core_seqid	core_source	core_type	core_start	core_end	core_bax_acc	core_contig_acc	core_bax_acc|contig_acc	core_bax_acc_contig_acc	cenote_input_name	cenote_contig	cenote_phage_region_id	cenote_gene_start	cenote_gene_stop	cenote_gene_name	original_cenote_gene_name	cenote_gene_orient	cenote_contig_length	cenote_dtr_seq	cenote_evidence_accession	cenote_evidence_description	cenote_translation	cenote_Evidence_source	cenote_vscore_category	cenote_chunk_name	cenote_chunk_length	cenote_chunk_start	cenote_chunk_stop	UNI_lookup_ID	pangenome_partition	pangenome_method	pangenome_confidence	pangenome_overlap_length	pangenome_overlap_fraction	pangenome_matching_locus_tag
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	1	480	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	2	481	GCA_002096735_1_9_1	GCA_002096735_1_9_1	-	7602	.	pfam18710	ComR tetratricopeptide. In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA.	MSNLEIGKRIRTLRTEKGLSREAFCGDEKHLTVRQLARIETGNNLPSLAKLDYIAEVLGVPISQLIDERLLIVPKEYLKLKTKLIRQSIHGDEEKIHQREAIFEDIQERFYDQLPEDEQVAVEVLQAIDDVYVSENAEFGEGLIEEYFEQTMLRTEYSTN	mmseqs_cdd	nonviral_gene	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0001	.	unmatched_CDS	none	0	0	.
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	1548	2483	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	1549	2484	GCA_002096735_1_9_2	GCA_002096735_1_9_2	+	7602	.	PDB:1Z19_B	Integrase	MDNENSKPKQNRWAKKRKARNRSKEKTYQNTVRKRLLEMFEDGKSSKRSLDKTKDDTKNKIYSEGTYRTYKKQLGYFIEWLDKEHPEALTIDDAYKYANDYLLYLIDKGDVSASTIATRKAAMAKVFGVSSNVFIDTPERTRAGIKRSRFAVKSDKHISEATERRLARFTSATGLRRAEMTRITSDDLFFEEGKAYLSVTKGTKGGKARIVEIMGISEEETEDIVKFIQSKKGRLFPKLHTNYDNHFYRASYAMRLYQHYARSEKDIPRADRYIMRKDRAGETYDKRAMAIVTKNLGHNRIDVIAQSYLYQ*	common_virus_hmm	common_virus	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0002	cloud	direct	high	935	0.999	GCA_002096735.1_01054
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	2927	3943	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	2928	3944	GCA_002096735_1_9_3	GCA_002096735_1_9_3	-	7602	.	PFAM:PF17288.1	Terminase_3C	MVAEVVKYHNDLNTVVMRTWTSEEMNFFFTILTKAKEQGVKKLVFNTDELKDLATSSRKYRWEETVTNAAKKIGQLTYFEQSERKFRVMTLFEFFEVDLDKKMVEVKVSSNFDYILNKLETQFTRYELEEFTSIRSTYAKTMYRLLKQWRTVGRKEFSVDDLKRILDTPESYRPSEIDRLILKPIKEQLSPYFVDLKVKKIKSNKRGTPVLGYEFTWKKEVTEAYDPNKYDKPKTVAKKPSKKATKKSNVPSWSNPNYKNELSQEFLDELIETQKILGIYGTPEAEAELAQKRAEIEKKRAELEAKKWELLGKLDKSSEPDVVPGQTDIYDFLEDDEK*	hallmark_hmm	common_virus	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0003	cloud	direct	high	1016	0.999	GCA_002096735.1_01055
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	4333	4545	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	4334	4546	GCA_002096735_1_9_4	GCA_002096735_1_9_4	-	7602	.	COG1476	DNA-binding transcriptional regulator, XRE-family HTH domain  [Transcription]. 	MLKKNNYQNKIKQFRVREGLTQDELAKKINISRQMIGLIENNKTIPSVEIALKLSTVLKEPIERLFLFAF*	mmseqs_cdd	nonviral_gene	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0004	cloud	direct	high	212	0.995	GCA_002096735.1_01056
