denitrification UniProt update

Nitrogen_metabolism/Denitrification/NapA/NapA_purity/TreeSAPP_purity_log.txt

@@ -0,0 +1,163 @@
+[2022-04-15 22:07:00] INFO: 
+##			Beginning purity analysis			##
+
+[2022-04-15 22:07:00] INFO: Arguments used:
+-n 4 -r NapA_UniProt_update/final_outputs/NapA_build.pkl --extra_info ../TIGRFAM_info.tsv -i ../TIGRFAM_seed_named.faa --output NapA_UniProt_update/NapA_purity
+
+[2022-04-15 22:07:00] DEBUG: Sequences appear to be 'prot'.
+
+[2022-04-15 22:07:01] DEBUG: Continuing with stage 'clean'
+
+[2022-04-15 22:07:01] DEBUG: Read 61111 headers from FASTA file '../TIGRFAM_seed_named.faa'.
+
+[2022-04-15 22:07:02] INFO: 
+##				Assigning sequences with TreeSAPP				##
+
+
+[2022-04-15 22:07:02] INFO: Arguments used:
+-i /root/data/imman/uniprot_data/NapA_UniProt_update/NapA_purity/intermediates/clean/TIGRFAM_seed_named_formatted.fasta -o /root/data/imman/uniprot_data/NapA_UniProt_update/NapA_purity/intermediates/assign/ -m prot -n 4 -t NapA --refpkg_dir /root/data/imman/uniprot_data/NapA_UniProt_update/final_outputs --overwrite --delete
+
+[2022-04-15 22:07:02] DEBUG: Continuing with stage 'clean'
+
+[2022-04-15 22:07:02] DEBUG: Gathering reference package files... 
+[2022-04-15 22:07:02] DEBUG: done.
+
+[2022-04-15 22:07:03] INFO: Reading and formatting /root/data/imman/uniprot_data/NapA_UniProt_update/NapA_purity/intermediates/clean/TIGRFAM_seed_named_formatted.fasta... 
+[2022-04-15 22:07:03] DEBUG: /root/data/imman/uniprot_data/NapA_UniProt_update/NapA_purity/intermediates/clean/TIGRFAM_seed_named_formatted.fasta read by pyfastx in 0.3 seconds.
+
+[2022-04-15 22:07:03] DEBUG: The following sequences were removed due to bad characters:
+TIGR01917_GP|14717791|gb|AAC43574.2/5-435
+TIGR00476_gi|158320767|ref|YP_001513274./1-309
+TIGR01918_GP|14717791|gb|AAC43574.2/5-435
+TIGR04483_gi|158319089|ref|YP_001511596./4-241
+TIGR04481_gi|310659538|ref/3-427
+TIGR00476_gi|342732113|ref|YP_004770952./1-307
+TIGR00476_gi|319956066|ref|YP_004167329./1-307
+TIGR04481_SELENO_ntcb02/5-434
+TIGR01917_GP|11065689|emb|CAC14301.1/5-435
+TIGR04483_gi|153933895|ref|YP_001384638./2-239
+TIGR01918_GP|11065689|emb|CAC14301.1/5-435
+TIGR00476_gi|317128844|ref|YP_004095126./1-311
+
+[2022-04-15 22:07:03] INFO: done.
+
+[2022-04-15 22:07:03] INFO: 	TreeSAPP will analyze the 61099 sequences found in input.
+
+[2022-04-15 22:07:03] INFO: Searching for marker proteins in ORFs using hmmsearch.
+
+[2022-04-15 22:07:04] INFO: Parsing HMMER domain tables for high-quality matches... 
+[2022-04-15 22:07:04] INFO: done.
+
+[2022-04-15 22:07:04] DEBUG: 	Initial alignments:	162
+	Alignments discarded:	23
+	Fragmented alignments:	144
+	Inversions detected:	0
+	Alignments scaffolded:	81
+	Multi-alignments:	0
+	Sequences identified:	58
+
+	Number of markers identified:
+		NapA	58
+
+[2022-04-15 22:07:04] INFO: Loading homologous sequences identified... 
+[2022-04-15 22:07:04] DEBUG: 61041 sequences were excluded after synchronizing FASTA.
+
+[2022-04-15 22:07:04] INFO: done.
+
+[2022-04-15 22:07:04] DEBUG: Instantiating the PQuery instances... 
+[2022-04-15 22:07:04] DEBUG: done.
+
+[2022-04-15 22:07:04] INFO: Extracting and grouping the quality-controlled sequences... 
+[2022-04-15 22:07:04] INFO: done.
