GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Reprolysin_2 - Metallo-peptidase family M12B Reprolysin-like
Pfam: PF13574 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0126
Length: 173
Sequences: 1886
Seq/Len: 10.9
HH_delta: 0.175 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
61_F64_W0.471143.304
58_Q61_F0.42492.980
117_H121_H0.394132.764
58_Q64_W0.378722.656
117_H127_H0.306842.152
121_H127_H0.302862.124
118_E121_H0.298512.094
160_S163_S0.287122.014
128_D162_C0.278861.956
61_F65_I0.277091.943
165_R169_A0.276761.941
72_I119_L0.2671.873
43_P46_N0.256291.797
11_V14_V0.250851.759
39_P42_D0.238931.676
117_H120_G0.227181.593
93_C162_C0.222611.561
118_E127_H0.21881.534
126_P166_Q0.21551.511
14_V115_F0.211781.485
74_H101_G0.211651.484
36_F44_Y0.210891.479
31_N34_I0.205231.439
7_I76_F0.204771.436
24_I30_N0.203231.425
31_N36_F0.199871.402
120_G125_A0.198021.389
92_V98_K0.197791.387
33_R36_F0.196541.378
38_D41_T0.195271.369
59_A63_S0.192781.352
88_Y97_Y0.191911.346
62_D65_I0.190661.337
116_A128_D0.185411.300
18_Y116_A0.182751.282
58_Q62_D0.181731.275
76_F115_F0.181731.275
31_N35_I0.180351.265
10_T111_G0.179671.260
40_S43_P0.178751.254
42_D46_N0.177641.246
36_F40_S0.172411.209
36_F41_T0.170761.198
15_N25_R0.169741.190
28_L37_T0.169591.189
17_I112_I0.168851.184
58_Q65_I0.167591.175
6_A13_R0.166351.167
42_D45_N0.16581.163
87_A118_E0.163291.145
128_D160_S0.162581.140
40_S44_Y0.158791.114
125_A163_S0.158571.112
124_G159_F0.15771.106
86_L89_V0.156371.097
132_G146_Y0.154811.086
27_E30_N0.154131.081
163_S166_Q0.1531.073
102_L105_P0.152081.067
84_G114_T0.149831.051
11_V15_N0.149561.049
165_R168_R0.149431.048
37_T40_S0.14651.027
64_W70_Y0.146451.027
127_H148_M0.146431.027
88_Y91_G0.146251.026
72_I122_Q0.146241.026
123_L168_R0.144571.014
32_D36_F0.143561.007
14_V26_L0.142631.000
85_G118_E0.141810.995
41_T44_Y0.141730.994
56_E60_N0.141630.993
62_D99_A0.141380.992
30_N33_R0.141360.991
10_T76_F0.140640.986
87_A101_G0.138730.973
94_S97_Y0.137440.964
74_H99_A0.137270.963
36_F42_D0.136480.957
125_A146_Y0.135910.953
74_H115_F0.135510.950
46_N61_F0.134660.944
56_E59_A0.134260.942
164_I171_L0.134260.942
25_R29_V0.132440.929
117_H148_M0.132210.927
129_F150_Y0.131960.925
57_N61_F0.131690.924
6_A9_T0.131280.921
39_P43_P0.130860.918
5_A16_Q0.12920.906
92_V170_V0.129160.906
132_G140_C0.129060.905
37_T43_P0.128920.904
72_I92_V0.1280.898
17_I21_D0.127620.895
13_R113_D0.127590.895
39_P44_Y0.127510.894
15_N19_E0.127220.892
104_S107_G0.1270.891
129_F166_Q0.1270.891
6_A10_T0.126870.890
18_Y123_L0.126760.889
148_M160_S0.126460.887
125_A170_V0.126210.885
77_G83_G0.125810.882
125_A166_Q0.125810.882
18_Y82_G0.125730.882
161_P169_A0.125570.881
125_A167_I0.125510.880
7_I11_V0.125140.878
65_I69_N0.125010.877
56_E61_F0.124420.873
145_G149_S0.124330.872
70_Y73_G0.124230.871
