correct peroxisome compartment

reconstruction/ecoli/dataclasses/getter_functions.py

@@ -27,7 +27,6 @@
 	'CCO-CE-BAC': 'm',
 	'CCO-BAC-NUCLEOID': 'c',
 	'CCO-RIBOSOME': 'c',
-	'CCO-PEROXISOME': 'c', ### TODO: DELETE AFTER 'CCO-PEROXISOME': 'c', is removed from "G7439-MONOMER"
 }
 
 IGNORED_DNA_SITE_TYPES = {

reconstruction/ecoli/flat/complexation_reactions.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:02:13
+# Date and time generated: July 19, 2024, 9:40:33
 "id"	"stoichiometry"	"common_name"	"cofactors"
 "1-PFK_RXN"	{"1-PFK": 1, "1-PFK-MONOMER": -2}	null	{"MG+2": 1}
 "2OXOGLUTARATEDEH-CPLX_RXN"	{"2OXOGLUTARATEDEH-CPLX": 1, "E1O": -1, "E2O": -1, "E3-CPLX": -1}	"2-oxoglutarate dehydrogenase complex"	{"LIPOIC-ACID": 1, "THIAMINE-PYROPHOSPHATE": 2, "FAD": 3, "MG+2": 2}

reconstruction/ecoli/flat/dna_sites.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:02:15
+# Date and time generated: July 19, 2024, 9:40:35
 "id"	"common_name"	"synonyms"	"type"	"left_end_pos"	"right_end_pos"	"direction"
 "BS-7046"	null	[]	"dna-binding-site"	1825765	1825784	null
 "BS-7048"	null	[]	"dna-binding-site"	3169748	3169760	null

reconstruction/ecoli/flat/equilibrium_reactions.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:02:16
+# Date and time generated: July 19, 2024, 9:40:36
 "id"	"stoichiometry"	"common_name"
 "CPLX-123_RXN"	{"CPLX-123": 1, "PC00033": null, "HYPOXANTHINE": null}	"DNA-binding transcriptional repressor PurR-hypoxanthine"
 "CPLX-124_CPD0-1112_RXN"	{"CPLX-124": 1, "CPD0-1112": null, "PC00086": null}	"RhaS-L-rhamnose DNA-binding transcriptional activator"

reconstruction/ecoli/flat/genes.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:02:22
+# Date and time generated: July 19, 2024, 9:40:40
 "id"	"symbol"	"synonyms"	"left_end_pos"	"right_end_pos"	"direction"	"rna_ids"
 "EG10001"	"alr"	["alr", "alr5", "b4053", "ECK4045"]	4265782	4266861	"+"	["EG10001_RNA"]
 "EG10002"	"modB"	["modB", "chlJ", "tslJ", "b0764", "ECK0753"]	795862	796551	"+"	["EG10002_RNA"]

reconstruction/ecoli/flat/metabolic_reactions.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:02:52
+# Date and time generated: July 19, 2024, 9:41:02
 "id"	"stoichiometry"	"direction"	"catalyzed_by"
 "1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN"	{"ACYL-SN-GLYCEROL-3P[CCO-CYTOSOL]": -1, "ACYL-ACP[CCO-CYTOSOL]": -1, "L-PHOSPHATIDATE[CCO-CYTOSOL]": 1, "ACP[CCO-CYTOSOL]": 1}	"L2R"	["1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER"]
 "1.1.1.127-RXN"	{"2-DEHYDRO-3-DEOXY-D-GLUCONATE[CCO-CYTOSOL]": -1, "NAD[CCO-CYTOSOL]": -1, "CPD-343[CCO-CYTOSOL]": 1, "NADH[CCO-CYTOSOL]": 1, "PROTON[CCO-CYTOSOL]": 1}	"BOTH"	["KDUD-MONOMER"]