+
+[2022-04-15 22:07:04] DEBUG: Number of query sequences in each marker's group:
+NapA	0	58
+
+
+[2022-04-15 22:07:04] INFO: Writing the grouped sequences to FASTA files... 
+[2022-04-15 22:07:04] INFO: done.
+
+[2022-04-15 22:07:06] DEBUG: 	hmmalign time required: 0.0:0.0:2.3
+
+[2022-04-15 22:07:06] DEBUG: Read 1175 headers from FASTA file '/root/data/imman/uniprot_data/NapA_UniProt_update/NapA_purity/intermediates/assign/intermediates/align/NapA_hmm_purified_group0.mfa'.
+
+[2022-04-15 22:07:36] INFO: Parsing the EPA-NG outputs... 
+[2022-04-15 22:07:37] INFO: done.
+
+[2022-04-15 22:07:37] DEBUG: 	JPlace parsing time required: 0.0:0.0:0.13
+
+[2022-04-15 22:07:37] DEBUG: 	1 JPlace files.
+
+[2022-04-15 22:07:37] INFO: Selecting the optimal query placements... 
+[2022-04-15 22:07:40] INFO: done.
+
+[2022-04-15 22:07:40] DEBUG: 	PQuery parsing time required: 0.0:0.0:3.54
+
+[2022-04-15 22:07:40] DEBUG: 	58 sequences placed into trees by EPA-NG.
+
+[2022-04-15 22:07:40] INFO: Filtering low-quality placements... 
+[2022-04-15 22:07:40] DEBUG: Maximum distance threshold for 'NapA' set to 6.428614.
+
+[2022-04-15 22:07:40] INFO: done.
+
+[2022-04-15 22:07:40] DEBUG: NapA	low_lwr	0
+NapA	distant	47
+NapA	big_pendant	0
+NapA	big_branch	0
+NapA	svm	0
+
+[2022-04-15 22:07:40] INFO: Generating inputs for iTOL... 
+[2022-04-15 22:07:40] INFO: done.
+
+[2022-04-15 22:07:40] DEBUG: A colours_style.txt file does not yet exist for markers:
+	NapA
+
+[2022-04-15 22:07:40] DEBUG: A colours_strip.txt file does not yet exist for markers:
+	NapA
+
+[2022-04-15 22:07:40] INFO: 
+Summarizing assignments for reference package NapA
+
+[2022-04-15 22:07:44] INFO: Ortholog	Hits	Leaves	Tree-coverage	Description
+--------------------------------------------------------------------------------
+TIGR01706	5	5	0.4	periplasmic nitrate reductase, large subunit
+TIGR01701	3	4	0.4	oxidoreductase alpha (molybdopterin) subunit
+TIGR02693	3	11	1.0	arsenite oxidase, large subunit
+
+
+[2022-04-15 22:07:44] DEBUG: TIGR01706:
+	Escherichia coli | tr|A0A376SHW7|A0A376SHW7_ECOLX
+	Root | SP|P39185|NAPA_ALCEU/2-831
+	Vibrio sp. JCM 18905 | tr|A0A829TJ52|A0A829TJ52_9VIBR
+	Campylobacter coli | tr|A0A5T1KEY4|A0A5T1KEY4_CAMCO
+	Root | SP|Q56350|NAPA_PARDT/2-831
+TIGR01701:
+	Corallococcus coralloides DSM 2259 | 1144275.COCOR_03558
+	Stigmatella aurantiaca DW4/3-1 | 378806.STAUR_4719
+	Sorangium cellulosum So0157-2 | 1254432.SCE1572_51875
+	Pseudoalteromonas atlantica T6c | 342610.Patl_2844
+	Corallococcus coralloides DSM 2259 | 1144275.COCOR_03558
+	Stigmatella aurantiaca DW4/3-1 | 378806.STAUR_4719
+	Sorangium cellulosum So0157-2 | 1254432.SCE1572_51875
+	Pseudoalteromonas atlantica T6c | 342610.Patl_2844
+	Corallococcus coralloides DSM 2259 | 1144275.COCOR_03558
+	Stigmatella aurantiaca DW4/3-1 | 378806.STAUR_4719
+	Sorangium cellulosum So0157-2 | 1254432.SCE1572_51875
+	Pseudoalteromonas atlantica T6c | 342610.Patl_2844
+TIGR02693:
+	Herminiimonas arsenicoxydans | 204773.HEAR0478
+	Agrobacterium albertimagni AOL15 | 1156935.QWE_02985
+	Herminiimonas arsenicoxydans | 204773.HEAR0478
+	Thiomonas sp. FB-Cd | 1158292.JPOE01000005_gene222
+	Rhodoferax ferrireducens T118 | 338969.Rfer_3084
+	Marinobacter sp. HL-58 | 1479237.JMLY01000001_gene255
+	Pseudomonas stutzeri TS44 | 477228.YO5_14640
+	Sinorhizobium americanum CCGM7 | 1408224.SAMCCGM7_c3965
+	Agrobacterium albertimagni AOL15 | 1156935.QWE_02985
+	Methylobacterium sp. GXF4 | 1096546.WYO_0073
+	Chelatococcus sp. GW1 | 1211115.ALIQ01000219_gene1389
+	Caulobacter segnis ATCC 21756 | 509190.Cseg_2507
+	Sulfurospirillum multivorans DSM 12446 | 1150621.SMUL_3120
+
+[2022-04-15 22:07:44] INFO: TreeSAPP has finished successfully.
