GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Filament - Intermediate filament protein
Pfam: PF00038 (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. )
Length: 312
Sequences: 2971
Seq/Len: 9.52
HH_delta: 0.54 (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
20_V23_L0.286542.574
105_L108_L0.272342.447
172_R176_A0.243752.190
56_L59_L0.223942.012
240_A244_R0.218851.966
171_L174_I0.214941.931
239_N242_L0.212451.909
299_I302_Y0.20681.858
63_I66_L0.20561.847
218_L221_L0.199051.788
288_L292_K0.197441.774
23_L27_N0.195571.757
80_L84_L0.191891.724
27_N30_L0.190521.712
256_E259_E0.190031.707
143_E147_L0.189681.704
98_R101_L0.189181.699
295_L302_Y0.188261.691
19_K23_L0.183981.653
126_I129_L0.182431.639
77_I80_L0.181171.628
246_L249_L0.180551.622
239_N243_E0.180161.618
95_L99_K0.179711.614
288_L302_Y0.178731.606
298_E302_Y0.176091.582
79_N83_E0.170681.533
145_E149_E0.16971.524
233_E236_R0.169641.524
63_I70_K0.167171.502
288_L291_V0.167031.501
53_E57_R0.164491.478
110_K114_E0.164141.475
13_L17_I0.164041.474
51_M55_E0.162571.460
32_S36_E0.162121.456
35_E39_E0.161961.455
232_L235_L0.161121.447
84_L87_L0.160781.444
277_E280_R0.159891.436
83_E86_D0.159651.434
168_S172_R0.158661.425
70_K74_E0.158181.421
72_R76_E0.156511.406
91_Y94_E0.156321.404
190_E193_Y0.156291.404
119_R123_E0.155681.399
251_Q254_D0.155621.398
16_Y20_V0.154671.389
271_L274_L0.154061.384
248_E252_R0.152091.366
175_R179_E0.149481.343
295_L298_E0.149141.340
12_R16_Y0.149051.339
16_Y23_L0.146891.320
61_R65_D0.146261.314
123_E127_Q0.143911.293
27_N34_I0.143581.290
87_L90_K0.142641.281
173_E177_Q0.141861.274
206_K210_E0.141531.271
24_E27_N0.141431.271
18_E21_R0.139591.254
42_G45_V0.13941.252
284_E292_K0.137631.236
110_K113_D0.136111.223
82_E86_D0.135761.220
193_Y197_L0.135621.218
300_A303_R0.135421.217
191_E195_S0.135021.213
29_R33_E0.134881.212
230_A234_S0.134761.211
292_K295_L0.134061.204
197_L200_L0.133871.203
176_A180_E0.132941.194
292_K302_Y0.132871.194
243_E247_R0.132841.193
121_D125_Q0.13271.192
287_E297_A0.132181.187
116_T120_V0.131631.182
62_Q65_D0.131451.181
144_I149_E0.129881.167
147_L151_I0.129721.165
275_R279_A0.129721.165
59_L62_Q0.12891.158
144_I147_L0.128431.154
54_E58_E0.127981.150
91_Y95_L0.127511.145
13_L16_Y0.127361.144
216_E219_K0.127271.143
261_Q264_I0.127241.143
298_E303_R0.12681.139
125_Q130_K0.126681.138
80_L83_E0.126361.135
11_D15_S0.126291.135
22_F26_E0.126071.133
286_Q296_D0.125561.128
198_E202_Q0.125311.126
292_K296_D0.125281.125
213_S216_E0.124951.122
44_E65_D0.123771.112
240_A243_E0.123511.110
12_R17_I0.123391.108
56_L60_R0.123211.107
260_Y264_I0.122991.105
266_E270_E0.12291.104
170_A173_E0.122781.103
65_D69_E0.122761.103
104_E107_S0.122371.099
178_Y181_I0.122011.096
178_Y182_A0.121711.093
23_L30_L0.121631.093
295_L299_I0.121051.087
131_E134_E0.121041.087
203_Q207_S0.120881.086
276_E279_A0.120661.084
283_R287_E0.120171.080
109_R113_D0.120011.078
78_D82_E0.11951.074
69_E72_R0.119351.072
46_S50_E0.11851.065
194_Q198_E0.118411.064
146_E149_E0.117711.057
170_A174_I0.1171.051
247_R250_E0.116991.051
211_L214_A0.116931.050
83_E87_L0.116871.050
