UHGV-2040872

Genome information

Genome length 40,938 bps

CDS count 67

Completeness 90.55% (high-quality)

geNomad score 0.9811

Prediction confidence Confident

Genome information
Genome ID	UHGV-2040872
vOTU ID	vOTU-067889
vOTU representative	Yes
Source dataset	IMG/VR v4
Original genome ID	3300029339\|Ga0242823_1000235\|provirus_3_40940
BioSample	SAMN05545071
Country	United States
Virus prediction confidence	Confident

Quality assessment
CheckV method	AAI-based
CheckV completeness	90.55% (high-quality)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	15
CheckV host markers	1
Recoded stop codon	No

Viral signal
geNomad score	0.9811
Virus hallmark genes (geNomad)	10
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	42.79
Jumbo phage	No

Genome content
Genome length	40,938 bps
GC content	40.78%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	67
CDS density	90.91%
Average CDS length	559.03 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-2040872_1	PHROG	phrog_6616	tail protein	tail
UHGV-2040872_1	UniRef90	UniRef90_A0A2V2D052	Peptidase S74 domain-containing protein	NA
UHGV-2040872_1	eggNOG-mapper	1121866.AUGK01000003_gene1439	Phage minor structural protein	NA
UHGV-2040872_1	COG	COG4926	Phage-related protein	NA
UHGV-2040872_1	Structural annotation	PF05113, NF033848, COG3500	NA	NA
UHGV-2040872_2	Structural annotation	PF20458, TIGR02126, COG3499	NA	NA
UHGV-2040872_3	PHROG	phrog_1535	tail length tape measure protein	tail
UHGV-2040872_3	UniRef90	UniRef90_A0A173R880	Phage-related protein	NA
UHGV-2040872_3	eggNOG-mapper	476272.RUMHYD_01785	phage tail tape measure protein	NA
UHGV-2040872_3	COG	COG1511	NA	NA
UHGV-2040872_3	Structural annotation	PF20155, TIGR01760, COG3941	NA	NA
UHGV-2040872_4	PHROG	phrog_706	NA	unknown function
UHGV-2040872_4	UniRef90	UniRef90_UPI001BAD00AD	Gp15 family bacteriophage protein	NA
UHGV-2040872_4	eggNOG-mapper	411459.RUMOBE_01383	Bacteriophage Gp15 protein	NA
UHGV-2040872_4	Pfam	PF06854	Bacteriophage Gp15 protein	Phage_Gp15
UHGV-2040872_4	Structural annotation	PF06854	NA	NA
UHGV-2040872_5	PHROG	phrog_11299	NA	unknown function
UHGV-2040872_5	eggNOG-mapper	33035.JPJF01000106_gene3125	NA	NA
UHGV-2040872_5	Structural annotation	PF10666	NA	NA
UHGV-2040872_6	PHROG	phrog_3099	NA	unknown function
UHGV-2040872_6	eggNOG-mapper	411902.CLOBOL_00129	NA	NA
UHGV-2040872_6	Structural annotation	PF06199, TIGR02126, COG5437	NA	NA
UHGV-2040872_7	PHROG	phrog_3266	tail completion	connector
UHGV-2040872_7	eggNOG-mapper	476272.RUMHYD_01781	NA	NA
UHGV-2040872_7	Structural annotation	PF12691	NA	NA
UHGV-2040872_9	PHROG	phrog_3366	NA	unknown function
UHGV-2040872_9	eggNOG-mapper	476272.RUMHYD_01779	NA	NA
UHGV-2040872_9	Structural annotation	PF20536, COG5614	NA	NA
UHGV-2040872_10	PHROG	phrog_1129	holin	lysis
UHGV-2040872_10	UniRef90	UniRef90_A0A395X7B2	Enolase	NA
UHGV-2040872_10	eggNOG-mapper	411461.DORFOR_00721	NA	NA
UHGV-2040872_10	Pfam	PF16079	Phage holin family Hol44, in holin superfamily V	Phage_holin_5_2