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	5029	5778	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	5030	5779	GCA_002096735_1_9_5	GCA_002096735_1_9_5	-	7602	.	PF03379.13	CcmB protein	MFKRILALIWLRTQVLLTNKNTLVQVVFPFFLVLLFQNFMNTDGTQGKVLLYSSLTMAFSFSSGSMISNSIAEEKEKRIFKTLILSGVRRGEYLVSVLFYPVIFALASVISFPIMVEVDFAKDYPVYLVVASLVALCTILLNLVIGAISETQTQAQVYGLIPMLGLSFLPMFAQVSSEVKKFMDTTFLGVYVDFFNKPDFKLNFDSLGITFAWVVALLALSYWGLKNKKKVPFGKLTLNQLQKLTFLKA*	hhsuite_tools	hypothetical_protein	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0005	shell	direct	high	749	0.999	GCA_002096735.1_01057
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	5771	6595	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	5772	6596	GCA_002096735_1_9_6	GCA_002096735_1_9_6	-	7602	.	COG1131	ABC-type multidrug transport system, ATPase component [Defense mechanisms]. 	MIKVERVTKRFGDNIALNQISFSINEGEIFGFLGPSGSGKTTMINILTGQLQANSGKTELLGKDSQKLLPSDFEELGLVGDTSGYYEKLSLYNNLLLFARLYGVSKSRIEEILKQVGLYDSKDTPAEKLSTGMRQRMLLARALINYPKVLFLDEPTSGLDPTTSKKIHKLLQELKERGTTIFLTTHDMNEATLLCDNLALLNKGDLIEQGSPSEIIQKYNTEKKVAVTYSDSTKKVVRFEDLQQEDYKKIMTIHSCEPTLEDIFIKLTGEKLDV*	mmseqs_cdd	nonviral_gene	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0006	shell	direct	high	824	0.999	GCA_002096735.1_01058
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	6678	6887	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	6679	6888	GCA_002096735_1_9_7	GCA_002096735_1_9_7	-	7602	.	.	hypothetical protein	MENINYHLEEKEVKSNYLIIKNCLDTRRLCKVTIDDKLFKLLLLLPNEVKEIKISPQFKNKVKVIDITE*	.	hypothetical_protein	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0007	cloud	direct	high	209	0.995	GCA_002096735.1_01059
GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote	cenote	CDS	7085	7600	GCA_002096735.1	NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735.1_NCVC01000006.1	GCA_002096735.1|NCVC01000006.1	GCA_002096735_1_9	GCA_002096735_1_9	7086	7601	GCA_002096735_1_9_8	GCA_002096735_1_9_8	-	7602	.	pfam18710	ComR tetratricopeptide. In Gram-positive bacteria, cell-to-cell communication mainly relies on extracellular signaling peptides. ComR is a member of the RNPP family, which positively controls competence for natural DNA transformation in streptococci. It is directly activated by the binding of its associated pheromone XIP. The crystal structure analysis of ComR shows that it contains an N-terminal helix-turn-helix (HTH), DNA binding domain (DBD) and a C-terminal tetratricopeptide repeat (TPR) domain. The TPR domain is composed of 11 alpha-helices forming 5 TPR motifs followed by an additional C-terminal alpha-helix 16 called CAP. The pheromone XIP binding site is found in the TPR region. Biochemical and mutational analysis indicate that, if the interacting XIP is accepted it can then trigger the conformational change of the TPR domain to open the DBD-TPR interface to allow dimer formation that is required to bind DNA.	DVYVSENAEFGEGLIEEYFEQTMLRTEYSTNDLLILYLYFLSLAVKSERDEITLKKVCLNIVSQTNYDDTNYIHLLQRVLLGLIFYQLDIDYHEFIPEILSMLREIMIDIGDTSLKPTVDFIEAKYYLYGEKDKEKALQYYEKAINGAEFLNDMNFKNRVIEEKNLDFQNI*	mmseqs_cdd	nonviral_gene	NaN	.	0	7602	GCA_002096735.1|NCVC01000006.1@region_1_7602@tool_cenote_CDS_0008	cloud	direct	moderate	450	0.872	GCA_002096735.1_01060