reconstruction/ecoli/flat/metabolites.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:03:09
+# Date and time generated: July 19, 2024, 9:41:18
 "id"	"common_name"	"synonyms"	"chemical_formula"	"mw"	"molecular_charge"	"_smiles"
 "--TRANS-ACENAPHTHENE-12-DIOL"	"(+/-)-<i>trans</i>-acenaphthene-1,2-diol"	["<i>trans</i>-1,2-acenaphthylene glycol"]	"C12H10O2"	186.21	0	"c2(cc1(cccc3(c1c(c2)[C@@H]([C@H]3O)O)))"
 "1-2-Beta-D-Glucans"	"a 1,2-&beta;-D-glucan"	[]	null	null	0	"C(O)[C@H]7(O[C@@H](O)[C@H](O[C@@H]6(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]5([C@H](O[C@@H]4(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]3([C@H](O[C@@H]2(O[C@H](CO)[C@@H](O)[C@H](O)[C@@H](O[C@H]1([C@H](O[R])[C@@H](O)[C@H](O)[C@@H](CO)O1))2))[C@@H](O)[C@H](O)[C@@H](CO)O3))4))[C@@H](O)[C@H](O)[C@@H](CO)O5))6))[C@@H](O)[C@H](O)7)"

reconstruction/ecoli/flat/proteins.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:03:28
+# Date and time generated: July 19, 2024, 9:41:37
 "id"	"common_name"	"synonyms"	"seq"	"experimental_compartment"	"computational_compartment"	"cleavage_of_initial_methionine"	"selenocysteine_at_opal"	"protein_feature_cofactors"	"in_complex"
 "1-ACYLGLYCEROL-3-P-ACYLTRANSFER-MONOMER"	"1-acylglycerol-3-phosphate <i>O</i>-acyltransferase PlsC"	["ParF", "PlsC"]	"MLYIFRLIITVIYSILVCVFGSIYCLFSPRNPKHVATFGHMFGRLAPLFGLKVECRKPTDAESYGNAIYIANHQNNYDMVTASNIVQPPTVTVGKKSLLWIPFFGQLYWLTGNLLIDRNNRTKAHGTIAEVVNHFKKRRISIWMFPEGTRSRGRGLLPFKTGAFHAAIAAGVPIIPVCVSTTSNKINLNRLHNGLVIVEMLPPIDVSQYGKDQVRELAAHCRSIMEQKIAELDKEVAEREAAGKV"	["CCO-PM-BAC-NEG"]	["CCO-MEMBRANE", "CCO-PM-BAC-NEG"]	0	[]	{}	0
 "1-PFK-MONOMER"	"1-phosphofructokinase"	["Fpk", "FruK"]	"MSRRVATITLNPAYDLVGFCPEIERGEVNLVKTTGLHAAGKGINVAKVLKDLGIDVTVGGFLGKDNQDGFQQLFSELGIANRFQVVQGRTRINVKLTEKDGEVTDFNFSGFEVTPADWERFVTDSLSWLGQFDMVCVSGSLPSGVSPEAFTDWMTRLRSQCPCIIFDSSREALVAGLKAAPWLVKPNRRELEIWAGRKLPEMKDVIEAAHALREQGIAHVVISLGAEGALWVNASGEWIAKPPSVDVVSTVGAGDSMVGGLIYGLLMRESSEHTLRLATAVAALAVSQSNVGITDRPQLAAMMARVDLQPFN"	[]	["CCO-CYTOSOL"]	0	[]	{}	1
@@ -2270,9 +2270,9 @@
 "G6700-MONOMER"	"outer membrane porin N"	["YnaG", "OmpN"]	"MKSKVLALLIPALLAAGAAHAAEVYNKDGNKLDLYGKVDGLHYFSDNSAKDGDQSYARLGFKGETQINDQLTGYGQWEYNIQANNTESSKNQSWTRLAFAGLKFADYGSFDYGRNYGVMYDIEGWTDMLPEFGGDSYTNADNFMTGRANGVATYRNTDFFGLVNGLNFAVQYQGNNEGASNGQEGTNNGRDVRHENGDGWGLSTTYDLGMGFSAGAAYTSSDRTNDQVNHTAAGGDKADAWTAGLKYDANNIYLATMYSETRNMTPFGDSDYAVANKTQNFEVTAQYQFDFGLRPAVSFLMSKGRDLHAAGGADNPAGVDDKDLVKYADIGATYYFNKNMSTYVDYKINLLDEDDSFYAANGISTDDIVALGLVYQF"	["CCO-MEMBRANE"]	["CCO-OUTER-MEM"]	0	[]	{}	0
