Sanders

#1.sh

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+for sc in gene_sequences/sporecoat0[1234].fasta
+do
+cat $sc >> gene_sequences/allsc.fasta
+echo \n >> gene_sequences/allsc.fasta
+done
+
+/afs/nd.edu/user25/vsanders/local/bin/muscle3.8.31_i86linux64 -in gene_sequences/allsc.fasta -out gene_sequences/allsc.align 
+
+for trans in gene_sequences/transporter0[1234].fasta
+do
+cat $trans >> gene_sequences/alltrans.fasta
+echo \n >> gene_sequences/alltrans.fasta
+done
+
+/afs/nd.edu/user25/vsanders/local/bin/muscle3.8.31_i86linux64 -in gene_sequences/alltrans.fasta -out gene_sequences/alltrans.align
+

#2.sh

@@ -0,0 +1,13 @@
+
+/afs/nd.edu/user25/vsanders/local/bin/hmmbuild transporter.hmm gene_sequences/alltrans.align
+
+for file in proteomes/*.fasta
+do
+/afs/nd.edu/user25/vsanders/local/bin/hmmsearch --tblout $file.hits transporter.hmm $file
+done
+
+for hits in proteomes/*.hits
+do
+echo $hits >> hmm_hits.txt
+cat $hits | grep -v "#" | wc -l >> hmm_hits.txt
+done 

