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					Investigating Gene Function
               Investigating Gene Function
You can identify genes of interest in a number of
ways:-

• Microarray analysis
• Proteomic studies
• Cloning

How can you investigate the function
of your sequence of interest?
              Investigating Gene Function
Bioinformatics can help address your
sequence of interests:-

• Genetic function      (Database > KO > Phenotype)

• Biochemical activity
• Subcellular localisation
• Protein structure
• Post-translational modification
                     Investigating AUX1 Gene Function

Using the AtEnsembl Database to find Knockout lines




               Insert your gene code or name
Investigating AUX1 Gene Function
Investigating AUX1 Gene Function
Investigating AUX1 Gene Function
Knock out mutations in AUX1
  disrupt root gravitropism




                       Pin


        WT     aux1
            Investigating Gene Function

Bioinformatics can help address your
sequence’s:-
• Genetic function
• Biochemical activity (Predicted from homology)
• Subcellular localisation
• Protein structure
• Post-translational modifications
                Investigating Protein Function
Examples of some tools that can SUGGEST
your protein’s function:-

• BLAST (search DB for homologous sequences)
• CLUSTAL W (relationships between homologues)
• Pfam   (highlight regions of suggested function)
• SMART
                             Investigating Protein Function
    Sequence of Interest



       BLAST




homologous sequences        (from chosen database)




             Functions of
                                (if known)
             homologues



                            Suggested function of protein of interest
Investigating Protein Function
Using BLAST P
Identifying related sequences
Identifying related sequences
             Generated alignment
For each
homologue:
Obtaining sequence for CLUSTAL W
Obtaining sequence
              Investigating Protein Function


Bioinformatics can help address your
sequence’s protein function using:-
• BLAST P
• CLUSTAL W (relationships between homologues)
• Pfam
• SMART
                            Investigating Protein Function
    Sequence of Interest                                            Seq1: M A R N D C E
                                                                    Seq2: M A L N D C E
                                               Clustal W            Seq3: M A P H H C L
       BLAST                Multiple Alignment            Phylogeny (Tree)


                                     Conserved                Understanding of
homologous sequences                 regions                  relationship
                                                              between
                                                              homologues

                                   Important
             Functions of          regions
             homologues



                            Suggested function of protein of interest
Generating multiple alignments
                Generating multiple alignments

(Scroll Down)
                            Obtaining sequence for CLUSTAL W
From BLAST search (or other source)




                                      Copy and Paste into Word
(MS Word)
            FASTA formatting text
FASTA formatting text
                             FASTA formatting text



