UHGV-1978519

Genome information

Genome length 43,697 bps

CDS count 57

Completeness 56.55% (medium-quality)

geNomad score 0.9479

Prediction confidence Confident

Genome information
Genome ID	UHGV-1978519
vOTU ID	vOTU-022422
vOTU representative	Yes
Source dataset	IMG/VR v4
Original genome ID	3300023484\|Ga0257055_10039\|provirus_32578_76274
BioSample	NA
Country	United States
Virus prediction confidence	Confident

Quality assessment
CheckV method	HMM-based
CheckV completeness	56.55% (medium-quality)
CheckV contamination	0.00%
Trimmed provirus	No
CheckV viral markers	5
CheckV host markers	2
Recoded stop codon	No

Viral signal
geNomad score	0.9479
Virus hallmark genes (geNomad)	5
Plasmid hallmark genes (geNomad)	0
viralVerify prediction	Virus
viralVerify score	20.71
Jumbo phage	No

Genome content
Genome length	43,697 bps
GC content	53.34%
Genetic code	The standard bacterial, archaeal and plant plastid code (11)
CDS count	57
CDS density	89.52%
Average CDS length	687.74 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-1978519_1	UniRef90	UniRef90_B2UQ77	Alginate_lyase domain-containing protein	NA
UHGV-1978519_1	eggNOG-mapper	349741.Amuc_0778	Alginate lyase	NA
UHGV-1978519_1	Pfam	PF05426	Alginate lyase	Alginate_lyase
UHGV-1978519_2	KOfam	K01174	nuc; micrococcal nuclease [EC:3.1.31.1]	NA
UHGV-1978519_2	PHROG	phrog_8809	NA	unknown function
UHGV-1978519_2	UniRef90	UniRef90_A0A2N8IRS5	TNase-like domain-containing protein	NA
UHGV-1978519_2	eggNOG-mapper	349741.Amuc_0779	Staphylococcal nuclease homologues	NA
UHGV-1978519_2	PADLOC	shah_acc_0212	SNc+LTD	CRISPR-CAS
UHGV-1978519_2	Pfam	PF00565	Staphylococcal nuclease homologue	SNase
UHGV-1978519_2	COG	COG1525	Endonuclease YncB, thermonuclease family	NA
UHGV-1978519_2	Structural annotation	PF00565, MF_00075, NF005083, COG1525	NA	NA
UHGV-1978519_4	PHROG	phrog_2159	ParB-like partition protein	DNA, RNA and nucleotide metabolism
UHGV-1978519_4	UniRef90	UniRef90_A0A2N8IDT6	Chromosome partitioning protein ParB	NA
UHGV-1978519_4	eggNOG-mapper	349741.Amuc_0782	ParB domain protein nuclease	NA
UHGV-1978519_4	Pfam	PF02195	ParB/Sulfiredoxin domain	ParBc
UHGV-1978519_4	COG	COG1475	Chromosome segregation protein Spo0J, contains ParB-like nuclease domain	NA
UHGV-1978519_4	Structural annotation	PF02195, MF_02015, TIGR04285, COG1475	NA	NA
UHGV-1978519_5	KOfam	K00390	cysH; phosphoadenosine phosphosulfate reductase [EC:1.8.4.8 1.8.4.10]	NA
UHGV-1978519_5	PHROG	phrog_2302	phosphoadenosine phosphosulfate reductase	moron, auxiliary metabolic gene and host takeover
UHGV-1978519_5	UniRef90	UniRef90_A0A2N8IRT3	Phosphoadenosine phosphosulfate reductase	NA
UHGV-1978519_5	eggNOG-mapper	349741.Amuc_0783	Phosphoadenosine phosphosulfate reductase	NA
UHGV-1978519_5	Pfam	PF01507	Phosphoadenosine phosphosulfate reductase family	PAPS_reduct
UHGV-1978519_5	Pfam	PF11922	NA	DUF3440
UHGV-1978519_5	COG	COG3969	NA	NA
UHGV-1978519_5	Structural annotation	PF11922, PF01507, MF_00063, NF006327, COG3969	NA	NA
