refactor, added examples

.gitignore

@@ -8,6 +8,7 @@ gbk_data/*
 data/*
 tree_test/
 demo_data/*
+traits/*
 
 # Files
 test.ipynb

README.md

@@ -1 +1,95 @@
-# Genbankpy
+# Downloading and parsing GenBank files from Python
+
+## Installation
+1. Fork git repo into local machine (click on fork) and clone, or simply clone main branch with
+```
+git clone https://github.com/Robaina/GenBankpy.git
+```
+2. CD to project directory and set conda environment if not already set:
+```
+conda env create -n genbankpy -f environment.yml
+```
+
+3. Activate environment:
+```
+conda activate genbankpy
+```
+
+
+```python
+from pathlib import Path
+from genbankpy.parser import GenBankFastaWriter, GBK
+
+
+sp_list = [
+    'Halobacterium salinarum',
+    'Escherichia coli',
+    'Pseudomonas aeruginosa',
+    'Proteus mirabilis',
+    'Klebsiella pneumoniae',
+    'Prochlorococcus marinus',
+    'Pelagibacter ubique'
+]
+
+gbkwriter = GenBankFastaWriter.fromSpecies(species_list=sp_list,
+                                           only_latest=True,
+                                           data_dir="demo_data") 
+
+# Alternatively, if already downloaded:
+# gbkwriter = GenBankFastaWriter.fromGBKdirectory(gbk_dir="demo_data")
+
+gbkwriter.writeSequencesInFasta(
+    gene_keywords={'product': ['pyruvate kinase']},
+    output_fasta='demo_results/pyruvate_kinase_demo.faa', 
+    sequence='protein'
+)
+```
+
+Now we infer a phylogenetic tree using [MUSCLE](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-113) and [fasttree](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009490). Results will be stored in /results/demo_tree.
+
+Next, we visualize the infered tree with [ETE3](http://etetoolkit.org/) (not included in the provided genbankpy conda environment):
+
+
+```python
+# Visualizing tree 
+from ete3 import Tree
+
+
+t = Tree("demo_results/demo_tree/ref_database.newick")
+t.render("%%inline")
+```
+
+
+
+
+
+![png](README_figures/output_3_0.png)
+
+
+
+
+# Additional examples of the filtering capabilities
+
+
+```python
+# Write fasta containing nucleotide sequences corresponding to Urease alpha
+gbkwriter.writeSequencesInFasta(
+    gene_keywords={'product': ['urease', 'alpha']},
+    output_fasta='demo_results/ureC.fasta', 
+    sequence='nucleotide'
+)
+
+# Write fasta containing peptide sequences corresponding to Urease alpha
+gbkwriter.writeSequencesInFasta(
+    gene_keywords={'product': ['urease', 'alpha']},
+    output_fasta='demo_results/ureC.faa', 