UHGV-2040872_10	Structural annotation	PF06946	NA	NA
UHGV-2040872_11	PHROG	phrog_355	nucleoside 2-deoxyribosyltransferase	DNA, RNA and nucleotide metabolism
UHGV-2040872_11	UniRef90	UniRef90_A0A415G5B2	NA	NA
UHGV-2040872_11	eggNOG-mapper	397290.C810_05229	NA	NA
UHGV-2040872_11	Structural annotation	PF14359	NA	NA
UHGV-2040872_12	PHROG	phrog_541	head-tail adaptor	connector
UHGV-2040872_12	eggNOG-mapper	476272.RUMHYD_01778	NA	NA
UHGV-2040872_13	PHROG	phrog_544	major head protein	head and packaging
UHGV-2040872_13	UniRef90	UniRef90_A0A395X7A1	S-l_SbsC_C domain-containing protein	NA
UHGV-2040872_13	eggNOG-mapper	1232453.BAIF02000011_gene3359	NA	NA
UHGV-2040872_13	Pfam	PF18316	S-layer protein SbsC C-terminal domain	S-l_SbsC_C
UHGV-2040872_13	Structural annotation	PF03864, PF18316, MF_04119, TIGR04387, COG4653	NA	NA
UHGV-2040872_14	PHROG	phrog_194	head scaffolding protein	head and packaging
UHGV-2040872_14	UniRef90	UniRef90_UPI001D14C9C8	phage scaffolding protein	NA
UHGV-2040872_14	eggNOG-mapper	476272.RUMHYD_01775	COG NOG36366 non supervised orthologous group	NA
UHGV-2040872_14	Pfam	PF06810	Phage minor structural protein GP20	Phage_GP20
UHGV-2040872_15	PHROG	phrog_28802	NA	unknown function
UHGV-2040872_15	eggNOG-mapper	476272.RUMHYD_01772	NA	NA
UHGV-2040872_16	PHROG	phrog_20016	NA	unknown function
UHGV-2040872_16	UniRef90	UniRef90_A0A285PT46	Tumour necrosis factor-like domain	NA
UHGV-2040872_16	eggNOG-mapper	397290.C810_05214	NA	NA
UHGV-2040872_16	Structural annotation	PF18573, NF033147	NA	NA
UHGV-2040872_17	PHROG	phrog_16490	NA	unknown function
UHGV-2040872_17	eggNOG-mapper	397290.C810_01328	NA	NA
UHGV-2040872_18	PHROG	phrog_22984	NA	unknown function
UHGV-2040872_19	PHROG	phrog_21718	NA	unknown function
UHGV-2040872_19	eggNOG-mapper	397290.C810_05210	NA	NA
UHGV-2040872_20	UniRef90	UniRef90_A0A395X7A4	CTP synthase	NA
UHGV-2040872_20	eggNOG-mapper	476272.RUMHYD_01766	NA	NA
UHGV-2040872_21	PHROG	phrog_3754	NA	unknown function
UHGV-2040872_21	eggNOG-mapper	476272.RUMHYD_01764	NA	NA
UHGV-2040872_22	PHROG	phrog_581	minor head protein	head and packaging
UHGV-2040872_22	UniRef90	UniRef90_UPI001C0EDE82	phage minor capsid protein	NA
UHGV-2040872_22	eggNOG-mapper	642492.Clole_0816	NA	NA
UHGV-2040872_22	Pfam	PF06152	Phage minor capsid protein 2	Phage_min_cap2
UHGV-2040872_22	COG	COG2369	NA	NA
UHGV-2040872_22	Structural annotation	PF06152	NA	NA
UHGV-2040872_23	PHROG	phrog_556	minor head protein	head and packaging
UHGV-2040872_23	UniRef90	UniRef90_UPI001C0ECC47	minor capsid protein	NA
UHGV-2040872_23	eggNOG-mapper	1449343.JQLQ01000002_gene1329	Minor capsid protein	NA
UHGV-2040872_23	Pfam	PF11114	Minor capsid protein	Minor_capsid_2
UHGV-2040872_23	Structural annotation	PF11114	NA	NA
UHGV-2040872_24	PHROG	phrog_533	portal protein	head and packaging
UHGV-2040872_24	UniRef90	UniRef90_A0A1C6CDM8	Phage portal protein, putative, A118 family	NA