UHGV-1978519_7	KOfam	K07726	K07726; putative transcriptional regulator	NA
UHGV-1978519_7	PHROG	phrog_2104	NA	unknown function
UHGV-1978519_7	UniRef90	UniRef90_A0A410S8Y9	Helix-turn-helix domain-containing protein	NA
UHGV-1978519_7	eggNOG-mapper	349741.Amuc_1361	sequence-specific DNA binding	NA
UHGV-1978519_7	Pfam	PF01381	Helix-turn-helix	HTH_3
UHGV-1978519_7	COG	COG1598	Antitoxin component HicB of the HicAB toxin-antitoxin system	NA
UHGV-1978519_8	UniRef90	UniRef90_A0A410SEJ2	Addiction module toxin, HicA family	NA
UHGV-1978519_8	eggNOG-mapper	349741.Amuc_1362	mRNA binding	NA
UHGV-1978519_8	Pfam	PF07927	HicA toxin of bacterial toxin-antitoxin,	HicA_toxin
UHGV-1978519_8	COG	COG1724	Predicted RNA binding protein YcfA, dsRBD-like fold, HicA-like mRNA interferase family	NA
UHGV-1978519_10	KOfam	K18626	TCHH; trichohyalin	NA
UHGV-1978519_10	Structural annotation	PF18654, TIGR00606, COG0268	NA	NA
UHGV-1978519_11	Structural annotation	PF18404, MF_01520, TIGR03469, COG1442	NA	NA
UHGV-1978519_12	Structural annotation	PF14594, TIGR01646, COG4379	NA	NA
UHGV-1978519_18	Structural annotation	PF21190, TIGR03511, COG4935	NA	NA
UHGV-1978519_19	UniRef90	UniRef90_A0A6J5N5S1	Major capsid protein	NA
UHGV-1978519_19	eggNOG-mapper	521674.Plim_2126	NA	NA
UHGV-1978519_19	Structural annotation	PF20911, MF_04133, NF041162, COG4397	NA	NA
UHGV-1978519_20	PHROG	phrog_328	head maturation protease	head and packaging
UHGV-1978519_20	UniRef90	UniRef90_UPI001C023827	phage protease	NA
UHGV-1978519_20	eggNOG-mapper	794903.OPIT5_08310	P22 coat protein - gene protein 5	NA
UHGV-1978519_20	Pfam	PF10123	Mu-like prophage I protein	Mu-like_Pro
UHGV-1978519_23	PHROG	phrog_113	portal protein	head and packaging
UHGV-1978519_23	UniRef90	UniRef90_A0A410S906	NA	NA
UHGV-1978519_23	eggNOG-mapper	794903.OPIT5_08305	NA	NA
UHGV-1978519_23	Pfam	PF06074	NA	DUF935
UHGV-1978519_23	COG	COG4383	NA	NA
UHGV-1978519_24	PHROG	phrog_315	endolysin	lysis
UHGV-1978519_24	UniRef90	UniRef90_A0A410SED1	PG_binding_3 domain-containing protein	NA
UHGV-1978519_24	eggNOG-mapper	349741.Amuc_1360	Glycosyl hydrolase 108	NA
UHGV-1978519_24	Pfam	PF09374	Predicted Peptidoglycan domain	PG_binding_3
UHGV-1978519_24	COG	COG3926	Lysozyme family protein	NA
UHGV-1978519_24	Structural annotation	PF09374, NF040573, COG3926	NA	NA
UHGV-1978519_27	UniRef90	UniRef90_UPI001EDF593B	NA	NA
UHGV-1978519_29	Structural annotation	PF05587, PF03388, COG3506	NA	NA
UHGV-1978519_30	PHROG	phrog_2	terminase large subunit	head and packaging
UHGV-1978519_30	UniRef90	UniRef90_A0A1C7PDG0	p-loop containing nucleoside triphosphate hydrolase	NA
UHGV-1978519_30	eggNOG-mapper	580331.Thit_1395	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD	NA
UHGV-1978519_30	COG	COG0507	ATPase/5'-3' helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V)	NA
UHGV-1978519_30	Structural annotation	PF04466, PF20441, MF_04145, TIGR01547, COG4373	NA	NA
UHGV-1978519_31	PHROG	phrog_1482	terminase small subunit	head and packaging