 "G6701-MONOMER"	"putative pyruvate-flavodoxin oxidoreductase"	["Pfo", "YdbK"]	"MITIDGNGAVASVAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDTPRVVEMQSEAGAIATVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGELTPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCAANVQEAQDFALISQIATLKSRVPFIHFFDGFRTSHEINKIVPLADDTILDLMPQVEIDAHRARALNPEHPVIRGTSANPDTYFQSREATNPWYNAVYDHVEQAMNDFSAATGRQYQPFEYYGHPQAERVIILMGSAIGTCEEVVDELLTRGEKVGVLKVRLYRPFSAKHLLQALPGSVRSVAVLDRTKEPGAQAEPLYLDVMTALAEAFNNGERETLPRVIGGRYGLSSKEFGPDCVLAVFAELNAAKPKARFTVGIYDDVTNLSLPLPENTLPNSAKLEALFYGLGSDGSVSATKNNIKIIGNSTPWYAQGYFVYDSKKAGGLTVSHLRVSEQPIRSAYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSADEVWSRLPQEVQAVLNQKKARFYVINAAKIARECGLAARINTVMQMAFFHLTQILPGDSALAELQGAIAKSYSSKGQDLVERNWQALALARESVEEVPLQPVNPHSANRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALPPDGTWPMGTTRWEKRNIAEEIPIWKEELCTQCNHCVAACPHSAIRAKVVPPEAMENAPASLHSLDVKSRDMRGQKYVLQVAPEDCTGCNLCVEVCPAKDRQNPEIKAINMMSRLEHVEEEKINYDFFLNLPEIDRSKLERIDIRTSQLITPLFEYSGACSGCGETPYIKLLTQLYGDRMLIANATGCSSIYGGNLPSTPYTTDANGRGPAWANSLFEDNAEFGLGFRLTVDQHRVRVLRLLDQFADKIPAELLTALKSDATPEVRREQVAALRQQLNDVAEAHELLRDADALVEKSIWLIGGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRKARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLIIAYSPCEEHGYDLALSHDQMRQLTATGFWPLYRFDPRRADEGKLPLALDSRPPSEAPEETLLHEQRFRRLNSQQPEVAEQLWKDAAADLQKRYDFLAQMAGKAEKSNTD"	[]	["CCO-PM-BAC-NEG"]	0	[]	{"CPD-7": 3}	0
 "G6702-MONOMER"	"lipoprotein implicated in Novobiocin resistance"	["YdbI", "HslJ"]	"MKKVAAFVALSLLMAGCVSNDKIAVTPEQLQHHRFVLESVNGKPVTSDKNPPEISFGEKMMISGSMCNRFSGEGKLSNGELTAKGLAMTRMMCANPQLNELDNTISEMLKEGAQVDLTANQLTLATAKQTLTYKLADLMN"	[]	["CCO-MEMBRANE"]	0	[]	{}	0
-"G6703-MONOMER"	"putative phospholipid transport factor YdbH"	["YdbH"]	"MLGKYKAVLALLLLIILVPLTLLMTLGLWVPTLAGIWLPLGTRIALDESPRITRKGLIIPDLRYLVGDCQLAHITNASLSHPSRWLLNVGTVELDSACLAKLPQTEQSPAAPKTLAQWQAMLPNTWINIDKLIFSPWQEWQGKLSLALTSDIQQLRYQGEKVKFQGQLKGQQLTVSELDVVAFENQPPVKLVGEFAMPLVPDGLPVSGHATATLNLPQEPSLVDAELDWQENSGQLIVLARDNGDPLLDLPWQITRQQLTVSDGRWSWPYAGFPLSGRLGVKVDNWQAGLENALVSGRLSVLTQGQAGKGNAVLNFGPGKLSMDNSQLPLQLTGEAKQADLILYARLPAQLSGSLSDPTLTFEPGALLRSKGRVIDSLDIDEIRWPLAGVKVTQRGVDGRLQAILQAHENELGDFVLHMDGLANDFLPDAGRWQWRYWGKGSFTPMNATWDVAGKGEWHDSTITLTDLSTGFDQLQYGTMTVEKPRLILDKPIVWVRDAQHPSFSGALSLDAGQTLFTGGSVLPPSTLKFSVDGRDPTYFLFKGDLHAGEIGPVRVNGRWDGIRLRGNAWWPKQSLTVFQPLVPPDWKMNLRDGELYAQVAFSAAPEQGFRAGGHGVLKGGSAWMPDNQVNGVDFVLPFRFADGAWHLGTRGPVTLRIAEVINLVTAKNITADLQGRYPWTEEEPLLLTDVSVDVLGGNVLMKQLRMPQHDPALLRLNNLSSSELVSAVNPKQFAMSGAFSGALPLWLNNEKWIVKDGWLANSGPMTLRLDKDTADAVVKDNMTAGSAINWLRYMEISRSSTKINLDNLGLLTMQANITGTSRVDGKSGTVNLNYHHEENIFTLWRSLRFGDNLQAWLEQNARLPGNDCPQGKECEEKQ"	["CCO-PM-BAC-NEG"]	["CCO-PM-BAC-NEG"]	0	[]	{}	0
-"G6704-MONOMER"	"lipoprotein YnbE"	["YnbE"]	"MKILLAALTSSFMLVGCTPRIEVAAPKEPITINMNVKIEHEIIIKADKDVEELLETRSDLF"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
-"G6705-MONOMER"	"DUF1318 domain-containing protein YdbL"	["YdbL"]	"MKKTLLLCAFLVGLVSSNVMALTLDEARTQGRVGETFYGYLVALKTDAETEKLVADINAERKASYQQLAKQNNVSVDDIAKLAGQKLVARAKPGEYVQGINGKWVRKF"	[]	[]	0	[]	{}	0
+"G6703-MONOMER"	"putative intermembrane phospholipid transport protein YdbH"	["YdbH"]	"MLGKYKAVLALLLLIILVPLTLLMTLGLWVPTLAGIWLPLGTRIALDESPRITRKGLIIPDLRYLVGDCQLAHITNASLSHPSRWLLNVGTVELDSACLAKLPQTEQSPAAPKTLAQWQAMLPNTWINIDKLIFSPWQEWQGKLSLALTSDIQQLRYQGEKVKFQGQLKGQQLTVSELDVVAFENQPPVKLVGEFAMPLVPDGLPVSGHATATLNLPQEPSLVDAELDWQENSGQLIVLARDNGDPLLDLPWQITRQQLTVSDGRWSWPYAGFPLSGRLGVKVDNWQAGLENALVSGRLSVLTQGQAGKGNAVLNFGPGKLSMDNSQLPLQLTGEAKQADLILYARLPAQLSGSLSDPTLTFEPGALLRSKGRVIDSLDIDEIRWPLAGVKVTQRGVDGRLQAILQAHENELGDFVLHMDGLANDFLPDAGRWQWRYWGKGSFTPMNATWDVAGKGEWHDSTITLTDLSTGFDQLQYGTMTVEKPRLILDKPIVWVRDAQHPSFSGALSLDAGQTLFTGGSVLPPSTLKFSVDGRDPTYFLFKGDLHAGEIGPVRVNGRWDGIRLRGNAWWPKQSLTVFQPLVPPDWKMNLRDGELYAQVAFSAAPEQGFRAGGHGVLKGGSAWMPDNQVNGVDFVLPFRFADGAWHLGTRGPVTLRIAEVINLVTAKNITADLQGRYPWTEEEPLLLTDVSVDVLGGNVLMKQLRMPQHDPALLRLNNLSSSELVSAVNPKQFAMSGAFSGALPLWLNNEKWIVKDGWLANSGPMTLRLDKDTADAVVKDNMTAGSAINWLRYMEISRSSTKINLDNLGLLTMQANITGTSRVDGKSGTVNLNYHHEENIFTLWRSLRFGDNLQAWLEQNARLPGNDCPQGKECEEKQ"	["CCO-PM-BAC-NEG"]	["CCO-PM-BAC-NEG"]	0	[]	{}	0
+"G6704-MONOMER"	"putative intermembrane phospholipid transport lipoprotein YnbE"	["YnbE"]	"MKILLAALTSSFMLVGCTPRIEVAAPKEPITINMNVKIEHEIIIKADKDVEELLETRSDLF"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
+"G6705-MONOMER"	"DUF1318 domain-containing protein YdbL"	["YdbL"]	"MKKTLLLCAFLVGLVSSNVMALTLDEARTQGRVGETFYGYLVALKTDAETEKLVADINAERKASYQQLAKQNNVSVDDIAKLAGQKLVARAKPGEYVQGINGKWVRKF"	[]	["CCO-PERI-BAC"]	0	[]	{}	0