msgekqaees   ivvsgedeva   grkvedsaae   edidgnggng   fsmksflwhg   gsawdawfsc
asnqvaqvll   tlpysfsqlg   mlsgillqif   yglmgswtay   lisvlyveyr   armekqeaks
fknhviqwfe   vldgllgpyw   kaaglafnct   fllfgsviql   iacasniyyi   ndrldkrtwt
yifgaccatt   vfipsfhnyr   iwsflglgmt   tytawyltia   sflhgqaegv   thsgptklvl
yftgatnily   tfgghavtve   imhamwkprk   fksiylmatl   yvftltlpsa   savywafgdq
llnhsnafsl   lpktrfrdta   vilmlihqfi   tfgfactply   fvwekaigmh   htkslclral
vrlpvvvpiw   flaiifpffg   pinsavgall   vtftvyiipa   lahmltyrta   sarrnaaekp
pffipswagv   yvinafivvw   vlvlgfgfgg   wasmtnfirq   idtfglfakc   yqckpppapi
aagahhrr
                         FASTA formatting text
>aux1
MSEGVEAIVANDNGTDQVNGNRTGKDNEEHDGSTGSNLSNFLWHGGSVWDAWFSCASNQVAQVLL
TLPYSFSQLGMLSGIVLQIFYGLLGSWTAYLISVLYVEYRARKEKEGKSFKNHVIQWFEVLDGLL
GSYWKALGLAFNCTFLLFGSVIQLIACASNIYYINDHLDKRTWTYIFGACCATTVFIPSFHNYRI
WSFLGLGMTTYTAWYLAIASIIHGQAEGVKHSGPTKLVLYFTGATNILYTFGGHAVTVEIMHAMW
KPQKFKYIYLMATLYVFTLTIPSAAAVYWAFGDALLDHSNAFSLMPKNAWRDAAVILMLIHQFIT
FGFACTPLYFVWEKVIGMHDTKSICLRALARLPVVIPIWFLAIIFPFFGPINSAVGALLVSFTVY
IIPSLAHMLTYRSASARQNAAEKPPFFMPSWTAMYVLNAFVVVWVLIVGFGFGGWASVTNFVRQV
DTFGLFAKCYQCKPAAAAAHAPVSALHHRL
>lax1
msgekqaees ivvsgedeva grkvedsaae edidgnggng fsmksflwhg gsawdawfsc
asnqvaqvll tlpysfsqlg mlsgillqif yglmgswtay lisvlyveyr armekqeaks
fknhviqwfe vldgllgpyw kaaglafnct fllfgsviql iacasniyyi ndrldkrtwt
yifgaccatt vfipsfhnyr iwsflglgmt tytawyltia sflhgqaegv thsgptklvl
yftgatnily tfgghavtve imhamwkprk fksiylmatl yvftltlpsa savywafgdq
llnhsnafsl lpktrfrdta vilmlihqfi tfgfactply fvwekaigmh htkslclral
vrlpvvvpiw flaiifpffg pinsavgall vtftvyiipa lahmltyrta sarrnaaekp
pffipswagv yvinafivvw vlvlgfgfgg wasmtnfirq idtfglfakc yqckpppapi
aagahhrr
>lax2
                Generating multiple alignments

(Scroll Down)
Generating multiple alignments
Generating multiple alignments




                        Inclusion of a
                        known outlier


More likely root
                       AUX1 belongs to the auxin-amino acid
                            permease (AAAP) family
                                ANT1

                                              ANT2


                     LAX3
       LAX2                                            ANT3


    LAX1
                                                                                                     OH
      AUX1

                                                                                                 O
                                                                                   N
                                                                AtSUC1




                                                                         Indole-3-acetic acid
                                                                                (IAA)
              AAP4

              AAP2

               AAP3
                                                     LHT1

                      AAP5             AAP1
1                            AAP6
                                                       Bennett et al (1996) Science, 273, 948;
                                                                                                                  Generating multiple alignments
1     M   S   -   -   -   E   G   V   E   A   I   V   A   N   D   N   G   T   D   Q   V   N   G   N   R   T   G   K   D   N   E   E   H   D   -   -   -   -   G   S   T   G   S   N   L   S   N   F   L   W   AUX1.pro
1     M   S   G   E   K   Q   A   E   E   S   I   V   V   S   -   -   G   E   D   E   V   A   G   R   K   V   E   D   S   A   A   E   E   D   I   D   G   N   G   G   N   G   F   S   M   K   S   F   L   W   LAX1.pro
1     M   E   N   G   E   K   A   A   E   T   V   V   V   G   N   Y   V   E   M   E   K   D   G   K   A   L   D   -   -   -   -   -   -   -   -   -   -   -   -   -   I   K   S   K   L   S   D   M   F   W   LAX2.pro
1     M   A   -   A   E   K   I   -   E   T   V   V   A   G   N   Y   L   E   M   E   R   E   E   E   N   I   S   G   N   K   -   -   -   -   -   -   -   K   S   S   T   K   T   K   L   S   N   F   F   W   LAX3.pro
1     M   K   S   F   N   T   E   G   H   N   H   S   T   A   E   -   -   -   -   -   -   S   G   D   A   Y   T   V   S   D   P   T   K   N   V   D   E   D   G   R   E   K   R   T   -   -   -   -   -   -   AAP1.pro