+

Nitrogen_metabolism/Denitrification/NapA/NapA_purity/intermediates/assign/final_outputs/TIGRFAM_seed_named_formatted_classified.faa

@@ -0,0 +1,22 @@
+>TIGR01701_OMNI|NTL02MLB0108/16-791|NapA|104_823
+WSDHDLEEQGRLTHPMRW.DAASDKYIPVAWSDAFDEIGRELRSLD.PHQVDLYTSGR.ASLETSYMYQLFARMYGSNNLPDSSNMCHEGSSVALPESIGSSVGTAILSDFENTDCIFYIAQNVGTSSPRMLHDLQDAVNRGVKIVTFNLLRERGLERFVNPQS.PQMLTGKETKISSEYYQVRSGGDIAALFGVCKALIEADDALKASGASRVAGQDGKPKDQDNAAMVAFAASMASADNKHVLDHDFIHEHTTGFEEFAQAARAHQWDELERVSGLSRAEMMQAATTYANASAVMMVYGMGLTQHLMGVENVHMVCNLALLRGNIGKPGANICAVRGHSNVQGQRTVGIT......EKPGLAPLDKLSQLYGFEPPTWTGRSTVETCEAIVN.....GQCRAFISLGGNFLKAIPDTAAMEEGWRKLHLSVQIATK..LNRSHVLHGEVAYLLPCLGRIEVDQQASGPQAVSIESSIAHFHGSRGKAKPAGAELLSEPAIVAGIAKATLG.ETKVPWDAWVGNYAQIRDAIERTYPETFKDFNKRLFQPGGFARPVPAR.ER.KWVTKTGKANFITPHRLFPEFSTSGRA...D.....VLHLSTLRSNDQFNTTIYGYSDRFRGVEGTRRVVFMNGEDISRLGFVDGEHIDVTTAIDDN....NIRKVTNLRIVQYNIPKGCCAAYYPEANPLFPFAHHDPKAKTPSYKLLPVRLTR
+>TIGR01701_SP|P77561|YDEP_ECOLI/11-758|NapA|105_824
+GDHELEAAGRLTQPLKY.DAVSDCYKPLSWQQAFDEIGARLQSYSDPNQVEFYTSGR.TSNEAAFLYQLFAREYGSNNFPDCSNMCHEPTSVGLAASIGVGKGTVLLEDFEKCDLVICIGHNPGTNHPRMLTSLRALVKRGAKMIAINPLQERGLERFTAPQNPFEMLTNSETQLASAYYNVRIGGDMALLKGMMRLLIERDDAASAAGRP..............................SLLDDEFIQTHTVGFDELRRDVLNSEWKDIERISGLSQTQIAELADAYAAAERTIICYGMGITQHEHGTQNVQQLVNLLLMKGNIGKPGAGICPLRGHSNVQGDRTVGIT......EKPSAEFLARLGERYGFTPPHAPGHAAIASMQAICT.....GQARALICMGGNFALAMPDREASAVPLTQLDLAVHVATK..LNRSHLLTARHSYILPVLGRSEIDMQKNGAQAVTVEDSMSMIHASRGVLKPAGVMLKSECAVVAGIAQAALP.QSVVAWEYLVEDYDRIRNDIEAVLP.EFADYNQRIRHPGGFHLINAAA.ER.RWMTPSGKANFITSKGLLEDPSSAFNS...K......LVMATVRSHDQYNTTIYGMDDRYRGVFGQRDVVFMSAKQAKICRVKNGERVNLIALTPDGKR..SSRRMDRLKVVIYPMADRSLVTYFPESNHMLTLDNHDPLSGIPGYKSIPVELEPS
+>TIGR01701_SP|Q10821|YT00_MYCTU/34-778|NapA|102_824
+SAKPEYWLSQQGRLAHPMVL.RPGDDHYRPISWDAAYQLIAEQLNGLDSPDRAVFYTSGR.TSNEAAFCYQLLVRSFGTNNLPDCSNMCHESSGAALTDSIGIGKGSVTIGDVEHADLIVIAGQNPGTNHPRMLSVLGKAKANGAKIIAVNPLPEAGLIRFKDPQK.VNGVVGHGIPIADEFVQIRLGGDMALFAGLGRLLLEAEERVP....G..............................SVVDRSFVDNHCAGFDGYRRRTLQVGLDTVMDATGIELAQLQRVAAMLMASQRTVICWAMGLTQHAHAVATIGEVTNVLLLRGMIGKPGAGVCPVRGHSNVQGDRTMGIW......EKMPEQFLAALDREFGITSPRAHGFDTVAAIRAMRD.....GRVSVFMGMGGNFASATPDTAVTEAALRRCALTVQVSTK..LNRSHLVHGATALILPTLGRTDRDTRNGRKQLVSVEDSMSMVHLSRGSLHPPSDQVRSEVQIICQLARALFGPGHPVPWERFADDYDTIRDAIAAVVP.GCDDYNHKVRVPDGFQLPHPPRDAR.EFRTSTGKANFAVNPLQWVPVPPGR............LVLQTLRSHDQYNTTIYGLDDRYRGVKGGRRVVFINPADIETFGLTAGDRVDLVSEWTDGQGGLQERRAKDFLVVAYSTPVGNAAAYYPETNPLVPLDHTAAQSNTPVSKAIIVRLEPT
