vOTU vOTU-018760

vOTU: vOTU-018760

Overview

Genome (FASTA) Annotation Track (GFF) Proteins (FASTA) Protein Annotation (TSV)

Cluster properties
vOTU ID	vOTU-018760
Number of genomes	5
Taxonomy (ICTV)	Bacteria → Firmicutes_A → Clostridia → Oscillospirales → Ruminococcaceae → Ruthenibacterium → Ruthenibacterium lactatiformans
Taxonomy (UHGV)	vFAM-00005 → vSUBFAM-05019 → vOTU-018760
Host lineage	Bacteria → Firmicutes_A → Clostridia → Oscillospirales → Ruminococcaceae → Ruthenibacterium → Ruthenibacterium lactatiformans
Host range breadth	Species
Lifestyle	temperate (Evidence: integrase)

Representative genome
Genome ID	UHGV-0261988
Biosample ID	SAMN13241759
Genome length (bp)	28,847 bps
CheckV completeness	84.88% (Medium-quality)
CDS count	45
CDS density	95.70%
tRNA count	0
Integrase	Yes
Viral confidence	Confident

Host assignment details
Assignment method	CRISPR
CRISPR-predicted host lineage	Bacteria → Firmicutes_A → Clostridia → Oscillospirales → Ruminococcaceae → Ruthenibacterium → Ruthenibacterium lactatiformans	Total connections	225	Host agreement	97.33
PHIST-predicted host lineage	Bacteria → Firmicutes_A → Clostridia → Oscillospirales → Ruminococcaceae → Ruthenibacterium → Ruthenibacterium lactatiformans	Total connections	5	Host agreement	100

Representative genome content

Select to view: Genome Viewer Functional Annotation

Genome view (completeness: 84.88)

