04448	NA	DUF551
UHGV-0040480_35	Structural annotation	PF04448, NF041588	NA	NA
UHGV-0040480_37	KOfam	K01494	dcd; dCTP deaminase [EC:3.5.4.13]	NA
UHGV-0040480_37	PHROG	phrog_1663	dCTP deaminase	DNA, RNA and nucleotide metabolism
UHGV-0040480_37	UniRef90	UniRef90_A0A3L7P3W4	dCTP deaminase, dUMP-forming	NA
UHGV-0040480_37	eggNOG-mapper	546269.HMPREF0389_00105	Belongs to the dCTP deaminase family	NA
UHGV-0040480_37	NCBIFam	TIGR02274.1	dCTP deaminase	NA
UHGV-0040480_37	COG	COG0717	dCTP deaminase	NA
UHGV-0040480_37	Structural annotation	PF06559, MF_00146, TIGR02274, COG0717	NA	NA
UHGV-0040480_38	KOfam	K01160	rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]	NA
UHGV-0040480_38	PHROG	phrog_34	RusA-like Holliday junction resolvase	DNA, RNA and nucleotide metabolism
UHGV-0040480_38	UniRef90	UniRef90_UPI0018ABA1B6	RusA family crossover junction endodeoxyribonuclease	NA
UHGV-0040480_38	eggNOG-mapper	796940.HMPREF9628_00163	Endodeoxyribonuclease RusA	NA
UHGV-0040480_38	Pfam	PF05866	Endodeoxyribonuclease RusA	RusA
UHGV-0040480_38	COG	COG4570	Holliday junction resolvase RusA (prophage-encoded endonuclease)	NA
UHGV-0040480_39	KOfam	K02314	dnaB; replicative DNA helicase [EC:5.6.2.3]	NA
UHGV-0040480_39	PHROG	phrog_19	DnaB-like replicative helicase	DNA, RNA and nucleotide metabolism
UHGV-0040480_39	UniRef90	UniRef90_A0A845R4R0	DNA helicase	NA
UHGV-0040480_39	eggNOG-mapper	742738.HMPREF9460_00852	Participates in initiation and elongation during chromosome replication	NA
UHGV-0040480_39	Pfam	PF00772	DnaB-like helicase N terminal domain	DnaB
UHGV-0040480_39	Pfam	PF03796	DnaB-like helicase C terminal domain	DnaB_C
UHGV-0040480_39	COG	COG0305	Replicative DNA helicase	NA
UHGV-0040480_39	Structural annotation	PF03796, PF00772, MF_04155, TIGR00665, COG0305	NA	NA
UHGV-0040480_40	eggNOG-mapper	411459.RUMOBE_01390	NA	NA
UHGV-0040480_41	PHROG	phrog_15768	NA	unknown function
UHGV-0040480_41	UniRef90	UniRef90_UPI0002D17810	helix-turn-helix domain-containing protein	NA
UHGV-0040480_41	eggNOG-mapper	658086.HMPREF0994_02124	NA	NA
UHGV-0040480_41	Pfam	PF13730	Helix-turn-helix domain	HTH_36
UHGV-0040480_41	COG	COG3935	DNA replication protein DnaD	NA
UHGV-0040480_41	Structural annotation	PF04492, MF_01819, NF040939, COG3355	NA	NA
UHGV-0040480_43	eggNOG-mapper	903814.ELI_1274	NA	NA
UHGV-0040480_43	Structural annotation	PF05037	NA	NA
UHGV-0040480_45	PHROG	phrog_2872	Sak4-like ssDNA annealing protein	DNA, RNA and nucleotide metabolism
UHGV-0040480_45	UniRef90	UniRef90_A0A8J6P193	AAA family ATPase	NA
UHGV-0040480_45	eggNOG-mapper	1449050.JNLE01000005_gene3946	AAA domain	NA
UHGV-0040480_45	Pfam	PF13479	AAA domain	AAA_24
UHGV-0040480_45	Structural annotation	PF13479, MF_00350, TIGR01618, COG0468	NA	NA
UHGV-0040480_48	Structural annotation	PF19157	NA	NA
UHGV-0040480_52	KOfam	K07741	antB; anti-repressor protein	NA
UHGV-0040480_52	PHROG	phrog_130	anti-repressor Ant	transcription regulation
UHGV-0040480_52	UniRef90	UniRef90_A0A6N2R468	Bro-N domain-containing protein	NA
UHGV-0040480_52	eggNOG-mapper	1321372.AQQB01000018_gene339	BRO family, N-terminal domain	NA
UHGV-0040480_52	Pfam	PF02498	BRO family, N-terminal domain	Bro-N
UHGV-0040480_52	Pfam	PF03374	Phage antirepressor protein KilAC domain	ANT
UHGV-0040480_52	COG	COG3617	Prophage antirepressor	NA
UHGV-0040480_52	Structural annotation	PF03374, PF02498, TIGR02681, COG3645	NA	NA
UHGV-0040480_53	PHROG	phrog_3	transcriptional repressor	transcription regulation
UHGV-0040480_53	UniRef90	UniRef90_UPI0005A988F9	helix-turn-helix domain-containing protein	NA
UHGV-0040480_53	eggNOG-mapper	460265.Mnod_2499	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-0040480_53	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-0040480_53	COG	COG1974	SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase)	NA
UHGV-0040480_53	Structural annotation	PF05339, NF002773, COG1476	NA	NA
UHGV-0040480_54	KOfam	K22299	rghR; HTH-type transcriptional regulator, competence development regulator	NA
UHGV-0040480_54	PHROG	phrog_8	transcriptional regulator	transcription regulation
UHGV-0040480_54	UniRef90	UniRef90_A0A6N3GQE1	Transcriptional repressor DicA	NA
UHGV-0040480_54	eggNOG-mapper	1567014.A0A0A7RTR3_9VIRU	protein disulfide oxidoreductase activity	NA
UHGV-0040480_54	Pfam	PF01381	Helix-turn-helix	HTH_3
UHGV-0040480_54	Structural annotation	PF13560, MF_00535, NF041951, COG3655	NA	NA
UHGV-0040480_55	KOfam	K14059	int; integrase	NA
UHGV-0040480_55	PHROG	phrog_1	integrase	integration and excision
UHGV-0040480_55	UniRef90	UniRef90_UPI00082B31A6	tyrosine-type recombinase/integrase	NA
UHGV-0040480_55	eggNOG-mapper	1507.HMPREF0262_00307	Phage integrase family	NA
UHGV-0040480_55	Pfam	PF00589	Phage integrase family	Phage_integrase
UHGV-0040480_55	COG	COG0582	Integrase/recombinase, includes phage integrase	NA
UHGV-0040480_55	Structural annotation	PF00589, PF14659, PF14657, MF_01808, TIGR02224, COG4974	NA	NA