285_Y288_L0.116171.044
11_D14_A0.116031.042
204_S208_S0.115881.041
207_S210_E0.115691.039
273_E277_E0.115391.037
33_E38_R0.115271.036
14_A17_I0.114981.033
265_A268_E0.114661.030
53_E56_L0.114531.029
75_L82_E0.114441.028
293_L297_A0.114271.027
267_L271_L0.113851.023
98_R102_E0.11381.022
166_D170_A0.113781.022
120_V124_N0.113641.021
291_V302_Y0.113611.021
68_K72_R0.113541.020
52_Y55_E0.113541.020
67_S70_K0.113451.019
94_E98_R0.113361.018
274_L277_E0.113271.018
220_E227_S0.113161.017
24_E33_E0.113111.016
222_R229_Q0.113061.016
149_E152_Q0.112981.015
17_I20_V0.112571.011
88_R92_E0.112291.009
87_L91_Y0.112171.008
49_K52_Y0.11211.007
197_L216_E0.111571.002
197_L201_R0.111571.002
63_I68_K0.11141.001
268_E275_R0.111150.999
28_K31_E0.110980.997
25_Q28_K0.110960.997
281_Q291_V0.110930.997
169_A173_E0.110850.996
248_E251_Q0.110480.992
20_V24_E0.110330.991
170_A175_R0.110080.989
290_D294_A0.110060.989
273_E276_E0.109730.986
28_K32_S0.109480.984
225_I228_L0.108890.978
39_E186_R0.108860.978
284_E296_D0.108730.977
104_E108_L0.108580.975
126_I130_K0.108560.975
112_L115_E0.108420.974
15_S19_K0.108380.974
295_L301_T0.108350.973
16_Y27_N0.10820.972
288_L298_E0.107580.966
199_E203_Q0.107360.964
285_Y296_D0.107240.963
197_L204_S0.107130.962
21_R24_E0.107080.962
289_L292_K0.106730.959
221_L224_Q0.106380.956
62_Q70_K0.106220.954
86_D90_K0.106210.954
211_L215_K0.106140.954
46_S53_E0.106110.953
261_Q265_A0.106080.953
285_Y292_K0.106070.953
264_I267_L0.105910.951
204_S207_S0.105880.951
266_E269_E0.10580.950
74_E78_D0.105660.949
16_Y19_K0.105390.947
138_Q142_E0.105220.945
67_S71_A0.105090.944
36_E40_K0.105020.943
132_E136_L0.104860.942
271_L275_R0.104820.942
192_W196_K0.104690.940
42_G46_S0.104650.940
288_L294_A0.10450.939
14_A19_K0.104470.939
20_V30_L0.104390.938
231_E234_S0.104360.938
128_S131_E0.104220.936
82_E90_K0.104130.935
20_V27_N0.104120.935
44_E49_K0.104050.935
290_D293_L0.103870.933
223_R226_Q0.103820.933
226_Q229_Q0.103750.932
12_R20_V0.10360.931
255_E258_E0.103530.930
78_D81_K0.103460.929
282_L286_Q0.102870.924
190_E196_K0.102750.923
178_Y188_E0.102670.922
284_E295_L0.102450.920
289_L294_A0.102380.920
296_D299_I0.102280.919
290_D301_T0.101610.913
25_Q29_R0.101490.912
299_I303_R0.10110.908
147_L150_Q0.100990.907
108_L125_Q0.100990.907
132_E135_F0.100520.903
262_A265_A0.100390.902
278_M282_L0.100240.901
290_D296_D0.100210.900
196_K199_E0.100170.900
298_E301_T0.099920.898
34_I37_L0.099820.897
199_E202_Q0.099820.897
22_F32_S0.099770.896
177_Q182_A0.099750.896
48_I51_M0.09970.896
294_A299_I0.099520.894
256_E260_Y0.099470.894
202_Q206_K0.099430.893
291_V298_E0.099410.893
285_Y289_L0.099380.893
99_K145_E0.09930.892
183_Q186_R0.098890.888
214_A218_L0.098890.888
142_E149_E0.098490.885
64_D67_S0.098240.883
31_E35_E0.098180.882
285_Y291_V0.098070.881
88_R94_E0.097750.878
174_I178_Y0.097750.878
23_L34_I0.097640.877
173_E176_A0.097610.877
213_S217_E0.097570.877
58_E62_Q0.097530.876
280_R284_E0.097230.873
212_E240_A0.0970.871
255_E261_Q0.096750.869
195_S199_E0.096660.868
283_R291_V0.096510.867
44_E47_R0.096320.865
79_N90_K0.096180.864
22_F25_Q0.095930.862
