Serine proteases: Evolutionary trees

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Catalog	Fitch/89	Fitch/extended	Subset
Taxonomy	Kitch/89	Kitch/extended
Tree of Life	PileUp/89	PileUp/extended

Make your own phylogenic tree of S1 serine proteases

A phylogenetic tree of 89 S1 serine proteases was built by Krem et al. (1999, JBC, in press) from residues 16 to 245 according to the chymotrypsin numbering. Original sequences were culled from GenBank. 89 non-redundant sequences were selected and aligned by Clustal-W 1.7. Protein distance matrices were calculated with PROTDIST from the PHYLIP package. Unrooted trees were built using the Fitch-Margoliash method with the PHYLIP program FITCH 3.572c. Distances from PRODIST are available here.

Now you can select sequences in the tree (all are selected by default) then specified the residues to take into account in the clustal multi-alignment using chymotrypsin as reference. You may submit this new subset to PROTDIST to calculate a new distance matrix then build a tree with FITCH or KITCH.

1- All the sequences of the tree below are selected by default (In). Il you want deselect some of them click on the radio button Out.

2- The sequence from the residue 16 to 245 are selected by default for each of the selected (In) serine proteases. It is possible to restrict the residues taken into account in the original clustal alignment. The numbering is refering to the bovin chymotrypsin (CTRB_BOVIN) .
Example : 57-102 189 195 214 221-225 238

Click to create a new edition of the multi-alignment and get forms for PROTDIST, FITCH and KITCH. Click to initialize by default.

 
  POSITIONS     FITCH-MARGOLIASH UNROOTED TREE (Krem et al.,1999, JBC, in press) 
 1234567890 Sequence names are linked to SwissProt. Numbers are knot references in the distance list.



