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_000162495.1|GG730094.1@region_50456_60183@tool_cenote	cenote	CDS	50455	51195	GCA_000162495.1	GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495.1_GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495_1_7	GCA_000162495_1_7@C1	1	741	GCA_000162495_1_7_52	GCA_000162495_1_7_52	+	96214	.	cd01106	Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an  N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Unique to this family, is a TipAL-like, lineage specific Bacilli subgroup, which has five conserved cysteines in the C-terminus of the protein.	MYHIKEAAQLSGVSVKTLHHYDKIGLLVPLKSENGYRTYSQEDLERLQVILYYKYLGFSLEKIAELLKEERTDLLPHLTRQLDYLTQERQHLDTLISTLQKTIQEQKGERKMTIEEKFTGFSYQDNQKYHQEAVEKYGQEVMDQALERQKGHEDEATAAFNQVFQALAQNLQAGLPATASENQEEAAKLLQAIRTYGFDCSIEVFGHIGKGYVYNPEFKENIDKFGLGTAQYTSDVIAHYVQTQIT*	mmseqs_cdd	nonviral_gene	C1	9728	50455	60183	GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote_CDS_0001	persistent	indirect	.	.	.	GCA_000178095.1_01537
GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote	cenote	CDS	51438	52001	GCA_000162495.1	GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495.1_GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495_1_7	GCA_000162495_1_7@C1	984	1547	GCA_000162495_1_7_53	GCA_000162495_1_7_53	+	96214	.	TIGR01440	TIGR01440 family protein. Members of this family are uncharacterized proteins of about 180 amino acids from the Bacillus/Clostridium group of Gram-positive bacteria, found in no more than one copy per genome. [Hypothetical proteins, Conserved]	MDKSRIKTETQQVIEDVLEKAGLREGALFVLGLSSSEVLGGQIGKDSSQEIGEIIVKTILDILEEKGIHLAVQGCEHVNRALVVERQVAEQFGLEIVSVLPTLHAGGSGQLAAFKFMKNPVEVEFIKAHAGLDIGDTAIGMHVKHVQVPIRPVLREIGHAHVTALASRPKLIGGARAQYPQDSIRKI*	mmseqs_cdd	nonviral_gene	C1	9728	50455	60183	GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote_CDS_0002	persistent	indirect	.	.	.	GCA_000225385.2_00237
GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote	cenote	CDS	51998	53329	GCA_000162495.1	GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495.1_GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495_1_7	GCA_000162495_1_7@C1	1544	2875	GCA_000162495_1_7_54	GCA_000162495_1_7_54	+	96214	.	PFAM:PF04883.11	type-I-neck-protein	MRMKKRKEQFQKNLKYSIRKLTVGVGPVAIGAFLVGASLLLTGKVQADELAEVNSVHYRYLAEQELTESEKALIHHEVPTEFHDEDIIYVVYRKKATNSQQLPYTGSKEFALAGLGLATASLAVFLVSKKQRQKVLGVLLIGSLGVSNFIPFATFAFENKELLSYNQTISASSNEELAKGVIDIGGYEYIGYFKGTDIKVASFSKKGKLLDQDSLPAYTGKLESKGTQESGKEGESLVQDSLPAYTEKLESKGTQEEDKEGQSLIQDSLPAYTGKLESKGTQEVGKEGDSLVQDSLPAYTEKLESKGTQEAGKEGESLVQEPRAEYTGKLESKGTQESGQEGDSLVQDSLPAYTEKLESKGTQESGKEGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX*	hallmark_hmm	common_virus	C1	9728	50455	60183	GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote_CDS_0003	shell	indirect	.	.	.	GCA_001808865.1_00774
GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote	cenote	CDS	53439	58400	GCA_000162495.1	GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495.1_GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495_1_7	GCA_000162495_1_7@C1	2985	7946	GCA_000162495_1_7_55	GCA_000162495_1_7_55	+	96214	.	