+>TIGR01706_OMNI|NTL01CJ00733/2-924|NapA|3_930
+NRRDFIKNTAIASAASVAGLSVP...SSMLGAQEE.DWKWDKAVCRFCGTGCGIMIARKDGKIVATKGDPAAPVNRGLNCIKGYFNAKIMYGEDRLVMPLLRMNEKGEFDKKGKFQQVSWQRAFDEMEKQFKKAYNELGVTGIGIFGSGQYTIQEGYAALKLAKAGFRTNNIDPNARHCMASAVVGFMQTFGVDEPSGCYDDIELTDTIITWGANMAEMHPILWSRVSDRKLSNLDKVKVVNLSTFSNRTSNIADIEIIFKPNTDLAIWNYIAREIVYNHPEAMDMKFIKDHCVFATGYADIGYGMRNNPNHPKFKESEKDTVEKENVITLDDEEATSLSYLGVKAGDKFEMKHQGVADKNWEISFDEFKKGLAPYTLEYTARVAKGDDNESLEDFKKKLQELANLYIEKNRKVVSFWTMGFNQHTRGSWVNEQAYMVHFLLGKQAKPGSGAFSLTGQPSACGTAREVGTFSHRLPADMVVANPKHREISEKIWKVPAKTINPKPGSPYLNIMRDLEDGKIKFAWVQVNNPWQNTANAN.HWIAAAREMDNFIVVSDCYPGISAKVADLILPSAMIYEKWGAYGNAERRTQHWKQQVLPVGAAMSDTWQILEFAKRFKLKEVWKEQKVDNKLTLPSVLEEAKAMGYSEDDTLFDVLFANKEAKSFNPNDAIAKGFDNTDVKGDERKIQGSDGKEFTGYGFFVQKYLWEEYRKFGLGHGHDLADFDTYHKVRGLRWPVVNGKETQWRFNTKFDYYAKKAAPNSDFAFYGDFNKMLTNGDLIAPKDEKEHSIKNKAKIFFRPFMKAPERPSKEYPFWLATGRVLEHWHSGTMTMRVPELYRAVPEALCYMSEKDGEKLGLNQGDLVWVESRRGKVKARVDMRGRNKPPVGLVYVPWFDENVYINKVTLDATCPLSKQTDFKKCAVKIYKA
+>TIGR01706_OMNI|NTL03EC3103/2-828|NapA|1_930
+KLSRRSFMKANAVAAAAAAAGLSVPG.VARAVVGQQE.AIKWDKAPCRFCGTGCGVLVGTQQGRVVACQGDPDAPVNRGLNCIKGYFLPKIMYGKDRLTQPLLRMKN.GKYDKEGEFTPITWDQAFDVMEEKFKTALKEKGPESIGMFGSGQWTIWEGYAASKLFKAGFRSNNIDPNARHCMASAVVGFMRTFGMDEPMGCYDDIEQADAFVLWGANMAEMHPILWSRITNRRLS.NQDVTVAVLSTYQHRSFELADNGIIFTPQSDLVILNYIANYIIQNN..AINQDFFSKHVNLRKGATDIGYGLR..PTHPLEKAAK..........NPGSDASEPMS.........................FEDYKAFVAEYTLEKTAEMTGVP........KDQLEQLAQLYADPNKKVISYWTMGFNQHTRGVWANNLVYNLHLLTGKISQPGCGPFSLTGQPSACGTAREVGTFAHRLPADMVVTNEKHRDICEKKWNIPSGTIPAKIGLHAVAQDRALKDGKLNVYWTMCTNNMQAGPNINEERMPGWRDPRNFIIVSDPYPTVSALAADLILPTAMWVEKEGAYGNAERRTQFWRQQVQAPGEAKSDLWQLVQFSRRFKTEEVWPEELLAKKPELR.............GKTLYEVLYATPEVSKFPVSELAED................QLNDESRELGFYLQKGLFEEYAWFGRGHGHDLAPFDDYHKARGLRWPVVNGKETQWRYSEGNDPYVKAGE...GYKFYGKP....................DGKAVIFALPFEPAAEAPDEEYDLWLSTGRVLEHWHTGSMTRRVPELHRAFPEAVLFIHPLDAKARDLRRGDKVKVVSRRGEVISIVETRGRNRPPQGLVYMPFFDAAQLVNKLTLDATDPLSKETDFKKCAVKLEKV
