GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M22 - Glycoprotease family
Pfam: PF00814 (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: CL0108
Length: 268
Sequences: 3263
Seq/Len: 12.18
HH_delta: 0.167 (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
224_S250_K0.688033.501
122_E125_D0.667463.396
120_L222_A0.6273.190
177_C219_K0.606663.087
165_G196_D0.574962.926
39_E43_E0.573172.916
56_V84_L0.530772.701
100_S255_P0.526622.680
145_A154_G0.500392.546
159_E235_K0.486352.475
151_P157_A0.477662.430
199_A203_E0.467082.377
242_R246_S0.457872.330
94_A108_V0.440162.240
54_I76_L0.419892.136
51_I82_I0.418192.128
37_I72_F0.416992.122
120_L127_E0.392741.998
122_E127_E0.390151.985
157_A160_K0.3891.979
203_E236_Y0.388871.979
94_A110_L0.388561.977
38_E42_K0.384181.955
48_L51_I0.370511.885
168_F191_L0.369971.882
170_F191_L0.368241.874
48_L80_L0.368051.873
158_L198_A0.364631.855
40_L44_A0.362661.845
206_A240_G0.355241.808
172_R207_D0.353461.798
163_S235_K0.353041.796
28_Q31_E0.350731.785
144_V188_V0.349691.779
217_L249_I0.344951.755
144_V201_F0.340791.734
90_L110_L0.340681.733
91_E126_Y0.339341.727
217_L225_L0.334911.704
97_A226_V0.332041.689
236_Y240_G0.32691.663
201_F205_I0.32671.662
47_S50_D0.326211.660
224_S252_F0.325441.656
203_E240_G0.323421.646
52_D82_I0.322821.643
171_P187_A0.313191.594
245_C251_L0.307381.564
53_A85_I0.306571.560
56_V70_L0.306491.559
189_Y193_E0.305681.555
210_A244_L0.299421.524
172_R204_A0.297531.514
213_A225_L0.293321.492
239_E243_K0.293261.492
164_E195_A0.289841.475
120_L220_P0.283091.440
137_I205_I0.281681.433
199_A202_Q0.278921.419
48_L76_L0.276041.405
202_Q236_Y0.275811.403
188_V197_I0.275531.402
161_L195_A0.27541.401
111_I237_L0.268091.364
190_R193_E0.266631.357
161_L164_E0.266041.354
196_D200_S0.263461.341
243_K247_E0.261111.329
111_I209_L0.253961.292
33_L72_F0.251941.282
211_K215_R0.251291.279
157_A161_L0.249431.269
233_A260_T0.249081.267
214_P244_L0.240891.226
133_L178_D0.237771.210
240_G244_L0.237541.209
159_E202_Q0.236031.201
46_I50_D0.234341.192
109_L213_A0.233791.190
56_V86_G0.232571.183
165_G199_A0.232341.182
91_E124_G0.231631.179
109_L118_V0.231381.177
227_V253_F0.229081.166
109_L209_L0.228831.164
210_A240_G0.228631.163
156_P160_K0.227981.160
41_L48_L0.227791.159
239_E242_R0.225781.149
170_F197_I0.225661.148
89_H93_H0.225521.147
59_G88_S0.225421.147
159_E163_S0.223811.139
77_A84_L0.223021.135
196_D199_A0.222631.133
141_F202_Q0.2221.130
159_E236_Y0.218181.110
119_Y126_Y0.217971.109
140_A201_F0.217161.105
119_Y128_I0.217131.105
240_G243_K0.216731.103
41_L46_I0.214581.092
160_K164_E0.214321.091
97_A228_S0.214111.089
236_Y239_E0.21361.087
163_S239_E0.21271.082
73_A84_L0.209431.066
233_A256_P0.209171.064
244_L247_E0.209071.064
87_V92_A0.208121.059
135_D185_K0.207671.057
144_V147_L0.207251.055
227_V241_L0.206711.052
160_K163_S0.206261.049
129_L220_P0.205851.047
58_R86_G0.204861.042
165_G200_S0.203991.038