 "G6706-MONOMER"	"DNA-binding transcriptional activator FeaR"	["MaoX", "YdbM", "MaoB", "FeaR"]	"MNPAVDNEFQQWLSQINQVCGNFTGRLLTERYTGVLDTHFAKGLKLSTVTTSGVNLSRTWQEVKGSDDAWFYTVFQLSGQAIMEQDERQVQIGAGDITLLDASRPCSLYWQESSKQISLLLPRTLLEQYFPHQKPICAERLDADLPMVQLSHRLLQESMNNPALSETESEAALQAMVCLLRPVLHQRESVQPRRERQFQKVVTLIDDNIREEILRPEWIAGETGMSVRSLYRMFADKGLVVAQYIRNRRLDFCADAIRHAADDEKLAGIGFHWGFSDQSHFSTVFKQRFGMTPGEYRRKFR"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
 "G6708-MONOMER"	"fused 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase and oxepin-CoA hydrolase"	["YdbN", "PaaZ", "MaoC", "oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase"]	"MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVARQHGDFVD"	[]	["CCO-CYTOSOL"]	0	[]	{}	1
 "G6709-MONOMER"	"phenylacetyl-CoA 1,2-epoxidase, monooxygenase subunit"	["YdbO", "PaaA"]	"MTQEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRKAILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGVIGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQMLQDAINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTVPDPDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHAQKQHARKVA"	[]	["CCO-CYTOSOL"]	0	[]	{}	1
@@ -2852,7 +2852,7 @@
 "G7434-MONOMER"	"putative anti-terminator regulatory protein"	["YgcP"]	"MPLLHLLRQNPVIAAVKDNASLQLAIDSECQFISVLYGNICTISNIVKKIKNAGKYAFIHVDLLEGASNKEVVIQFLKLVTEADGIISTKASMLKAARAEGFFCIHRLFIVDSISFHNIDKQVAQSNPDCIEILPGCMPKVLGWVTEKIRQPLIAGGLVCDEEDARNAINAGVVALSTTNTGVWTLAKKLL"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
 "G7435-MONOMER"	"putative flavoprotein"	["YgcQ"]	"MNIAIVTINQENAAIASWLAAQDFSGCTLAHWQIEPQPVVAEQVLDALVEQWQRTPADVVLFPPGTFGDELSTRLAWRLHGASICQVTSLDIPTVSVRKSHWGNALTATLQTEKRPLCLSLARQAGAAKNATLPSGMQQLNIVPGALPDWLVSTEDLKNVTRDPLAEARRVLVVGQGGEADNQEIAMLAEKLGAEVGYSRARVMNGGVDAEKVIGISGHLLAPEVCIVVGASGAAALMAGVRNSKFVVAINHDASAAVFSQADVGVVDDWKVVLEALVTNIHADCQ"	[]	["CCO-MEMBRANE"]	0	[]	{}	0
 "G7436-MONOMER"	"putative flavoprotein"	["YgcR"]	"MNILLAFKAEPDAGMLAEKEWQAAAQGKSGPDISLLRSLLGADEQAAAALLLAQRKNGTPMSLTALSMGDERALHWLRYLMALGFEEAVLLETAADLRFAPEFVARHIAEWQHQNPLDLIITGCQSSEGQNGQTPFLLAEMLGWPCFTQVERFTLDALFITLEQRTEHGLRCCRVRLPAVIAVRQCGEVALPVPGMRQRMAAGKAEIIRKTVAAEMPAMQCLQLARAEQRRGATLIDGQTVAEKAQKLWQDYLRQRMQP"	[]	["CCO-PM-BAC-NEG", "CCO-CYTOSOL"]	0	[]	{}	0