allsc.align

@@ -0,0 +1,104 @@
+>Q12FX3_POLSJ/50194
+TWGVLLAAGTAHATISCSV-SGNGFT-SVYDPIS------TVPNDNVSSVTINCS-R---
+-ASGDPTTTTYSLASTNGLYPQGQNNRAY--YPTNKYLKYDIYKDAAYSSRWGPG--GSA
+PFTGTLNFGSGT-SA-SLTLPYYNRVAA-QQSAVAADYTDTMTAT-
+>Q60C08_METCA/20167
+LLACPKIS--DADPYQCDI-GNISVPHAVYDPTDS-----NPNSSGVGTVGITCHLKNAK
+QTQQVQYTIALSRGSSGSYNP--RRMSG-----GRGSLGYNLYLDAARVTIWGDGSGGTF
+PLRGTLLLNPTTPVQ-QVIHNIYGLIPP-LQDVYAGTYTDTVTIT-
+>A9CH19_AGRFC/11158
+IAAAFVAS--PVLAQSCTF-SMSDMNFGFVNLAG------GAAVDTTATLSVTCN-NPLS
+LA--LSIRICPNINAGGGGQSGGIRRMLQ----GSNILNYQLYQTSARTTAWGSVTQPAL
+GAPPPIDMALPLLIN-STTRTVYGRINAGQASAARGLYLSSFAGG-
+>Q985D8_RHILO/37183
+SAALLLPT--VAWAQSCSF-GVSAMNFGLVDTLS------GSSSNSTATLSVNCT-G---
+-LLLQRILVCPNLGTGSGGATASARQMLS----GANDLNYQLYSDSARSVVWGSYAWPYP
+PTAPGFALTLNVLGSGSASQTIYGAILGGQATAVPSTYLSTFSGS-
+>Q8XPY9_RALSO/25163
+-----------ASAQSCSV-ASASLNFGSISPVQ------AGNTDTSTTLTVSCS-GFLL
+QG--TVARACLNLGVGSGDTGISPRVLSA----GANQLQYNLYADSARSVVWGGRTTPAT
+PAIQVD-VSLGLLGFGSATVTVYGRVPGGQTTVPAGAYTQSFSGTN
+>Q8XVY3_RALSO/23163
+VLVALASWAPGALAVSCSV-SANALSFGAYNT--------TSNLTGTTTVTITCG-A---
+WGGASSINYTLSASVGSGTYANRQVLN------GSNVIAYNLYTTSADTSIWGDGN-GDG
+TVTLSGTVTKQ--VG-TVNLTIYGKING-GQNVVPGSYATTIPIT-
+>A1VIJ0_POLNA/19170
+ALFLLLATAGPAQAGSCTV-GSSGLAFGAYQPLTFAGKLTSSAVTSNASISVVCT-GIAS
+GG---AYSIALGPSTTGSGDRISTRYLGN--SNGGDDMSFNIYTSASYSTVWGNGTTG-G
+LVGGSIPV--G--DS-NQSQPVYGRIAASQNTLRAGSYSGSLTMTN
+>Q0AAK6_ALKEH/8153
+SLFLVAAGSGSAQAYTCSI-SADPLAFGQYDPIT------GAQVDGASEVSVSCS-LLGL
+VSLLVSYEISLDPGTGGSYHPRALSS-------ATDTLDYNLYVDTARTEIWGDGTDDTA
+TVTDSYTLGVL--TV-TRYYPVYGRVFA-DQNVAAGVYDDTITAT-
+>Q1D5L1_MYXXD/13153
+AVAGVCGLLPGLAGAVCQIRSTIGVSFGTYLTTD------LLPRDSAGSITYRCE-G---
+QI--TPITIDFSAGGSG--TPLARSMAGP----GAQRLEYNLYVDATRLIVWGNGTSGTG
+RYGPVVPL--F--GV-EVTVPIFGRIPA-GQAIPAGAYADTVVMT-
+>Q3A2W0_PELCD/10150
+IIVLLFAV--DAYAFHCEV-TTTPVSFGAYDVFS------SFSLDTTGRISVSCN-NPEK
+KR--MPVTISISRGAANSFSPRQMRRIG-----GSDRMDYYLFVDASRTAVWGDGTGGSS
+TYVGMID---R--TS-PLNVPIYGRIPA-RQNLRAGSYQDILVVTN
+>Q0C623_HYPNA/23151
+ANGTLDVQ--ATVVNTCVV-LTAPVVFASVG---------LDEVTANGSITVNCT-N---
+-T--SAFTVALDGGDSGDISARSLTHAS-----LPASFNYQLYTDAGLTTVWGDGVTGSQ
+ANGS---------GP-SQTLTVYGRTTS--TPDTAGAYADEVQVT-
+>A7H7Q5_ANADF/16150
+APRAVDAAQPPSPGPSCSV-SAGSVAFGAYDPLS------PTHLDSTGTIGLTCA-V---
+-R--QLVTISLGTGQSG---TFARELRGP----GGAALRYDLYTDATRTQVWGDGTAGTA
+TWPFET-------ER-GRYVPVYARVLA-GQDVPAGPYSDTIVVT-
+>Q2IFK8_ANADE/19157
+ATALSLVAPAAARAASCSLTMGTSIAFGAYDPLS------PVPLTTTGMLQYRCS-R---
+-G--QPIRITFTAGSSGDVYARTLRQ-------GPWTLAYNLYADAGFGTVWGDGTGGTA
+AAPAVTTLS-N--GL-TVAY-VFGRIPA-RQEPPVGPYSDTIVVT-