UHGV-2040872_24	eggNOG-mapper	33035.JPJF01000106_gene3135	phage minor capsid protein	NA
UHGV-2040872_24	Structural annotation	PF05133, MF_04120, TIGR01542, COG5511	NA	NA
UHGV-2040872_26	KOfam	K06909	xtmB; phage terminase large subunit	NA
UHGV-2040872_26	PHROG	phrog_3717	terminase large subunit	head and packaging
UHGV-2040872_26	UniRef90	UniRef90_A0A395X9V4	PBSX family phage terminase large subunit	NA
UHGV-2040872_26	eggNOG-mapper	397291.C804_01612	Phage terminase large subunit	NA
UHGV-2040872_26	Pfam	PF04466	Phage terminase large subunit	Terminase_3
UHGV-2040872_26	NCBIFam	TIGR01547.1	PBSX family phage terminase large subunit	NA
UHGV-2040872_26	COG	COG1783	Phage terminase large subunit	NA
UHGV-2040872_26	Structural annotation	PF04466, PF17288, MF_04145, TIGR01547, COG1783	NA	NA
UHGV-2040872_27	PHROG	phrog_606	terminase small subunit	head and packaging
UHGV-2040872_27	UniRef90	UniRef90_UPI00195648BB	DNA-packaging protein	NA
UHGV-2040872_27	eggNOG-mapper	397290.C810_05185	DNA-packaging protein gp3	NA
UHGV-2040872_27	Pfam	PF16677	DNA-packaging protein gp3	GP3_package
UHGV-2040872_27	Structural annotation	PF16677	NA	NA
UHGV-2040872_28	eggNOG-mapper	411459.RUMOBE_01385	NA	NA
UHGV-2040872_28	AcrCatalog	cluster_11670	NA	NA
UHGV-2040872_29	PHROG	phrog_10714	NA	unknown function
UHGV-2040872_32	eggNOG-mapper	1235793.C809_02210	NA	NA
UHGV-2040872_32	Structural annotation	PF09038	NA	NA
UHGV-2040872_34	PHROG	phrog_20593	NA	unknown function
UHGV-2040872_35	PHROG	phrog_22740	NA	unknown function
UHGV-2040872_35	UniRef90	UniRef90_A0A174XE96	DNA N-6-adenine-methyltransferase of bacteriophage	NA
UHGV-2040872_35	eggNOG-mapper	411468.CLOSCI_00567	DNA N-6-adenine-methyltransferase	NA
UHGV-2040872_35	PADLOC	oMTase_00015	orphan methyltransferase	RM
UHGV-2040872_35	Pfam	PF05869	DNA N-6-adenine-methyltransferase (Dam)	Dam
UHGV-2040872_37	PHROG	phrog_4601	NA	unknown function
UHGV-2040872_37	Structural annotation	PF17888	NA	NA
UHGV-2040872_38	KOfam	K19779	ralR; endodeoxyribonuclease RalR [EC:3.1.-.-]	NA
UHGV-2040872_38	PHROG	phrog_599	Lar-like restriction alleviation protein	moron, auxiliary metabolic gene and host takeover
UHGV-2040872_38	UniRef90	UniRef90_A0A317UED7	Restriction alleviation protein, Lar family	NA
UHGV-2040872_38	Pfam	PF14354	Restriction alleviation protein Lar	Lar_restr_allev
UHGV-2040872_38	NCBIFam	TIGR03655.1	Lar family restriction alleviation protein	NA
UHGV-2040872_38	dbAPIS	APIS033	Lar is functionally similar to RaI, is able to alleviate restriction and enhance modification by EcoKI. And the nucleotide sequences of their genes share 47% identity, indicating a common origin.	NA
UHGV-2040872_39	Structural annotation	NF041070	NA	NA
UHGV-2040872_40	KOfam	K00558	DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37]	NA
UHGV-2040872_40	PHROG	phrog_116	DNA methyltransferase	other
UHGV-2040872_40	UniRef90	UniRef90_A0A3E5ENN5	DNA (cytosine-5-)-methyltransferase	NA