+    sequence='protein'
+)
+
+# Write fasta containing nucleotide sequences to 16S
+gbkwriter.writeSequencesInFasta(
+    gene_keywords={'product': ['16S']},
+    output_fasta='demo_results/16s.fasta', 
+    sequence='nucleotide'
+)
+```

demo_results/demo_tree/ref_database.faln

@@ -0,0 +1,132 @@
+>GCF_004799605_Halobacterium_salinarum_WP_010902196.1_pyruvate_kinase
+------MRNAKIVCTLGPATNDDASVRALADAGMTVARINASHGDAAARRELIETTRAVD
+AQTDKPLAVMLDTQGPEVRTAPIDDDGTIHIETGSDVAFV---EGDTATPDRIGISTS--
+IAAAEPGDTVLLDDGRIEADVDRVA--GDTVHATVVSGGSLGSRKGVNVPGVELDVDVVT
+EKDRRDLALAAELDVDYVAASFVRDADDVLAVNRVLESH-GADIPIVAKIERAGAV---E
+NLDGIIDAAQGVMVARGDLGVECPMEDVPMIQKRIIAQCRDAGVPVITATEMLDSMVHAR
+RPTRAEASDVANAVLDGTDGVMLSAETAVGDNPTRVVETMDRIVREVEGSAEYSERQEQ-
+AVPTADGTAKTDALARSARYLARDID-ASAVVVASESGYTARKAAKFRPSVPVVCATPSH
+DVRRQLALNWGVHANYAAVAEGDATTVVERAVQAAVDSGVVASGDTVVVLVGMMTELEGA
+STTNTLKVHVAAETLSTGRAVVDGRTTGRTYRAD----SGDLSDAPENAVVLLAHGFDGE
+FDGDLSKIGAIVSADAGLTGYPAVIARELDVPMVGDVDVDAVPAGDLVTVDGERGVVYEA
+DQ---------
+>GCF_000069965_Proteus_mirabilis_WP_004245632.1_pyruvate_kinase
+------MRKTKIVATLGPASCSEQMIEKLILAGANVFRLNFSHGTREQHQSTAATIRQVA
+KKHRVFIGILADLQGPKIRIASFKNN-AIQLTQGDSFILNADLDSTQGDEQQVGLDYPQL
+VQEVTPGNILLLDDGNIQLKVRAVN--NNNIETVVTVGGKLSNRKGINLLGGGLSAPALT
+DKDKQDIHTAAAIQADYIAVSFPRNGADIEYARRLIVAA-GSQAKIVAKVERAEVVSCQA
+NMDDIIQASDVIMVARGDLAVEIGDACLPGAQKQLIARCRALGCPVITATQMMESMIENP
+MPTRAEVMDIANAVGDGTDAVMLSAETAAGKYPEEAVRAMARVAEGA--ERSFAANAENP
+WQSPSYYSQTGRWIALAATTAAFHNDKHLSVAALTDNGQSVTLLSRFMPNNNIYALTDNP
+ALAGQLTVLRGVTPVTYQRQN--NNDGDENIMQKLQTEGLLTDIHSLLITRLSTFEKTG-
+-ESDCCHLVPVKQVTTALT-----------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000006765_Pseudomonas_aeruginosa_NP_253019.1_pyruvate_kinase
+----MSVRRTKIVATLGPASNSPEVLEQLILAGIDVARLNFSHGTPDEHRARARLVRELA
+AKHGRFVALLGDLQGPKIRIAKFANK-RIELQVGDKFRFSTSHARDAGTQEVVGIDYPDL
+VKDCGVGDELLLDDGRVVMVVEEVA--ADELRCRVLIGGPLSDHKGINRRGGGLTAPALT
+DKDKADIKLAADMDLDYVAVSFPRDAKDMEYARRLLTEA-GGKAWLVAKIERAEAVADDD
+ALDGLIRASDAVMVARGDLGVEIGDAELVGIQKKIILHARRNNKVVITATQMMESMIHSP
+MPTRAEVSDVANAVLDYTDAVMLSAESAAGEYPVEAVKAMARVCQGA--EKHPTSQKSS-
+HRLGQTFDRCDESIALASMYTANHFPGIKAIICLTESGFTPLIMSRIRSSVPIYAYSPHR
+ETQARVAMFRGVETIPFDPAALPAEKVSQAAVDELLKRGVVTKGDWVILTKGDSYTAQG-
+-GTNTMKVLHVGDLLV--------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000069965_Proteus_mirabilis_WP_004242765.1_pyruvate_kinase
+--MSRRLRRTKIVTTLGPATDRDNNLEKIITAGANVVRLNFSHGSAEDHLARANRTREIA
+ARLGRHVAILGDLQGPKIRVSTFKEG-KVFLNVGDKFLLDANLEKGEGDQTKVGIDYKGL
