UHGV-0001399

Genome information

Genome length 33,437 bps

CDS count 56

Completeness 94.38% (high-quality)

geNomad score 0.9665

Prediction confidence Confident

Genome information
Genome ID	UHGV-0001399
vOTU ID	vOTU-014697
vOTU representative	Yes
Source dataset	Hadza
Original genome ID	Hadza_MoBio_hadza-E-H_E_6_1848__NODE_62_length_123979_cov_10.712797_1
BioSample	SAMEA4766070
Country	Tanzania
Virus prediction confidence	Confident

Quality assessment
CheckV method	AAI-based
CheckV completeness	94.38% (high-quality)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	19
CheckV host markers	1
Recoded stop codon	No

Viral signal
geNomad score	0.9665
Virus hallmark genes (geNomad)	10
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	54.48
Jumbo phage	No

Genome content
Genome length	33,437 bps
GC content	30.47%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	56
CDS density	93.76%
Average CDS length	561.86 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-0001399_1	eggNOG-mapper	1235802.C823_00136	NA	NA
UHGV-0001399_2	PHROG	phrog_6988	NA	unknown function
UHGV-0001399_2	UniRef90	UniRef90_G5F8B5	NA	NA
UHGV-0001399_2	eggNOG-mapper	635013.TherJR_2008	NA	NA
UHGV-0001399_2	PADLOC	ThsB1_00013	TIR-like	Thoeris
UHGV-0001399_2	Pfam	PF08937	Thoeris protein ThsB, TIR-like domain	ThsB_TIR
UHGV-0001399_2	Structural annotation	PF08937, MF_03036, TIGR03646, COG0758	NA	NA
UHGV-0001399_3	KOfam	K22299	rghR; HTH-type transcriptional regulator, competence development regulator	NA
UHGV-0001399_3	PHROG	phrog_8	transcriptional regulator	transcription regulation
UHGV-0001399_3	UniRef90	UniRef90_UPI001BCE5B8B	helix-turn-helix transcriptional regulator	NA
UHGV-0001399_3	eggNOG-mapper	340099.Teth39_2244	transcriptional regulator, XRE family	NA
UHGV-0001399_3	PADLOC	retron_type_VI_hth_cluster2_1	NA	Retron
UHGV-0001399_3	Pfam	PF01381	Helix-turn-helix	HTH_3
UHGV-0001399_3	COG	COG1476	DNA-binding transcriptional regulator, XRE-family HTH domain	NA
UHGV-0001399_3	Structural annotation	PF12844, MF_00535, NF041951, COG1476	NA	NA
UHGV-0001399_4	UniRef90	UniRef90_A0A3D0X5L0	HTH cro/C1-type domain-containing protein	NA
UHGV-0001399_4	eggNOG-mapper	272563.CD630_09071	sequence-specific DNA binding	NA
UHGV-0001399_4	Pfam	PF12844	Helix-turn-helix domain	HTH_19
UHGV-0001399_4	COG	COG3620	Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair)	NA
UHGV-0001399_4	Structural annotation	PF01381, NF041951, COG1476	NA	NA
UHGV-0001399_5	PHROG	phrog_989	NA	unknown function
UHGV-0001399_5	eggNOG-mapper	1540257.JQMW01000013_gene708	NA	NA
UHGV-0001399_5	Structural annotation	PF11372	NA	NA
UHGV-0001399_9	KOfam	K02086	dnaD; DNA replication protein	NA
UHGV-0001399_9	PHROG	phrog_186	DnaD-like helicase loader	DNA, RNA and nucleotide metabolism
UHGV-0001399_9	UniRef90	UniRef90_A0A318KSV9	DnaD/phage-associated family protein	NA
UHGV-0001399_9	eggNOG-mapper	428127.EUBDOL_01512	DnaD domain protein	NA
UHGV-0001399_9	Pfam	PF07261	Replication initiation and membrane attachment	DnaB_2
UHGV-0001399_9	NCBIFam	TIGR01446.1	DnaD domain protein	NA
UHGV-0001399_9	COG	COG3935	DNA replication protein DnaD	NA
UHGV-0001399_9	Structural annotation	PF10771, MF_01177, TIGR01610, COG0640	NA	NA
UHGV-0001399_10	PHROG	phrog_674	NA	unknown function