161_P164_I0.12390.869
139_T143_S0.123550.866
91_G97_Y0.122960.862
93_C128_D0.122890.862
83_G104_S0.122880.862
85_G89_V0.122880.862
37_T41_T0.122870.862
89_V126_P0.122830.861
168_R171_L0.12180.854
87_A122_Q0.121240.850
28_L71_D0.121170.850
29_V70_Y0.120910.848
35_I38_D0.120830.847
140_C144_G0.120120.842
23_N164_I0.120090.842
8_V12_N0.119720.840
80_S90_G0.119440.838
140_C146_Y0.11840.830
34_I37_T0.118160.829
128_D148_M0.117460.824
60_N63_S0.116460.817
21_D24_I0.116230.815
87_A102_L0.116110.814
25_R95_K0.115930.813
10_T13_R0.115830.812
34_I41_T0.11550.810
74_H122_Q0.115060.807
22_I29_V0.114960.806
164_I168_R0.114760.805
34_I42_D0.114570.804
166_Q169_A0.114510.803
22_I30_N0.114490.803
161_P168_R0.113550.796
57_N64_W0.113160.794
3_A8_V0.112810.791
105_P108_D0.112620.790
60_N64_W0.112330.788
78_T83_G0.112330.788
64_W67_S0.112010.786
4_L11_V0.111930.785
87_A114_T0.111530.782
36_F39_P0.111470.782
120_G148_M0.111460.782
101_G104_S0.111450.782
13_R17_I0.111070.779
59_A62_D0.110550.775
159_F167_I0.110520.775
25_R28_L0.109880.771
32_D42_D0.109830.770
81_G84_G0.109510.768
82_G169_A0.109490.768
7_I10_T0.109470.768
2_N90_G0.109260.766
73_G76_F0.109140.765
65_I70_Y0.109010.765
87_A91_G0.108820.763
27_E32_D0.108770.763
57_N62_D0.108620.762
44_Y57_N0.108340.760
74_H103_S0.108090.758
57_N60_N0.107650.755
11_V28_L0.107550.754
40_S45_N0.1070.750
5_A109_F0.106810.749
83_G89_V0.10680.749
158_K161_P0.106610.748
61_F66_G0.106060.744
145_G158_K0.10580.742
38_D43_P0.105670.741
35_I57_N0.105660.741
73_G83_G0.105620.741
122_Q125_A0.105440.739
88_Y124_G0.105080.737
9_T13_R0.1050.736
8_V11_V0.104970.736
26_L119_L0.104770.735
61_F75_L0.104430.732
119_L122_Q0.104120.730
63_S66_G0.103530.726
106_Y114_T0.103510.726
15_N145_G0.103430.725
118_E123_L0.103230.724
129_F141_P0.103020.723
33_R37_T0.103010.722
32_D44_Y0.102720.720
41_T45_N0.102560.719
147_I159_F0.102230.717
18_Y46_N0.101940.715
34_I38_D0.101790.714
10_T112_I0.101460.712
90_G119_L0.101440.711
159_F166_Q0.101420.711
18_Y165_R0.10110.709
132_G142_G0.100930.708
158_K164_I0.100110.702
25_R30_N0.099760.700
63_S69_N0.09970.699
89_V150_Y0.099680.699
43_P56_E0.099590.698
166_Q170_V0.099380.697
28_L152_G0.099350.697
93_C116_A0.099230.696
152_G155_N0.099140.695
120_G127_H0.098850.693
25_R32_D0.098810.693
144_G165_R0.098780.693
148_M159_F0.098730.692
120_G142_G0.098060.688
63_S67_S0.098030.688
84_G120_G0.098030.688
71_D99_A0.09790.687
10_T115_F0.097830.686
9_T159_F0.097710.685
121_H148_M0.097670.685
109_F156_N0.097520.684
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3g5cA0.94221000.175
3k7lA0.90171000.195
3k7nA0.90171000.196
2e3xA0.90171000.199
2rjqA0.9481000.202
2eroA0.90171000.204
2dw0A0.90171000.204
1r55A0.92491000.205
2v4bA0.9481000.205
1atlA0.90171000.21

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