UHGV-2040872_40	eggNOG-mapper	1499683.CCFF01000017_gene2594	PFAM C-5 cytosine-specific DNA methylase	NA
UHGV-2040872_40	PADLOC	MTase_II_00058	Type II methyltransferase	RM
UHGV-2040872_40	Pfam	PF00145	C-5 cytosine-specific DNA methylase	DNA_methylase
UHGV-2040872_40	NCBIFam	TIGR00675.1	DNA (cytosine-5-)-methyltransferase	NA
UHGV-2040872_40	COG	COG0270	DNA-cytosine methylase	NA
UHGV-2040872_40	Structural annotation	PF00145, PF05203, PF13847, MF_01420, TIGR00675, NF005852, COG1372, COG0270	NA	NA
UHGV-2040872_43	UniRef90	UniRef90_A0A6L8SWV5	Winged helix-turn-helix transcriptional regulator	NA
UHGV-2040872_43	Structural annotation	PF01726, COG0640	NA	NA
UHGV-2040872_45	KOfam	K15255	PIF1; ATP-dependent DNA helicase PIF1 [EC:5.6.2.3]	NA
UHGV-2040872_45	PHROG	phrog_325	Dda-like helicase	DNA, RNA and nucleotide metabolism
UHGV-2040872_45	UniRef90	UniRef90_A0A2V2D011	AAA domain-containing protein	NA
UHGV-2040872_45	eggNOG-mapper	1121333.JMLH01000003_gene334	PIF1-like helicase	NA
UHGV-2040872_45	PADLOC	cluster10	RecD_0_IVD	CRISPR-CAS
UHGV-2040872_45	Pfam	PF05970	PIF1-like helicase	PIF1
UHGV-2040872_45	COG	COG0507	ATPase/5'-3' helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V)	NA
UHGV-2040872_45	Structural annotation	PF05970, PF16277, MF_03176, TIGR01448, COG0507	NA	NA
UHGV-2040872_46	PHROG	phrog_8841	DNA primase/helicase	DNA, RNA and nucleotide metabolism
UHGV-2040872_46	UniRef90	UniRef90_A0A3A6GQS5	NA	NA
UHGV-2040872_46	eggNOG-mapper	411460.RUMTOR_02070	NA	NA
UHGV-2040872_46	Pfam	PF06048	NA	DUF927
UHGV-2040872_46	Pfam	PF18662	Cch helix turn helix domain	HTH_56
UHGV-2040872_46	COG	COG5519	NA	NA
UHGV-2040872_46	Structural annotation	PF06048, PF18662, MF_00016, NF011296, COG5519	NA	NA
UHGV-2040872_47	KOfam	K02316	dnaG; DNA primase [EC:2.7.7.101]	NA
UHGV-2040872_47	PHROG	phrog_11992	NA	unknown function
UHGV-2040872_47	UniRef90	UniRef90_A0A3A6GSV7	DNA primase	NA
UHGV-2040872_47	eggNOG-mapper	411460.RUMTOR_02069	CHC2 zinc finger	NA
UHGV-2040872_47	PADLOC	drt-UG29	DRT	DRT
UHGV-2040872_47	Pfam	PF01807	CHC2 zinc finger	zf-CHC2
UHGV-2040872_47	COG	COG0358	DNA primase (bacterial type)	NA
UHGV-2040872_47	Structural annotation	PF01807, PF00401	NA	NA
UHGV-2040872_48	PHROG	phrog_3490	ERCC4-type nuclease	DNA, RNA and nucleotide metabolism
UHGV-2040872_48	UniRef90	UniRef90_R9KEE1	ERCC4 domain-containing protein	NA
UHGV-2040872_48	eggNOG-mapper	397290.C810_05169	ERCC4 domain	NA
UHGV-2040872_48	Pfam	PF02732	ERCC4 domain	ERCC4
UHGV-2040872_48	Structural annotation	PF03834, NF040956, COG1948	NA	NA
UHGV-2040872_49	PHROG	phrog_28936	NA	unknown function
UHGV-2040872_49	eggNOG-mapper	573061.Clocel_3563	NA	NA
UHGV-2040872_49	Structural annotation	PF11645, MF_01490, NF040854	NA	NA
UHGV-2040872_50	PHROG	phrog_18107	NA	unknown function
UHGV-2040872_50	eggNOG-mapper	1256908.HMPREF0373_00659	NA	NA
UHGV-2040872_50	Structural annotation	PF05037	NA	NA
UHGV-2040872_51	PHROG	phrog_2872	Sak4-like ssDNA annealing protein	DNA, RNA and nucleotide metabolism