UHGV-0001399_10	UniRef90	UniRef90_A0A374N9T8	NA	NA
UHGV-0001399_10	eggNOG-mapper	1408437.JNJN01000039_gene373	NA	NA
UHGV-0001399_10	Pfam	PF07083	NA	DUF1351
UHGV-0001399_10	Structural annotation	PF07083	NA	NA
UHGV-0001399_11	KOfam	K07455	recT; recombination protein RecT	NA
UHGV-0001399_11	PHROG	phrog_148	RecT-like ssDNA annealing protein	DNA, RNA and nucleotide metabolism
UHGV-0001399_11	UniRef90	UniRef90_UPI00137B13AE	recombinase RecT	NA
UHGV-0001399_11	eggNOG-mapper	1095750.HMPREF9970_1675	RecT family	NA
UHGV-0001399_11	Pfam	PF03837	RecT family	RecT
UHGV-0001399_11	NCBIFam	TIGR00616.1	recombinase, phage RecT family	NA
UHGV-0001399_11	COG	COG3723	Recombinational DNA repair protein RecT	NA
UHGV-0001399_11	Structural annotation	PF03837, TIGR00616, COG3723	NA	NA
UHGV-0001399_12	KOfam	K06167	phnP; phosphoribosyl 1,2-cyclic phosphate phosphodiesterase [EC:3.1.4.55]	NA
UHGV-0001399_12	PHROG	phrog_392	metal-dependent hydrolase	other
UHGV-0001399_12	UniRef90	UniRef90_A0A353JB44	Lactamase_B domain-containing protein	NA
UHGV-0001399_12	eggNOG-mapper	665956.HMPREF1032_03101	May be involved in the transport of PQQ or its precursor to the periplasm	NA
UHGV-0001399_12	Pfam	PF12706	Beta-lactamase superfamily domain	Lactamase_B_2
UHGV-0001399_12	COG	COG1235	Phosphoribosyl 1,2-cyclic phosphate phosphodiesterase	NA
UHGV-0001399_12	Structural annotation	PF12706, MF_01818, TIGR03307, COG1234	NA	NA
UHGV-0001399_15	KOfam	K03111	ssb; single-strand DNA-binding protein	NA
UHGV-0001399_15	PHROG	phrog_44	single strand DNA binding protein	DNA, RNA and nucleotide metabolism
UHGV-0001399_15	UniRef90	UniRef90_A0A350H2L8	Single-stranded DNA-binding protein	NA
UHGV-0001399_15	eggNOG-mapper	698758.AXY_23960	Plays an important role in DNA replication, recombination and repair. Binds to ssDNA and to an array of partner proteins to recruit them to their sites of action during DNA metabolism	NA
UHGV-0001399_15	Pfam	PF00436	Single-strand binding protein family	SSB
UHGV-0001399_15	NCBIFam	TIGR00621.2	single-stranded DNA-binding protein	NA
UHGV-0001399_15	COG	COG0629	Single-stranded DNA-binding protein	NA
UHGV-0001399_15	HAMAP	MF_00984	Single-stranded DNA-binding protein	NA
UHGV-0001399_15	Structural annotation	PF00436, MF_00984, NF005241, COG0629	NA	NA
UHGV-0001399_18	KOfam	K07741	antB; anti-repressor protein	NA
UHGV-0001399_18	PHROG	phrog_63	anti-repressor Ant	transcription regulation
UHGV-0001399_18	UniRef90	UniRef90_A0A1C6EMR2	Phage anti-repressor protein	NA
UHGV-0001399_18	eggNOG-mapper	1035196.HMPREF9998_01733	NA	NA
UHGV-0001399_18	Pfam	PF08346	AntA/AntB antirepressor	AntA
UHGV-0001399_18	Pfam	PF03374	Phage antirepressor protein KilAC domain	ANT
UHGV-0001399_18	COG	COG3561	Phage anti-repressor protein Ant	NA
UHGV-0001399_18	Structural annotation	PF03374, PF08346, TIGR02681, TIGR04176, COG3561, COG3645	NA	NA
UHGV-0001399_19	KOfam	K01160	rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]	NA
UHGV-0001399_19	PHROG	phrog_1682	RusA-like Holliday junction resolvase	DNA, RNA and nucleotide metabolism
UHGV-0001399_19	UniRef90	UniRef90_G4D5I8	Prophage Lp2 protein 24	NA
UHGV-0001399_19	eggNOG-mapper	997350.HMPREF9129_1668	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-0001399_19	Pfam	PF05866	Endodeoxyribonuclease RusA	RusA