+>Q0AAK3_ALKEH/24160
+DTATFDVT--ATVDPTCTV-DADNLVFGTYDPFS------DTPLDENSEIRVQCT-S---
+-D--TPYDIGLDDGDNTGAEGERRMALAD----ESDFLEYDLYHDNHGGTSWGDIDSGAE
+LTGLSG----T--GS-EQSYVVYGRIFA-EQSVAVGNYVDTIEVT-
+>A7H7Q6_ANADF/25150
+ATAQFQVT--ATVVKKCKI-SATTIAFGNYDP--------ATILSAEGTLTLKCT-K---
+-G--TLYSVALDGGSTGS-----RQMTQ-----AAEVLDYELYSDAGHTAVWPSTAAAPS
+VAAA---------GA-DEALIIFAQVPA-DQYPAPGAYADTVTAT-
+>Q2IFL0_ANADE/27162
+ATATLDVT--ATVVPSCTI-AATPVAFGSYDPLVTN---AATALDAQGTVTVTCT-T---
+-G--TAYTVGLGAGNSGSGSRAMQHASI-----AGAQLPYELYQEAARTTVWDSTVMQAG
+TAAS---------IT-PVQYTVYGRIPA-AQNVPTGNYADAVVAT-
+>Q985D8_RHILO/205338
+DRPTFTIN--AIVPANCLL-AIQNIDFGSNGIL-------GANVDATGGVSITCT-P---
+-G--TPYTVSLSNGT-TGSAPTARKMSK-----GVETVTYGLYKDNARSQVWGDAAMPGS
+TVAGSG----S--GA-AQNLTIYGRVPA-QTTPSAGVYTDTVVVT-
+>Q8XVY0_RALSO/26164
+TTTTFSVS--TTVNATCVINSASALTFAAFDPS-------QGAQASTSSISVNCT-N---
+-T--TPFNIGLNAGTGTGATVASRVMTS-----GANTLTYSLYQDSGHASVWGN-TVGTN
+TVAGTGAGMAA--GN-AITKTVYGLIPS-QPNTVPGNYADTVTVT-
+>Q0BSH7_GRABC/37169
+TTTTFQVT--ATVQASCII-QATNLSFGNYS---------GSQTDATSTIQVTCT-N---
+-S--TPYNVGLSAGTGSGATVSNRKMSLN----STSALPYALYSDASRSTNWGN-TPNQD
+TVSGTG----N--GS-AQSLTVYGRIQT-GNYPTPGSYADTITAT-
+>Q8XPY6_RALSO/36170
+KTTTFTVS--LTLQADCSI-SANALNFGTQGVL-------AANVDQTATLSVTCS-N---
+-T--APYNVGFDAGTTTGSTIAARLLAGS----GAATVGFQLYSDSARTQIWGN-TVGTD
+TVSGTG----S--GT-AQVLTVYGRVPS-QNSPAAGTYSTTITAT-
+>Q63W79_BURPS/31169
+ATATFTVS--LTIQANCTI-SANALSFGTNGVL-------ATAVNQQTTLSVTCS-N---
+-T--TSYNVGLDAGNVSGSTVSSRLLAGTTTGNTSTTVSFQLYQDSGHTTIWGN-TVGTN
+TVSGTG----N--GT-AQTLSVYGQVPA-QTTPKPDTYESTVTATN
+>Q7CVQ4_AGRFC/27162
+ATTNFNVQ--ITIQAACQINSAGNLDFGTNGVI-------GAPIDVTSQIVVQCT-A---
+-S--TPFSLGLSAGAGSGATVANRLMTSA----AGATISYSLYTTAAHSTVWGN-TVGTD
+RQTGTG----T--GA-PQNFTVFGRVPA-QTTPAVGVYTDTVTAT-
+>Q985D5_RHILO/27162
+ATGNMTVR--ITIQAECKVQTATDMDFGTNGVI-------DANVDQTSTISVQCT-N---
+-S--TPYNVGLSAGVGAGATVAVRKMTGP----AAAVLNYSLYRDVARAQLWGT-TIGTD
+TVAGTG----N--GA-AQPLTVYGRVPP-QTTPGAGVYTDTVAIT-
+>A6X8A6_OCHA4/27162
+ATGNMNVR--ITIQAECKIVTATDLDFGTKGVI-------DVNVDQTSTISVQCT-N---
+-G--TPYTVGLSAGGGAGATVAMRKMTGA----ASATINYTIYRDAARTQVWGV-TAGTD
+VVSGTG----N--GN-AQSITAYGRVPA-QTTPAPGVYSDVVSVT-
+>A9CH19_AGRFC/182313
+TQVPFTVS--AAVAPTCII-SAQNINFGSHGVL-------NTAVDANGAINLTCT-N---
+-G--LNYSVALNGGLSNS-PPAARQMVQ-----GAASIIYGLYRDVSRTNVWG--SAAGQ
+IATGTG----N--GS-LQTLTVFGRVPA-QNTPAPGNYADTVVVT-
+>Q63W78_BURPS/193326
+-TFAFTAS--ATVVNDCFI-NATNVAFGSTGVI-------QGALTATGTISAQCT-N---
+-G--DAFRIALNGGASGNVAARAMQRTG-----GGGAVNYQLYLDAAHSTIWGDGTAGTS
+TATGTG----S--GL-SQSLTVYGQVPA-QTTPAPGTYSDTITAT-