UHGV-2040872_51	UniRef90	UniRef90_UPI0015715A02	AAA family ATPase	NA
UHGV-2040872_51	eggNOG-mapper	397290.C810_05165	AAA domain	NA
UHGV-2040872_51	Pfam	PF13479	AAA domain	AAA_24
UHGV-2040872_51	Structural annotation	PF13479, MF_00350, TIGR01618, COG0468	NA	NA
UHGV-2040872_52	UniRef90	UniRef90_R6RDX0	Arginyl-tRNA synthetase	NA
UHGV-2040872_53	Structural annotation	NF011879	NA	NA
UHGV-2040872_62	UniRef90	UniRef90_A0A395X814	XRE family transcriptional regulator	NA
UHGV-2040872_62	eggNOG-mapper	1121289.JHVL01000079_gene1187	Helix-turn-helix XRE-family like proteins	NA
UHGV-2040872_62	Pfam	PF13443	Cro/C1-type HTH DNA-binding domain	HTH_26
UHGV-2040872_62	Structural annotation	PF12844, NF041951, COG1396	NA	NA
UHGV-2040872_63	KOfam	K22300	dicA; HTH-type transcriptional regulator, cell division transcriptional repressor	NA
UHGV-2040872_63	PHROG	phrog_8	transcriptional regulator	transcription regulation
UHGV-2040872_63	UniRef90	UniRef90_A0A395X7H2	XRE family transcriptional regulator	NA
UHGV-2040872_63	eggNOG-mapper	397288.C806_00131	Transcriptional	NA
UHGV-2040872_63	PADLOC	retron_type_VI_hth_cluster2_1	NA	Retron
UHGV-2040872_63	Pfam	PF01381	Helix-turn-helix	HTH_3
UHGV-2040872_63	COG	COG1396	Transcriptional regulator, contains XRE-family HTH domain	NA
UHGV-2040872_63	Structural annotation	PF01381, MF_02017, NF041951, COG3655	NA	NA
UHGV-2040872_65	PHROG	phrog_8545	superinfection exclusion Sie-like	moron, auxiliary metabolic gene and host takeover
UHGV-2040872_65	UniRef90	UniRef90_UPI001C0EAFDF	OB-fold putative lipoprotein	NA
UHGV-2040872_65	eggNOG-mapper	1304866.K413DRAFT_0836	tRNA_anti-like	NA
UHGV-2040872_65	Pfam	PF12869	tRNA_anti-like	tRNA_anti-like
UHGV-2040872_65	Structural annotation	PF12869, PF10571, MF_01959, TIGR03943, COG5235	NA	NA
UHGV-2040872_66	KOfam	K06400	spoIVCA; site-specific DNA recombinase	NA
UHGV-2040872_66	PHROG	phrog_95	integrase	integration and excision
UHGV-2040872_66	UniRef90	UniRef90_A0A2V2D7K6	Recombinase family protein	NA
UHGV-2040872_66	eggNOG-mapper	33035.JPJF01000109_gene439	Resolvase, N terminal domain	NA
UHGV-2040872_66	Pfam	PF00239	Resolvase, N terminal domain	Resolvase
UHGV-2040872_66	Pfam	PF07508	Recombinase	Recombinase
UHGV-2040872_66	Pfam	PF13408	Recombinase zinc beta ribbon domain	Zn_ribbon_recom
UHGV-2040872_66	COG	COG1961	Site-specific DNA recombinase SpoIVCA/DNA invertase PinE	NA
UHGV-2040872_66	Structural annotation	PF07508, PF00239, NF041201, COG1961	NA	NA
UHGV-2040872_67	KOfam	K06334	cotJC; spore coat protein JC	NA
UHGV-2040872_67	PHROG	phrog_7573	NA	unknown function
UHGV-2040872_67	UniRef90	UniRef90_A0A1C6BUE8	Probable manganese catalase	NA
UHGV-2040872_67	eggNOG-mapper	1121115.AXVN01000006_gene2180	NA	NA
UHGV-2040872_67	Pfam	PF05067	Manganese containing catalase	Mn_catalase
UHGV-2040872_67	COG	COG3546	Mn-containing catalase (includes spore coat protein CotJC)	NA
UHGV-2040872_67	Structural annotation	PF02185, MF_01506, TIGR04535, COG3546	NA	NA