44    H   G   G   S   V   W   D   A   W   F   S   C   A   S   N   Q   V   A   Q   V   L   -   -   -   -   L   T   L   P   Y   S   F   S   Q   L   G   M   L   S   G   I   V   L   Q   I   F   Y   G   L   L   AUX1.pro
49    H   G   G   S   A   W   D   A   W   F   S   C   A   S   N   Q   V   A   Q   V   L   -   -   -   -   L   T   L   P   Y   S   F   S   Q   L   G   M   L   S   G   I   L   L   Q   I   F   Y   G   L   M   LAX1.pro
38    H   G   G   S   A   Y   D   A   W   F   S   C   A   S   N   Q   V   A   Q   V   L   -   -   -   -   L   T   L   P   Y   S   F   S   Q   L   G   M   L   S   G   I   L   F   Q   L   F   Y   G   I   L   LAX2.pro
42    H   G   G   S   V   Y   D   A   W   F   S   C   A   S   N   Q   V   A   Q   V   L   -   -   -   -   L   T   L   P   Y   S   F   S   Q   L   G   M   M   S   G   I   L   F   Q   L   F   Y   G   L   M   LAX3.pro
39    -   -   -   -   -   -   G   T   W   L   T   A   S   A   H   I   I   T   A   V   I   G   S   G   V   L   S   L   A   W   A   I   A   Q   L   G   W   I   A   G   T   S   I   L   L   I   F   S   F   I   AAP1.pro