+>TIGR01706_OMNI|VCA0678/2-828|NapA|1_930
+KMTRRAFVKANAAASAAAVAGITLPASATNLIASSDQTAIHWDKAPCRFCGTGCSVLVGTQDGRVVATQGDPEAPVNKGLNCIKGYFLSKIMYGQDRLKTPLLRMKD.GQYHKDGEFTPVSWDTAFDVMAEKWKASLKTKGPTSVGMFGSGQWTVMEGYAAVKLMKAGFRSNNIDPNARHCMASAVVGFMRTFGIDEPMGCYDDFEHADAFVLWGSNMAEMHPVLWTRITDRRLS.HPHVKVNVLSTYYHRSFELADHGYIFHPQSDLAIANFIANYIIQND..AVNWDFVNKHTHFKQAVTDIGYGLR..DDHPLQKKAK..........NANSGDVSDIS.........................FEEYKKSVAPYTVEKASEISGVS........PDKLITLAKQYADPNTKVMSLWTMGMNQHTRGVWMQSLVYNLHLLTGKIATPGNSPFSLTGQPSACGTAREVGTFAHRLPADMVVANPKHRAIAEKVWKLPEGTIPEKPGFHAVQQDRMLKDGVLNCYWVQCNNNMQAGPNINEERLPGYRNPENFIVVSDAYPTVTAQAADLVLPTAMWVEKEGAYGNAERRTQVWYQQVKTVGESHSDSWQVIEFSKRFKVEDVWPEELLAKAPQYR.............GKTLYDVLFKNGQVDKFPLSEAR..................ELNDDAHHFGFYIQKGLFEEYAEFGRGHGHDLAPYDVYHQVRGLRWPVVDGKETKWRFKEGSDPYAKAGS...GWDFYGKP....................DGKAWIISSPYEAPPEMPNEEYDLWLCTGRVLEHWHTGTMTRRVPELYKAVPDALCFMHHEDAQARGLRRGDEVLISNSRGEVRVRVETRGRNKPPKGLVFVPFFDARILVNKLILDATDPLSKQTDFKKCPVKITKV
+>TIGR01706_SP|P39185|NAPA_ALCEU/2-831|NapA|1_930
+KISRRDFIKQTAITATASVAGVTLPAGAANFVTDSEVTKLKWSKAPCRFCGTGCGVTVAVKDNKVVATQGDPQAEVNKGLNCVKGYFLSKIMYGQDRLTRPLMRMKN.GKYDKNGDFAPVTWDQAFDEMERQFKRVLKEKGPTAVACSAPAQWTVWEGYAAAKLYKAGFRSNNIDPNARHCMASAAAGFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWTRVTDRRLS.HPKTRVVVLSTFTHRCFDLADIGIIFKPQTDLAMLNYIANYIIRNN..KVNKDFVNKHTVFKEGVTDIGYGLR..PDHPLQKAAK..........NASDPGAAKVIT........................FDEFAKFVSKYDADYVSKLSAVP........KAKLDQLAELYADPNIKVMSLWTMGFNQHTRGTWANNMVYNLHLLTGKIATPGNSPFSLTGQPSACGTAREVGTFSHRLPADMVVTNPKHREEAERIWKLPPGTIPDKPGYDAVLQNRMLKDGKLNAYWVQVNNNMQAAANLMEEGLPGYRNPANFIVVSDAYPTVTALAADLVLPSAMWVEKEGAYGNAERRTQFWHQLVDAPGEARSDLWQLVEFAKRFKVEEVWPPELIAKKPEYK.............GKTLYDVLYRNGQVDKFPLKDVNAE................YHNAEAKAFGFYLQKGLFEEYATFGRGHGHDLAPFDAYHEARGLRWPVVNGKETRWRYREGSDPYVKAGT...GFQFYGNP....................DGKAVIFALPYEPPAESPDKEYPYWLVTGRVLEHWHSGSMTRRVPELYRSFPNAVVFMHPEDAKALGLRRGVEVEVVSRRGRMRSRIETRGRDAPPRGLVFVPWFDASQLINKVTLDATCPISLQTDFKKCAVKIVKV
+>TIGR01706_SP|Q56350|NAPA_PARDT/2-831|NapA|1_930