 I  O  +-- chymoshrmp (S1)
             ! 
 I  O  !          +------ chymomosq (S1)  
             !       +-69 
 I  O  !       !  +------- ser1fly (S1)  
             !       ! 
 I  O  !       !  +----- factorD (S1)    
             !       !  ! 
 I  O  !       !  !        +-- chymase (S1)  
             !    +-59  !     +-33  
 I  O  !    !  !  !     !  !  +-- MCP-like (S1) 
             !    !  !  !     !  +-32  
 I  O  !    !  !  !     !     +-- MCP-1 (S1)  
             !    !  !  !     !  
 I  O  !    !  !  !     !            +-- granzymeF (S1) 
             !    !  !  !     !        +--30  
 I  O  !    !  +-57     !        !   +-- granzymeD (S1)  
             !    !     !     !        !  
 I  O  !    !     !  +-31        !                         +------------------------- proteaseC (S2A)  
             !    !     !  !  !     +-26                      +-76   
 I  O  !    !     !  !  !     !  !                      !  +----- granz-l-II (S1)  
             !    !     !  !  !     !  !   +----------------25  
 I  O  !    !     !  !  !     !  !   !                  !                   +-- proteaseA (S2A)  
             !    !     !  !  !     !  !   !                  !                +-52   
 I  O  !    !     !  !  !  +-27  +--51                  +---------------53  +---- proteaseD (S2A)  
             !    !     !  !  !  !  !      !                                   !   
 I  O  !    !     !  !  !  !  !      !                                   +-- proteaseB (S2A)  
             !    !     +-24  !  !  !      !  
 I  O  !    !        !  +-29  !      +-- MCP-8 (S1)  
             !    !        !     !  !  
 I  O  !    !        !     !  +--- cathepsinG (S1)  
             !    !        !     !  
 I  O  !    !        !     !  +-- NKCP-1 (S1)  
             !    !        !     +-28  
 I  O  !    !        !        +-- granzymeB (S1)  
             !    !        !  
 I  O  !    !        !  +------ granzymeA (S1)  
             !    !        +-58  
 I  O  !    !           !   +--- pmn-elasta (S1)  
             !    !           +--22  
 I  O  !    !               !  +----- azurocidin (S1)  
             !    !               +-23   
 I  O  !    !                  +--- myeloblast (S1)  
             !    !  
 I  O !    !     +-------------------------------  Nsp4-EAV (?)  
             !    !  +-86  
 I  O  !    !  !  !        +----- scatter (S1)  
             !    !  !  +-------37  
 I  O  1---21  !           +----- HGF-like (S1)  
             !    !  !  
 I  O  !    !  !        +------------------ cercarial (S1)  
             !    !  !        !  
 I  O  !    !  !     +-38   +---- SCCE (S1)  
             !    !  !     !  !   !   
 I  O  !    !  !     !  !   !        +-- kallikrein (S1)  
             !    !  !     !  +--17     +-13  
 I  O  !    !  !     !      !  +-15  +-- PSA (S1)  
             !    !  !     !      !  !  !  
 I  O  !    !  !     !      +-14  +-- Resterase (S1)  
             !    !  !     !         !  
 I  O  !    !  !     !         !  +-- tonin (S1)  
             !    !  !     !         +-16  
 I  O  !    !  !     !            +--- g-renin (S1)  
             !    !  !     !  
 I  O  !    !  !     !                 +-- plasmin (S1)  
             !    !  !     !           +----35  
 I  O  !    !  !     !           !     +-- apolipo-A (S1)  
             !    !  !     !           !  
 I  O  !    !  !     !           !  +--------- factorI (S1)  
             !    !  !     !           !  !  
 I  O  !    !  !     !        +-36  !       +-- elastase2 (S1)  
             !    !  !     !        !  !  !  +---39  
 I  O  !    !  !     !        !  !  !  !    +--- caldecrin (S1)  
             !    !  !     !        !  !  !  !  
 I  O  !    !  !     !        !  !  !  !        +----- u-PA (S1)  
             !    !  !     !        !  +-74  !     +--5  
 I  O  !    !  !     !        !     !  !     !  !   +-- t-PA (S1)  
             !    !  !     !        !     !  !     !  +---4  
 I  O  !    !  !     !        !     !  !     !      +-- s-PA (S1)  
             !    !  !     !        !     !  !  +--6   
 I  O  !    !  !     !        !     !  !  !  !            +------ C2 (S1)  
             !    !  !     !        !     !  !  !  !  +--------84  
 I  O  !    !  !     !        !     !  !  !  !  !         +------- factorB (S1)  
             !    !  !     !        !     +-63  !  +-83  
 I  O  !    !  !     !        !        !  !     !  +---- HGFA (S1)  
             !    !  !     !        !        !  !     +--2  
 I  O  !    !  !     !        !        !  !        +---- factorXII (S1)  
             !    !  !     !        !        !  !  
 I  O  !    +-34     !        !        !  !     +--------- easter (S1)  
             !       !     !        !        !  !  +-78  
 I  O  !       !     !        !        !  !  !  +--------- SP24Dmosq (XX)  
             !       !     !        !        !  !  !  
 I  O  !       !     !        !        !  !  !                 +----- trypStrep (S2A)  
             !       !     !        !        !  !  !              +-62  
 I  O  !       !     !        !        !  !  !              !  +--- trypFoxy (S1)  
             !       !     !        !        !  !  !           +-61  
 I  O  !       !     !        !        +-47  !           !  !  +----------------- Elegans208 (XX)  
             !       !  +--8        !           !  !           !  !  !  
 I  O  !       !  !  !        !           !  !           !  +-85  +-------- nudel (S1)  
             !       !  !  !        !           !  !           !     !  !  