141_F159_E0.203791.037
147_L189_Y0.20281.032
101_E250_K0.201631.026
108_V228_S0.20091.022
39_E42_K0.199031.013
141_F201_F0.197971.007
46_I51_I0.196811.001
107_L222_A0.196451.000
74_K84_L0.194360.989
72_F75_G0.194090.988
225_L245_C0.193730.986
167_A196_D0.192230.978
214_P217_L0.19210.977
209_L241_L0.191920.977
175_K211_K0.190880.971
75_G79_A0.189380.964
223_K249_I0.189110.962
223_K250_K0.187180.952
148_L198_A0.186770.950
210_A213_A0.186550.949
161_L198_A0.185930.946
172_R211_K0.184750.940
170_F187_A0.183640.934
191_L197_I0.181780.925
54_I82_I0.181670.924
89_H261_D0.181560.924
107_L213_A0.180940.921
42_K45_G0.17770.904
217_L221_R0.176940.900
95_L121_A0.176650.899
179_F208_H0.176430.898
162_A198_A0.17520.891
204_A208_H0.174470.888
118_V179_F0.174370.887
258_Y264_A0.174280.887
166_E203_E0.173120.881
245_C249_I0.172780.879
145_A151_P0.171240.871
71_S75_G0.170560.868
128_I131_E0.169040.860
34_P72_F0.168940.860
208_H212_K0.168670.858
108_V226_V0.168610.858
230_G234_N0.168170.856
203_E207_D0.167820.854
26_S64_T0.166770.849
135_D139_E0.166390.847
56_V73_A0.166370.847
144_V148_L0.166270.846
187_A190_R0.165890.844
184_L205_I0.164930.839
28_Q131_E0.164570.837
70_L74_K0.164440.837
172_R203_E0.164130.835
220_P223_K0.164070.835
118_V216_A0.163240.831
139_E143_K0.162740.828
227_V232_A0.161790.823
217_L220_P0.160870.819
214_P218_E0.160680.818
93_H234_N0.160530.817
168_F196_D0.159830.813
36_L40_L0.159740.813
41_L44_A0.159710.813
107_L217_L0.158730.808
117_E128_I0.158680.807
91_E95_L0.158230.805
110_L119_Y0.15730.800
53_A86_G0.156980.799
262_N265_M0.156630.797
111_I137_I0.156050.794
202_Q234_N0.155270.790
99_L226_V0.155260.790
76_L80_L0.154950.788
34_P263_A0.154910.788
167_A200_S0.154730.787
187_A191_L0.154220.785
93_H261_D0.153750.782
172_R208_H0.153350.780
76_L82_I0.153320.780
101_E252_F0.152640.777
181_F205_I0.152570.776
137_I206_A0.152460.776
62_S139_E0.152170.774
117_E131_E0.151350.770
177_C215_R0.150930.768
191_L194_K0.150890.768
94_A121_A0.150770.767
234_N261_D0.150210.764
94_A126_Y0.149420.760
243_K246_S0.149120.759
89_H234_N0.148740.757
232_A259_C0.148620.756
242_R253_F0.148070.753
258_Y262_N0.148040.753
118_V212_K0.147840.752
77_A82_I0.147620.751
255_P258_Y0.147250.749
238_R253_F0.1470.748
209_L237_L0.146290.744
63_F66_L0.145930.743
70_L84_L0.145930.743
139_E185_K0.145570.741
61_G66_L0.145210.739
235_K239_E0.145020.738
49_S82_I0.14480.737
49_S80_L0.144680.736
200_S203_E0.144230.734
115_H265_M0.144170.734
54_I73_A0.143360.729
213_A241_L0.14250.725
150_L161_L0.141690.721
254_P259_C0.141610.721
242_R250_K0.141460.720
148_L158_L0.141390.719
98_R226_V0.140850.717
96_S228_S0.140680.716
74_K77_A0.140670.716
147_L192_I0.14050.715
98_R103_L0.13940.709
90_L115_H0.138320.704
231_V234_N0.137410.699
228_S254_P0.137070.697
97_A254_P0.136490.694
144_V197_I0.136390.694
65_G88_S0.13560.690
188_V201_F0.135580.690
217_L244_L0.135540.690
162_A165_G0.134730.686
174_L204_A0.134420.684
107_L220_P0.134320.683
51_I80_L0.134260.683
107_L209_L0.133770.681
55_A86_G0.13350.679
67_R71_S0.133390.679
104_K250_K0.133190.678
55_A85_I0.133070.677
93_H230_G0.133070.677
121_A126_Y0.132880.676
210_A214_P0.132690.675
57_T90_L0.132230.673
90_L117_E0.132180.673
112_S115_H0.131730.670
230_G261_D0.131520.669
173_P176_N0.129150.657
48_L82_I0.12890.656
215_R218_E0.128670.655
125_D225_L0.128590.654
27_R64_T0.128510.654
232_A255_P0.128370.653
120_L129_L0.128220.652
207_D244_L0.128030.651
229_G234_N0.127230.647
96_S254_P0.127160.647
54_I77_A0.126820.645
172_R175_K0.126360.643
70_L73_A0.125740.640
95_L126_Y0.125540.639
48_L54_I0.124620.634
105_F123_G0.124580.634
238_R260_T0.124430.633
205_I208_H0.124260.632
59_G87_V0.123920.631
42_K49_S0.123660.629
90_L119_Y0.123520.628
62_S153_P0.123280.627
162_A236_Y0.123170.627
62_S185_K0.122880.625
146_R152_Y0.122840.625
110_L117_E0.122650.624
49_S243_K0.122630.624
74_K86_G0.122340.622
89_H230_G0.121850.620
95_L98_R0.121240.617
207_D240_G0.120940.615
99_L264_A0.120780.615
24_I28_Q0.120760.614
118_V213_A0.120540.613
38_E166_E0.120520.613
214_P225_L0.120360.612
135_D141_F0.120170.611
44_A50_D0.120040.611
66_L106_P0.119910.610
108_V117_E0.119640.609
90_L112_S0.119330.607
58_R71_S0.119250.607
105_F121_A0.119170.606
42_K47_S0.119160.606
24_I31_E0.118820.605
143_K185_K0.118780.604
115_H155_G0.118720.604
89_H113_A0.11850.603
139_E153_P0.118160.601
185_K189_Y0.118030.601
214_P249_I0.117870.600
180_S183_G0.117360.597
225_L251_L0.116910.595
130_G134_D0.116450.593
186_T189_Y0.116070.591
49_S246_S0.115430.587
241_L251_L0.115420.587
132_T180_S0.114990.585
107_L118_V0.114820.584
36_L44_A0.114780.584
145_A156_P0.114760.584
98_R252_F0.114370.582
32_N35_P0.114320.582
234_N259_C0.113960.580
215_R219_K0.113880.579
38_E247_E0.113670.578
37_I41_L0.113640.578
130_G178_D0.11350.578
36_L39_E0.112990.575
98_R121_A0.112990.575
158_L201_F0.112960.575
254_P258_Y0.112960.575
103_L226_V0.11280.574
57_T142_D0.112570.573
28_Q117_E0.112490.572
138_G142_D0.112370.572
72_F76_L0.112060.570
239_E246_S0.111830.569
242_R251_L0.111770.569
138_G230_G0.111710.568
98_R257_R0.111670.568
110_L115_H0.111510.567
135_D143_K0.110840.564
173_P184_L0.11050.562
134_D180_S0.110160.561
111_I231_V0.109940.559
125_D164_E0.109750.558
156_P260_T0.109470.557
27_R31_E0.109420.557
37_I76_L0.109410.557
187_A197_I0.109160.555
110_L121_A0.109070.555
30_S253_F0.108760.553
41_L51_I0.108670.553
96_S100_S0.108630.553
97_A253_F0.108470.552
141_F145_A0.108370.551
111_I232_A0.108070.550
51_I76_L0.108070.550
257_R263_A0.107970.549
39_E166_E0.107830.549
95_L105_F0.107160.545
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
3enoA0.98881000.167
3en9A0.98131000.197
3zeuB11000.213
2ivnA0.98511000.219
4k25A0.98881000.231
3venA0.98881000.286
3ttcA0.94031000.358
4g9iA0.96271000.358
3vthA0.94031000.359
4ehuA0.835899.80.652

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