+PADVVPGDILLLDDGRVQLKVLKVE--GLKVFTEVTVGGPLSNNKGINKLGGGLSAEALT
+EKDKQDIITAAKIGVDYLAVSFPRTGEDLNYARRLARDA-GCECQIVAKVERAEAVANDE
+IIDEIILASDVVMVARGDLGVEIGDPELVGVQKKLIRRARQLNRVVITATQMMESMITNP
+MPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPAETVAAMAQVCLGA--EKMPAANVSK-
+HRLDMVFDNAEEAIAMSTMYAANHMKGVNAIIAMTESGRTARMMSRISTGLPIFSMSRHE
+KTLNQTALYRGVTPVYCSTHT-DGIAAANEAIMRLCEKGFLVSGDLVLVTQGDQMGTIG-
+-STNTCRILTVE------------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000008865_Escherichia_coli_NP_310591.1_pyruvate_kinase
+--MSRRLRRTKIVTTLGPATDRDNNLEKVIAAGANVVRMNFSHGSPEDHKMRADKVREIA
+AKLGRHVAILGDLQGPKIRVSTFKEG-KVFLNIGDKFLLDANLGKGEGDKEKVGINYKGL
+PADVVPGDILLLDDGRVQLKVLEVQ--GMKVFTEVTVGGPLSNNKGINKLGGGLSAEALT
+EKDKADIKTAALIGVDYLAVSFPRCGEDLNYARRLARDA-GCDAKIVAKVERAEAVCSQD
+AMDDIILASDVVMVARGDLGVEIGDPELVGIQKALIRRARQLNRAVITATQMMESMITNP
+MPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPSETVAAMARVCLGA--EKIPSINVSK-
+HRLDVQFDNVEEAIAMSAMYAANHLKGVTAIITMTESGRTALMTSRISSGLPIFAMSRHE
+RTLNLTALYRGVTPVHFDSAN-DGVAAASEAVNLLRDKGYLMSGDLVIVTQGDVMSTVG-
+-STNTTRILTVE------------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000240185_Klebsiella_pneumoniae_YP_005227690.1_pyruvate_kinase
+--MSRRLRRTKIVTTLGPATDRDNNLEKVIAAGANVVRMNFSHGTPEDHQLRADKVREIA
+AKLGRHVAILGDLQGPKIRVSTFKEG-KIFLNVGDKFLLDANLGKGEGDKEKVGIDYKGL
+PADVVPGDILLLDDGRVQLKVLEVQ--GMKVFTEVTVGGPLSNNKGINKLGGGLSAEALT
+DKDKADIVTAAKIGVDYLAVSFPRCGEDLNYARRLARDA-GCDAKIVAKVERAEAVCDQD
+AMDDVILASDVVMVARGDLGVEIGDPELVGIQKALIRRARQLNRSVITATQMMESMITNP
+MPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPSETVAAMARVCLGA--EKIPSLNVSK-
+HRLDVQFDNVEEAIAMSAMYAANHLKGITAIITMTESGRTALMTSRISSGLPIFALSRHE
+RTLNLTALYRGVTPVFFDSQN-DGVAAAHDAVNLLRDKGYLVSGDLVVVTQGDVMSTIG-
+-STNTTRILTVE------------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000006765_Pseudomonas_aeruginosa_NP_250189.1_pyruvate_kinase
+MTA---DKKAKILATLGPATRSRDDIRALVEAGANLLRLNFSHGDYADHAQRFAWVREVE
+AELNYPIGVLMDLQGPKLRVGRFAAG-AVQLQRGQTFTLDLS-DAP-GDERRVNLPHPEI
+IHALEPGMSLLLDDGKIRLEVVNCH--SDAIETRVAVGGELSDRKGVNVPEAVLQLSPLT
+DKDRRDLAFGLELGVDWVALSFVQRPEDIDEARGLI----GDKAFLMAKIEKPSAV---S
+AIEAIAERADAIMVARGDLGVEVPAESVPGIQKRIVQVCRQLGKPVVVATQMLESMRFSP
+APTRAEVTDVATAVGAGADAVMLSAETASGQYPREAVEMMAKIVRQVEAEPDYHVQLEV-
+NRPQPDA-TVSDAISCAIRRVSRILP-VAVLVNYTESGNSTLRAARERPKAPILSLTPNL
+RTARRLTVAWGVYSVVNEQLA-HVDEICSTALDIALAQRMARRGDTVVVTAGVPFGRPG-
+-STNMLRIETV---------------------------APPLGDL---------------
+------------------------------------------------------------
+-----------
+>GCF_000007925_Prochlorococcus_marinus_WP_011125075.1_pyruvate_kinase