 I  O  !       !  !  !        !           !  !           !     +-70  +------ stubble (S1)  
             !       !  !  !        !           !  !           !        !  !  
 I  O  !       !  !  !        !           !  !           !        +-64  +----------- snake (S1)  
             !       !  !  !        !           !  !           !           !  !  
 I  O  !       !  !  !        !           !  !           !           !  !     +---- trypsinfly (S1)  
             !       !  !  !        !           !  !           !           +-79  +-46  
 I  O  !       !  !  !        !           !  !           !              !  !  !  +-- hypodermB (S1)  
             !       !  !  !        !           !  !        +-75              !  !  +-45  
 I  O  !       !  !  !     +-42           !  !        !  !              +-44     +-- hypodermA (S1)  
             !       !  !  !     !  !           !  !        !  !                 !   
 I  O  !       !  !  !     !  !           !  !        !  !                 !  +------ vitellin (S1)  
             !       !  !  !     !  !           !  !        !  !                 +-60   
 I  O  !       !  !  !     !  !           !  !        !  !                    !    +-- allergen2 (S1)  
             !       !  !  !     !  !           +-71        !  !                    +---43   
 I  O  !       !  !  !     !  !              !        !  !                         +-- allergen1 (S1)  
             !       !  !  !     !  !              !        !  !  
 I  O  !       !  !  !     !  !              !        !  !     +------- proteinC (S1)  
             !       !  !  !     !  !              !        !  !  +-67  
 I  O  !       !  !  !     !  !              !        !  !  !  +------ factorIX (S1)  
             !       !  !  !     !  !              !        !  !  !  
 I  O  !       !  !  !     !  !              !        !  +-68     +--------- Elegans157 (XX)  
             !       !  !  !     !  !              !        !     !  +-56  
 I  O  !       !  !  !     !  !              !        !     !  !  +------ factorVII (S1)  
             !       !  !  !     !  !              !     +-40     +-82  
 I  O  !       !  !  !     !  !              !     !  !        !  +-------- Elegans132 (XX)  
             !       !  !  !     !  !              !     !  !        !  !   
 I  O  !       !  !  !     !  !              !     !  !        +-50     +------ MASP-1 (S1)  
             !       !  !  !     !  !              !     !  !           !  +-73  
 I  O  !       !  !  !     !  !              !     !  !           !  !  +----- clotfactC (S1)  
             !       !  !  !  +-87  !              !     !  !           +-72  
 I  O  !       !  !  !  !  !  !              !     !  !              !  +------ MASP-2 (S1)  
             !       +-12  !  !  !  !              !     !  !              !  !   
 I  O  !          !  !  !  !  !              !  +-77  !              +-66     +-------- haptoglobin (?)  
             !          !  !  !  !  !              !  !  !  !                 !  +-80  
 I  O  !          !  !  !  !  !              !  !  !  !                 !  !  !    +-- C1s (S1)  
             !          !  !  !  !  !              !  !  !  !                 +-49  +---48  
 I  O  !          !  !  !  !  !              !  !  !  !                    !       +-- CASP (S1)  
             !          !  !  !  !  !              !  !  !  !                    !   
 I  O  !          !  !  !  !  !              +-54  !  !                    +------ C1r (S1)  
             !          !  !  !  !  !                 !  !  !  
 I  O  !          !  !  !  !  !                 !  !  +------- thrombin (S1)  
             !          !  !  !  !  !                 !  !  
 I  O  !          !  !  !  !  !                 !  +------- proclottin (S1)  
             !          !  +--3  !  !                 !   
 I  O  !          !     !  !  !                 +------- factorX (S1)  
             !          !     !  !  !  
 I  O  !          !     !  !  !  +-- chymo-lhum (S1)  
             !          !     !  !  +-41  
 I  O  !          !     !  !     +-- chymohuman (S1)  
             !          !     !  !  
 I  O  !          !     !  +------ tryptase (S1)  
             !          !     !   
 I  O  !          !     !     +----- prostasin (S1)  
             !          !     !     !  
 I  O  !          !     !  +-55     +------ acrosin (S1)  
             !          !     !  !  !  +-65  
 I  O  !          !     !  !  !  !  +---- hepsin (S1)  
             !          !     !  !  +-10  
 I  O  !          !     +--7     !   +-- p-kallikre (S1)  
             !          !        !     +---9  
 I  O  !          !        !         +-- factorXI (S1)  
             !          !        !  
 I  O  !          !        +----- enterokina (S1)
             !          !  
 I  O  !          !  +---------- chymo-laba (XX)  
             !          !  !  
 I  O  !          +-81         +-- batroxobin (S1)  
             !             !  +-----11  
 I  O  !             !  !      +--- ancrod (S1)  
             !             +-18   
 I  O  !                !  +-- trypsincod (S1)  
             !                +-20   
 I  O  !                   !  +-- trypIIhum (S1)  
             !                   +-19   
 I  O  !                      +-- tryp1hum (S1)  
             !  
 I  O  +-- brachyurin (S1)

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Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
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