90
95
      G
      G
          S
          S
              W
              W
                  T
                  T
                      A
                      A
                          Y
                          Y
                              L
                              L
                                  I
                                  I
                                      S
                                      S
                                          V
                                          V
                                              L
                                              L
                                                  Y
                                                  Y
                                                      V
                                                      V
                                                          E
                                                          E
                                                              -
                                                              -
                                                                  Y
                                                                  Y
                                                                      R
                                                                      R
                                                                          A
                                                                          A
                                                                              R
                                                                              R
                                                                                  K
                                                                                  M
                                                                                      E
                                                                                      E
                                                                                          K
                                                                                          K
                                                                                              -
                                                                                              Q
                                                                                                  E
                                                                                                  E
                                                                                                      G
                                                                                                      A
                                                                                                          K
                                                                                                          K
                                                                                                              S
                                                                                                              S
                                                                                                                  F
                                                                                                                  F
                                                                                                                      K
                                                                                                                      K
                                                                                                                          N
                                                                                                                          N
                                                                                                                              H
                                                                                                                              H
                                                                                                                                  V
                                                                                                                                  V
                                                                                                                                      I
                                                                                                                                      I
                                                                                                                                          Q
                                                                                                                                          Q
                                                                                                                                              W
                                                                                                                                              W
                                                                                                                                                  F
                                                                                                                                                  F
                                                                                                                                                      E
                                                                                                                                                      E
                                                                                                                                                          V
                                                                                                                                                          V
                                                                                                                                                              L
                                                                                                                                                              L
                                                                                                                                                                  D
                                                                                                                                                                  D
                                                                                                                                                                      G
                                                                                                                                                                      G
                                                                                                                                                                          L
                                                                                                                                                                          L
                                                                                                                                                                              L
                                                                                                                                                                              L
                                                                                                                                                                                  G
                                                                                                                                                                                  G
                                                                                                                                                                                      S
                                                                                                                                                                                      P
                                                                                                                                                                                          Y
                                                                                                                                                                                          Y
                                                                                                                                                                                              W
                                                                                                                                                                                              W
                                                                                                                                                                                                  K
                                                                                                                                                                                                  K
                                                                                                                                                                                                      A
                                                                                                                                                                                                      A
                                                                                                                                                                                                          L
                                                                                                                                                                                                          A       If point mutations (shaded) occur at
                                                                                                                                                                                                              AUX1.pro
                                                                                                                                                                                                              LAX1.pro
84    G   S   W   T   A   Y   L   I   S   I   L   Y   V   E   -   Y   R   T   R   K   E   R   -   E   K   V   N   F   R   N   H   V   I   Q   W   F   E   V   L   D   G   L   L   G   K   H   W   R   N   V   LAX2.pro
88
83
      G
      -
          S
          -
              W
              -
                  T
                  -
                      A
                      T
                          Y
                          Y
                              L
                              F
                                  I
                                  T
                                      S
                                      S
                                          V
                                          T
                                              L
                                              M
                                                  Y
                                                  L
                                                      V
                                                      A
                                                          E
                                                          D
                                                              -
                                                              C
                                                                  Y
                                                                  Y
                                                                      R
                                                                      R
                                                                          T
                                                                          A
                                                                              R
                                                                              P
                                                                                  K
                                                                                  D
                                                                                      E
                                                                                      P
                                                                                          R
                                                                                          V
                                                                                              -
                                                                                              T
                                                                                                  E
                                                                                                  G
                                                                                                      K
                                                                                                      K
                                                                                                          F
                                                                                                          R
                                                                                                              D
                                                                                                              N
                                                                                                                  F
                                                                                                                  Y
                                                                                                                      R
                                                                                                                      T
                                                                                                                          N
                                                                                                                          -
                                                                                                                              H
                                                                                                                              -
                                                                                                                                  V
                                                                                                                                  -
                                                                                                                                      I
                                                                                                                                      -
                                                                                                                                          Q
                                                                                                                                          -
                                                                                                                                              W
                                                                                                                                              Y
                                                                                                                                                  F
                                                                                                                                                  M
                                                                                                                                                      E
                                                                                                                                                      D
                                                                                                                                                          V
                                                                                                                                                          V
                                                                                                                                                              L
                                                                                                                                                              V
                                                                                                                                                                  D
                                                                                                                                                                  R
                                                                                                                                                                      G
                                                                                                                                                                      S
                                                                                                                                                                          L
                                                                                                                                                                          Y
                                                                                                                                                                              L
                                                                                                                                                                              L
                                                                                                                                                                                  G
                                                                                                                                                                                  G
                                                                                                                                                                                      K
                                                                                                                                                                                      G
                                                                                                                                                                                          H
                                                                                                                                                                                          -
                                                                                                                                                                                              W
                                                                                                                                                                                              -
                                                                                                                                                                                                  R
                                                                                                                                                                                                  R
                                                                                                                                                                                                      N
                                                                                                                                                                                                      K
                                                                                                                                                                                                          L
                                                                                                                                                                                                          V
                                                                                                                                                                                                                  conserved loci (boxed) they are likely to
                                                                                                                                                                                                              LAX3.pro
                                                                                                                                                                                                              AAP1.pro

138   G   L   A   F   N   C   T   F   L   L   F   G   S   V   I   Q   -   -   -   -   -   -   -   -   -   -   -   -   L   I   A   C   A   S   N   I   Y   Y   I   N   D   H   L   D   K   -   -   -   -   R       be cause more severe phenotypes
                                                                                                                                                                                                              AUX1.pro
144   G   L   A   F   N   C   T   F   L   L   F   G   S   V   I   Q   -   -   -   -   -   -   -   -   -   -   -   -   L   I   A   C   A   S   N   I   Y   Y   I   N   D   R   L   D   K   -   -   -   -   R   LAX1.pro
132   G   L   A   F   N   C   T   F   L   L   F   G   S   V   I   Q   -   -   -   -   -   -   -   -   -   -   -   -   L   I   A   C   A   S   N   I   Y   Y   I   N   D   N   L   D   K   -   -   -   -   R   LAX2.pro
136   G   L   I   F   N   C   T   F   L   L   F   G   S   V   I   Q   -   -   -   -   -   -   -   -   -   -   -   -   L   I   A   C   A   S   N   I   Y   Y   I   N   D   K   L   D   K   -   -   -   -   R   LAX3.pro
122   Q   L   -   -   -   C   G   V   A   Q   Y   G   N   L   I   G   V   T   V   G   Y   T   I   T   A   S   I   S   L   V   A   V   G   K   S   N   C   F   H   D   K   G   H   T   A   D   C   T   I   S
                                                                                                                                                                                                                  This can aid structure-function studies
                                                                                                                                                                                                              AAP1.pro