+MTTIDLKRRTKIVATIGPATESPEKITELIKAGATTFRLNFSHGDHEEHAKRIKTIRSVA
+SDLGVNIGILQDLQGPKIRLGRFKEG-PVNLKTGDVFALTSE-NKDC-NQEIANVTYENL
+VNEVEKGKRILLDDGRVEMIVENVDKKNKSLICKVTVGGILSNNKGVNFPDVQLSINALT
+EKDKIDLSFGLKQGVDWVALSFVRNPADIQEIKELIRRH-GYTTPIVAKIEKFEAI---D
+QIDSILSLCDGVMVARGDLGVEMDAEEVPLLQKELIKKANSLGIPIITATQMLDSMASSP
+RPTRAEVSDVANAILDGTDAVMLSNETAVGDYPIEAVETMAKIARRI--ERDYPQRALE-
+SHLPST---IPNAISAAVSTIARQLN-AAAILPLTKSGATAHNVSKFRPATPILAITSEI
+SVARRLQLVWGVSPLLIDAQK-STSKTFGIAMEQAMDMKLLKPGDQVVETAGTLTGISG-
+-STDLIKVGIVSKIVASGKTKPIVKEGTISGKLRVINKATDLSDLKSGEILVLAENVQYN
+LDTKTHISAMIFEGEYSLINTNNQIEDNNIIPAIYNVEGACTKFKNGEIVTLDLKDGNII
+KGLAQDLKTYN
+>GCF_000069965_Proteus_mirabilis_WP_004248168.1_pyruvate_kinase_PykF
+------MKKTKIVCTIGPKTESEEKLTQLLDAGMNVMRLNFSHGDYEEHGNRIKNLRNVC
+AKTGKKAAILLDTKGPEIRTIKLEGGNDVSLVAGQTFTFTTD-TSVVGNKDRVAVTYDGF
+ARDLTVGNTVLVDDGLIGMKVIKVT--DTEVVCEVLNNGDLGENKGVNLPGVSIGLPALA
+EKDKQDLIFGCEQGVDFVAASFIRKRSDVEEMRAHLKAHGGENIMIISKIENQEGL---N
+NFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCNAARKVVITATQMLDSMIKNP
+RPTRAEAGDVANAILDGTDAVMLSGESAKGKYPVEAVTIMATICDRT--DRIMKSRLES-
+YQLGAKL-RVTEAVCRGAVEMAEKLD-APLIVVATYGGKSARSIRKYFPTAPILALTNNE
+ETARQLLLVKGVTTQLVNKIA-STDDFYRIGKDAALSSGLAHAGDRVVMVTGALVD-SG-
+-TTNTSSVHVL-------------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000008865_Escherichia_coli_NP_310410.1_pyruvate_kinase
+------MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVM
+SKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTD-KSVIGNSEMVAVTYEGF
+TTDLSVGNTVLVDDGLIGMEVTAIE--GNKVICKVLNNGDLGENKGVNLPGVSIALPALA
+EKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQEGL---N
+NFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNP
+RPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERT--DRVMNSRLEF-
+NNDNRKL-RITEAVCRGAVETAEKLD-APLIVVATQGGKSARAVRKYFPDATILALTTNE
+KTAHQLVLSKGVVPQLVKEIT-STDDFYRLGKELALQSGLAHKGDVVVMVSGALVP-SG-
+-TTNTASVHVL-------------------------------------------------
+------------------------------------------------------------
+-----------
+>GCF_000240185_Klebsiella_pneumoniae_YP_005227418.1_pyruvate_kinase
+------MKKTKIVCTIGPKTESEEMLTKMLEAGMNVMRLNFSHGDYAEHGQRIQNLRNVM
+SKTGKKAAILLDTKGPEIRTIKLEGGNDVSLKAGQTFTFTTD-KSVIGNNEIVAVTYEGF
+TSDLAVGNTVLVDDGLIGMEVTAIE--GNKVICKVLNNGDLGENKGVNLPGVSIALPALA
+EKDKQDLIFGCEQGVDFVAASFIRKRSDVVEIREHLKAHGGENIQIISKIENQEGL---N
+NFDEILEASDGIMVARGDMGVEIPVEEVIFAQKMIIEKCIRARKVVITATQMLDSMIKNP
+RPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVTIMATICERT--DRVMTSRLDF-