+TISRRDLLKAQAAGIAAMAANIPLSSQAPAVPGGVESLQITWSKAPCRFCGTGCGVMVGVKEGRVVATHGDLLAEVNRGLNCVKGYFLSKIMYGADRLTQPLLRKKD.GVYAKDGEFTPVSWEEAFDTMAAQAKRVLRDKGPTALGMFGSGQWTIFEGYAATKLMRAGFRSNNLDPNARHCMASAAYAFMRTFGMDEPMGCYDDFEAADAFVLWGSNMAEMHPILWTRVADRRLG.HPHVKVAVLSTFTHRSSDLADIPIVFKPGTDLAILNYIANHIIQTG..RVNRDFVDRHTTFVAGATGIGYGLR..DDDPREMAAR..........TAEDPAATTPST........................FEEFAELVSEYTLDKVSELSGVE........PAFLEQLAELYADPDRKVMSLWTMGFNQHVRGVWANQMVYNLHLLTGKISEPGNSPFSLTGQASACGTARQVGTFRHRLPSDMTVTNPERRQDAEEIWRIPHGVIPEQPGLHAVAQDRALHDGTLNFYWIQVNNNLQASPNNDGEAWPGYRNPDNFIVVSDAYPTVTALAADLILPAAMWVEKEGAYGNAERRTHVWHQLVEAPGEARSDLWQMMEFSTRFTTDEVWPEEILAANPNYR.............GQSLFDVLFRNGSVDRFDLSELNPV................TPTAESNAFGFYVQKGLFEEYAPFGRGHGHDLAPYDTYHEVRGLRWPVVDGKETLWRYREGLDPYVEPGA...GVQFYGNP....................DGKARIIAVPYEPPAEPPDEEYNIWLVTGRVLEHWHSGSMTMRVPELYRAFPGARCFMNPEDARDMGFNQGAEVRIVSRRGEIRSRVETRGRNRMPRGVVFVPWFDASQLINKVTLDATDPISKQTDFKKCAVKILPV
+>TIGR02693_GB|AAR05656.1|37962697/9-825|NapA|4_839
+IIPADAKKHNVTCHFCIVGCGYHAYTWPINKQGGTDPQNNIFGVDLSEQQQAESDAWYSPSMYNVVKQ.DGRDVHVVIKPDHECVVNSGLGSVRGARMAETSFSEARNTQQQRLTDPLVWRYGQMQPTSWDDALDLVARVTAKIVKEKGEDA.LIVSAFDHGGAGGGYENTWGTGKLYFEAMKVKNIRIHNRPAYNSEVHGTRDMGVGELNNCYEDAELADTIVAVGTNALETQTNYFLNHWIPNLRGESLGKKKELM.PEEPHEAGRIIIVDPRRTVTVNACEQTAGADNVLHLAINSGTDLALFNALFTYIADKGWVDRDFIDKSTLREGTARPPLYPARGVSEANPGHLSSFED.AVEGCRMS......IEEAAEITGLDAAQIIKAAEWIGMPKEGGKRRRVMFGYEKGLIWGNDNYRTNGALVNLALATGNIGRPGGGVVRLGGHQEGYVRPSD.....AHVGRPAAYVDQLLIGGQGGVHHIWGCDHYKTTLNAHEFKRVYKKRTDMVKDAMSAAPY.GDREAMVNAIVDAINQG..GLFAVNVDIIPTKIGEACHVILPAATSGEMNLTSMNG.ERRMRLTERYMDPPGQSMPDCLIAARLANTMERVLTEMGDVGYAAQFK.GFDWQTEEDAFMDGYNKN...........AHGG...EFVTYERLSAMGTNGFQEPATGFTDGK.IEGTQRLYTDGVFSTDDGKARFM.DAPWRGLQAPGKQQQK....DSHKYLINNGRANVVWQSAYLDQENDFVMDRFPYPFIEMNPEDMAEAGLKEGDLVEIYNDAGATQAMAYPTPTARRGETFMLFGFPTGVQGNVTSAGT
+>TIGR02693_GB|BAD71923.1|55773483/9-841|NapA|4_858
+IPPKNAKVYNQVCQYCTVGCGYKVYVWPVGEEGGVKPEQNAFGLDLSTPQPPLAGQSYTETMHAVTVGRDGRQYNVVIVPAKDSPINRGNYSIRGGTNALTVWSLDRGTQD.RLTYPLLRVGDQFQAITWQDALTLMGLLIKGIRDRDGNDDNIAVKCFDHGGSGQGFEDNYAAGKLFFAALSVKHIAIHNRPAYNSEVWGSRERGVHELNYTYEDARLADTIVLWGANSYETATVFYVEHMLPNIQGATVAEKQQAFDPGEPAEPGYLIVIDPRKTSSYTVAAQVA.PDRVMLLRPNLGTDYILANAIARAVWEKGYYDMAYLQAR......................