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_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	93	983	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	94	984	GCA_003640305_1_139_1	GCA_003640305_1_139_1	-	9740	.	.	hypothetical protein	MNENLFKTRSVLANMKTTINTLLQHYPTLFYKTLIPYLVAAMALTTLLFNGTNAVVNFYSGDDPSLLQVLLSLVALPLVLLLPAVAMGIVFGKLHQQPRARCIKRNLVAALAFALLTLALYLLLEWAQYGVQTLWPSLIRENDLNDTQNIETIKYALTFILLLPFCPLNFAFTKYIITPTLPLRKALKEAFTTGRRNWGYLVSNQAAICFLCGVAYCLISIPVRILLNAYYLNAIGMLQGDANGLPAHFVPMMFAVCTLIGLLLFQLLNVYAAFEYFMYGAAEQRALEKQQQQHLR*	.	hypothetical_protein	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0001	persistent	direct	high	890	0.999	GCA_003640305.1_00990
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	1007	1762	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	1008	1763	GCA_003640305_1_139_2	GCA_003640305_1_139_2	-	9740	.	cd18109	SAM-dependent RNA methylase related to SpoU-TrmH. RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.	MISKAKIKFIKSLQLKKNRLRERLFIAEGHKVVGDLLTVMPAHTLVATEEWTETHEVPQTTALHIVSEDELQSVSLLQHPQQVLGLFPYPDVSDFDIPLTQLSLALDGIQDPGNLGTIIRMADWFGIAHIFCSPNTAEAYNPKVVQATMGSIAHVAIHYTELPPLLAALPHNFPIYGTMLDGENIYQKTLSPTGIIIMGNEGNGLSPETRAWVNQRLLIPNCSAATNKAESLNVAIATAIVCSEFRRQTFL*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0002	persistent	direct	high	755	0.999	GCA_003640305.1_00991
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	1836	4049	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	1837	4050	GCA_003640305_1_139_3	GCA_003640305_1_139_3	+	9740	.	PFAM:PF02123.15	RNA-dependent-RNA-polymerase	MEYCKIYSVLFATLLTACSASKFVPENQYMLESVKIKSDRKDLDASTLSAYVRQTANSKWFSLFKIPLGTYALAGRDSTKWMNRTLKHIGEAPVIFDTAQARLSVQDLTSAMRNMGYMQAKTQLKTTVKGKKVKVVFRLQPGEPYLIHTLKYDIQDSVIAALLARKEKRNMFKPTLAAGSRFTVDALNAERKNITDFLLNHGYYKFHRDFIQYSADSARNSRDINITLHLLPYRTNEQKHDTLHPCYVIDSIYYRMNEDGGAIRLRKSVLRNATMLEAHEPYDANKLEQTYNKFARFQVVRYTNITFKERPDTTLLDCEIQLNTNKANTLSFQPEGTNTAGDLGAAASLTWENRNLFHGAELLSVQLRGAFEAIRGLEGYKNQNYVEYGFETKLQFPRFLAPFLSRTFKHRSLATSELATGYNLQNRPEFHRRVFSAAWRYRWAEPHHHISYRADVLDLSYVYMPWISATFKHDYLDGTSNRNAILRYNYEDLFIMKIGMGLTYNDNVNVVRANIETAGNILNGLSHLFRFKQNANQQATLFNIAFAQYVKFDVDLTHLICFDARNALAMHVGLGVAWPYGNSTILPFEKRYFSGGANSVRGWSVRELGPGKFKGSGGRIDFINQTGDMKLDLNVEYRTYLFWKFNGAAFVDAGNIWTLRNYVDQPGGQFKFDTFYKQMAVAYGLGLRLNFDYFILRFDMAMRAINPAYADVHEHYPIFHPKFSRDFAFHFAVGLPF*	rdrp_hall_hmm	common_virus	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0003	persistent	direct	high	2213	1.0	GCA_003640305.1_00992
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	4217	5245	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	4218	5246	GCA_003640305_1_139_4	GCA_003640305_1_139_4	+	9740	.	cd05247	UDP-glucose 4 epimerase, subgroup 1, extended (e) SDRs. UDP-glucose 4 epimerase (aka UDP-galactose-4-epimerase), is a homodimeric extended SDR. It catalyzes the NAD-dependent conversion of UDP-galactose to UDP-glucose, the final step in Leloir galactose synthesis. This subgroup has the characteristic active site tetrad and NAD-binding motif of the extended SDRs. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.	MKQTILVTGGTGFIGSHTVVELMEAGYEVVIIDNLSNSKIEVLDGIAQITGQKPAFEKVDLRDKEATEGVFKKYPHIAGIIHFAASKAVGESVQKPLLYYRNNIVSLINLLELMPQYGVKGFIFSSSCTVYGQPKPENLPVTEDAPHQKATSPYGNTKEINEQIIYDYIHSGANIKSIVLRYFNPIGAHPTALIGELPNGVPANLIPFVTQTAAGIRKELTIFGNDYNTPDGTCIRDYIYVVDLAKAHVAAMQRVLNADAEPIEYFNIGTGKGNTTKEIVDTFEKATGVKVNWKYGPRREGDIEKIWGDCSKANAVLGWEAKTPLNEVLATAWKWQQKLKEV*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0004	persistent	direct	high	1028	0.999	GCA_003640305.1_00993
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	5364	6059	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	5365	6060	GCA_003640305_1_139_5	GCA_003640305_1_139_5	+	9740	.	COG0290	Translation initiation factor IF-3 [Translation, ribosomal structure and biogenesis]. 	MKNDKLKNQYRVNEQIRAREVRIVGDEGSEVVSTKKALDMARQQGVDLVEISPNAQPPVCRLIDYSKFLYQQKKHQKEIKQKQVKVEVKEIRFGPQTDEHDYNFKLKHAKEFLEDGNKVRAYVFFRGRSILFKEQGEVLLLRFANDLEEFGKVEQMPRLEGKKMFLFIAPKKSGVAKKSQQKLDREKRDAEAKLASDMQREANLEKTGLFANAKNGEKALDQLKDSAATNE*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0005	persistent	direct	high	695	0.999	GCA_003640305.1_00994