Functional Annotation

Reference	Gene ID	Reference ID	Bit-score	E-value	Information	Category
PHROG	UHGV-0261988_1	phrog_757	60.7	2.3e-17	DNA methyltransferase	other
UniRef90	UHGV-0261988_1	UniRef90_A0A7J2R6L5	74.7	1.11e-16	DNA cytosine methyltransferase (Fragment)	N/A
eggNOG-mapper	UHGV-0261988_1	742733.HMPREF9469_01835	119.0	4.14e-33	DNA (cytosine-5-)-methyltransferase activity	N/A
COG	UHGV-0261988_1	COG0270	N/A	N/A	DNA-cytosine methylase	N/A
PHROG	UHGV-0261988_3	phrog_599	48.0	0.00000000000019	Lar-like restriction alleviation protein	moron, auxiliary metabolic gene and host takeover
UniRef90	UHGV-0261988_3	UniRef90_U2DJA0	50.4	0.00000453	Restriction alleviation protein, Lar family	N/A
Pfam	UHGV-0261988_3	PF14354	N/A	N/A	Restriction alleviation protein Lar	Lar_restr_allev
structural_annotation	UHGV-0261988_3	PF14354,TIGR03655	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_6	phrog_244	78.8	8.6e-23	RusA-like Holliday junction resolvase	DNA, RNA and nucleotide metabolism
eggNOG-mapper	UHGV-0261988_6	33035.JPJF01000122_gene2460	169.0	0	N/A	N/A
structural_annotation	UHGV-0261988_6	PF01870,MF_01490,NF040854,COG1591	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_8	K02314	212.2	0	dnaB; replicative DNA helicase [EC:5.6.2.3]	N/A
PHROG	UHGV-0261988_8	phrog_19	223.5	0	DnaB-like replicative helicase	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_8	UniRef90_A0A3A6E5J4	780.0	0	DNA helicase	N/A
eggNOG-mapper	UHGV-0261988_8	1203606.HMPREF1526_01325	139.0	3.37e-34	Participates in initiation and elongation during chromosome replication	N/A
Pfam	UHGV-0261988_8	PF00772	N/A	N/A	DnaB-like helicase N terminal domain	DnaB
Pfam	UHGV-0261988_8	PF03796	N/A	N/A	DnaB-like helicase C terminal domain	DnaB_C
COG	UHGV-0261988_8	COG0305	N/A	N/A	Replicative DNA helicase	N/A
structural_annotation	UHGV-0261988_8	PF03796,PF00772,MF_04155,TIGR00665,COG0305	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_9	phrog_20437	157.4	0	DNA replication initiation	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_9	UniRef90_A0A3A6E2X3	498.0	0	N/A	N/A
eggNOG-mapper	UHGV-0261988_9	97138.C820_00626	194.0	0	N/A	N/A
Pfam	UHGV-0261988_9	PF14297	N/A	N/A	Lin1244/Lin1753-like, N-terminal	Lin1244_N
COG	UHGV-0261988_9	COG3935	N/A	N/A	DNA replication protein DnaD	N/A
structural_annotation	UHGV-0261988_9	PF14297	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_10	K03111	136.7	2.8e-40	ssb; single-strand DNA-binding protein	N/A
PHROG	UHGV-0261988_10	phrog_44	145.0	4.40008e-43	single strand DNA binding protein	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_10	UniRef90_A0A0W7TNC8	277.0	0	Single-stranded DNA-binding protein	N/A
eggNOG-mapper	UHGV-0261988_10	665956.HMPREF1032_00430	191.0	0	Single-stranded DNA-binding protein	N/A
Pfam	UHGV-0261988_10	PF00436	N/A	N/A	Single-strand binding protein family	SSB
NCBIFam	UHGV-0261988_10	TIGR00621.2	N/A	N/A	single-stranded DNA-binding protein	N/A
COG	UHGV-0261988_10	COG0629	N/A	N/A	Single-stranded DNA-binding protein	N/A
HAMAP	UHGV-0261988_10	MF_00984	N/A	N/A	Single-stranded DNA-binding protein	N/A
structural_annotation	UHGV-0261988_10	PF00436,MF_00984,NF005242,COG0629	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_11	phrog_7370	67.2	2.1e-19	HNH endonuclease	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_11	UniRef90_A0A498CPV0	143.0	2.11036e-42	HNH endonuclease	N/A
eggNOG-mapper	UHGV-0261988_11	1123058.KB894266_gene1536	52.0	0.0000036	HNH endonuclease	N/A
COG	UHGV-0261988_11	COG1403	N/A	N/A	5-methylcytosine-specific restriction endonuclease McrA	N/A
PHROG	UHGV-0261988_12	phrog_72	53.7	0.0000000000000036	NinB/ Orf homologous recombination mediator	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_12	UniRef90_A0A2Z4Q9W9	156.0	2.8026e-45	NinB	N/A
eggNOG-mapper	UHGV-0261988_12	445972.ANACOL_01825	139.0	2.46e-39	N/A	N/A