172   T   W   T   Y   -   -   I   F   G   A   C   C   A   T   T   V   F   I   P   S   F   H   N   Y   R   I   W   S   F   L   G   L   G   M   T   -   T   Y   T   A   W   Y   -   -   L   A   I   A   S   I   AUX1.pro
178   T   W   T   Y   -   -   I   F   G   A   C   C   A   T   T   V   F   I   P   S   F   H   N   Y   R   I   W   S   F   L   G   L   G   M   T   -   T   Y   T   A   W   Y   -   -   L   T   I   A   S   F   LAX1.pro
166   T   W   T   Y   -   -   I   F   G   A   C   C   A   T   T   V   F   I   P   S   F   H   N   Y   R   I   W   S   F   L   G   L   L   M   T   -   T   Y   T   A   W   Y   -   -   L   T   I   A   S   I   LAX2.pro
170   T   W   T   Y   -   -   I   F   G   A   C   C   A   T   T   V   F   I   P   S   F   H   N   Y   R   I   W   S   F   L   G   L   A   M   T   -   T   Y   T   S   W   Y   -   -   L   T   I   A   S   L   LAX3.pro
169   N   Y   P   Y   M   A   V   F   G   I   I   Q   V   I   L   S   Q   I   P   N   F   H   K   L   S   F   L   S   I   M   A   A   V   M   S   F   T   Y   A   T   I   G   I   G   L   A   I   A   T   V   AAP1.pro

217   -   -   -   -   -   -   -   -   -   I   H   G   Q   A   E   G   V   K   H   S   G   P   T   K   L   V   L   Y   F   T   G   A   T   N   I   L   Y   T   F   G   G   H   A   V   T   V   E   I   M   H   AUX1.pro
223   -   -   -   -   -   -   -   -   -   L   H   G   Q   A   E   G   V   T   H   S   G   P   T   K   L   V   L   Y   F   T   G   A   T   N   I   L   Y   T   F   G   G   H   A   V   T   V   E   I   M   H   LAX1.pro
211   -   -   -   -   -   -   -   -   -   L   H   G   Q   V   E   G   V   K   H   S   G   P   S   K   L   V   L   Y   F   T   G   A   T   N   I   L   Y   T   F   G   G   H   A   V   T   V   E   I   M   H   LAX2.pro
215   -   -   -   -   -   -   -   -   -   L   H   G   Q   A   E   D   V   K   H   S   G   P   T   T   M   V   L   Y   F   T   G   A   T   N   I   L   Y   T   F   G   G   H   A   V   T   V   E   I   M   H   LAX3.pro
219   A   G   G   K   V   G   K   T   S   M   T   G   T   A   V   G   V   D   V   T   A   A   Q   K   I   W   R   S   F   Q   A   V   G   Y   I   A   F   A   Y   A   Y   A   T   V   L   I   E   I   Q   D   AAP1.pro