UHGV-1978519_31	UniRef90	UniRef90_UPI000C9ACC23	ubiquitin carboxyl-hydrolase	NA
UHGV-1978519_31	eggNOG-mapper	1072685.IX83_07125	NA	NA
UHGV-1978519_31	Pfam	PF20901	Bacteriophage Sf6, terminase small subunit-like	Sf6_terminase
UHGV-1978519_31	Structural annotation	PF20901	NA	NA
UHGV-1978519_33	UniRef90	UniRef90_A0A4Q5IVQ1	ADPrib_exo_Tox domain-containing protein	NA
UHGV-1978519_35	KOfam	K02314	dnaB; replicative DNA helicase [EC:5.6.2.3]	NA
UHGV-1978519_35	PHROG	phrog_19	DnaB-like replicative helicase	DNA, RNA and nucleotide metabolism
UHGV-1978519_35	UniRef90	UniRef90_A0A410S8Z8	DNA helicase	NA
UHGV-1978519_35	eggNOG-mapper	349741.Amuc_1377	DnaB-like helicase C terminal domain	NA
UHGV-1978519_35	Pfam	PF00772	DnaB-like helicase N terminal domain	DnaB
UHGV-1978519_35	Pfam	PF03796	DnaB-like helicase C terminal domain	DnaB_C
UHGV-1978519_35	COG	COG0305	Replicative DNA helicase	NA
UHGV-1978519_35	Structural annotation	PF03796, PF00772, MF_04155, TIGR00665, COG0305	NA	NA
UHGV-1978519_36	PHROG	phrog_5810	replication initiation protein	DNA, RNA and nucleotide metabolism
UHGV-1978519_36	UniRef90	UniRef90_UPI0015841E4F	conserved phage C-terminal domain-containing protein	NA
UHGV-1978519_36	eggNOG-mapper	402626.Rpic_2326	ROK family	NA
UHGV-1978519_36	COG	COG3355	Predicted transcriptional regulator	NA
UHGV-1978519_36	Structural annotation	PF10771, NF041413, COG0735	NA	NA
UHGV-1978519_37	PHROG	phrog_954	DNA methyltransferase	other
UHGV-1978519_37	UniRef90	UniRef90_A0A410S9A2	Class I SAM-dependent methyltransferase	NA
UHGV-1978519_37	eggNOG-mapper	1395513.P343_12775	DNA (cytosine-5-)-methyltransferase activity	NA
UHGV-1978519_37	PADLOC	MTase_II_00074	Type II methyltransferase	RM
UHGV-1978519_37	Pfam	PF13649	Methyltransferase domain	Methyltransf_25
UHGV-1978519_37	Pfam	PF08241	Methyltransferase domain	Methyltransf_11
UHGV-1978519_37	COG	COG0500	SAM-dependent methyltransferase	NA
UHGV-1978519_37	Structural annotation	PF01170, MF_01057, TIGR00446, COG4123	NA	NA
UHGV-1978519_38	KOfam	K00558	DNMT1, dcm; DNA (cytosine-5)-methyltransferase 1 [EC:2.1.1.37]	NA
UHGV-1978519_38	PHROG	phrog_116	DNA methyltransferase	other
UHGV-1978519_38	UniRef90	UniRef90_UPI001CA4D280	DNA cytosine methyltransferase	NA
UHGV-1978519_38	eggNOG-mapper	1005994.GTGU_00272	Belongs to the class I-like SAM-binding methyltransferase superfamily. C5-methyltransferase family	NA
UHGV-1978519_38	PADLOC	MTase_II_00058	Type II methyltransferase	RM
UHGV-1978519_38	Pfam	PF00145	C-5 cytosine-specific DNA methylase	DNA_methylase
UHGV-1978519_38	NCBIFam	TIGR00675.1	DNA (cytosine-5-)-methyltransferase	NA
UHGV-1978519_38	COG	COG0270	DNA-cytosine methylase	NA
UHGV-1978519_38	Structural annotation	PF00145, MF_02100, TIGR00675, COG0270	NA	NA
UHGV-1978519_39	PHROG	phrog_3136	NA	unknown function
UHGV-1978519_39	UniRef90	UniRef90_UPI001C02F5BC	ASCH domain-containing protein	NA
UHGV-1978519_39	eggNOG-mapper	97139.C824_00742	The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome	NA