structural_annotation	UHGV-0261988_12	PF05772	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_13	phrog_7838	137.0	1.10001e-40	exonuclease	DNA, RNA and nucleotide metabolism
UniRef90	UHGV-0261988_13	UniRef90_A0A8D9UGW3	190.0	0	DNA repair protein RAD52-like protein	N/A
eggNOG-mapper	UHGV-0261988_13	742767.HMPREF9456_02397	149.0	2.40042e-42	N/A	N/A
structural_annotation	UHGV-0261988_13	PF04098,TIGR00607,COG4380	N/A	N/A	N/A	N/A
eggNOG-mapper	UHGV-0261988_15	1235802.C823_04724	73.6	0.00000000000152	N/A	N/A
PHROG	UHGV-0261988_16	phrog_1123	46.2	0.00000000000062	N/A	unknown function
structural_annotation	UHGV-0261988_16	PF02002,MF_01804,NF040939,COG3355	N/A	N/A	N/A	N/A
AcrCatalog	UHGV-0261988_17	cluster_35670	134.0	8.40779e-45	NA	N/A
structural_annotation	UHGV-0261988_17	PF11998	N/A	N/A	N/A	N/A
structural_annotation	UHGV-0261988_18	PF12728	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_23	K22300	41.3	0.000000000028	dicA; HTH-type transcriptional regulator, cell division transcriptional repressor	N/A
PHROG	UHGV-0261988_23	phrog_8	43.2	0.0000000000082	transcriptional regulator	transcription regulation
UniRef90	UHGV-0261988_23	UniRef90_G9YSE4	95.5	1.54e-24	DNA-binding helix-turn-helix protein	N/A
eggNOG-mapper	UHGV-0261988_23	585501.HMPREF6123_2084	52.4	0.000000326	Helix-turn-helix XRE-family like proteins	N/A
Pfam	UHGV-0261988_23	PF01381	N/A	N/A	Helix-turn-helix	HTH_3
COG	UHGV-0261988_23	COG1476	N/A	N/A	DNA-binding transcriptional regulator, XRE-family HTH domain	N/A
structural_annotation	UHGV-0261988_23	PF01381,NF041951,COG1476	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_24	K01356	69.9	5.1e-20	lexA; repressor LexA [EC:3.4.21.88]	N/A
PHROG	UHGV-0261988_24	phrog_4	114.4	1.2e-33	transcriptional repressor	transcription regulation
UniRef90	UHGV-0261988_24	UniRef90_A0A3A6ECX9	416.0	0	Helix-turn-helix domain-containing protein	N/A
eggNOG-mapper	UHGV-0261988_24	665956.HMPREF1032_01654	220.0	0	Peptidase S24-like	N/A
Pfam	UHGV-0261988_24	PF01381	N/A	N/A	Helix-turn-helix	HTH_3
Pfam	UHGV-0261988_24	PF00717	N/A	N/A	Peptidase S24-like	Peptidase_S24
COG	UHGV-0261988_24	COG1396	N/A	N/A	Transcriptional regulator, contains XRE-family HTH domain	N/A
structural_annotation	UHGV-0261988_24	PF00717,PF12844,MF_00015,TIGR00498,TIGR03070,COG1974,COG1476	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_25	phrog_4980	179.7	0	superinfection exclusion	moron, auxiliary metabolic gene and host takeover
UniRef90	UHGV-0261988_25	UniRef90_R7HFV1	77.0	0.000000000000485	Surface lipoprotein-related family protein	N/A
eggNOG-mapper	UHGV-0261988_25	742818.HMPREF9451_01281	95.9	1.81e-21	Host cell surface-exposed lipoprotein	N/A
Pfam	UHGV-0261988_25	PF10400	N/A	N/A	Virulence activator alpha C-term	Vir_act_alpha_C
Pfam	UHGV-0261988_25	PF07553	N/A	N/A	Host cell surface-exposed lipoprotein	Lipoprotein_Ltp
COG	UHGV-0261988_25	COG3064	N/A	N/A	Membrane protein TolA involved in colicin uptake	N/A
structural_annotation	UHGV-0261988_25	PF02631,MF_01114,NF001062,COG2137	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_26	K14059	209.3	0	int; integrase	N/A
PHROG	UHGV-0261988_26	phrog_1	200.9	0	integrase	integration and excision
UniRef90	UHGV-0261988_26	UniRef90_A0A6L6LPA2	663.0	0	Tyrosine-type recombinase/integrase	N/A
eggNOG-mapper	UHGV-0261988_26	1507.HMPREF0262_00307	521.0	0	Phage integrase family	N/A
Pfam	UHGV-0261988_26	PF14659	N/A	N/A	Phage integrase, N-terminal SAM-like domain	Phage_int_SAM_3
Pfam	UHGV-0261988_26	PF00589	N/A	N/A	Phage integrase family	Phage_integrase
COG	UHGV-0261988_26	COG0582	N/A	N/A	Integrase/recombinase, includes phage integrase	N/A
structural_annotation	UHGV-0261988_26	PF00589,PF14659,MF_02055,TIGR02224,COG4974	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_28	phrog_1129	75.5	4.3e-22	holin	lysis