+NNDNRKL-RITEAVCRGAVETAEKLE-APLIVVATQGGKSARAVRKYFPDATILALTTNE
+TTARQLVLSKGVVPQLVEEIA-STDDFYHLGKDLALKSGLARKGDVVVMVSGALVP-SG-
+-TTNTASVHVL-------------------------------------------------
+------------------------------------------------------------
+-----------

demo_results/demo_tree/ref_database.newick

@@ -0,0 +1 @@
+((GCF_000069965_Proteus_mirabilis_WP_004245632.1_pyruvate_kinase:0.540564072,(GCF_000006765_Pseudomonas_aeruginosa_NP_253019.1_pyruvate_kinase:0.462181802,(GCF_000069965_Proteus_mirabilis_WP_004242765.1_pyruvate_kinase:0.097084550,(GCF_000008865_Escherichia_coli_NP_310591.1_pyruvate_kinase:0.024134197,GCF_000240185_Klebsiella_pneumoniae_YP_005227690.1_pyruvate_kinase:0.023515710)0.931:0.057851236)1.000:0.280157502)0.957:0.161444222)1.000:0.415252181,(GCF_004799605_Halobacterium_salinarum_WP_010902196.1_pyruvate_kinase:0.849641007,(GCF_000069965_Proteus_mirabilis_WP_004248168.1_pyruvate_kinase_PykF:0.068872124,(GCF_000008865_Escherichia_coli_NP_310410.1_pyruvate_kinase:0.025305557,GCF_000240185_Klebsiella_pneumoniae_YP_005227418.1_pyruvate_kinase:0.025183099)0.984:0.100534754)1.000:0.556959195)0.948:0.156115197,(GCF_000006765_Pseudomonas_aeruginosa_NP_250189.1_pyruvate_kinase:0.660070918,GCF_000007925_Prochlorococcus_marinus_WP_011125075.1_pyruvate_kinase:0.520263194)0.879:0.120950005);

demo_results/pyruvate_kinase_demo.faa

@@ -0,0 +1,22 @@
+>GCF_004799605_Halobacterium_salinarum_WP_010902196.1_pyruvate_kinase
+MRNAKIVCTLGPATNDDASVRALADAGMTVARINASHGDAAARRELIETTRAVDAQTDKPLAVMLDTQGPEVRTAPIDDDGTIHIETGSDVAFVEGDTATPDRIGISTSIAAAEPGDTVLLDDGRIEADVDRVAGDTVHATVVSGGSLGSRKGVNVPGVELDVDVVTEKDRRDLALAAELDVDYVAASFVRDADDVLAVNRVLESHGADIPIVAKIERAGAVENLDGIIDAAQGVMVARGDLGVECPMEDVPMIQKRIIAQCRDAGVPVITATEMLDSMVHARRPTRAEASDVANAVLDGTDGVMLSAETAVGDNPTRVVETMDRIVREVEGSAEYSERQEQAVPTADGTAKTDALARSARYLARDIDASAVVVASESGYTARKAAKFRPSVPVVCATPSHDVRRQLALNWGVHANYAAVAEGDATTVVERAVQAAVDSGVVASGDTVVVLVGMMTELEGASTTNTLKVHVAAETLSTGRAVVDGRTTGRTYRADSGDLSDAPENAVVLLAHGFDGEFDGDLSKIGAIVSADAGLTGYPAVIARELDVPMVGDVDVDAVPAGDLVTVDGERGVVYEADQ
+>GCF_000008865_Escherichia_coli_NP_310410.1_pyruvate_kinase
+MKKTKIVCTIGPKTESEEMLAKMLDAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKTAAILLDTKGPEIRTMKLEGGNDVSLKAGQTFTFTTDKSVIGNSEMVAVTYEGFTTDLSVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVIEIREHLKAHGGENIHIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVSIMATICERTDRVMNSRLEFNNDNRKLRITEAVCRGAVETAEKLDAPLIVVATQGGKSARAVRKYFPDATILALTTNEKTAHQLVLSKGVVPQLVKEITSTDDFYRLGKELALQSGLAHKGDVVVMVSGALVPSGTTNTASVHVL