PFAM:PF04883.11	type-I-neck-protein	MPAYTEKLESKGTQESGKEGESLIQDSLPAYTEKLESKGTQETGKEGDSLVQDSLLAYTEKLEGKGTQETGKEGQSLIQDSLPTYTGKLESKGTQEPGKEGDSLVQEDLSEYTVTEGTITKDTIAEIDYQTEIIDDPTKYTDEETVVQNGEKGIQVTKTTYKTVEGVETDQVLNTTTTVIKEPVTKKISHGTKPIEGTLVEESLEKIPFKEIVEEDAQLKKGDKVTVQEGKDGQKKVIKTYKTIKGIKTQEAPEILEQVIELAQNRIVKLGTKNFEKPVLTFSRVDIQDLKRSSQIYYNLENPSKAAIKSITLTLKKGNEVVKTMTVSPNNLTATLTDLQYYKDYKLETKMVYDRGEGNEEEILKEEPLRIDLKKVEVKNIKETSLISVDDNGVETDSSFLTSVPSDVRPYYLKIATRDNKMTRLAIDKIEEVTVDGKTLYKVTAKAPDLVQHTDGNQLSEEYVHYFAKPKTHEENVYYDFNELVKAMQVNPSGEFKIGADLNAVNVPAAGKSYVTTKFRGKLSSVDGQQYTIHNLERPLLGDTEGAHIHDLNLGKVNIHMPWANRVAPLAAVIKNTTINNVKVTGIVVGNNDVSGLINKIDNNGRLTNVAFIGKLHAGGNQGAFLAGIVGENWKGSVEKAYVDAQITGNKAKVAGIAYWSQNGGDNHAVYRDGAIKKSVAKGTIDVREPISAGGVVGSTNALGSVEDTVSMMKVKNGEIFYGSSDIDDDPYWTGDRLNRNFVVTGVSEGKSSYRYSKQQHRIKSISQEEADKKIAALGITAHEYEINEPIVDKLNRLTHREDEYKAIQDYRADRELAYRNIEKLQPFYNKEWIVNQANKLDASSKLVTKEVLSVTGLKNGQFVTDLSAIDQIMIHYADGTKEESAVTAKADSDVKQVKEYEVTNQNIVYTPNVLVKDRAGLIAKAKETLSSVELISPEVRALMDKRNKPQENTDERKNGYIRDLFLEESFAEVKQNLGNLVKQIVENEDHQLNDDEAAQRAFIKKVEDNKANIMMGLAYLNQYYAIKYDGLSIKDIMMFKPDFYGKNVNVLDRLITIGSKENNLKGDQSQDAYNRVIAGATGKGSLHEFLTYNMKLFTNETDMNVWFKKAIEKNAYVVEQPSLNPDFVHKKYRLYEGINNGVHGRMILPLLNLKNSHLFMISTYNTISFSAFEKYGKNTEEAREAFKSEINKRAKEQVNYLDFWSKLAADNVRNKLLKSENSVPTPVWDNHDAPGIGWANRYGHKDGKPDYAPIREFFGRIHKYHGYQYGYGAYAYIFAAPNQQDAVYFVMTELISDFGTSAFTHETTHVNDRMAYYGGWYHREGTDLESFAQGMLQSPSLTNPNGEYGALGLNMAYERQNDGNQIYNYDPNKLKNREEIDHYMKNYNEALMMLDHLEADAVIGKHLNDNSKWFKKMDREWRTNAERNNLKGEPHQWDKLRDLTDNEKKLTITSIDQLVDHNFVTKHGMPGNGRYRSEGFDSAYQTVNMMSGIFGGNTSKSTVGSISFKHNAFRMWGYYGYLNGFIGYASNKYKAEANKENKGLLGDDFIIKKVSDGQFDTLEAWKKHWYKEVYDKAQNGFTTIEINGRSISTYAELKSLFDEAVQKDLDSMENPNIKNHYKNTEDLKWKVYKQLLQKSDGFSGNLFAKASL*	hallmark_hmm	common_virus	C1	9728	50455	60183	GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote_CDS_0004	cloud	indirect	.	.	.	GCA_021497885.1_01499
GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote	cenote	CDS	58467	60182	GCA_000162495.1	GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495.1_GG730094.1	GCA_000162495.1|GG730094.1	GCA_000162495_1_7	GCA_000162495_1_7@C1	8013	9728	GCA_000162495_1_7_56	GCA_000162495_1_7_56	+	96214	.	TIGR00553	aminodeoxychorismate synthase, component I, bacterial clade. Members of this family, aminodeoxychorismate synthase, component I (PabB), were designated para-aminobenzoate synthase component I until it was recognized that PabC, a lyase, completes the pathway of PABA synthesis. This family is closely related to anthranilate synthase component I (trpE), and both act on chorismate. The clade of PabB enzymes represented by this model includes sequences from Gram-positive and alpha and gamma Proteobacteria as well as Chlorobium, Nostoc, Fusobacterium and Arabidopsis. A closely related clade of fungal PabB enzymes is identified by TIGR01823, while another bacterial clade of potential PabB enzymes is more closely related to TrpE (TIGR01824). [Biosynthesis of cofactors, prosthetic groups, and carriers, Folic acid]	MHRKTVIDFRALGERYTFIQPIKELKTRDLSEVANLLAQVESYQEQGYYVVGYVSYEAAPAFEEKLAVHTAPLLGEYLLYFTVHDSVETSPIPLTYEEVDLPSNWQEVTSAEDYEKAIAQIHHHLRQGDTYQVNYTVQLKQDLSANPFSIYNRMVVEQEAGYNAYVEHDEMAVISMSPELFFEQNDRELTTRPMKGTTQRGVTDDEDLKEAAWLEQDPKNRSENMMIVDLLRNDMNRISEVGSEHVERLCQVEQYSTVWQMTSTIKSQLREDVDLVVIFRSLFPCGSITGAPKIATMEIIKDLEPQPRGVYCGTIGILLPNGRRIFNVAIRTIQLHQGKAIYGVGGGITWDSTWESEYREVHQKAAVLYRKQARFQLISTGKISQKQLLFEDQHLERLTKASRYFAYPFDPEDLRQRIEEECQACDSHQDYRLRITLNKSGELELSRQVLTPLSPGFCQAKLCLQETDLNQAFTYFKTTYRPHLSIGEQEKIYHNKSEELLETSIGNLVLKIAGKFYTPPIRLGILPGIYRQHLLETGQVEEKVLTLADLNQAETIYGCNAVRGLYELKVI*	mmseqs_cdd	nonviral_gene	C1	9728	50455	60183	GCA_000162495.1|GG730094.1@region_50456_60183@tool_cenote_CDS_0005	persistent	indirect	.	.	.	GCA_000162495.1_01276