UniRef90	UHGV-0261988_28	UniRef90_UPI00051B7422	125.0	1.05e-35	phage holin family protein	N/A
eggNOG-mapper	UHGV-0261988_28	1232453.BAIF02000030_gene2527	119.0	9.74e-34	N/A	N/A
Pfam	UHGV-0261988_28	PF16079	N/A	N/A	Phage holin family Hol44, in holin superfamily V	Phage_holin_5_2
structural_annotation	UHGV-0261988_28	PF16079	N/A	N/A	N/A	N/A
eggNOG-mapper	UHGV-0261988_29	33035.JPJF01000090_gene94	72.4	0.0000000000000025	N/A	N/A
KOfam	UHGV-0261988_30	K19304	97.5	1.8e-28	mepM; murein DD-endopeptidase [EC:3.4.24.-]	N/A
PHROG	UHGV-0261988_30	phrog_7767	97.5	8.9e-29	metallo-endopeptidase	other
UniRef90	UHGV-0261988_30	UniRef90_A0A3A6EBG8	471.0	0	M23 family peptidase	N/A
eggNOG-mapper	UHGV-0261988_30	1041147.AUFB01000010_gene1454	92.4	7.3e-19	Membrane proteins related to metalloendopeptidases	N/A
Pfam	UHGV-0261988_30	PF01551	N/A	N/A	Peptidase family M23	Peptidase_M23
COG	UHGV-0261988_30	COG0739	N/A	N/A	Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain	N/A
structural_annotation	UHGV-0261988_30	PF01551,NF040883,COG0739,COG5492	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_31	phrog_16573	62.5	4.4e-18	N/A	unknown function
UniRef90	UHGV-0261988_31	UniRef90_UPI001967E4F4	671.0	0	BppU family phage baseplate upper protein	N/A
eggNOG-mapper	UHGV-0261988_31	1160721.RBI_I01572	78.2	0.000000000000236	N/A	N/A
Pfam	UHGV-0261988_31	PF10651	N/A	N/A	BppU N-terminal domain	BppU_N
PHROG	UHGV-0261988_32	phrog_1067	379.8	0	minor head protein	head and packaging
UniRef90	UHGV-0261988_32	UniRef90_UPI001968120D	926.0	0	phage tail protein	N/A
eggNOG-mapper	UHGV-0261988_32	1123263.AUKY01000068_gene489	405.0	0	Phage minor structural protein	N/A
Pfam	UHGV-0261988_32	PF06605	N/A	N/A	Prophage endopeptidase tail	Prophage_tail
NCBIFam	UHGV-0261988_32	TIGR01665.1	N/A	N/A	phage tail spike protein	N/A
COG	UHGV-0261988_32	COG4926	N/A	N/A	Phage-related protein	N/A
structural_annotation	UHGV-0261988_32	PF14594,TIGR01665,COG4926	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_33	phrog_33	57.3	4.4e-16	distal tail protein Dit	tail
UniRef90	UHGV-0261988_33	UniRef90_A0A1C6H6D2	187.0	0	Phage-related protein	N/A
eggNOG-mapper	UHGV-0261988_33	1032362.F6K8S1_9CAUD	110.0	8.29e-27	Phage tail protein	N/A
structural_annotation	UHGV-0261988_33	PF20195,TIGR01633,COG4722	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_34	phrog_1272	110.9	0	tail length tape measure protein	tail
UniRef90	UHGV-0261988_34	UniRef90_A0A1Y4R6K5	300.0	0	PhageMin_Tail domain-containing protein	N/A
eggNOG-mapper	UHGV-0261988_34	1140001.I571_01843	189.0	0	phage tail tape measure protein	N/A
COG	UHGV-0261988_34	COG5412	N/A	N/A	Phage-related protein	N/A
structural_annotation	UHGV-0261988_34	PF20155,COG5280	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_36	phrog_88	100.3	1.8e-29	major tail protein	tail
UniRef90	UHGV-0261988_36	UniRef90_G9YSC5	127.0	1.56e-33	Phage major tail protein, phi13 family	N/A
NCBIFam	UHGV-0261988_36	TIGR01603.1	N/A	N/A	major tail protein	N/A
COG	UHGV-0261988_36	COG5492	N/A	N/A	N/A	N/A
structural_annotation	UHGV-0261988_36	PF04630,TIGR01603,COG3498	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_37	phrog_5	48.1	0.00000000000028	tail completion or Neck1 protein	connector
UniRef90	UHGV-0261988_37	UniRef90_A0A1C6FG30	158.0	0	Phage protein, HK97 gp10 family	N/A
eggNOG-mapper	UHGV-0261988_37	908340.HMPREF9406_2573	122.0	4.34e-33	N/A	N/A
NCBIFam	UHGV-0261988_37	TIGR01725.1	N/A	N/A	HK97-gp10 family putative phage morphogenesis protein	N/A
structural_annotation	UHGV-0261988_37	TIGR01725	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_38	phrog_78	46.3	0.00000000000087	tail terminator	connector
eggNOG-mapper	UHGV-0261988_38	1232446.BAIE02000002_gene829	101.0	1.28e-26	N/A	N/A
structural_annotation	UHGV-0261988_38	PF05657,COG3167	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_39	phrog_19734	57.0	3.5e-16	N/A	unknown function