+>GCF_000008865_Escherichia_coli_NP_310591.1_pyruvate_kinase
+MSRRLRRTKIVTTLGPATDRDNNLEKVIAAGANVVRMNFSHGSPEDHKMRADKVREIAAKLGRHVAILGDLQGPKIRVSTFKEGKVFLNIGDKFLLDANLGKGEGDKEKVGINYKGLPADVVPGDILLLDDGRVQLKVLEVQGMKVFTEVTVGGPLSNNKGINKLGGGLSAEALTEKDKADIKTAALIGVDYLAVSFPRCGEDLNYARRLARDAGCDAKIVAKVERAEAVCSQDAMDDIILASDVVMVARGDLGVEIGDPELVGIQKALIRRARQLNRAVITATQMMESMITNPMPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPSETVAAMARVCLGAEKIPSINVSKHRLDVQFDNVEEAIAMSAMYAANHLKGVTAIITMTESGRTALMTSRISSGLPIFAMSRHERTLNLTALYRGVTPVHFDSANDGVAAASEAVNLLRDKGYLMSGDLVIVTQGDVMSTVGSTNTTRILTVE
+>GCF_000006765_Pseudomonas_aeruginosa_NP_250189.1_pyruvate_kinase
+MTADKKAKILATLGPATRSRDDIRALVEAGANLLRLNFSHGDYADHAQRFAWVREVEAELNYPIGVLMDLQGPKLRVGRFAAGAVQLQRGQTFTLDLSDAPGDERRVNLPHPEIIHALEPGMSLLLDDGKIRLEVVNCHSDAIETRVAVGGELSDRKGVNVPEAVLQLSPLTDKDRRDLAFGLELGVDWVALSFVQRPEDIDEARGLIGDKAFLMAKIEKPSAVSAIEAIAERADAIMVARGDLGVEVPAESVPGIQKRIVQVCRQLGKPVVVATQMLESMRFSPAPTRAEVTDVATAVGAGADAVMLSAETASGQYPREAVEMMAKIVRQVEAEPDYHVQLEVNRPQPDATVSDAISCAIRRVSRILPVAVLVNYTESGNSTLRAARERPKAPILSLTPNLRTARRLTVAWGVYSVVNEQLAHVDEICSTALDIALAQRMARRGDTVVVTAGVPFGRPGSTNMLRIETVAPPLGDL
+>GCF_000006765_Pseudomonas_aeruginosa_NP_253019.1_pyruvate_kinase
+MSVRRTKIVATLGPASNSPEVLEQLILAGIDVARLNFSHGTPDEHRARARLVRELAAKHGRFVALLGDLQGPKIRIAKFANKRIELQVGDKFRFSTSHARDAGTQEVVGIDYPDLVKDCGVGDELLLDDGRVVMVVEEVAADELRCRVLIGGPLSDHKGINRRGGGLTAPALTDKDKADIKLAADMDLDYVAVSFPRDAKDMEYARRLLTEAGGKAWLVAKIERAEAVADDDALDGLIRASDAVMVARGDLGVEIGDAELVGIQKKIILHARRNNKVVITATQMMESMIHSPMPTRAEVSDVANAVLDYTDAVMLSAESAAGEYPVEAVKAMARVCQGAEKHPTSQKSSHRLGQTFDRCDESIALASMYTANHFPGIKAIICLTESGFTPLIMSRIRSSVPIYAYSPHRETQARVAMFRGVETIPFDPAALPAEKVSQAAVDELLKRGVVTKGDWVILTKGDSYTAQGGTNTMKVLHVGDLLV
+>GCF_000069965_Proteus_mirabilis_WP_004242765.1_pyruvate_kinase
+MSRRLRRTKIVTTLGPATDRDNNLEKIITAGANVVRLNFSHGSAEDHLARANRTREIAARLGRHVAILGDLQGPKIRVSTFKEGKVFLNVGDKFLLDANLEKGEGDQTKVGIDYKGLPADVVPGDILLLDDGRVQLKVLKVEGLKVFTEVTVGGPLSNNKGINKLGGGLSAEALTEKDKQDIITAAKIGVDYLAVSFPRTGEDLNYARRLARDAGCECQIVAKVERAEAVANDEIIDEIILASDVVMVARGDLGVEIGDPELVGVQKKLIRRARQLNRVVITATQMMESMITNPMPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPAETVAAMAQVCLGAEKMPAANVSKHRLDMVFDNAEEAIAMSTMYAANHMKGVNAIIAMTESGRTARMMSRISTGLPIFSMSRHEKTLNQTALYRGVTPVYCSTHTDGIAAANEAIMRLCEKGFLVSGDLVLVTQGDQMGTIGSTNTCRILTVE
+>GCF_000069965_Proteus_mirabilis_WP_004248168.1_pyruvate_kinase_PykF