TDMTLFEEYKAKSLKLSVPYDEFMAQAERITGVSRAEIEKAADWIAKPKAGRFKRRTLTIYEKGIIWNMKNYDQVAAIVQLAVLTHNIGRPGTGCGRQGGHQEGYVRPPAPTPGSIYRGGPPVNVDKFLIEGKGKFYWVIANDPYLSTPNNQVFRKRIHERTEKLTKALGAGGEPGTIQERAQKILDILYQDPDALFLVVQDIYMTETARDAHLILPAAGWGEANETSINCNSRLLRLYEKFMDPPGEAKPDWEIFKWVGLRIAELYRAEGKFEEAKKFEFGKNWKTDEDVFLAGAEEFRDNTVSEEDEAVLEAENYKGVTYKLLKELGQKGIQTPVRRDPKTGKLVGTVRRYTYR.FGTEDGKFKWYGTDDWEGYPAEVAKYLEPGMAEKYPFWVTTGRAQTIWQTAYHDRHLPEKALALPLPYVEVNPEDAKRLGLKSGDLVEVYNEEGNGTFLVYVTDAVKPGTLFLVMYHWRGTSNSLVTGYTDPKTTIPWYKGTRANLRKV
+>TIGR02693_SP|Q8GGJ6|ARSL_CENAS/7-806|NapA|3_840
+ALPPVNAQKTNMTCHFCIVGCGYHVYKWDENKEGGRAANQNALGLDFT.KQLPPFATTLTPAMTNVITAKNGKRSNIMIIPDKECVVNQGLSSTRGGKMAGYMYAADGMTAD.RLKYPRFYAGDQWLDTSWDHAMAIYAGLTKKILDQGNVRD.IMFATFDHGGAGGGFENTWGSGKLMFSAIQTPTVRIHNRPAYNSECHATREMGIGELNNSYEDAQVADVIWSIGNNPYETQTNYFLNHWLPNLNGSTEEKKKQWF.AGEPVGPGLMIFVDPRRTTSIAIAEQTA.KDRVLHLDINPGTDVALFNGLLTYVLQQGWIAKEFIAQ........................HTVGFED.AVKTNQMS......LADCSRITGVSEDKLRQAAEWSYKPKAAGKMPRTMHAYEKGIIWGNDNYNIQSSLLDLVIATQNVGRRGTGCVRMGGHQEGYVRPP.......HPTGEKIYVDQEIIQGKGRMMTWWGCNNFQTSNNAQALREVSLRRSQIVKDAMSKARG.ASAAEMVDIIYDATSKG..GLFVTSINLYPTKLSEAAHLMLPAAHPGEMNLTSMNG.ERRMRLSEKFMDAPGDALPDCLIAAKAANTLKAMYEAEGKPEMVKRFS.GFDWKTEEDAFNDGFRSAGQPGAEPID..SQGGSTGVLATYTLLRAAGTNGVQLPIKRVENGK.MIGTAIHYDDNKFDTKDGKAHFK.PAPWNGLPKP.VEEQK....AKHKFWLNNGRANEVWQSAYHDQYNDFVKSRYPLAYIELNPGDAQSLGVAAGDVVEVFNDYGSTFAMAYPVKDMKPSHTFMLFGYVNGIQGDVTTDWVD

Nitrogen_metabolism/Denitrification/NapA/NapA_purity/intermediates/assign/final_outputs/classifications.tsv

@@ -0,0 +1,12 @@
+Sample	Query	Marker	Start_pos	End_pos	Taxonomy	Abundance	iNode	E-value	LWR	EvoDist	Distances
+TIGRFAM_seed_named_formatted	TIGR01701_SP|P77561|YDEP_ECOLI/11-758	NapA	105	824	r__Root	1.0	115	4.5e-64	1.0	2.1982	0.5689,1.1263,0.503
+TIGRFAM_seed_named_formatted	TIGR01706_OMNI|NTL03EC3103/2-828	NapA	1	930	r__Root; d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacterales; f__Enterobacteriaceae; g__Escherichia; s__Escherichia coli	1.0	1718	0.0	1.0	0.0902	0.0066,0.0836,0.0
+TIGRFAM_seed_named_formatted	TIGR01706_SP|P39185|NAPA_ALCEU/2-831	NapA	1	930	r__Root	1.0	2021	0.0	1.0	0.0757	0.0009,0.0749,0.0