-"G7439-MONOMER"	"putative FAD-containing dehydrogenase"	["YgcV", "YgcU", "YgcT"]	"MSLSRAAIVDQLKEIVGADRVITDETVLKKNSIDRFRKFPDIHGIYTLPIPAAVVKLGSTEQVSRVLNFMNAHKINGVPRTGASATEGGLETVVENSVVLDGSAMNQIINIDIENMQATAQCGVPLEVLENALREKGYTTGHSPQSKPLAQMGGLVATRSIGQFSTLYGAIEDMVVGLEAVLADGTVTRIKNVPRRAAGPDIRHIIIGNEGALCYITEVTVKIFKFTPENNLFYGYILEDMKTGFNILREIMVEGYRPSIARLYDAEDGTQHFTHFADGKCVLIFMAEGNPRIAKVTGEGIAEIVARYPQCQRVDSKLIETWFNNLNWGPDKVAAERVQILKTGNMGFTTEVSGCWSCIHEIYESVINRIRTEFPHADDITMLGGHSSHSYQNGTNMYFVYDYNVVDCKPEEEIDKYHNPLNKIICEETIRLGGSMVHHHGIGKHRVHWSKLEHGSAWALLEGLKKQFDPNGIMNTGTIYPIEK"	[]	["CCO-PEROXISOME", "CCO-CYTOSOL"]	0	[]	{}	0
+"G7439-MONOMER"	"putative FAD-containing dehydrogenase"	["YgcV", "YgcU", "YgcT"]	"MSLSRAAIVDQLKEIVGADRVITDETVLKKNSIDRFRKFPDIHGIYTLPIPAAVVKLGSTEQVSRVLNFMNAHKINGVPRTGASATEGGLETVVENSVVLDGSAMNQIINIDIENMQATAQCGVPLEVLENALREKGYTTGHSPQSKPLAQMGGLVATRSIGQFSTLYGAIEDMVVGLEAVLADGTVTRIKNVPRRAAGPDIRHIIIGNEGALCYITEVTVKIFKFTPENNLFYGYILEDMKTGFNILREIMVEGYRPSIARLYDAEDGTQHFTHFADGKCVLIFMAEGNPRIAKVTGEGIAEIVARYPQCQRVDSKLIETWFNNLNWGPDKVAAERVQILKTGNMGFTTEVSGCWSCIHEIYESVINRIRTEFPHADDITMLGGHSSHSYQNGTNMYFVYDYNVVDCKPEEEIDKYHNPLNKIICEETIRLGGSMVHHHGIGKHRVHWSKLEHGSAWALLEGLKKQFDPNGIMNTGTIYPIEK"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
 "G7440-MONOMER"	"putative deoxygluconate dehydrogenase"	["YgcW"]	"MSIESLNAFSMDFFSLKGKTAIVTGGNSGLGQAFAMALAKAGANIFIPSFVKDNGETKEMIEKQGVEVDFMQVGITAEGAPQKIIAACCERFGTVDILVNNAGICKLNKVLDFGRADWDPMIDVNLTAAFELSYEAAKIMIPQKSGKIINICSLFSYLGGQWSPAYSATKHALAGFTKAYCDELGQYNIQVNGIAPGYYATDITLATRSNPETNQRVLDHIPANRWGDTQDLMGAAVFLASPASNYVNGHLLVVDGGYLVR"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
 "G7442-MONOMER"	"putative sugar kinase YgcE"	["YgcE"]	"MSKKYIIGIDGGSQSTKVVMYDLEGNVVCEGKGLLQPMHTPDADTAEHPDDDLWASLCFAGHDLMSQFAGNKEDIVGIGLGSIRCCRALLKADGTPAAPLISWQDARVTRPYEHTNPDVAYVTSFSGYLTHRLTGEFKDNIANYFGQWPVDYKSWAWSEDAAVMDKFNIPRHMLFDVQMPGTVLGHITPQAALATHFPAGLPVVCTTSDKPVEALGAGLLDDETAVISLGTYIALMMNGKALPKDPVAYWPIMSSIPQTLLYEGYGIRKGMWTVSWLRDMLGESLIQDARAQDLSPEDLLNKKASCVPPGCNGLMTVLDWLTNPWEPYKRGIMIGFDSSMDYAWIYRSILESVALTLKNNYDNMCNEMNHFAKHVIITGGGSNSDLFMQIFADVFNLPARRNAINGCASLGAAINTAVGLGLYPDYATAVDNMVRVKDIFIPIESNAKRYDAMNKGIFKDLTKHTDVILKKSYEVMHGELGNVDSIQSWSNA"	[]	["CCO-CYTOSOL"]	0	[]	{}	0
 "G7443-MONOMER"	"putative 7-carboxy-7-deazaguanine synthase QueE"	["QueE", "YgcF", "putative CDG synthase"]	"MQYPINEMFQTLQGEGYFTGVPAIFIRLQGCPVGCAWCDTKHTWEKLEDREVSLFSILAKTKESDKWGAASSEDLLAVIGRQGYTARHVVITGGEPCIHDLLPLTDLLEKNGFSCQIETSGTHEVRCTPNTWVTVSPKLNMRGGYEVLSQALERANEIKHPVGRVRDIEALDELLATLTDDKPRVIALQPISQKDDATRLCIETCIARNWRLSMQTHKYLNIA"	["CCO-CYTOSOL"]	["CCO-CYTOSOL"]	0	[]	{"CPD-7": 1, "MG+2": 1}	0