+MKKTKIVCTIGPKTESEEKLTQLLDAGMNVMRLNFSHGDYEEHGNRIKNLRNVCAKTGKKAAILLDTKGPEIRTIKLEGGNDVSLVAGQTFTFTTDTSVVGNKDRVAVTYDGFARDLTVGNTVLVDDGLIGMKVIKVTDTEVVCEVLNNGDLGENKGVNLPGVSIGLPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVEEMRAHLKAHGGENIMIISKIENQEGLNNFDEILEASDGIMVARGDLGVEIPVEEVIFAQKMMIEKCNAARKVVITATQMLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPVEAVTIMATICDRTDRIMKSRLESYQLGAKLRVTEAVCRGAVEMAEKLDAPLIVVATYGGKSARSIRKYFPTAPILALTNNEETARQLLLVKGVTTQLVNKIASTDDFYRIGKDAALSSGLAHAGDRVVMVTGALVDSGTTNTSSVHVL
+>GCF_000069965_Proteus_mirabilis_WP_004245632.1_pyruvate_kinase
+MRKTKIVATLGPASCSEQMIEKLILAGANVFRLNFSHGTREQHQSTAATIRQVAKKHRVFIGILADLQGPKIRIASFKNNAIQLTQGDSFILNADLDSTQGDEQQVGLDYPQLVQEVTPGNILLLDDGNIQLKVRAVNNNNIETVVTVGGKLSNRKGINLLGGGLSAPALTDKDKQDIHTAAAIQADYIAVSFPRNGADIEYARRLIVAAGSQAKIVAKVERAEVVSCQANMDDIIQASDVIMVARGDLAVEIGDACLPGAQKQLIARCRALGCPVITATQMMESMIENPMPTRAEVMDIANAVGDGTDAVMLSAETAAGKYPEEAVRAMARVAEGAERSFAANAENPWQSPSYYSQTGRWIALAATTAAFHNDKHLSVAALTDNGQSVTLLSRFMPNNNIYALTDNPALAGQLTVLRGVTPVTYQRQNNNDGDENIMQKLQTEGLLTDIHSLLITRLSTFEKTGESDCCHLVPVKQVTTALT
+>GCF_000240185_Klebsiella_pneumoniae_YP_005227418.1_pyruvate_kinase
+MKKTKIVCTIGPKTESEEMLTKMLEAGMNVMRLNFSHGDYAEHGQRIQNLRNVMSKTGKKAAILLDTKGPEIRTIKLEGGNDVSLKAGQTFTFTTDKSVIGNNEIVAVTYEGFTSDLAVGNTVLVDDGLIGMEVTAIEGNKVICKVLNNGDLGENKGVNLPGVSIALPALAEKDKQDLIFGCEQGVDFVAASFIRKRSDVVEIREHLKAHGGENIQIISKIENQEGLNNFDEILEASDGIMVARGDMGVEIPVEEVIFAQKMIIEKCIRARKVVITATQMLDSMIKNPRPTRAEAGDVANAILDGTDAVMLSGESAKGKYPLEAVTIMATICERTDRVMTSRLDFNNDNRKLRITEAVCRGAVETAEKLEAPLIVVATQGGKSARAVRKYFPDATILALTTNETTARQLVLSKGVVPQLVEEIASTDDFYHLGKDLALKSGLARKGDVVVMVSGALVPSGTTNTASVHVL
+>GCF_000240185_Klebsiella_pneumoniae_YP_005227690.1_pyruvate_kinase
+MSRRLRRTKIVTTLGPATDRDNNLEKVIAAGANVVRMNFSHGTPEDHQLRADKVREIAAKLGRHVAILGDLQGPKIRVSTFKEGKIFLNVGDKFLLDANLGKGEGDKEKVGIDYKGLPADVVPGDILLLDDGRVQLKVLEVQGMKVFTEVTVGGPLSNNKGINKLGGGLSAEALTDKDKADIVTAAKIGVDYLAVSFPRCGEDLNYARRLARDAGCDAKIVAKVERAEAVCDQDAMDDVILASDVVMVARGDLGVEIGDPELVGIQKALIRRARQLNRSVITATQMMESMITNPMPTRAEVMDVANAVLDGTDAVMLSAETAAGQYPSETVAAMARVCLGAEKIPSLNVSKHRLDVQFDNVEEAIAMSAMYAANHLKGITAIITMTESGRTALMTSRISSGLPIFALSRHERTLNLTALYRGVTPVFFDSQNDGVAAAHDAVNLLRDKGYLVSGDLVVVTQGDVMSTIGSTNTTRILTVE
+>GCF_000007925_Prochlorococcus_marinus_WP_011125075.1_pyruvate_kinase
+MTTIDLKRRTKIVATIGPATESPEKITELIKAGATTFRLNFSHGDHEEHAKRIKTIRSVASDLGVNIGILQDLQGPKIRLGRFKEGPVNLKTGDVFALTSENKDCNQEIANVTYENLVNEVEKGKRILLDDGRVEMIVENVDKKNKSLICKVTVGGILSNNKGVNFPDVQLSINALTEKDKIDLSFGLKQGVDWVALSFVRNPADIQEIKELIRRHGYTTPIVAKIEKFEAIDQIDSILSLCDGVMVARGDLGVEMDAEEVPLLQKELIKKANSLGIPIITATQMLDSMASSPRPTRAEVSDVANAILDGTDAVMLSNETAVGDYPIEAVETMAKIARRIERDYPQRALESHLPSTIPNAISAAVSTIARQLNAAAILPLTKSGATAHNVSKFRPATPILAITSEISVARRLQLVWGVSPLLIDAQKSTSKTFGIAMEQAMDMKLLKPGDQVVETAGTLTGISGSTDLIKVGIVSKIVASGKTKPIVKEGTISGKLRVINKATDLSDLKSGEILVLAENVQYNLDTKTHISAMIFEGEYSLINTNNQIEDNNIIPAIYNVEGACTKFKNGEIVTLDLKDGNIIKGLAQDLKTYN