UHGV-1978519_39	COG	COG4933	Predicted transcriptional regulator, contains an HTH and PUA-like domains	NA
UHGV-1978519_39	Structural annotation	PF04266, MF_00684, NF008917, COG4933	NA	NA
UHGV-1978519_40	Structural annotation	PF09465, MF_00667, TIGR00739, COG5475	NA	NA
UHGV-1978519_42	KOfam	K01160	rusA; crossover junction endodeoxyribonuclease RusA [EC:3.1.21.10]	NA
UHGV-1978519_42	PHROG	phrog_140	RusA-like Holliday junction resolvase	DNA, RNA and nucleotide metabolism
UHGV-1978519_42	UniRef90	UniRef90_A0A4Q5ITS8	RusA family crossover junction endodeoxyribonuclease	NA
UHGV-1978519_42	eggNOG-mapper	608534.GCWU000341_02308	endodeoxyribonuclease RusA	NA
UHGV-1978519_42	Pfam	PF05866	Endodeoxyribonuclease RusA	RusA
UHGV-1978519_42	COG	COG4570	Holliday junction resolvase RusA (prophage-encoded endonuclease)	NA
UHGV-1978519_42	Structural annotation	PF05866, NF007305, COG4570	NA	NA
UHGV-1978519_44	UniRef90	UniRef90_A0A410S925	NA	NA
UHGV-1978519_44	eggNOG-mapper	1403819.BATR01000122_gene4275	NA	NA
UHGV-1978519_44	Pfam	PF10926	NA	DUF2800
UHGV-1978519_45	PHROG	phrog_124	Sak4-like ssDNA annealing protein	DNA, RNA and nucleotide metabolism
UHGV-1978519_45	UniRef90	UniRef90_A0A8F1HRX2	ATP-binding protein	NA
UHGV-1978519_45	eggNOG-mapper	1111454.HMPREF1250_0030	AAA domain	NA
UHGV-1978519_45	Pfam	PF13479	AAA domain	AAA_24
UHGV-1978519_45	Structural annotation	PF13479, MF_00350, TIGR01618, COG0468	NA	NA
UHGV-1978519_51	KOfam	K01356	lexA; repressor LexA [EC:3.4.21.88]	NA
UHGV-1978519_51	PHROG	phrog_4	transcriptional repressor	transcription regulation
UHGV-1978519_51	UniRef90	UniRef90_A0A4Q5ITN5	Peptidase_S24 domain-containing protein	NA
UHGV-1978519_51	eggNOG-mapper	349741.Amuc_1794	Peptidase S24-like	NA
UHGV-1978519_51	Pfam	PF00717	Peptidase S24-like	Peptidase_S24
UHGV-1978519_51	COG	COG1974	SOS-response transcriptional repressor LexA (RecA-mediated autopeptidase)	NA
UHGV-1978519_51	Structural annotation	PF00717, PF01381, MF_00015, NF007621, NF041951, COG2932	NA	NA
UHGV-1978519_52	PHROG	phrog_1762	NA	unknown function
UHGV-1978519_52	UniRef90	UniRef90_A0A8E2TXY3	NA	NA
UHGV-1978519_52	eggNOG-mapper	261292.Nit79A3_3106	NA	NA
UHGV-1978519_52	Pfam	PF11185	NA	DUF2971
UHGV-1978519_56	PHROG	phrog_5783	NA	unknown function
UHGV-1978519_56	UniRef90	UniRef90_UPI00138E8EA5	NYN domain-containing protein	NA
UHGV-1978519_56	eggNOG-mapper	107636.JQNK01000009_gene1263	NYN domain	NA
UHGV-1978519_56	Pfam	PF01936	NYN domain	NYN
UHGV-1978519_56	COG	COG1432	NYN domain, predicted PIN-related RNAse, tRNA/rRNA maturation	NA
UHGV-1978519_57	KOfam	K14059	int; integrase	NA
UHGV-1978519_57	PHROG	phrog_1	integrase	integration and excision
UHGV-1978519_57	UniRef90	UniRef90_A0A7G6DT43	Tyrosine-type recombinase/integrase	NA
UHGV-1978519_57	eggNOG-mapper	349741.Amuc_2006	Belongs to the 'phage' integrase family	NA
UHGV-1978519_57	Pfam	PF00589	Phage integrase family	Phage_integrase
UHGV-1978519_57	COG	COG0582	Integrase/recombinase, includes phage integrase	NA