UHGV-0001399_19	COG	COG4570	Holliday junction resolvase RusA (prophage-encoded endonuclease)	NA
UHGV-0001399_19	Structural annotation	PF19595, NF007305, COG4570	NA	NA
UHGV-0001399_20	PHROG	phrog_1233	NA	unknown function
UHGV-0001399_20	UniRef90	UniRef90_R7IWF8	Peptidase_M78 domain-containing protein	NA
UHGV-0001399_20	Pfam	PF06114	IrrE N-terminal-like domain	Peptidase_M78
UHGV-0001399_20	Structural annotation	PF13058	NA	NA
UHGV-0001399_24	PHROG	phrog_10455	NA	unknown function
UHGV-0001399_24	UniRef90	UniRef90_R7IT47	Conserved domain protein	NA
UHGV-0001399_26	KOfam	K03744	lemA; LemA protein	NA
UHGV-0001399_26	PHROG	phrog_1383	virion structural protein	head and packaging
UHGV-0001399_26	UniRef90	UniRef90_A0A1Q6M2C0	LemA family protein	NA
UHGV-0001399_26	eggNOG-mapper	742735.HMPREF9467_00879	LemA family	NA
UHGV-0001399_26	Pfam	PF04011	LemA family	LemA
UHGV-0001399_26	COG	COG1704	Magnetosome formation protein MamQ, lipoprotein antigen LemA family	NA
UHGV-0001399_26	Structural annotation	PF04011, NF040966, COG1704	NA	NA
UHGV-0001399_27	PHROG	phrog_3886	NA	unknown function
UHGV-0001399_27	eggNOG-mapper	1497679.EP56_05675	NA	NA
UHGV-0001399_28	Structural annotation	PF10654	NA	NA
UHGV-0001399_29	Structural annotation	PF16535, PF04545	NA	NA
UHGV-0001399_30	PHROG	phrog_606	terminase small subunit	head and packaging
UHGV-0001399_30	UniRef90	UniRef90_A0A6M3XSH7	Putative terminase small subunit	NA
UHGV-0001399_30	eggNOG-mapper	931276.Cspa_c57180	DNA-packaging protein gp3	NA
UHGV-0001399_30	Pfam	PF16677	DNA-packaging protein gp3	GP3_package
UHGV-0001399_30	Structural annotation	PF16677	NA	NA
UHGV-0001399_31	KOfam	K06909	xtmB; phage terminase large subunit	NA
UHGV-0001399_31	PHROG	phrog_3717	terminase large subunit	head and packaging
UHGV-0001399_31	UniRef90	UniRef90_A0A6N7QVH7	PBSX family phage terminase large subunit	NA
UHGV-0001399_31	eggNOG-mapper	40522.A8ASJ2_BPA50	Pfam:Terminase_3C	NA
UHGV-0001399_31	Pfam	PF04466	Phage terminase large subunit	Terminase_3
UHGV-0001399_31	Pfam	PF17288	Terminase RNAseH like domain	Terminase_3C
UHGV-0001399_31	NCBIFam	TIGR01547.1	PBSX family phage terminase large subunit	NA
UHGV-0001399_31	Structural annotation	PF04466, PF17288, MF_04145, TIGR01547, COG1783	NA	NA
UHGV-0001399_32	PHROG	phrog_533	portal protein	head and packaging
UHGV-0001399_32	UniRef90	UniRef90_I3DY03	Putative portal protein	NA
UHGV-0001399_32	eggNOG-mapper	997296.PB1_16244	Phage portal protein, SPP1 Gp6-like	NA
UHGV-0001399_32	Pfam	PF05133	Phage portal protein, SPP1 Gp6-like	Phage_prot_Gp6
UHGV-0001399_32	Structural annotation	PF05133, MF_04120, TIGR01542, COG5511	NA	NA
UHGV-0001399_33	PHROG	phrog_581	minor head protein	head and packaging
UHGV-0001399_33	UniRef90	UniRef90_A0A6N7QW86	Minor capsid protein	NA
UHGV-0001399_33	eggNOG-mapper	997296.PB1_16234	Phage minor capsid protein 2	NA
UHGV-0001399_33	Pfam	PF06152	Phage minor capsid protein 2	Phage_min_cap2
UHGV-0001399_33	COG	COG2369	NA	NA
UHGV-0001399_33	Structural annotation	PF06152	NA	NA
UHGV-0001399_35	PHROG	phrog_918	NA	unknown function
UHGV-0001399_35	UniRef90	UniRef90_UPI00115A7D93	NA	NA
UHGV-0001399_35	eggNOG-mapper	469618.FVAG_01307	NA	NA
UHGV-0001399_35	Pfam	PF19791	NA	DUF6275