258   A   M   W   K   P   -   -   -   -   Q   K   F   K   Y   I   Y   L   M   A   T   L   Y   V   F   T   L   T   I   P   S   A   A   A   V   Y   W   A   F   G   D   A   -   -   -   -   L   L   D   H   S   AUX1.pro
264   A   M   W   K   P   -   -   -   -   R   K   F   K   S   I   Y   L   M   A   T   L   Y   V   F   T   L   T   L   P   S   A   S   A   V   Y   W   A   F   G   D   Q   -   -   -   -   L   L   N   H   S   LAX1.pro
252   A   M   W   K   P   -   -   -   -   Q   K   F   K   S   I   Y   L   F   A   T   L   Y   V   L   T   L   T   L   P   S   A   S   A   V   Y   W   A   F   G   D   L   -   -   -   -   L   L   N   H   S   LAX2.pro
256   A   M   W   K   P   -   -   -   -   Q   K   F   K   A   I   Y   L   L   A   T   I   Y   V   L   T   L   T   L   P   S   A   S   A   V   Y   W   A   F   G   D   K   -   -   -   -   L   L   T   H   S   LAX3.pro
269   T   L   R   S   S   P   A   E   N   K   A   M   K   R   A   S   L   V   G   V   S   T   T   T   F   F   Y   I   L   C   G   C   I   G   Y   A   A   F   G   N   N   A   P   G   D   F   L   T   D   F   AAP1.pro

300   N   A   F   S   L   M   P   K   N   A   W   R   D   A   A   V   I   L   M   L   I   H   Q   F   I   T   F   G   F   A   C   T   P   L   Y   -   F   V   W   E   K   V   I   G   M   H   D   T   K   S   AUX1.pro
306   N   A   F   S   L   L   P   K   T   R   F   R   D   T   A   V   I   L   M   L   I   H   Q   F   I   T   F   G   F   A   C   T   P   L   Y   -   F   V   W   E   K   A   I   G   M   H   H   T   K   S   LAX1.pro
294   N   A   F   A   L   L   P   K   N   L   Y   R   D   F   A   V   V   L   M   L   I   H   Q   F   I   T   F   G   F   A   C   T   P   L   Y   -   F   V   W   E   K   L   I   G   M   H   E   C   R   S   LAX2.pro
298   N   A   L   S   L   L   P   K   T   G   F   R   D   T   A   V   I   L   M   L   I   H   Q   F   I   T   F   G   F   A   S   T   P   L   Y   -   F   V   W   E   K   L   I   G   V   H   E   T   K   S   LAX3.pro
319   G   F   F   E   P   F   W   L   I   D   F   A   N   A   C   I   A   V   H   L   I   G   A   Y   Q   V   F   A   -   -   -   Q   P   I   F   Q   F   V   -   -   -   -   -   -   -   -   -   -   E   K   AAP1.pro

349   I   C   L   R   A   L   A   R   L   P   V   V   I   P   I   W   F   L   A   I   I   F   P   F   F   G   P   I   N   S   A   V   G   A   L   L   V   S   F   T   V   Y   I   I   P   S   L   A   H   M   AUX1.pro
355   L   C   L   R   A   L   V   R   L   P   V   V   V   P   I   W   F   L   A   I   I   F   P   F   F   G   P   I   N   S   A   V   G   A   L   L   V   T   F   T   V   Y   I   I   P   A   L   A   H   M   LAX1.pro
343
347
      M
      M
          C
          F
              K
              K
                  R
                  R
                      A
                      A
                          A
                          M
                              A
                              A
                                  R
                                  R
                                      L
                                      L
                                          P
                                          P
                                              V
                                              V
                                                  V
                                                  V
                                                      I
                                                      V
                                                          (This alignment was generated with DNAstar not CLustalW)
                                                          P
                                                          P
                                                              I
                                                              I
                                                                  W
                                                                  W
                                                                      F
                                                                      F
                                                                          L
                                                                          L
                                                                              A
                                                                              A
                                                                                  I
                                                                                  I
                                                                                      I
                                                                                      I
                                                                                          F
                                                                                          F
                                                                                              P
                                                                                              P
                                                                                                  F
                                                                                                  F
                                                                                                      F
                                                                                                      F
                                                                                                          G
                                                                                                          G
                                                                                                              P
                                                                                                              P
                                                                                                                  I
                                                                                                                  I
                                                                                                                      N
                                                                                                                      N
                                                                                                                          S
                                                                                                                          S
                                                                                                                              T
                                                                                                                              A
                                                                                                                                  V
                                                                                                                                  V
                                                                                                                                      G
                                                                                                                                      G
                                                                                                                                          S
                                                                                                                                          S
                                                                                                                                              L
                                                                                                                                              L
                                                                                                                                                  L
                                                                                                                                                  L
                                                                                                                                                      V
                                                                                                                                                      V
                                                                                                                                                          S
                                                                                                                                                          S
                                                                                                                                                              F
                                                                                                                                                              F
                                                                                                                                                                  T
                                                                                                                                                                  T
                                                                                                                                                                      V
                                                                                                                                                                      V
                                                                                                                                                                          Y
                                                                                                                                                                          Y
                                                                                                                                                                              I
                                                                                                                                                                              I
                                                                                                                                                                                  I
                                                                                                                                                                                  I
                                                                                                                                                                                      P
                                                                                                                                                                                      P
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                                                                                                                                                                                                  A
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                                                                                                                                                                                                      H
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                                                                                                                                                                                                          I
                                                                                                                                                                                                          M
                                                                                                                                                                                                              LAX2.pro
                                                                                                                                                                                                              LAX3.pro
356   K   C   N   R   N   Y   P   D   N   K   F   I   T   S   E   Y   S   V   N   V   -   -   P   F   L   G   K   F   N   I   S   L   F   R   L   -   V   W   R   T   A   Y   V   V   I   T   T   V   V   A   AAP1.pro
                 Investigating Protein Function