alltrans.align

@@ -0,0 +1,32 @@
+>A0A026RKY7_ECOLX/4411
+NIPFRNAYYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFM
+MFYGIVQDKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLA
+GCGLLDSFTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVF
+-MMINMRFKDKDHQCIAADAGGVKKEDF-----IAVFKDRNFWVFVIFIVGTWSFYNIFD
+QQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIM
+ALRILSCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASS
+LGIVLLSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLSKKREQIVMETPVN
+>RAFB_ECOLX/4415
+ASTHKNTDFWIFGLFFFLYFFIMATCFPFLPVWLSDVVGLSKTDTGIVFSCLSLFAISFQ
+PLLGVISDRLGLKKNLIWSISLLLVFFAPFFLYVFAPLLHLNIWAGALTGGVFIGFVFSA
+GAGAIEAYIERVSRSSGFEYGKARMFGCLGWALCATMAGILFNVDPSLVFWMGSGGALLL
+LLLLYLARPSTSQTAMVMNALGANSSLISTRMVFSLFRMRQMWMFVLYTIGVACVYDVFD
+QQ-FAIFFRSFFDTPQAGIKAFGFATTAGEICNAIIMFCTPWIINRIGAKNTLLVAGGIM
+TIRITGSAFATTMTEVVILKMLHALEVPFLLVGAFKYITGVFDTRLSATVYLIGFQFSKQ
+LAAILLSTFAGHLYDRMGFQNTYFVLGMIVLTVTVISAFTLS-SSPGIVHPSVEN
+>LACY_CITFR/1412
+MYYLKNTNFWMFGFFFFFYFFIMGAYFPFFPIWLHEVNHISKGDTGIIFACISLFSLLFQ
+PIFGLLSDKLGLRKHLLWVITGMLVMFAPFFIYVFGPLLQVNILLGSIVGGIYLGFIYNA
+GAPAIEAYIEKASRRSNFEFGRARMFGCVGWALCASIAGIMFTINNQFVFWLGSGCAVIL
+ALLLLFSKTDVPSSAKVADAVGANNSAFSLKLALELFKQPKLWLISLYVVGVSCTYDVFD
+QQ-FANFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIVNRIGGKNALLLAGTIM
+SVRIIGS-HSHTALEVVILKTLHMFEIPFLIVGCFKYITSQFEVRFSATIYLVCFCFFKQ
+LAMIFMSVLAGKMYESIGFQGAYLVLGIIRVSFTLISVFTLSGPGPFSLLRRREN
+>LACY_KLEOX/6416
+LAPRERHNFIYFMLFFFFYYFIMSAYFPFFPVWLAEVNHLTKTETGIVFSCISLFAIIFQ
+PVFGLISDKLGLRKHLLWTITILLILFAPFFIFVFSPLLQMNIMAGALVGGVYLGIVFSS
+RSGAVEAYIERVSRANRFEYGKVRVSGCVGWALCASITGILFSIDPNITFWIASGFALIL
+GVLLWVSKPESSNSAEVIDALGANRQAFSMRTAAELFRMPRFWGFIIYVVGVASVYDVFD
+QQ-FANFFKGFFSSPQRGTEVFGFVTTGGELLNALIMFCAPAIINRIGAKNALLIAGLIM
+SVRILGSSFATSAVEVIILKMLHMFEIPFLLVGTFKYISSAFKGKLSATLFLIGFNLSKQ
+LSSVVLSAWVGRMYDTVGFHQAYLILGCITLSFTVISLFTL--KGSKTLLPATAN

hmm_hits.txt

@@ -0,0 +1,16 @@
+proteomes/Arthrobacter.fasta.hits
+1
+proteomes/Bacillus.fasta.hits
+1
+proteomes/Clostridium.fasta.hits
+0
+proteomes/Flavobacterium.fasta.hits
+1
+proteomes/Limnohabitans.fasta.hits
+1
+proteomes/Rhizobium.fasta.hits
+0
+proteomes/Roseobacter.fasta.hits
+1
+proteomes/Verrucomicrobia.fasta.hits
+0