Bonjour,

Nous avons un problème pour classer notre séquence dans une catégorie.
Notre séquence à de fortes homologies avec des alpha-protéo et des eucaryotes. De plus, le domaine protéique est:"Stabilizer of iron transporter SufD", impliqué dans le transport du fer. On s'attend donc à retrouver notre séquence dans des bactéries à l'origine de mitochondries ou chloroplaste.

Notre arbre avec la méthode parcimonie est abhérent (arbre a). Notre arbre par NJ (arbre b) nous donne la séquence dans les CFB bactéries.
Nous avons suivi les conseils de madame Brochier, nous avons fait des arbres non racinés avec plus de séquences de bactéries ( arbre c par parcimonie et arbre d par NJ). Ils sont totalement incohérents.
Monsieur Hingamp nous a dit de faire un arbre avec la méthode phyML qui donne encore quelque chose de différent: elle est proche des alpha-protéo (arbre e).
Madame Brochier nous a dit qu'elle connaissait cette séquence, pourriez-vous nous donner des pistes de recherches pour nous éclairer???

Merci

arbre a

  a)                                                                           +------Fbacterium2    [CFB group bacteria]
                                                                        +--1.0-|
                                                                 +--1.0-|      +------Fbacterium1   [CFB group bacteria]
                                                                 |      |
                                                          +--1.0-|      +-------------tenacibaculum    [CFB group bacteria]
                                                          |      |
                                                          |      |      +-------------Aproteobact    [a-proteobacteria]
                                                          |      +--1.0-|
                                                          |             |      +------Fpelagi    [a-proteobacteria]
                                                          |             +--1.0-|
                                                   +--0.8-|                    +------Msilvestris    [a-proteobacteria]
                                                   |      |
                                                   |      |                    +------Kpneumoniae    [enterobacteria]
                                                   |      |             +--1.0-|
                                                   |      |      +--1.0-|      +------Ecoli     [enterobacteria]
                                            +--0.8-|      |      |      |
                                            |      |      +--0.8-|      +-------------salmonallaT     [enterobacteria]
                                            |      |             |
                                            |      |             +--------------------Xfastidiosa    [g-proteobacteria]
                                     +--0.5-|      |
                                     |      |      |                           +------CAPgenomovar   [CFB group bacteria]
                                     |      |      +-----------------------1.0-|
                                     |      |                                  +------Bfragilis    [CFB group bacteria]
                                     |      |
                              +--0.8-|      +-----------------------------------------Cburnetii    [g-proteobacteria]
                              |      |
                              |      |                                         +------synechococcus    [cyanobacteria]
                              |      |                           +---------1.0-|
                              |      |                           |             +------Pmarinus    [cyanobacteria]
                              |      +-----------------------1.0-|
                       +--0.8-|                                  |             +------Npunctiforme    [cyanobacteria]
                       |      |                                  |      +--1.0-|
                       |      |                                  +--1.0-|      +------Maeruginosa    [cyanobacteria]
                       |      |                                         |
                +--1.0-|      |                                         +-------------synechocystis    [cyanobacteria]
                |      |      |
                |      |      +-------------------------------------------------------polaromonas    [b-proteobacteria]
         +--1.0-|      |
         |      |      +--------------------------------------------------------------Bthailandensis    [b-proteobacteria]
         |      |
         |      |                                                              +------Tpendens    [crenarchaeotes]
  +------|      +----------------------------------------------------------0.8-|
  |      |                                                                     +------Npharaonis    [euryarchaeotes]
  |      |
  |      |                                                                     +------Mmaripaludis    [euryarchaeotes]
  |      +-----------------------------------------------------------------1.0-|
  |                                                                            +------SEQinconnue
  |
  +-----------------------------------------------------------------------------------Aboonei    [euryarchaeotes]


arbre b

                   +-----------Tpendens     [crenarchaeotes]  
                   !
                   !                   +Ecoli    [enterobacteria]    
                   !                 +-4
                   !          +------5 +Kpneumoniae     [enterobacteria]    
               +---3          !      !
               !   !          !      +-salmonallaT   [enterobacteria]  
               !   !          !  
               !   !          !          +SEQinconnue    
               !   !          !        +-6
               !   !          !     +--7 +-Fbacterium2    [CFB group bacteria]  
               !   +---------13     !  !
               !              !  +-10  +-Fbacterium1     [CFB group bacteria]  
               !              !  !  !  
               !              !  !  +---tenacibaculum     [CFB group bacteria]  
               !              !  !  
               !              !  !        +----Fpelagi  [a-proteobacteria]
    
