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Catalog
Fitch/89
Fitch/extended
Taxonomy
Kitch/89
Kitch/extended
Tree of Life
PileUp/89
PileUp/extended
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Phylogenic tree of S1 serine proteases, Fitch-Margoliash method, 89 sequences
Details of computation
A phylogenic tree of serine proteases was built by Maxwell Krem (WUSM St. Louis) from residues 16 to 245 according to the chymotrypsin numbering. 89 non-redundant sequences were were culled from GenBank 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.
Parameters: 
                        __ __            2
                        \  \  (Obs - Exp) 
      Sum of squares =  /_ /_ ------------ 
                         i  j        2 
                                  Obs
Negative branch lengths allowed
Global optimization
Unrooted tree

Result:

Sum of squares = 68.76126
Average percent standard deviation = 9.37111
Examined -21687 trees
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Between And

Length
1 chymoshrmp 0.12209
1 21 0.47773
21 59 -0.16513
59 69 0.15212
69 chymomosq 0.71712
69 ser1fly 0.84060
59 57 0.20241
57 factorD 0.62645
57 24 0.07238
24 31 0.20353
31 33 0.15230
33 chymase 0.32617
33 32 0.10451
32 MCP-like 0.26500
32 MCP-1 0.22821
31 29 0.09022
29 27 -0.05606
27 26 -0.08385
26 30 0.37406
30 granzymeF 0.16765
30 granzymeD 0.22101
26 51 0.40793
51 25 1.81057
25 76 -2.30086
76 proteaseC 2.60939
76 granz-l-II 0.58917
25 53 1.71099
53 52 0.31594
52 proteaseA 0.16847
52 proteaseD 0.51562
53 proteaseB 0.00070
51 MCP-8 0.14496
27 cathepsinG 0.41773
29 28 0.15006
28 NKCP-1 0.17985
28 granzymeB 0.20850
24 58 -0.09171
58 granzymeA 0.70497
58 22 0.36572
22 pmn-elasta 0.41463
22 23 -0.10128
23 azurocidin 0.60138
23 myeloblast 0.40304
21 34 0.08324
34 86 -0.41313
86 Nsp4-EAV 3.16036
86 37 0.85498
37 scatter 0.56376
37 HGF-like 0.55493
34 12 0.06850
12 8 -0.07749
8 38 -0.22067
38 cercarial 1.93536
38 17 0.37391
17 SCCE 0.51943
17 14 0.19013
14 15 0.03554
15 13 0.04550
13 kallikrein 0.28294
13 PSA 0.29916
15 Resterase 0.31185
14 16 0.13189
16 tonin 0.21288
16 g-renin 0.40255
8 3 0.19022
3 87 -0.09280
87 42 0.01710
42 36 -0.05149
36 35 0.59171
35 plasmin 0.06979
35 apolipo-A 0.05861
36 74 0.14348
74 factorI 1.01835
74 63 -0.15542
63 39 0.47611
39 elastase2 0.16988
39 caldecrin 0.35063
63 47 0.08680
47 6 0.17857
6 5 0.14632
5 u-PA 0.56728
5 4 0.38576
4 t-PA 0.12230
4 s-PA 0.12048
6 83 -0.16727
83 84 1.01824
84 C2 0.65526
84 factorB 0.83513
83 2 0.31176
2 HGFA 0.44599
2 factorXII 0.46833
47 71 0.02882
71 78 -0.11803
78 easter 1.03179
78 SP24Dmosq 0.99626
71 54 0.16732
54 77 -0.13967
77 40 0.06869
40 75 -0.10804
75 61 0.17153
61 62 0.21744
62 trypStrep 0.57348
62 trypFoxy 0.40233
61 85 -0.19176
85 Elegans208 1.78366
85 70 0.04541
70 nudel 0.91241
70 64 0.03566
64 stubble 0.68862
64 79 -0.15550
79 snake 1.18644
79 44 0.27509
44 46 0.20256
46 trypsinfly 0.51620
46 45 0.23933
45 hypodermB 0.28166
45 hypodermA 0.29331
44 60 -0.08679
60 vitellin 0.67205
60 43 0.51445
43 allergen2 0.10489
43 allergen1 0.11115
75 68 0.13508
68 67 -0.05941
67 proteinC 0.78744
67 factorIX 0.65552
68 82 -0.10452
82 56 0.10779
56 Elegans157 0.98906
56 factorVII 0.71582
82 50 -0.01555
50 Elegans132 0.87593
50 72 0.09622
72 73 0.12189
73 MASP-1 0.65692
73 clotfactC 0.60360
72 66 0.15066
66 MASP-2 0.66750
66 49 0.11899
49 80 -0.11718
80 haptoglobi 0.89001
80 48 0.45252
48 C1s 0.21802
48 CASP 0.18814
49 C1r 0.64065
40 thrombin 0.78736
77 proclottin 0.81090
54 factorX 0.78004
42 41 0.22375
41 chymo-lhum 0.31808
41 chymohuman 0.32257
87 tryptase 0.70001
3 7 0.14444
7 55 -0.04804
55 prostasin 0.61947
55 10 0.00344
10 65 0.10654
65 acrosin 0.72480
65 hepsin 0.48940
10 9 0.40481
9 p-kallikre 0.18401
9 factorXI 0.24193
7 enterokina 0.58688
12 81 -0.13564
81 chymo-laba 1.11113
81 18 0.20565
18 11 0.67020
11 batroxobin 0.19370
11 ancrod 0.43317
18 20 0.21158
20 trypsincod 0.31205
20 19 0.15867
19 trypIIhum 0.05469
19 tryp1hum 0.05929
1 brachyurin 0.12218

 
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Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
Saint Louis, MO, U.S.A.
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