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	6124	6321	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	6125	6322	GCA_003640305_1_139_6	GCA_003640305_1_139_6	+	9740	.	COG0291	Ribosomal protein L35 [Translation, ribosomal structure and biogenesis]. 	MPKVKTNSGAKKRFSFTGTGKVKRHHAYHSHILTKKTKKQKRNLVHQTLVDRTNMKQVRDLLCLR*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0006	persistent	direct	high	197	0.995	GCA_003640305.1_00995
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	6359	6703	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	6360	6704	GCA_003640305_1_139_7	GCA_003640305_1_139_7	+	9740	.	PRK05185	50S ribosomal protein L20; Provisional	MPRSVNHVASKAKRTRILKLTKGYYGARKNVWTVAKNTWEKGLTYAYRDRRNKKRNFRALWIQRINAAARLENMSYSTLMGALHKAGIEINRKVLADLAVNNPEAFKAIVDKVK*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0007	persistent	direct	high	344	0.997	GCA_003640305.1_00996
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	6732	6857	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	6733	6858	GCA_003640305_1_139_8	GCA_003640305_1_139_8	+	9740	.	.	hypothetical protein	MGMYVAYILIFFVYILCRKGNNYTRIAPSLCLIEIGVFKKI*	.	hypothetical_protein	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0008	persistent	direct	high	125	0.992	GCA_003640305.1_00997
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	6825	7175	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	6826	7176	GCA_003640305_1_139_9	GCA_003640305_1_139_9	-	9740	.	.	hypothetical protein	MDYHQEILRILIEADCEGLSVKKIVNHVYNACNSLFAPIAYDSVYKAVMQDLITHAKKPNSLIVRTAKRGTYRINTENPLSNQLLLQFKEHNEEERNMEEIKKEMPLNLFEDTNLY*	.	hypothetical_protein	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0009	persistent	direct	high	350	0.997	GCA_003640305.1_00998
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	7255	7551	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	7256	7552	GCA_003640305_1_139_10	GCA_003640305_1_139_10	-	9740	.	pfam10771	Winged helix-turn-helix domain (DUF2582). This family is conserved in bacteria and archaea. The function is not known. The structure of two proteins in this family were solved using NMR and shown to adopt a winged helix-turn-helix fold. Structural analysis shows that these proteins form an unusual dimeric conformation. This dimer was shown to be similar to that found in the FadR and TubR wHTH domains. It was suggested that these proteins are not very likely to bind to DNA.	MTEKKATSKATAPKKVAVKKAAAPKKAASATPVLYINAESVGFRAGDVYQALAAAEGALSVAEIAKAAKISVEEAYLGIGWLFKEGKVKDENNLLTLA*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0010	persistent	direct	high	296	0.997	GCA_003640305.1_00999
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	7707	9470	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	7708	9471	GCA_003640305_1_139_11	GCA_003640305_1_139_11	-	9740	.	COG0173	Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]. 	MYRTKTCGELRLADAGTSVTLAGWVQRIRKMGGMTFIDLRDRYGITQLVFNSTADSSLFDAANRLGREYCIQVVGRVSERESKNPKMDTGDIEILAERLQILSPSLTPPFTIEDETDGGDDLRMKYRYLDLRRNAVRRNIELRHRMTILIRNFLDAQQFMEVETPVLIGSTPEGARDFVVPSRMNPGQFYALPQSPQTLKQLLMVAGFDRYFQIAKCFRDEDLRADRQPEFTQIDCEMSFVDQDDVLELFERMARHLFKEIRGVELPPLERMTWQEAMKRFGSDKPDLRFGMEFVELKEAFAGKGSFSVFDDAQYIGGICVPGCAHYSRKQLDELTDFVKRPQIGAKGLVYIKYNEDGSVKSSIDKFYREEVLRSVLQKGDAKPGDLMLILSGDKPNATRIQLCALRLEMGDRLGLRNKDVFKCLWIIDFPLFEWSDEEQRLMATHHPFTMPNPDDLPLLDEHPEQVRAKAYDFVCNGIEVGGGSLRIHDTQLQEKMFEVLGFTKERAEAQFGFLMNAFKYGAPPHAGLAFGLDRFVSIMAGLDSIRDCIAFPKNNSGRDVMLDAPGVLDDKQLEELQIRLNPSTKD*	mmseqs_cdd	nonviral_gene	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0011	persistent	direct	high	1763	0.999	GCA_003640305.1_01000
GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote	cenote	CDS	9483	9737	GCA_003640305.1	RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305.1_RBKH01000139.1	GCA_003640305.1|RBKH01000139.1	GCA_003640305_1_139	GCA_003640305_1_139	9484	9738	GCA_003640305_1_139_12	GCA_003640305_1_139_12	-	9740	.	.	hypothetical protein	FVHRDGQTQEMIAGEGLADGQTQEMYAGEVLADEDKMRFAAISKSFWSVCQDGQPIFLDFAHSSGLYDLMLHLFRNFAQQNSNS*	.	hypothetical_protein	NaN	.	0	9740	GCA_003640305.1|RBKH01000139.1@region_1_9740@tool_cenote_CDS_0012	cloud	direct	moderate	225	0.882	GCA_003640305.1_01001