UniRef90	UHGV-0261988_39	UniRef90_A0A316NL63	112.0	1.01e-29	Head-tail adaptor protein	N/A
eggNOG-mapper	UHGV-0261988_39	1232446.BAIE02000002_gene828	55.8	0.0000000207	N/A	N/A
structural_annotation	UHGV-0261988_39	PF05521,TIGR01563,COG5614	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_40	phrog_2550	58.8	6.5e-17	N/A	unknown function
UniRef90	UHGV-0261988_40	UniRef90_UPI0008717716	68.2	0.00000000000059	phage head-tail connector protein	N/A
eggNOG-mapper	UHGV-0261988_40	1226322.HMPREF1545_00117	69.3	0.0000000000000357	N/A	N/A
structural_annotation	UHGV-0261988_40	PF05135,TIGR01560	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_41	phrog_10	200.3	0	major head protein	head and packaging
UniRef90	UHGV-0261988_41	UniRef90_UPI000679B959	1065.0	0	phage major capsid protein	N/A
eggNOG-mapper	UHGV-0261988_41	1226322.HMPREF1545_00116	642.0	0	phage major capsid protein, HK97 family	N/A
Pfam	UHGV-0261988_41	PF05065	N/A	N/A	Phage capsid family	Phage_capsid
NCBIFam	UHGV-0261988_41	TIGR01554.2	N/A	N/A	phage major capsid protein	N/A
COG	UHGV-0261988_41	COG4653	N/A	N/A	Predicted phage phi-C31 gp36 major capsid-like protein	N/A
structural_annotation	UHGV-0261988_41	PF05065,MF_04119,TIGR01554,COG4653	N/A	N/A	N/A	N/A
KOfam	UHGV-0261988_42	K06904	148.7	5.04467e-44	N/A	N/A
PHROG	UHGV-0261988_42	phrog_80	168.7	0	head maturation protease	head and packaging
UniRef90	UHGV-0261988_42	UniRef90_A0A0D8IYC2	385.0	0	HK97 family phage prohead protease	N/A
eggNOG-mapper	UHGV-0261988_42	1226322.HMPREF1545_00115	253.0	0	Phage prohead protease, HK97 family	N/A
Pfam	UHGV-0261988_42	PF04586	N/A	N/A	Caudovirus prohead serine protease	Peptidase_S78
NCBIFam	UHGV-0261988_42	TIGR01543.1	N/A	N/A	HK97 family phage prohead protease	N/A
COG	UHGV-0261988_42	COG3740	N/A	N/A	Phage head maturation protease	N/A
structural_annotation	UHGV-0261988_42	PF04586,TIGR01543,COG3740	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_43	phrog_12	196.2	0	portal protein	head and packaging
UniRef90	UHGV-0261988_43	UniRef90_A0A0D8IVL0	806.0	0	Phage portal protein	N/A
eggNOG-mapper	UHGV-0261988_43	1226322.HMPREF1545_00114	535.0	0	Phage portal protein, HK97 family	N/A
Pfam	UHGV-0261988_43	PF04860	N/A	N/A	Phage portal protein	Phage_portal
NCBIFam	UHGV-0261988_43	TIGR01537.1	N/A	N/A	phage portal protein	N/A
COG	UHGV-0261988_43	COG4695	N/A	N/A	Phage portal protein BeeE	N/A
structural_annotation	UHGV-0261988_43	PF04860,MF_04120,TIGR01537,COG4695	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_44	phrog_9	286.4	0	terminase large subunit	head and packaging
UniRef90	UHGV-0261988_44	UniRef90_A0A0D8IV16	1163.0	0	Terminase	N/A
eggNOG-mapper	UHGV-0261988_44	1226322.HMPREF1545_00113	891.0	0	Phage Terminase	N/A
Pfam	UHGV-0261988_44	PF03354	N/A	N/A	Terminase large subunit, ATPase domain	TerL_ATPase
Pfam	UHGV-0261988_44	PF20441	N/A	N/A	Terminase large subunit, endonuclease domain	TerL_nuclease
COG	UHGV-0261988_44	COG4626	N/A	N/A	Phage terminase-like protein, large subunit, contains N-terminal HTH domain	N/A
structural_annotation	UHGV-0261988_44	PF20441,PF03354,MF_04013,TIGR01547,COG4626	N/A	N/A	N/A	N/A
PHROG	UHGV-0261988_45	phrog_361	67.9	1.7e-19	terminase small subunit	head and packaging
UniRef90	UHGV-0261988_45	UniRef90_A0A1C6H6I9	197.0	0	Phage terminase, small subunit	N/A
Pfam	UHGV-0261988_45	PF05119	N/A	N/A	Phage terminase, small subunit	Terminase_4
COG	UHGV-0261988_45	COG3747	N/A	N/A	Phage terminase, small subunit	N/A
structural_annotation	UHGV-0261988_45	PF05119,TIGR01558,COG3747	N/A	N/A	N/A	N/A

All viral genomes

ID	Representative?	Length (bps)	% GC Content	CheckV Completeness	geNomad Score
UHGV-0261988	Yes	28,847	46	85	1
UHGV-1337914	No	27,330	46	80	1
UHGV-0427719	No	27,155	46	80	1
UHGV-0388470	No	16,341	45	48	1
UHGV-0392692	No	14,388	46	42	1