               !              +-17     +-14  
               !                 !  +-15  +---Msilvestris   [a-proteobacteria]
    
               !                 !  !  !  
               !                 !  !  +----Aproteobact     [a-proteobacteria]
    
               !                 !  !  
               !                 !  !     +------Xfastidiosa    [g-proteobacteria]    
               !                 +-19  +-16  
  +------------2                    !  !  +------Bthailandensis     [b-proteobacteria]
    
  !            !                    !  !  
  !            !                    !  !             +-synechocystis    [cyanobacteria]    
  !            !                    !  !           +-9
  !            !                    +-20        +-11 +--Maeruginosa    [cyanobacteria]    
  !            !                       !        !  !  
  !            !                       !     +-12  +--Npunctiforme     [cyanobacteria]  
  !            !                       !     !  !  
  !            !                       !  +-18  +----synechococcus     [cyanobacteria]  
  !            !                       !  !  !  
  !            !                       +-21  +----Pmarinus      [cyanobacteria]
  !            !                          !  
  !            !                          !  +----Cburnetii     [g-proteobacteria]  
  !            !                          +-22  
  !            !                             !  +----polaromonas     [b-proteobacteria]
  
  !            !                             +-23  
  !            !                                !  +--Bfragilis    [CFB group bacteria]    
  !            !                                +--8
  !            !                                   +----------------CAPgenomovar    [CFB group bacteria]    
  !            !
  !            +---------------Npharaonis    [euryarchaeotes]    
  !
  1------------------------Aboonei   [euryarchaeotes]  
  !
  +---------------------------------------------------------Mmaripaludis    [euryarchaeotes]    


arbre c

        +-----------------------------------------------------SEQinconnue    
        |  
        |  +--------------------------------------------------Fjohnsoniae   [CFB group bacteria]
        |  |  
        |  |                                               +--Rhizobium    [a-proteobacteria]
     +-15  |                                         +----12  
     |  |  |                                         |     +--Mchloromethanicum    [a-proteobacteria]
     |  |  |                                   +----11  
     |  |  |                                   |     |     +--Roseobacter    [a-proteobacteria]
     |  |  |                                   |     +----13  
     |  +-14  +-------------------------------10           +--Gdiazotrophicus    [a-proteobacteria]
     |     |  |                                |  
     |     |  |                                |           +--Rrubrum    [a-proteobacteria]
     |     |  |                                +-----------9  
     |     |  |                                            +--Aproteo     [a-proteobacteria]
     |     |  |  
     |     |  |                                   +-----------CBlochmanniafloridanus    [enterobacteria]
     |     |  |                                +-20  
     |     |  |                                |  |  +--------Pluminescens    [enterobacteria]
     |     +--8                                |  +-19  
     |        |                                |     |  +-----Kpneunomonia    [enterobacteria]
  +--2        |                             +-16     +-18  
  |  |        |                             |  |        |  +--Ealbertii    [enterobacteria]
  |  |        |                             |  |        +-17  
  |  |        |                 +-----------7  |           +--Ecoli    [enterobacteria]
  |  |        |                 |           |  |  
  |  |        |                 |           |  +--------------Lyngbya     [cyanobacteria]
  |  |        |                 |           |  
  |  |        +-----------------6           +-----------------Bplebeius     [CFB group bacteria]
  |  |                          |  
  1  |                          |                          +--Gviolaceus   [cyanobacteria]  
  |  |                          |                    +-----5  
  |  |                          |                    |     +--Noceani     [g-proteobacteria]
  |  |                          +--------------------4  
  |  |                                               |     +--Saurantiaca     [d-proteobacteria]
  |  |                                               +-----3  
  |  |                                                     +--Anaeromyxobacter     [d-proteobacteria]
  |  |  
  |  +--------------------------------------------------------Marinomas     [g-proteobacteria]
  |  
  +-----------------------------------------------------------Cjaponicus     [g-proteobacteria]


arbre d



+------Marinomas  [g-proteobacteria]  
  !
  !      +-----------Fjohnsoniae    [CFB group bacteria]  
  !      !  
  !      !   +SEQinconnue    
  !   +-13   !
  !   !  !   !              +Ecoli    [enterobacteria]
  !   !  !   !            +-1
  !   !  +---6        +---2 +Ealbertii   [enterobacteria]
  !   !      !        !   !
  !   !      !     +--3   +-Kpneunomonia   [enterobacteria]  
  !   !      !     !  !
  !   !      +-----4  +----Pluminescens    [enterobacteria]  
  !   !            !
  !   !            +--------------CBlochmanniafloridanus    [enterobacteria]
  !   !  
  7--14           +-----Aproteo   [a-proteobacteria]  
  !   !        +-10  
  !   !     +-11  +-----Rrubrum   [a-proteobacteria]
  !   !     !  !  
  !   !     !  +--------Gdiazotrophicus    [a-proteobacteria]
  !   !  +-12  
  !   !  !  !    +-----Mchloromethanicum     [a-proteobacteria]
  !   !  !  ! +--5
  !   !  !  +-8  +----Rhizobium    [a-proteobacteria]
  !   !  !    !
  !   !  !    +-----------Roseobacter    [a-proteobacteria]
  !   +-15  
  !      !       +-----Anaeromyxobacter     [d-proteobacteria]
  !      !     +-9
  !      !     ! +-------Saurantiaca     [d-proteobacteria]
  !      !  +-17  
  !      !  !  !  +------Noceani     [g-proteobacteria]
  !      !  !  +-16  
  !      +-18     +------Gviolaceus     [cyanobacteria]
  !         !  
  !         !  +----------Bplebeius     [CFB group bacteria]
  !         +-19  
  !            +----------Lyngbya     [cyanobacteria]
  !
  +----Cjaponicus   [g-proteobacteria]  


arbre e


                                  +-------------------------------------------------------------------------Mmaripaludis
+--------------------------------+
|                                +----------------------------------------------------------Aboonei
|
|                         +------------------------------------------------------------Tpendens
|+------------------------+
||                        +-----------------------------------------Npharaonis
||
||
||                                                      +----Fpelagi
++                                                 +----+
  |                                                 |    +---------Msilvestris
  |                                                 |
  |                                                 |     +------------------------Bthailandensis
  |                                                 |     |
  +-------------------------------------------------+     |               +-----------CAPgenomovar
                                                    |     |         +-----+
                                                    |     |         |     +---Bfragilis
                                                    |     |         |
                                                    |     |  +------+      +---tenacibaculum
                                                    +-----+  |      |    +-+
                                                          |  |      |    | +---Fbacterium2
                                                          |  |      +----+
                                                          |  |           +Fbacterium1
                                                          |  |
                                                          |  |      +------Aproteobact
                                                          |  |      |
                                                          +--+   +--+
                                                             |   |  +-------SEQinconnue
                                                             |   |
                                                             |   |               +-Ecoli
                                                             |   |               |
                                                             |   |      +--------+salmonallaT
                                                             |   |      |        |
                                                             |   |      |        +-Kpneumoniae
                                                             +---+      |
                                                                 |  +---+             +---synechocystis
                                                                 |  |   |           +-+
                                                                 |  |   |           | +---Maeruginosa
                                                                 |  |   |           |
                                                                 |  |   +-----------+ +-----Npunctiforme
                                                                 |  |               | |
                                                                 |  |               +-+
                                                                 +--+                 |        +------------Pmarinus
                                                                    |                 +--------+
                                                                    |                          +----------synechococcus
                                                                    |
                                                                    |   +--------polaromonas
                                                                    | +-+
                                                                    +-+ +---------------Xfastidiosa
                                                                      |
                                                                      +-------Cburnetii
          

Taxonomie         Bacteria

Il faut en effet faire attention car dans l'aln multiple on voit un groupe de séquences très atypique (archae je crois, homologue certes, mais vraiment différentes) et ce type de configuration peut entrainer des artéfacts lors des inférences d'arbre. On voit que la méthode PhYML ne s'est pas laissée piéger comme la parcimonie et n'a pas envoyer l'ORF dans le groupe ext. Malheureusement le dernier arbre par PhyML n'est pas étiqueté, donc j'ai du mal à voir la cohérence avec la phylogénie de référence... Aussi il est intéressant de noter avec PhyML les valeurs en rouge aux noeuds: ils donnent une idée de la fiabilité de chaque noeud dans l'arbre et cela permet qqfois de se rendre compte qu'il y a des régions de l'arbre très mal résolues (ou le contraire).
Sinon personnellement, je ne reconnais pas la séquence:(