Bioinformatics can help address your
sequence’s protein function using:-
• BLAST P
• CLUSTAL W
• Pfam
           (highlight regions of suggested function)
• SMART
                            Investigating Protein Function
    Sequence of Interest                                                     SMART

                                             Clustal W
       BLAST                Multiple Alignment      Phylogeny (Tree)


                                   Conserved             Understanding of
homologous sequences               regions               relationship
                                                         between
                                                         homologues

                                 Important
             Functions of        regions                                    Suggested
             homologues                                                     functions of
                                                                            regions
                   Predicted structure
                          Suggested function of protein of interest
                   regions conserved within families
                   regions with biochemical properties
                   signal peptides for localisation
Investigating Protein Function
Investigating Protein Function
              Investigating Gene Function


Bioinformatics can help address your
sequence’s:-
• Genetic function
• Biochemical activity
• Subcellular localisation
• Protein structure
• Post-translational modifications
Investigating localisation
        Investigating Protein Localisation



                     Transgenic Arabidopsis Roots
                     Showing:

                     Co-localisation
A   B           C    of
                     YFP tagged AUX1
                     and
                     GFP tagged membrane marker

                     I.E. AUX1 localises to membranes

                     BIOINFORMATICS ONLY
D   E            F   GUIDES YOUR ENQUIRIES.
               Investigating Gene Function

Bioinformatics can help address your
sequence’s:-
• Genetic function
• Biochemical activity
• Subcellular localisation
• Protein structure       Eg TM helix prediction


• Post-translational modifications
Modelling Protein Structure
Modelling Protein Structure
Modelling Protein Structure




              Predicts 10 TM regions
             Practical Lab Work shows that:
AUX1 contains 11 membrane spanning domains
               Investigating Gene Function


Bioinformatics can help address your
sequence’s:-
• Genetic function
• Biochemical activity
• Subcellular localisation
• Protein structure
• Post-translational modifications
Post-translational modifications
Post-translational modifications
Post-translational modifications
           Investigating Gene Function

Bioinformatics can help address your
sequence’s:-
• Genetic function
•Biochemical activity
• Subcellular localisation
• Protein structure
• Promoter Analysis
                                 Promoter Analysis
Can search for known transcription factor binding sites in a sequence, e.g TRES
                      Promoter Analysis
Paste promoter sequences (can be obtained from AtEnsembl)
Promoter Analysis
           Investigating Gene Function

Bioinformatics can help address your
sequence’s:-
• Genetic function
• Biochemical activity
• Subcellular localisation
• Protein structure
• Post-translational modifications

				
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posted:10/2/2012
language:English
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