reconstruction/ecoli/flat/rnas.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:03:33
+# Date and time generated: July 19, 2024, 9:41:42
 "id"	"common_name"	"synonyms"	"type"	"modified_forms"	"gene_id"	"monomer_ids"	"anticodon"	"coding_segments"
 "EG10001_RNA"	"alr"	["alr", "alr5", "b4053", "ECK4045"]	"mRNA"	[]	"EG10001"	["ALARACEBIOSYN-MONOMER"]	null	[]
 "EG10002_RNA"	"modB"	["modB", "chlJ", "tslJ", "b0764", "ECK0753"]	"mRNA"	[]	"EG10002"	["MODB-MONOMER"]	null	[]

reconstruction/ecoli/flat/transcription_units.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:03:37
+# Date and time generated: July 19, 2024, 9:41:46
 "id"	"common_name"	"genes"	"left_end_pos"	"right_end_pos"	"direction"	"evidence"
 "TU-8381"	"spy"	["G6939"]	1825057	1825688	"-"	["EV-EXP-IDA-TRANSCRIPT-LEN-DETERMINATION", "EV-EXP-IDA-BOUNDARIES-DEFINED"]
 "TU-8382"	"ycaC"	["EG11241"]	944931	945557	"-"	["EV-COMP-AINF-SINGLE-DIRECTON"]

reconstruction/ecoli/flat/trna_charging_reactions.tsv

@@ -1,7 +1,7 @@
 # Organism: Escherichia coli K-12 substr. MG1655
 # Database: EcoCyc
 # Version: 28.5
-# Date and time generated: July 18, 2024, 11:03:38
+# Date and time generated: July 19, 2024, 9:41:47
 "id"	"stoichiometry"	"catalyzed_by"	"common_name"
 "ALANINE--TRNA-LIGASE-RXN_alaT-tRNA"	{"L-ALPHA-ALANINE": -1, "ATP": -1, "alaT-tRNA": -1, "PPI": 1, "AMP": 1, "charged-alaT-tRNA": 1}	["ALAS-CPLX"]	"ALANYL-TRNA SYNTHETASE"
 "ALANINE--TRNA-LIGASE-RXN_alaU-tRNA"	{"L-ALPHA-ALANINE": -1, "ATP": -1, "alaU-tRNA": -1, "PPI": 1, "AMP": 1, "charged-alaU-tRNA": 1}	["ALAS-CPLX"]	"ALANYL-TRNA SYNTHETASE"