+TIGRFAM_seed_named_formatted	TIGR01701_SP|Q10821|YT00_MYCTU/34-778	NapA	102	824	r__Root	1.0	115	1.3e-68	1.0	1.7834	0.3464,0.934,0.503
+TIGRFAM_seed_named_formatted	TIGR01706_OMNI|VCA0678/2-828	NapA	1	930	r__Root; d__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Vibrionales; f__Vibrionaceae; g__Vibrio	1.0	1821	0.0	0.996792722	0.2169	0.0436,0.1733,0.0
+TIGRFAM_seed_named_formatted	TIGR01701_OMNI|NTL02MLB0108/16-791	NapA	104	823	r__Root	1.0	115	3.7e-51	1.0	2.2516	0.4048,1.3438,0.503
+TIGRFAM_seed_named_formatted	TIGR02693_SP|Q8GGJ6|ARSL_CENAS/7-806	NapA	3	840	r__Root; d__Bacteria; p__Proteobacteria; c__Betaproteobacteria; o__Burkholderiales; f__Oxalobacteraceae; g__Herminiimonas	1.0	131	1.8e-86	1.0	0.1327	0.0031,0.1296,0.0
+TIGRFAM_seed_named_formatted	TIGR02693_GB|AAR05656.1|37962697/9-825	NapA	4	839	r__Root; d__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Hyphomicrobiales; f__Rhizobiaceae; g__Agrobacterium	1.0	120	4.1e-102	1.0	0.1884	0.0051,0.1832,0.0
+TIGRFAM_seed_named_formatted	TIGR02693_GB|BAD71923.1|55773483/9-841	NapA	4	858	r__Root	1.0	136	6.9e-104	1.0	2.5784	0.5013,1.1574,0.9197
+TIGRFAM_seed_named_formatted	TIGR01706_OMNI|NTL01CJ00733/2-924	NapA	3	930	r__Root; d__Bacteria; p__Proteobacteria; c__Epsilonproteobacteria; o__Campylobacterales; f__Campylobacteraceae; g__Campylobacter; s__Campylobacter coli	1.0	1362	2.6e-281	1.0	0.071	0.013,0.058,0.0
+TIGRFAM_seed_named_formatted	TIGR01706_SP|Q56350|NAPA_PARDT/2-831	NapA	1	930	r__Root	1.0	1923	8.9e-300	1.0	0.1063	0.0001,0.1063,0.0

Nitrogen_metabolism/Denitrification/NapA/NapA_purity/intermediates/assign/iTOL_output/NapA/NapA_abundance_simplebar.txt

@@ -0,0 +1,25 @@
+DATASET_SIMPLEBAR
+SEPARATOR COMMA
+DATASET_LABEL,ABUNDANCE
+COLOR,#ff0000
+DATA
+588_NapA,0.75
+586_NapA,0.75
+591_NapA,0.75
+756_NapA,0.75
+844_NapA,1.0
+1_NapA,1.0
+1087_NapA,1.0
+468_NapA,1.0909090909090908
+134_NapA,1.0909090909090908
+365_NapA,0.09090909090909091
+452_NapA,0.09090909090909091
+732_NapA,0.09090909090909091
+1027_NapA,0.09090909090909091
+161_NapA,0.09090909090909091
+100_NapA,0.09090909090909091
+84_NapA,0.09090909090909091
+34_NapA,0.09090909090909091
+641_NapA,0.09090909090909091
+615_NapA,1.0
+2_NapA,1.0