Using WikiBCB

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Assignment for 10/01/2015

The gene I chose to focus on is Spo11 in Saccharomyces Cerevisiae. Spo11 is a 45 kDa protein that creates the double stranded DNA breaks in meiotic recombination.

.fasta Formatted Protein Sequence

>sp|P23179|SPO11_YEAST Meiosis-specific protein SPO11 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SPO11 PE=1 SV=1
MALEGLRKKYKTRQELVKALTPKRRSIHLNSNGHSNGTPCSNADVLAHIKHFLSLAANSL
EQHQQPISIVFQNKKKKGDTSSPDIHTTLDFPLNGPHLCTHQFKLKRCAILLNLLKVVME
KLPLGKNTTVRDIFYSNVELFQRQANVVQWLDVIRFNFKLSPRKSLNIIPAQKGLVYSPF
PIDIYDNILTCENEPKMQKQTIFPGKPCLIPFFQDDAVIKLGTTSMCNIVIVEKEAVFTK
LVNNYHKLSTNTMLITGKGFPDFLTRLFLKKLEQYCSKLISDCSIFTDADPYGISIALNY
THSNERNAYICTMANYKGIRITQVLAQNNEVHNKSIQLLSLNQRDYSLAKNLIASLTANS
WDIATSPLKNVIIECQREIFFQKKAEMNEIDARIFEYK

On the NCBI website I found an interesting tool in the CDD (conserved domain database) called CD-search that checks for conserved domains in your protein sequence. I input the sequence for my protein Spo11 and obtained interesting information on some domains and other areas of interest on the protein.

The conserved domain database has a fantastic help section that details everything in great detail.

Assignment for 10/06/2015

The goal of this assignment was to produce a phylogenetic tree using 10 related sequences to your gene of interest.

Obtain the fasta formatted sequence of your protein by either accessing it from the database of your organism, or through UniProt.

>sp|P23179|SPO11_YEAST Meiosis-specific protein SPO11 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SPO11 PE=1 SV=1
MALEGLRKKYKTRQELVKALTPKRRSIHLNSNGHSNGTPCSNADVLAHIKHFLSLAANSL
EQHQQPISIVFQNKKKKGDTSSPDIHTTLDFPLNGPHLCTHQFKLKRCAILLNLLKVVME
KLPLGKNTTVRDIFYSNVELFQRQANVVQWLDVIRFNFKLSPRKSLNIIPAQKGLVYSPF
PIDIYDNILTCENEPKMQKQTIFPGKPCLIPFFQDDAVIKLGTTSMCNIVIVEKEAVFTK
LVNNYHKLSTNTMLITGKGFPDFLTRLFLKKLEQYCSKLISDCSIFTDADPYGISIALNY
THSNERNAYICTMANYKGIRITQVLAQNNEVHNKSIQLLSLNQRDYSLAKNLIASLTANS
WDIATSPLKNVIIECQREIFFQKKAEMNEIDARIFEYK

Enter your sequence into blastp at the NCBI website and press “blast”.

In the results page, select 10 sequenes from related organisms, press download, and select “FASTA” format.

>gi|190405760|gb|EDV09027.1| meiosis-specific protein SPO11 [Saccharomyces cerevisiae RM11-1a] >gi|256274400|gb|EEU09304.1| Spo11p [Saccharomyces cerevisiae JAY291] >gi|259147003|emb|CAY80258.1| Spo11p [Saccharomyces cerevisiae EC1118] >gi|323337401|gb|EGA78653.1| Spo11p [Saccharomyces cerevisiae Vin13] >gi|365765317|gb|EHN06828.1| Spo11p [Saccharomyces cerevisiae x Saccharomyces kudriavzevii VIN7] >gi|584476265|gb|EWH18015.1| Spo11p [Saccharomyces cerevisiae P283] >gi|628217461|gb|AHY77674.1| Spo11p [Saccharomyces cerevisiae YJM993] >gi|761437246|gb|AJP39074.1| Spo11p [Saccharomyces cerevisiae YJM1078] >gi|768506205|gb|AJU19320.1| Spo11p [Saccharomyces cerevisiae YJM1415] >gi|768507232|gb|AJU20343.1| Spo11p [Saccharomyces cerevisiae YJM1433] >gi|768507973|gb|AJU21081.1| Spo11p [Saccharomyces cerevisiae YJM1443] >gi|768509474|gb|AJU22576.1| Spo11p [Saccharomyces cerevisiae YJM1477] >gi|768512969|gb|AJU26060.1| Spo11p [Saccharomyces cerevisiae YJM193] >gi|768513476|gb|AJU26565.1| Spo11p [Saccharomyces cerevisiae YJM244] >gi|768513728|gb|AJU26816.1| Spo11p [Saccharomyces cerevisiae YJM248] >gi|768513986|gb|AJU27073.1| Spo11p [Saccharomyces cerevisiae YJM270] >gi|768514747|gb|AJU27831.1| Spo11p [Saccharomyces cerevisiae YJM326] >gi|768515765|gb|AJU28845.1| Spo11p [Saccharomyces cerevisiae YJM453] >gi|768516526|gb|AJU29603.1| Spo11p [Saccharomyces cerevisiae YJM541] >gi|768517535|gb|AJU30608.1| Spo11p [Saccharomyces cerevisiae YJM681] >gi|768517788|gb|AJU30860.1| Spo11p [Saccharomyces cerevisiae YJM682] >gi|768518043|gb|AJU31114.1| Spo11p [Saccharomyces cerevisiae YJM683] >gi|768518299|gb|AJU31369.1| Spo11p [Saccharomyces cerevisiae YJM689] >gi|768519683|gb|AJU32749.1| Spo11p [Saccharomyces cerevisiae YJM975] >gi|768520557|gb|AJU33621.1| Spo11p [Saccharomyces cerevisiae YJM981] >gi|768520816|gb|AJU33879.1| Spo11p [Saccharomyces cerevisiae YJM984] >gi|768521940|gb|AJU35000.1| Spo11p [Saccharomyces cerevisiae YJM996] >gi|768810156|gb|AJV26764.1| Spo11p [Saccharomyces cerevisiae YJM1083] >gi|768811103|gb|AJV27707.1| Spo11p [Saccharomyces cerevisiae YJM1190] >gi|768811861|gb|AJV28462.1| Spo11p [Saccharomyces cerevisiae YJM1208] >gi|768812114|gb|AJV28714.1| Spo11p [Saccharomyces cerevisiae YJM1242] >gi|768812374|gb|AJV28973.1| Spo11p [Saccharomyces cerevisiae YJM1244] >gi|768812875|gb|AJV29472.1| Spo11p [Saccharomyces cerevisiae YJM1250] >gi|768813124|gb|AJV29720.1| Spo11p [Saccharomyces cerevisiae YJM1252] >gi|768814403|gb|AJV30994.1| Spo11p [Saccharomyces cerevisiae YJM1326] >gi|768814660|gb|AJV31250.1| Spo11p [Saccharomyces cerevisiae YJM1332] >gi|768815179|gb|AJV31767.1| Spo11p [Saccharomyces cerevisiae YJM1338] >gi|768815435|gb|AJV32022.1| Spo11p [Saccharomyces cerevisiae YJM1341] >gi|919303102|gb|KOH50182.1| SPO11p Meiosis-specific protein that initiates meiotic recombination [Saccharomyces sp. 'boulardii']
MALEGLRKKYKTRQELVKALTPKRRSIHLNSNGHSNGTPCSNADVLAHIKHFLSLAANSLEQHQQPISIVFQNKKRKGDT
SSPDIHTTLDFPLNGPHLCTHQFKLKRCAILLNLLKVVMEKLPLGKNTTVRDIFYSNVELFQRQANVVQWLDVIRFNFKL
SPRKSLNIIPAQKGLVYSPFPIDIYDNILTCANEPKMQKQTIFPGKPCLIPFFQDDAVIKLGTTSMCNIVIVEKEAVFTK
LVNNYHKLSTNTMLITGKGFPDFLTRLFLKKLEQYCSNLISDCSIFTDADPYGISIALNYTHSNERNAYICTMANYKGIR
ITQVLAQNNEVHNKSIQLLSLNQRDYSLAKNLIASLTANSWDIATSPLKNVIIECQREIFFQKKAEMNEIDARIFKYK
>gi|918730502|gb|KOG96497.1| SPO11-like protein [Saccharomyces eubayanus]
MALQRLRKKHRTRQELLKALTPRTRSIHLSPNEHSNGSAGSNAEVLSHIKQILSLAANSLEQHQQPISIIFDNKTKGNSG
GNKVSTTLDFPLTGPHLFTHQFKLKRCSILLNLLKIVMEKLPLGQNTTIRDIFYSNVELFQRQANVVQWLDVIRFNFKLS
PRKSLNIIPAQKGLIYSPFPIYVYDSITKCEDEFQVEKQTVSPGKPCLIPFFQDEAVIRLETTSHCNIVIVEKEAVFTKL
VSNYNKLNANTVLITGKGFPDFLTRLFLKKLEQDCSNLISNCSIFTDADPYGISIALNYINSNANASYNCPMVNYKGVYI
TQILAQNNRTGSKFVQLLSLNQRDYSLAKNLVVSLTNNGGGVISSPFKNFIIECQREIFFQKKAEMNEIDVSMFRLQ
>gi|693903678|dbj|BAP72530.1| meiosis-specific protein SPO11 [Kluyveromyces marxianus]
MDCSLRTLMDGCHSRAELKQRMLPRSRVVEFSKIKSEEECQRQITNNMRFMRLALKEHGIPIEIRFHNSRNNEVSWKYPE
FGSNWKKCSKVPQLLQLLSIVNERLKLKKTSTTVRDIYYGNVELFGNQSTVEQLLQRLESMFQVEKQFFNIVSTQKGLLF
AGPKLSIEGQIFHQECQLVPYMNKEEVPISIGAGESCAKVVVLEKDAIFQQLIQCKNLVQNWIVITGKGYPDLLTRQLLH
HMGQKLPQEVEFLIYTDSDPYGIDIVTKYMSHATLRNVQCSRIKHKGVLLSQLIARNRPGTHQMLVLLPLSLRDSTFAMN
LIRRMMCQDTQIEEKTKRSLRDELQKQLFFQRKGEMNVVNNGDLEQYFSEEALRDTT
>gi|317148419|ref|XP_001822758.2| meiotic recombination protein spo11 [Aspergillus oryzae RIB40]
MEDHLEYMGLVFYHPTTQDSYMSTPLRQVKRYINETLSSAFDELSKPDGRPAITLKRSSRNASLFINPTSRALESSGTDT
YITYSWPGANTFEAWKFTVVFRVLAVVADAIGTGVVVSKRDIYYSDPACFGTQRIVDTIVDDLAYTIGVDRSALNVEAAA
KGLVAGYCSLLTKSGETMDVQLPAKDCLVPSSQDDRELNISDASWVLIIEKEAIYRRLTRSNYHTRAAAGKGILITGKGY
PDLSTRAFIRKLYENSRRSDKALRFYGLVDNDPDGMAIMSIYKYGSMAHTNQNGRLNIPCLWWLGLRTSDVVSGAPSNDD
RALNRLTVRDRTKIVTMLSNNPVWAAEGPELEWRAELQQMLMLNLKAEIEILYDWDGGLEGWIDQKMAGFSLPED
>gi|425773684|gb|EKV12019.1| Meiosis-specific topoisomerase Spo11, putative [Penicillium digitatum Pd1] >gi|425775995|gb|EKV14234.1| Meiosis-specific topoisomerase Spo11, putative [Penicillium digitatum PHI26]
MAEPTTIHTLEMDDDRDPSVQGFINNTLAAFVHGLSQSPTEANISITLKRRASPTACAINTLTGALEPIPRVETYRKYSW
PGKTAHEAWKFTVILRILAILDQAIRTGQLISKRDIYYIDPEFFRVQYIVDHIVDDLAYTIGVNRTALNVEAAAKGLVTG
DYRLIRGSHILIDAHSVIEDSLIPRIENGDKIDISRIRWVLVIEKEAVFHRLARISYHTRALAGEGIMVTGKGYPDFMTR
TFLRAISDSASKQSRSQPRFYALTDGDPHGMAIMSTYKYGSAAHLHQNARLSIPRLQWLGLRVTDIIAVPEVLGDTALLS
LTMQDRKKIMAMLRNSPVWASDGPEPEWRAELQRMMILNLKAEIEILYGCQGGLEGWINRRMFRQE
>gi|317032060|ref|XP_001393922.2| meiotic recombination protein spo11 [Aspergillus niger CBS 513.88]
MEASHLDGMEAEAFERLTIIATIPQTPVQSYIQETLAAILDEVSFREGHLSITLKQRGKKFASLFINPRTLALETSEIQT
YTTYRWPGGDMNEALKFTAALRVLAAIAEAVQAGLVVSKRDIYYSDPICFGSQKTVDTLVDDLAHTMGVDRAALYVGAAA
KGLVVGYYQMTTTSAGVVDARLSNQDTLVPRMQDIHKVDLKDVAWVLVLEKEAVYRRLASSNYHIRSAAGKGVLVTGKGY
PDLSTRAFVRKLFDHSHQLTKKPQFYALVDGDPDGMAIMATYKYGSVAFAHENRNLNVPGLHWLGLRLAEVVAGADPLGD
GTLLHLTKRDRKKAIDMLSKNPVWEADGPEPEWRVELQRMLMLNVKAEMEILYDMEGGLTGWLDRKLVHLIQNSK
>gi|407925927|gb|EKG18901.1| Spo11/DNA topoisomerase VI subunit A [Macrophomina phaseolina MS6]
MELDDNDDDMLYGSMSLRNSSRESLTDATTALWAISEDDDHLLLPNAHQHISPSQPSGTLRTASLDLESQWLEEDLFAFA
EASPRQELRFSNTAPVARRVCHKERLISSIESVFESMLDVLLAKEESLTILVKSRPRALTPVNTSVRLIRFPGKTAEEAW
RFTVLIRILEIVHEALITDRVISKREIYYRHPALFTTQVIVDRYIDDIAYTFGTYRSLLNVCAAAKGLVSGPVSIQKGDN
TAFQKLDDHAGHLIPNNDGEGIIQTTAKWILVVEKEALFRSISASSSWEVLRHQGVMVTGKGYPDLSTRAFLRQLCAASV
TGHPHIPIYALVDFDPDGLSIMCTYKYGSSALAHEGDAARLPSMQWLGVKSTQAFPPKSSGLTASSVHQNQGLLHLTHRD
RKKAVSILCKACCCETDISHEIARELQIMLMLNLKAETELLESRDDGLAGWLMEQLPT
>gi|6716731|gb|AAF26720.1|AF214638_1 Spo11 [Coprinopsis cinerea]
MVLSFLKQIEACGAVILDDGEESQGKKQRPKLEIQLADRKRLTVDGEPAKRSLKFPKRFATGSSRSMAQLFRVLDIMHEG
LVTGTPTTKRDIYYKDVALFGRQSVVDTLVDDLAATWGTQRCDLNVRAASKGLVCGAGITINLYSGEVVQGNDTEPSNIP
AGEDIESFGVDEDIAWVLVVEKEAVFQTLCQLGVTHGLNIGKGIMVTGKGYPDIATRHLVKSLGDALPKHVALAALVDCD
PYGIDILSVYRYGSQSMRHENDTLATRRIKWLGLRISEVMEWDLDPSLLLPLTDYDENKIRSMLKRPHLPRRWRDELEAT
QARGRKAEIEVLCSLPRDQALRIGVGDSMNNPLLAYVEQKLHSLISRAS
>gi|915659766|gb|KOC62684.1| Meiotic recombination protein SPO11 [Habropoda laboriosa]
MNREGFRFTDSQPADVEEKKIDIPVVDNTESRTQLVARIESITFSIIQQICSGRLPKISYSSSQNYASTGTQTTEEINFE
SQFPEDSEQITEESEQHERKSVISFARKRGKDKFALMITVMAAAHRLLITNSSITRRSLYYDLKKEKTSNLVPEQRNLDQ
AVNHVANLLNCAPWELNLLPTSKGLVAGELILTLNDNRIIDCKVPGGALIPMISSNVISVRARAKMVLIVEKDAVFQKLL
ENDCTTSLNSIIVTGKGYPDVATRMLVKLLSEKLELPLYAIVDADPFGVDIMCVYRFGSATLSRERESLACPSVRWLGIH
PSELLALGVNTVPLTEFDLSKLLALECRPYMRDAFLRELRVLRTGKAEIESVSSFLGKFLAATYLPCKIKGDDYV
>gi|33304618|gb|AAQ02689.1| meiosis-specific topoisomerase Spo11 [Sordaria macrospora]
MYFCPIRNQFLQPRSQPPSQPPSQPPSQLPSQPNSQPGTRTGHGQPNPPLMQGNSVGVGRGRVSRNIVTIPQSHFNDDAL
AKIETLFETILDAVSVGGPVVIPYRRSTNAQTFNATAFTSNPSDGRHIDSVRFPGRNPQELRRFEALFRIIELSHEALLS
GTLITKRNIYYQNMELFRSQSMVDEMVDNLAFTLGVGRGDLNIVATAKGLIAGQVQLMMRGGTSINCAESSDSGVLLPSI
SAVEKIDFQSVKWLLVIEKEATFRTLSASRYHAVSRAGSGILVTGKGYPDLATRKFLATLHFVQPRLPMFALVDFDTHGI
SILRTYQYGSQRLDHEERTKVPRLRWLGIRSSDVLSQTMVTQDPSANNQDSQSSQDLSSQESIAYSVDALQDERPTKRPR
TRRTKSHPSDSTAPLNEGDREKAVSVLRDICTTARLDSSGREHKLELQRMLLLNVKAEIQAVDDFGDITNWLDERLLSQS
R

Go to Mobyl @ Pasteur clustalw multialign, input your sequences, and run.

You should get an output of your sequences aligned.

>gi|190405760|gb|EDV09027.1| meiosis-specific protein SPO11 [Saccharomyces cerevisiae RM11-1a]
------------------------------------------------------------
------------------------MALEGLRKKYKTRQELVKALTPKRRSIHLNSNGHSN
GTPCSNADVLAHIKHFLSLAANSLEQH--QQPISIVFQNK--------------------
-----KRKGDTSSPDIHTTLDFPLNGPHLCTHQFKLKRCAILLNLLKVVMEKLPLGK-NT
TVRDIFYSN-----VELFQRQANVVQWLDVIRFNFKLSPRKSLNIIPAQKGLVYSPFPID
I-YD-NILTCANEPKMQKQTIFPGKPCLIPFFQD-DAVIKLGTTSMCN-IVIVEKEAVFT
KLVNNYHK---LSTNTMLITGKGFPDFLTRLFLKKLEQYCSN---LISDCSIFTDADPYG
ISIALNYT-----HSNERNAYICTMANYKGIRITQVLAQNNEV-----------------
---------------------------HNKSIQLLSLNQRDYSLAKNLIASLTANSWDIA
TSPLKNVIIECQREIFFQKKAEMNEIDARIFKYK--------------------------
---
>gi|918730502|gb|KOG96497.1| SPO11-like protein [Saccharomyces eubayanus]
------------------------------------------------------------
------------------------MALQRLRKKHRTRQELLKALTPRTRSIHLSPNEHSN
GSAGSNAEVLSHIKQILSLAANSLEQH--QQPISIIFDNK--------------------
-----T-KGNSGGNKVSTTLDFPLTGPHLFTHQFKLKRCSILLNLLKIVMEKLPLGQ-NT
TIRDIFYSN-----VELFQRQANVVQWLDVIRFNFKLSPRKSLNIIPAQKGLIYSPFPIY
V-YD-SITKCEDEFQVEKQTVSPGKPCLIPFFQD-EAVIRLETTSHCN-IVIVEKEAVFT
KLVSNYNK---LNANTVLITGKGFPDFLTRLFLKKLEQDCSN---LISNCSIFTDADPYG
ISIALNYI-----NSNANASYNCPMVNYKGVYITQILAQNNRT-----------------
---------------------------GSKFVQLLSLNQRDYSLAKNLVVSLTNNGGGVI
SSPFKNFIIECQREIFFQKKAEMNEIDVSMFRLQ--------------------------
---
>gi|693903678|dbj|BAP72530.1| meiosis-specific protein SPO11 [Kluyveromyces marxianus]
------------------------------------------------------------
----------------------MDCSLRTLMDGCHSRAELKQRMLPRSRVVEFSKIKSE-
------EECQRQITNNMRFMRLALKEH--GIPIEIRFHNS--------------------
-----RNNE--------VSWKYPEFGSN----WKKCSKVPQLLQLLSIVNERLKLKKTST
TVRDIYYGN-----VELFGNQSTVEQLLQRLESMFQVE-KQFFNIVSTQKGLLFAGPKLS
I-EG-QIF--------------HQECQLVPYMNKEEVPISIGAGESCAKVVVLEKDAIFQ
QLIQ-CKN---LVQNWIVITGKGYPDLLTRQLLHHMGQKLPQ---E-VEFLIYTDSDPYG
IDIVTKYM-----SHATLRNVQCSRIKHKGVLLSQLIARNRPG-----------------
---------------------------THQMLVLLPLSLRDSTFAMNLIRRMMCQDTQIE
EKTKRSLRDELQKQLFFQRKGEMNVVNNGDLEQYF----------------SEEALRDTT
---
>gi|317148419|ref|XP_001822758.2| meiotic recombination protein spo11 [Aspergillus oryzae RIB40]
------------------------------------------------------------
------------------MEDHLEYMGLVFYHP-TTQDSY-------------MST-PL-
------RQVKRYINETLSSAFDELSKP--DGRPAITLKRS-------SRNASLFI-----
--NPTSRALESSGTDTYITYSWPGANTF------EAWKFTVVFRVLAVVADAIGTGV-VV
SKRDIYYSD-----PACFGTQRIVDTIVDDLAYTIGVD-RSALNVEAAAKGLVAGYCSLL
T-KSGETMD-V---------QLPAKDCLVPSSQDDREL---N-ISDASWVLIIEKEAIYR
RLTRSNYHTRAAAGKGILITGKGYPDLSTRAFIRKLYEN-SRRSDKALRFYGLVDNDPDG
MAIMSIYKYGSMAHTNQNGRLNIPCLWWLGLRTSDVVS-------GAP------------
---------------------------SNDDRALNRLTVRDRTKIVTMLSNNP--VWA-A
EGPELEWRAELQQMLMLNLKAEIEILYDWDG--------------GLEGWIDQKMAGFSL
PED
>gi|425773684|gb|EKV12019.1| Meiosis-specific topoisomerase Spo11, putative [Penicillium digitatum Pd1] >gi|425775995|gb|EKV14234.1| Meiosis-specific topois
------------------------------------------------------------
-----------------------------MAEP-TTIHTLEM-----------DDD-RD-
------PSVQGFINNTLAAFVHGLSQSPTEANISITLKRR------ASPTACAIN-----
--TLTGALEPIPRVETYRKYSWPGKTAH------EAWKFTVILRILAILDQAIRTGQ-LI
SKRDIYYID-----PEFFRVQYIVDHIVDDLAYTIGVN-RTALNVEAAAKGLVTGDYRLI
R-GSHILID-A---------HSVIEDSLIPRIENGDKI---D-ISRIRWVLVIEKEAVFH
RLARISYHTRALAGEGIMVTGKGYPDFMTRTFLRAISDSASKQSRSQPRFYALTDGDPHG
MAIMSTYKYGSAAHLHQNARLSIPRLQWLGLRVTDIIA-------VPE------------
---------------------------VLGDTALLSLTMQDRKKIMAMLRNSP--VWA-S
DGPEPEWRAELQRMMILNLKAEIEILYGCQG--------------GLEGWINRRMFRQE-
---
>gi|317032060|ref|XP_001393922.2| meiotic recombination protein spo11 [Aspergillus niger CBS 513.88]
------------------------------------------------------------
-----------------MEASHLDGMEAEAFE---RLTII-------------ATI-PQ-
------TPVQSYIQETLAAILDEVSFR--EGHLSITLKQR------GKKFASLFI-----
--NPRTLALETSEIQTYTTYRWPGGDMN------EALKFTAALRVLAAIAEAVQAGL-VV
SKRDIYYSD-----PICFGSQKTVDTLVDDLAHTMGVD-RAALYVGAAAKGLVVGYYQMT
T-TSAGVVD-A---------RLSNQDTLVPRMQDIHKV---D-LKDVAWVLVLEKEAVYR
RLASSNYHIRSAAGKGVLVTGKGYPDLSTRAFVRKLFDH-SHQLTKKPQFYALVDGDPDG
MAIMATYKYGSVAFAHENRNLNVPGLHWLGLRLAEVVA-------GAD------------
---------------------------PLGDGTLLHLTKRDRKKAIDMLSKNP--VWE-A
DGPEPEWRVELQRMLMLNVKAEMEILYDMEG--------------GLTGWLDRKLVHLIQ
NSK
>gi|407925927|gb|EKG18901.1| Spo11/DNA topoisomerase VI subunit A [Macrophomina phaseolina MS6]
MELDDNDDDMLYGSMSLRNSSRESLTDATTALWAISEDDDHLLLPNAHQ-HISPSQPSGT
LRTASLD----------LESQWLEEDLFAFAEA-SPRQELRF-----------SNTAPVA
RRVCHKERLISSIESVFESMLDVLLAK--EESLTILVKSR--------------------
-----PRA-LTPVNTSVRLIRFPGKTAE------EAWRFTVLIRILEIVHEALITDR-VI
SKREIYYRH-----PALFTTQVIVDRYIDDIAYTFGTY-RSLLNVCAAAKGLVSGPVSIQ
K-GDNTAFQ-K---------LDDHAGHLIPN-NDGEGI---I-QTTAKWILVVEKEALFR
SISASSS-WEVLRHQGVMVTGKGYPDLSTRAFLRQLCAA-SVTGHPHIPIYALVDFDPDG
LSIMCTYKYGSSALAHEGDAARLPSMQWLGVKSTQAFPPKSSGLTASS------------
---------------------------VHQNQGLLHLTHRDRKKAVSILCKAC--CCE-T
D-ISHEIARELQIMLMLNLKAETELLESRDD--------------GLAGWLMEQLPT---
---
>gi|6716731|gb|AAF26720.1|AF214638_1 Spo11 [Coprinopsis cinerea]
------------------------------------------------------------
------------------------------------------------------------
----MVLSFLKQIEACGAVILDDG-------EESQGKKQR------PKLEIQLAD-----
-----RKRLTVDGEPAKRSLKFPKRFAT-----GSSRSMAQLFRVLDIMHEGLVTGT-PT
TKRDIYYKD-----VALFGRQSVVDTLVDDLAATWGTQ-RCDLNVRAASKGLVCGAGITI
NLYSGEVVQ-----------GNDTEPSNIPAGEDIESF---GVDEDIAWVLVVEKEAVFQ
TLCQLGVTHGLNIGKGIMVTGKGYPDIATRHLVKSLGDA----LPKHVALAALVDCDPYG
IDILSVYRYGSQSMRHENDTLATRRIKWLGLRISEVMEW---------------------
---------------------------DLDPSLLLPLTDYDENKIRSMLKRPH-------
--LPRRWRDELEATQARGRKAEIEVLCSLPRDQALRIGVGDSMNNPLLAYVEQKLHSLIS
RAS
>gi|915659766|gb|KOC62684.1| Meiotic recombination protein SPO11 [Habropoda laboriosa]
------------------------------------------------------------
----------------------MNREGFRFTDS-QPADVEEK-----------KIDIPVV
DNTESRTQLVARIESITFSIIQQICSG---RLPKISYSSSQNYASTGTQTTEEINFESQF
PEDSEQITEESEQHERKSVISFARKR--------GKDKFALMITVMAAAHRLLITNS-SI
TRRSLYYDLKKEKTSNLVPEQRNLDQAVNHVANLLNCA-PWELNLLPTSKGLVAGELILT
L-NDNRIIDCK---------V--PGGALIPMISS-NVI---SVRARAKMVLIVEKDAVFQ
KLLENDCTTS---LNSIIVTGKGYPDVATRMLVKLLSEK------LELPLYAIVDADPFG
VDIMCVYRFGSATLSRERESLACPSVRWLGIHPSELLALGV-------------------
--------------------------------NTVPLTEFDLSKLLALECRPY--MRD--
-----AFLREL--RVLRTGKAEIESVSSFLGKFLAATYLPCKIK--GDDYV---------
---
>gi|33304618|gb|AAQ02689.1| meiosis-specific topoisomerase Spo11 [Sordaria macrospora]
-------------------------------MYFC-PIRNQFLQPRSQPPSQPPSQPPSQ
LPSQPNSQPGTRTGHGQPNPPLMQGNSVGVGRGRVSRNIV---------------TIPQ-
--SHFNDDALAKIETLFETILDAVSVG---GPVVIPYR--------RSTNAQTFN-----
--AT-AFTSNPSDGRHIDSVRFPGRNPQ------ELRRFEALFRIIELSHEALLSGT-LI
TKRNIYYQN-----MELFRSQSMVDEMVDNLAFTLGVG-RGDLNIVATAKGLIAGQVQLM
M-RGGTSINCA---------ESSDSGVLLPSISAVEKI---D-FQSVKWLLVIEKEATFR
TLSASRYHAVSRAGSGILVTGKGYPDLATRKFLATLHF-----VQPRLPMFALVDFDTHG
ISILRTYQYGSQRLDHEE-RTKVPRLRWLGIRSSDVLSQTMVTQDPSANNQDSQSSQDLS
SQESIAYSVDALQDERPTKRPRTRRTKSHPSDSTAPLNEGDREKAVSVLRDIC--TTARL
DSSGREHKLELQRMLLLNVKAEIQAVDDF-G--------------DITNWLDERLLSQSR
---

Go to Mobyl @ Pasteur protdist enter, your alignemnt, and select run. You should get a distance matrix as an output.

    10
gi|1904057  0.000000  0.273555  1.521075  2.036143  1.935387  2.073157
  2.013416  2.314664  2.242249  1.998031
gi|9187305  0.273555  0.000000  1.497646  2.114223  1.961088  2.122944
  2.072802  2.346647  2.226902  1.965679
gi|6939036  1.521075  1.497646  0.000000  2.289752  2.102218  2.157135
  2.077586  1.922648  2.268390  2.056180
gi|3171484  2.036143  2.114223  2.289752  0.000000  0.756860  0.656571
  1.297607  1.574023  1.910127  1.393124
gi|4257736  1.935387  1.961088  2.102218  0.756860  0.000000  0.828876
  1.223347  1.488076  1.790926  1.352155
gi|3170320  2.073157  2.122944  2.157135  0.656571  0.828876  0.000000
  1.308540  1.463853  1.979154  1.284165
gi|4079259  2.013416  2.072802  2.077586  1.297607  1.223347  1.308540
  0.000000  1.557884  1.707755  1.302945
gi|6716731  2.314664  2.346647  1.922648  1.574023  1.488076  1.463853
  1.557884  0.000000  1.818979  1.611165
gi|9156597  2.242249  2.226902  2.268390  1.910127  1.790926  1.979154
  1.707755  1.818979  0.000000  1.623545
gi|3330461  1.998031  1.965679  2.056180  1.393124  1.352155  1.284165
  1.302945  1.611165  1.623545  0.000000

Go to Mobyl @ Pasteur neighbor and input your distance matrix, and run. This should give you a tree file.

(gi|9187305:0.14764,(gi|6939036:0.76627,((((((gi|3171484:0.33845,
gi|3170320:0.31812):0.10621,gi|4257736:0.35837):0.25741,
gi|4079259:0.60937):0.05381,gi|3330461:0.63876):0.07517,
gi|6716731:0.83368):0.01340,gi|9156597:0.96346):0.53335):0.60631,gi|1904057:0.12591);

To get a visual display of an unrooted tree, go to Mobyl @ Pasteur drawtree, input your tree file, and pess run. You should now have a visual representation of your tree in unrooted format.

Assignment for 10/06/2015

Cn3D 4.3.1 was used to view the structure of my protein of interest. Although the structure of Spo11 does not appear to have been resolved, I found the DNA binding domain of another protein that interests me, hESRR2, has been resolved. I found this my going to the NCBI structure database which found this result.

I used the 1000 genomes browser to look at the landscape of mutations uncovered in Spo11 from the sequencing of 1000 human genomes. The variations table showed a robust dataset of different mutations types.

I checked under phenotypes and found 2 somatic deletions in breast cancer patients.

I can hide messages in your images!

 The biggest thing here is to make your pictures larger so that people can read them. You can manually change the size by editing the number after the .png?. I changed the last picture size to something I could read. Nice use of a table of contents and the separate headings. Also I hid a message in your pictures
b2gof15/students/rpolicas/start.txt · Last modified: 2015/10/08 13:25 by gteeters
 
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