Finding protein motifs by running sequence analysis in protein BLAST

Question

I've run the following sequence (bottom of page) in NCBI protein BLAST and its been identified as Zn-dependent alcohol dehydrogenase. Next I want to see what protein motifs are in this protein. Where in the programme is it possible to see the motifs?

Thanks in advance!

Sequence:

MDRNRLAIVFPIFARCISAADFSTDLYLSEIYQQKVVTMKAAVITKDHTIDVKDTKLRPLNYGEALLEIE YCGVCHTDLHVKNGDFGDETGRISGHEGIGIVKQDGEGVTSLNAGDRASVAWFFKGCGHCEYCVSGNETL CRNVENAGYTVDGAIAEECIVVAEYSVRVPDGLDPAVASRITCAGVTTYKAVKVSQLQPGQWLAIYGYGR FRQSSPSICQDMYFNAKDEQLAYYAKELGGADMVINPKNEAAKIIQEKLGGAHATVVTAVAKSAFNSAVE AIRAGGRVVVVVAVGLPPPEKMDLSIPPRLVLVGIEVLGSLVGTREKEAFQFAAEGKVKPKVTKRKVEEI NQIFDEMEHGKFTGRMILPTHHIWIVIGWQSFSLYSQDVSQPQIFRLTSISPRYINKRSPKQPSLLKIIR STKTPNYALITGKRFWKSNIAGYVIPISMKTGISAMKPAEFQGMKVVSSSRTGKGLLLMPVTAPVLHGSS KAAAIANIVSAGMKRFAATLKMPVIRLTALQKNASSSPNTRSACQMVLILRLPAGSLARVPPIKQRFLSY SPDNGWPSMATGGLGNLALRYAKTCISTPKMNSSHTTPKSWAAQIWSSIRKTKLPKSFRKSSGEHTRRWR LLPNPPLTRLLRLSARVAVLLLLSPLVCLLLKKWIAFLLVWCLSVSKSVPWSERGKRRPSSLQPKVRSSR KLPSVKSKKSTKSLTKWNMVNSQAVYYQPITYGSSAGNRFPYIRKMYLSRRFFDPLSLRDISTKGSHHES SRHYRSYDRRERHQITPSELRGSASGNRILRGMSYRSPCEKRGFRRNRQNFRARYRYRQAGRGRGYFSEC RPRQCCMVLQRLRPLRILCQRENALPQRKCRLYGRRYSRRMHRRRRILGPRARWSSCGCQQDHLRGCNHL SSKGFSATARTMAGHLWLRAVAIPFDMETPRHVFQRQRTARILRQRVGRRRYGHQSEKRSCQNHSGKARG STRDGGDGCCQIRLLGCGYPRGWPCCCCCRRWSASSKNGFEHSSSFGACRYRSPRFLGRNAGKGGLPVCS RRGQAESYQASRRNQPNLRNGTWIHRPYDITNPSHILYVMGWYHTACEFTMFHFVKDLVDFFDFTLGNFR LDLTFGCKLEGLLFPRSDQGTDFDTDKHQTRRNAQIHFFRRRQTNGDNNNNTATRADSLNSRVKGGFGNS RHHRRVCSPELFLNDFGSFVFRIDDHICAAQLFGVVCELFIFGVEIHVLAYRRARLPKPPVAIDGQPLSG LLRNLYCFIGGYTRASDPAGNRRIKTIWHADRVFGDDDAFFCYSAVNRITGIFNVAAKRFIPADTIFAMA AAFEEPCNTGAVTGIQRSNPFPVLLDDTYTFMPNSAGFIAEIPVFHMEIGMTYPAIFDFQKRFPVIQRAF GVFHVDRMIFSNDGCFHGDYLLLIYLGEIEVSRKICGDTSCEYRENDCQPITIHYMWVGNIIRPVNLPCS ISSKIWLISSTLRLVTFGLTLPSAANWKASFSRVPTKEPRTSIPTSTKRGGMLKSIFSGGGRPTATTTTT RPPARIASTAELKADLATAVTTVACAPPSFSMILAASFFGLMTISAPPNSLAYASCSSLALKYMSWHIEG LDCLNRPPMASHCPGCSETFTALVVTPAQVILLATAGSRPSGTRTEYSATTMHSSAIAPSTVPAFSTLRQ SVSFPLTQYSQWPQPLKNHATLARSPAFREVTPSPSCLTIPIPSCPEILPVSSPKSPFFTWRSVHTPQYS ISRSASPFRGRNLVSFTSIVSLVMTAAFMVTTFCYISERRSVEKSAAEIHLANIGKTIASRLRSICDGLV ISYGLIYHVPFRQRFGFLRLYAWLSAPYLRLQTGRPPFPAFRPRNLGLRYRQAPNEEECSNPFFQEEADQ RRQQQQHGHPRGPQQPSRRIWQQPSPPSRVLPRAFPEFWQLRFSDPYLRRPTLWRSMRAVHLWRNTCLGI SKGIATARSHRWPAIVRAVAEKPLLLYRWLHPRKSCWQPQDQDHLARGPSIRRRRCILLLRRQPYNRHFQ RCGKAFHSRHNIRNGRSLRTMQHWRGHRHSEKPLPRPARYLYLHALKFCRFHRRNPRFSHGDRYDIPRNI RFPEALPRNSEGVIWCLSRRSYDLRLLSWLPFVDISRRDRGQSKNLRLRYILRIGKRLPADYDP

Answer 1

MOTIF search
First of all this is not possbile in BLAST (at least nog direclty). There are a lot of tools to search for motifs in your sequence. I think a good way to start is to use MOTIF search. This searches for motifs in your sequence based on infomration in: Pfam, NCBI-CDD, PROSTIE PATTERN and PROSITE PROFILE (you can select which of these you want to use). Further you can also use INTERPRO (which also searches through serveral database, note that INTERPO searching can take a while but will give a nice graphical view). If you want to find new motifs you can use MEME (as suggest by @mxwsn). However to do this you have to find (or have) a set of sequences which resemble your seqence to find motifs. Because off course the algorithm is not able to find motifs in one sequence because it needs to compare a set of sequences to find some frequently occuring motifs, which could be of your interest.
So to summarize you can use MOTIF search (or INTERPRO etc...) to find motifs in your sequence which are already known. Or gather a set of sequences and find new motifs in them using MEME or a similair tool.

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However, how did you conclude that your sequence is a Zn-dependent alcohol dehydrogenase? Because BLASTing the sequence you provided will give matches with this enzyme but only covering ~17%. Nonetheless a good way to find information about your sequence is indeed to find motifs and compare the sequence with HMM's or PSSM's of known proteins. For example MOTIF search will give these results:

PROSITE:
    Zinc-containing alcohol dehydrogenases signature.
PFAM:
    Zinc-binding dehydrogenase
    Alcohol dehydrogenase GroES-like domain
AND A LOT MORE>>>

Searching PFAM will give you this:

Notice that the second domain (Zinc-binding dehydrogenase) is not completely present, more information can be seen in the detail overview:

I would advice to also take a look at how important these "missing" residu's are (e.g. using a MSA and look at conservation). Because your sequence could contain these domains but that does not necessarily mean that this IS A Zn-dependent alcohol dehydrogenase. It could be non-functional for example.

Answer 2

To find de novo motifs present in your protein sequences, you should use MEME or some other motif-finding tool instead of BLAST.

MEME discovers novel, ungapped motifs (recurring, fixed-length patterns) in your sequences.