UHGV-0001399_35	Structural annotation	PF19791	NA	NA
UHGV-0001399_36	PHROG	phrog_2303	head scaffolding protein	head and packaging
UHGV-0001399_36	UniRef90	UniRef90_W7YV79	NA	NA
UHGV-0001399_36	eggNOG-mapper	1460640.JCM19046_3518	NA	NA
UHGV-0001399_37	UniRef90	UniRef90_D4LDZ8	p22 coat protein-gene protein 5	NA
UHGV-0001399_37	eggNOG-mapper	411471.SUBVAR_06993	NA	NA
UHGV-0001399_37	Pfam	PF09479	Listeria-Bacteroides repeat domain (List_Bact_rpt)	Flg_new
UHGV-0001399_40	PHROG	phrog_793	head-tail adaptor	connector
UHGV-0001399_40	UniRef90	UniRef90_UPI001A9D18B6	putative minor capsid protein	NA
UHGV-0001399_40	eggNOG-mapper	935836.JAEL01000021_gene1491	Minor capsid protein	NA
UHGV-0001399_40	Pfam	PF10665	Minor capsid protein	Minor_capsid_1
UHGV-0001399_40	COG	COG5652	VanZ-like family protein (function unknown)	NA
UHGV-0001399_40	Structural annotation	PF10665, TIGR01563, COG5614	NA	NA
UHGV-0001399_41	PHROG	phrog_556	minor head protein	head and packaging
UHGV-0001399_41	eggNOG-mapper	935836.JAEL01000086_gene48	Minor capsid protein	NA
UHGV-0001399_42	PHROG	phrog_2595	head-tail connector protein	connector
UHGV-0001399_42	Pfam	PF12691	Bacteriophage minor capsid protein	Minor_capsid_3
UHGV-0001399_45	PHROG	phrog_706	NA	unknown function
UHGV-0001399_45	Pfam	PF06854	Bacteriophage Gp15 protein	Phage_Gp15
UHGV-0001399_46	PHROG	phrog_1272	tail length tape measure protein	tail
UHGV-0001399_46	eggNOG-mapper	573061.Clocel_3533	tail tape measure protein	NA
UHGV-0001399_46	Pfam	PF10145	Phage-related minor tail protein	PhageMin_Tail
UHGV-0001399_46	NCBIFam	TIGR01760.1	phage tail tape measure protein	NA
UHGV-0001399_46	COG	COG5280	Phage-related minor tail protein	NA
UHGV-0001399_46	Structural annotation	PF10145, TIGR01760, COG5280	NA	NA
UHGV-0001399_47	eggNOG-mapper	1188235.MBVG_6920	NA	NA
UHGV-0001399_47	Structural annotation	PF14594, NF033848, COG4379	NA	NA
UHGV-0001399_48	Structural annotation	PF18975, MF_03022, TIGR04528, COG2706	NA	NA
UHGV-0001399_49	PHROG	phrog_24267	NA	unknown function
UHGV-0001399_49	UniRef90	UniRef90_R5LPM8	Putative truncated prophage LambdaSa1 minor structural protein	NA
UHGV-0001399_49	eggNOG-mapper	1035184.HMPREF1042_1210	NA	NA
UHGV-0001399_49	COG	COG4675	Phage tail collar domain	NA
UHGV-0001399_49	Structural annotation	COG4675	NA	NA
UHGV-0001399_51	PHROG	phrog_1863	NA	unknown function
UHGV-0001399_51	eggNOG-mapper	768486.EHR_09640	NA	NA
UHGV-0001399_53	KOfam	K01447	xlyAB; N-acetylmuramoyl-L-alanine amidase [EC:3.5.1.28]	NA
UHGV-0001399_53	PHROG	phrog_3088	amidase	lysis
UHGV-0001399_53	UniRef90	UniRef90_A0A3E3JYJ7	N-acetylmuramoyl-L-alanine amidase domain-containing protein	NA
UHGV-0001399_53	eggNOG-mapper	428125.CLOLEP_01782	N-acetylmuramoyl-L-alanine amidase	NA
UHGV-0001399_53	Pfam	PF01510	N-acetylmuramoyl-L-alanine amidase	Amidase_2
UHGV-0001399_53	COG	COG5632	N-acetylmuramoyl-L-alanine amidase CwlA	NA
UHGV-0001399_53	Structural annotation	PF01510, MF_04111, NF008758, COG5632	NA	NA
UHGV-0001399_56	eggNOG-mapper	1284352.AOIG01000022_gene3821	Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase	NA
UHGV-0001399_56	COG	COG0739	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain	NA
UHGV-0001399_56	Structural annotation	PF01832, NF007681, COG1705	NA	NA