demo_results/ureC.faa

@@ -0,0 +1,8 @@
+>GCF_000008865_Escherichia_coli_NP_309351.2_urease_subunit_alpha
+MSNISRQAYADMFGPTTGDKIRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLSAGCADLVLTNALIIDYWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGVSTEIIAAEGRIVTAGGVDTHIHWICPQQAEEALTSGITTMIGGGTGPTAGSNATTCTPGPWYIYQMLQAADSLPVNIGLLGKGNCSNPDALREQVAAGVIGLKIHEDWGATPAVINCALTVADEMDVQVALHSDTLNESGFVEDTLTAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTVNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRQETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVVLRTWQVAHRMKVQRGPLPEESGDNDNVRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVLWSPAFFGVKPATIVKGGMIAMAPMGDINGSIPTPQPVHYRPMFAALGSARHRCRVTFLSQAAAANGVAEQLNLHSTTAVVKGCRTVQKADMRHNSLLPDITVDSQTYEVRINGELITSEPADILPMAQRYFLF
+>GCF_000006765_Pseudomonas_aeruginosa_NP_253555.1_urease_subunit_alpha
+MKISRQAYADMFGPTVGDRVRLADTDLWIEVERDFTVYGEEVKFGGGKVIRDGMGQSQLGAAQVVDTVITNALILDHWGVVKADVGLKDGRIQAIGKAGNPDIQPGVNIAIGAGTEVIAGEGMILTAGGIDTHIHFICPQQIEEALMSGVTTMIGGGTGPAAGTNATTCTSGPWHMARMLQAADAFPMNIGFTGKGNASLPLPLEEQVLAGAIGLKLHEDWGSTPAAIDNCLEVAERHDIQVAIHTDTLNESGFVETTLGAFKGRTIHTYHTEGAGGGHAPDIIKACGFANVLPSSTNPTRPFTRNTIDEHLDMLMVCHHLDPAIAEDVAFAESRIRRETIAAEDILHDLGAFSMISSDSQAMGRVGEVITRTWQTADKMKRQRGRLDGDGARNDNFRARRYIAKYTINPAITHGISHEVGSVEAGKWADLVLWRPAFFGVKPSLILKGGAIAASLMGDINGSIPTPQPVHYRPMFASYAGSRHATSLTFVSQAAFAAGVPQQLGLRKAIGVVSGCRGVQKTDLIHNGYLPTIEVDAQNYQVRADGQLLWCEPADVLPMAQRYFLF
+>GCF_000069965_Proteus_mirabilis_WP_004245262.1_urease_subunit_alpha
+MKTISRQAYADMFGPTTGDRLRLADTELFLEIEKDFTTYGEEVKFGGGKVIRDGMGQSQVVSAECVDVLITNAIILDYWGIVKADIGIKDGRIVGIGKAGNPDVQPNVDIVIGPGTEVVAGEGKIVTAGGIDTHIHFICPQQAQEGLVSGVTTFIGGGTGPVAGTNATTVTPGIWNMYRMLEAVDELPINVGLFGKGCVSQPEAIREQITAGAIGLKIHEDWGATPMAIHNCLNVADEMDVQVAIHSDTLNEGGFYEETVKAIAGRVIHVFHTEGAGGGHAPDVIKSVGEPNILPASTNPTMPYTINTVDEHLDMLMVCHHLDPSIPEDVAFAESRIRRETIAAEDILHDMGAISVMSSDSQAMGRVGEVILRTWQCAHKMKLQRGTLAGDSADNDNNRIKRYIAKYTINPALAHGIAHTVGSIEKGKLADIVLWDPAFFGVKPALIIKGGMVAYAPMGDINAAIPTPQPVHYRPMYACLGKAKYQTSMIFMSKAGIEAGVPEKLGLKSLIGRVEGCRHITKASMIHNNYVPHIELDPQTYIVKADGVPLVCEPATELPMAQRYFLF
+>GCF_000240185_Klebsiella_pneumoniae_YP_005228898.1_urease_subunit_alpha
+MSNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGASTEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLKIHEDWGATPAAIDCALTVADEMDIQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF