GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pectate_lyase22 - Oligogalacturonate lyase
Pfam: PF14583 (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: CL0186
Length: 386
Sequences: 7099
Seq/Len: 18.39
HH_delta: 0.171 (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
51_L88_L0.66163.006
97_Y107_V0.596332.709
108_D111_T0.575722.615
196_S199_D0.557282.532
326_D329_A0.548912.494
52_F65_L0.518052.353
51_L95_L0.49482.248
79_P97_Y0.489192.222
270_D273_T0.485362.205
254_Y269_Y0.478152.172
253_W290_S0.475952.162
85_G98_V0.473562.151
355_H368_R0.471062.140
66_D69_T0.46992.135
298_V358_F0.466862.121
216_Q219_W0.46542.114
291_S358_F0.458492.083
299_G325_F0.448312.037
40_Q53_A0.446622.029
51_L64_L0.445662.025
62_L97_Y0.437781.989
222_N225_G0.423871.926
96_Y139_L0.417441.896
96_Y130_W0.416431.892
369_S372_E0.413081.877
174_D177_T0.409131.859
121_P141_G0.404631.838
196_S245_W0.402731.830
104_L141_G0.402641.829
253_W297_F0.398281.809
121_P125_K0.39781.807
253_W268_G0.385551.751
338_H367_F0.383491.742
44_T88_L0.379981.726
204_M252_I0.370021.681
96_Y106_R0.367671.670
105_R114_E0.363411.651
41_N52_F0.362961.649
266_I299_G0.357261.623
216_Q220_T0.353531.606
287_H300_D0.350821.594
256_S263_D0.349371.587
45_D92_D0.345071.568
298_V324_L0.3451.567
94_A106_R0.344261.564
49_K64_L0.34361.561
242_H255_D0.340391.546
253_W288_F0.339961.544
216_Q221_I0.336381.528
186_D205_F0.336241.527
63_Y72_I0.335681.525
96_Y104_L0.33161.506
215_D219_W0.329151.495
251_T268_G0.326531.483
90_P136_C0.324231.473
359_S363_K0.32281.466
186_D190_L0.317931.444
359_S362_G0.315141.432
170_I205_F0.31381.426
54_S59_N0.313011.422
322_I367_F0.310961.413
246_V290_S0.30811.400
51_L86_G0.305641.388
319_D323_Y0.304511.383
88_L358_F0.303031.377
42_C87_F0.30011.363
289_M357_S0.297611.352
301_G319_D0.297381.351
89_S130_W0.295881.344
292_P358_F0.292881.331
59_N63_Y0.291311.323
140_V195_F0.289371.315
247_P290_S0.283561.288
323_Y334_K0.279811.271
298_V365_V0.279621.270
62_L86_G0.27921.268
43_F50_L0.278661.266
287_H356_P0.278451.265
133_N136_C0.275171.250
52_F63_Y0.275021.249
372_E376_A0.274631.248
99_K103_S0.274261.246
246_V250_S0.273091.241
292_P362_G0.269591.225
204_M245_W0.269571.225
44_T48_R0.26911.222
291_S295_K0.267391.215
97_Y105_R0.266961.213
127_Y142_I0.266491.211
254_Y267_A0.266151.209
105_R117_V0.26461.202
93_R110_D0.263471.197
195_F245_W0.262871.194
45_D88_L0.261811.189
167_H171_F0.260991.186
367_F378_Y0.258341.174
215_D221_I0.257421.169
252_I271_P0.256931.167
44_T47_G0.250061.136
338_H369_S0.248811.130
84_F100_N0.246051.118
217_R221_I0.245261.114
140_V172_T0.245121.114
93_R108_D0.245111.113
197_P249_G0.245061.113
359_S366_L0.244861.112
375_P378_Y0.244381.110
50_L67_L0.244261.110
291_S294_G0.243331.105
87_F129_T0.241161.096
96_Y128_G0.240591.093
86_G97_Y0.238631.084
244_F289_M0.238131.082
298_V356_P0.236651.075
48_R68_A0.235631.070
171_F180_R0.235581.070
90_P130_W0.23541.069
99_K102_R0.234581.066
78_G97_Y0.234221.064
52_F59_N0.233751.062
268_G290_S0.232811.058
44_T51_L0.232491.056
289_M356_P0.232141.055
54_S61_N0.231941.054
75_L78_G0.231731.053
359_S364_W0.231291.051
323_Y332_F0.231151.050
267_A276_R0.230151.046
356_P367_F0.229851.044
195_F203_I0.229041.040
372_E375_P0.228941.040
247_P294_G0.226191.028
39_Y55_D0.223741.016
246_V249_G0.222071.009
63_Y75_L0.220671.002
44_T49_K0.220631.002
240_V243_E0.219520.997
338_H353_H0.218980.995
330_G333_R0.216680.984
95_L109_L0.216650.984
89_S94_A0.216520.984
263_D267_A0.216320.983
256_S265_W0.216260.982
234_R254_Y0.216130.982
88_L109_L0.215720.980
121_P143_E0.214160.973
245_W271_P0.213710.971
86_G95_L0.213650.971
49_K94_A0.211860.962
104_L128_G0.211740.962
245_W290_S0.211410.960
101_G105_R0.211380.960
281_E299_G0.21110.959
194_Q244_F0.211010.959
357_S366_L0.210750.957
59_N65_L0.210320.955
244_F288_F0.210270.955
219_W230_K0.209770.953
217_R230_K0.209650.952
89_S92_D0.209630.952
205_F219_W0.209310.951
295_K326_D0.208640.948
72_I180_R0.205610.934
234_R269_Y0.205080.932
255_D285_C0.204920.931
276_R332_F0.204340.928
114_E117_V0.203830.926
364_W379_L0.203170.923
53_A86_G0.202890.922
240_V254_Y0.202240.919
42_C86_G0.202220.919
254_Y263_D0.201260.914
134_S200_P0.201150.914
196_S201_T0.200960.913
98_V102_R0.200680.912
46_D49_K0.200650.912
194_Q243_E0.199340.906
243_E252_I0.19920.905
299_G323_Y0.198230.901
246_V251_T0.198040.900
192_H206_C0.197070.895
353_H367_F0.196890.894
218_I254_Y0.196530.893
52_F72_I0.19620.891
135_D138_K0.195920.890
215_D220_T0.195650.889
40_Q86_G0.194590.884
272_D328_E0.194250.882
285_C288_F0.193640.880
49_K66_D0.193520.879
329_A333_R0.192960.877
43_F290_S0.191510.870
41_N50_L0.190710.866
43_F245_W0.19070.866
358_F365_V0.189860.863
108_D112_L0.189710.862
91_D94_A0.189250.860
87_F96_Y0.189150.859
195_F223_T0.188280.855
231_V234_R0.187380.851
197_P245_W0.187010.850
254_Y276_R0.18650.847
251_T270_D0.186120.846
88_L130_W0.185630.843
201_T224_D0.185440.842
268_G327_V0.185380.842
217_R220_T0.183770.835
83_T97_Y0.183550.834
99_K105_R0.183090.832
140_V203_I0.183060.832
281_E319_D0.182370.828
129_T194_Q0.182330.828
361_D364_W0.182260.828
354_P370_D0.180980.822
48_R201_T0.180330.819
270_D277_R0.17970.816
79_P99_K0.179030.813
175_L178_G0.178970.813
125_K128_G0.178880.813
296_L324_L0.178710.812
216_Q254_Y0.178290.810
269_Y276_R0.178190.809
207_H215_D0.176870.803
375_P379_L0.176770.803
295_K328_E0.17660.802
288_F297_F0.176520.802
130_W139_L0.176270.801
114_E276_R0.176080.800
89_S93_R0.175890.799
173_I180_R0.175680.798
245_W252_I0.175520.797
324_L358_F0.175380.797
369_S374_P0.174660.793
286_S302_G0.174610.793
110_D272_D0.173260.787
229_K274_G0.173020.786
141_G173_I0.172890.785
242_H287_H0.172860.785
94_A108_D0.172610.784
326_D330_G0.172510.784
353_H369_S0.171410.779
290_S358_F0.171130.777
174_D178_G0.17080.776
301_G321_W0.170570.775
325_F332_F0.170270.774
281_E301_G0.170210.773
79_P101_G0.169740.771
255_D288_F0.169530.770
250_S363_K0.169230.769
354_P368_R0.169160.768
120_V141_G0.168860.767
369_S373_G0.168690.766
66_D70_G0.168090.764
66_D72_I0.168070.764
288_F299_G0.167850.763
120_V125_K0.167680.762
190_L193_V0.167680.762
300_D320_P0.167310.760
128_G141_G0.167160.759
54_S60_R0.166950.758
51_L62_L0.166390.756
298_V322_I0.166370.756
143_E167_H0.166320.756
250_S270_D0.166310.756
54_S63_Y0.165820.753
143_E169_R0.165510.752
202_L220_T0.164930.749
79_P83_T0.164740.748
289_M298_V0.164240.746
65_L72_I0.16410.745
300_D353_H0.16370.744
83_T86_G0.163620.743
327_V330_G0.163620.743
204_M243_E0.163470.743
43_F67_L0.163190.741
280_M283_P0.162830.740
234_R263_D0.16280.740
285_C299_G0.162750.739
133_N138_K0.16230.737
60_R63_Y0.161840.735
271_P274_G0.161480.734
110_D176_K0.161260.733
168_C185_E0.161030.732
366_L379_L0.160920.731
353_H356_P0.160680.730
205_F221_I0.160590.730
255_D264_F0.160580.729
256_S267_A0.160250.728
301_G323_Y0.160070.727
326_D331_R0.159930.727
199_D202_L0.159870.726
72_I75_L0.159760.726
290_S327_V0.159680.725
76_T79_P0.159550.725
53_A60_R0.159490.725
121_P124_W0.159240.723
94_A296_L0.158990.722
42_C88_L0.158930.722
188_D207_H0.158760.721
108_D113_E0.158390.720
62_L83_T0.157560.716
88_L95_L0.157490.715
180_R332_F0.157440.715
280_M325_F0.157330.715
46_D92_D0.157110.714
243_E254_Y0.156970.713
107_V114_E0.156750.712
64_L73_T0.156590.711
84_F98_V0.156210.710
321_W334_K0.156080.709
270_D326_D0.155860.708
203_I223_T0.155680.707
224_D272_D0.155430.706
189_W239_S0.154910.704
233_R269_Y0.154860.704
48_R66_D0.15450.702
78_G99_K0.153940.699
53_A83_T0.153260.696
204_M220_T0.153150.696
367_F376_A0.152770.694
299_G319_D0.151910.690
64_L88_L0.15180.690
97_Y101_G0.151690.689
73_T112_L0.151540.688
246_V294_G0.151440.688
167_H173_I0.151380.688
87_F128_G0.150990.686
368_R375_P0.150930.686
250_S272_D0.15090.686
329_A332_F0.150770.685
109_L271_P0.150340.683
175_L327_V0.150090.682
179_E275_E0.150070.682
172_T195_F0.149840.681
84_F126_G0.149590.680
266_I288_F0.149410.679
42_C244_F0.149110.677
53_A97_Y0.148880.676
61_N74_Q0.148590.675
68_A110_D0.148420.674
290_S297_F0.148420.674
43_F358_F0.148310.674
275_E331_R0.148160.673
248_D294_G0.148150.673
49_K110_D0.147760.671
245_W358_F0.147660.671
88_L290_S0.1470.668
263_D269_Y0.146550.666
192_H242_H0.146270.664
43_F195_F0.146020.663
43_F360_P0.145430.661
75_L79_P0.145370.660
366_L377_V0.144840.658
338_H372_E0.144830.658
89_S106_R0.144760.658
251_T290_S0.144690.657
59_N64_L0.14460.657
372_E378_Y0.144230.655
251_T327_V0.144210.655
108_D115_R0.143660.653
324_L333_R0.143590.652
129_T193_V0.14320.651
121_P167_H0.14310.650
88_L245_W0.143050.650
223_T226_S0.142980.650
49_K138_K0.142560.648
196_S200_P0.142560.648
84_F241_G0.141940.645
253_W266_I0.141940.645
93_R137_T0.141660.644
236_E240_V0.141630.643
47_G51_L0.140690.639
120_V143_E0.140690.639
186_D207_H0.140450.638
89_S96_Y0.140380.638
133_N137_T0.13970.635
195_F290_S0.139640.634
251_T277_R0.139470.634
67_L109_L0.139110.632
335_L338_H0.138640.630
114_E180_R0.138560.629
70_G73_T0.138470.629
191_G208_E0.138040.627
176_K224_D0.137760.626
326_D333_R0.137760.626
54_S65_L0.136310.619
291_S298_V0.135980.618
141_G171_F0.135940.618
110_D328_E0.135690.616
134_S137_T0.135670.616
94_A115_R0.135480.615
121_P128_G0.135180.614
222_N227_N0.135140.614
66_D108_D0.135050.614
138_K172_T0.135020.613
116_V182_V0.134790.612
206_C243_E0.134770.612
53_A59_N0.13450.611
356_P365_V0.13440.611
273_T276_R0.134230.610
279_L282_M0.133890.608
334_K338_H0.133430.606
241_G257_Y0.133210.605
171_F182_V0.133150.605
295_K363_K0.133080.605
43_F47_G0.132980.604
191_G241_G0.132790.603
202_L245_W0.132770.603
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
1nr0A0.85491000.171
1nr0A0.86791000.172
2ymuA0.77721000.212
1vyhC0.79271000.223
3iz6a0.81351000.227
3sfzA0.86531000.229
2ymuA0.79531000.242
3pe7A0.98191000.245
3sfzA0.82641000.252
4j87A0.74871000.252

Page generated in 0.0379 seconds.