93_E97_E0.095840.861
198_E201_R0.095750.860
297_A300_A0.095670.859
114_E138_Q0.09560.859
225_I229_Q0.095480.858
114_E127_Q0.095470.858
187_E191_E0.095310.856
288_L295_L0.095240.856
257_R260_Y0.095140.855
32_S39_E0.094560.849
263_E266_E0.094440.848
273_E279_A0.094130.846
231_E236_R0.094110.845
228_L231_E0.09410.845
193_Y200_L0.094040.845
27_N33_E0.093970.844
37_L111_D0.093970.844
190_E194_Q0.093880.843
85_E88_R0.093660.841
105_L109_R0.093640.841
228_L232_L0.093590.841
287_E294_A0.093430.839
269_E273_E0.093190.837
65_D68_K0.093110.836
44_E51_M0.092560.832
167_L173_E0.09250.831
281_Q288_L0.092050.827
77_I83_E0.091890.825
14_A21_R0.091540.822
286_Q297_A0.091480.822
216_E233_E0.091280.820
156_T162_F0.091260.820
220_E236_R0.091240.820
291_V295_L0.091220.819
40_K43_E0.09120.819
194_Q210_E0.091180.819
181_I192_W0.091150.819
260_Y267_L0.090910.817
135_F143_E0.090840.816
51_M54_E0.090780.816
16_Y21_R0.090660.814
90_K94_E0.090540.813
78_D90_K0.090380.812
137_K141_E0.09030.811
27_N44_E0.090140.810
145_E148_R0.090030.809
62_Q66_L0.089940.808
151_I180_E0.089850.807
206_K216_E0.089820.807
143_E148_R0.089740.806
95_L103_E0.089720.806
154_S158_E0.089710.806
27_N31_E0.089680.806
267_L270_E0.089660.805
64_D69_E0.089640.805
39_E45_V0.089290.802
112_L116_T0.089270.802
264_I279_A0.089240.802
131_E138_Q0.0890.800
47_R65_D0.088970.799
201_R205_E0.088770.797
74_E83_E0.088750.797
130_K133_L0.088670.797
218_L222_R0.088670.797
199_E205_E0.088530.795
222_R225_I0.088320.793
141_E145_E0.08830.793
18_E22_F0.088280.793
106_E110_K0.088140.792
255_E265_A0.088040.791
287_E291_V0.087980.790
275_R286_Q0.087920.790
275_R297_A0.08790.790
79_N82_E0.087890.790
76_E79_N0.087890.790
263_E267_L0.087640.787
96_A127_Q0.087270.784
83_E88_R0.087180.783
293_L301_T0.087090.782
129_L133_L0.087030.782
53_E60_R0.086870.780
220_E223_R0.08680.780
82_E101_L0.086710.779
106_E274_L0.086640.778
294_A303_R0.086640.778
246_L250_E0.086540.777
44_E48_I0.086530.777
206_K209_E0.086380.776
258_E262_A0.086270.775
165_S169_A0.085850.771
40_K44_E0.085820.771
124_N128_S0.085750.770
84_L88_R0.085680.770
107_S115_E0.085610.769
183_Q187_E0.085610.769
264_I268_E0.085180.765
157_V160_D0.085170.765
99_K108_L0.085140.765
287_E293_L0.085010.764
292_K299_I0.084980.763
162_F167_L0.084960.763
75_L79_N0.084920.763
35_E38_R0.08490.763
289_L293_L0.084870.762
209_E220_E0.084830.762
163_R166_D0.084810.762
92_E97_E0.084750.761
47_R51_M0.084730.761
272_A276_E0.084730.761
201_R204_S0.084670.761
57_R61_R0.084620.760
292_K301_T0.084550.760
17_I23_L0.084320.757
199_E235_L0.084050.755
257_R274_L0.084030.755
289_L295_L0.083970.754
33_E37_L0.083730.752
254_D258_E0.083610.751
226_Q237_A0.083530.750
132_E140_H0.083530.750
13_L34_I0.083520.750
145_E194_Q0.083380.749
123_E141_E0.083270.748
296_D301_T0.083270.748
87_L94_E0.083130.747
256_E263_E0.083120.747
257_R261_Q0.082970.745
117_L120_V0.082950.745
251_Q255_E0.082930.745
105_L112_L0.08290.745
287_E300_A0.082820.744
127_Q138_Q0.082770.744
144_I148_R0.082770.744
57_R60_R0.082630.742
48_I52_Y0.082610.742
13_L24_E0.082270.739
74_E77_I0.08220.738
45_V49_K0.082150.738
286_Q298_E0.082020.737
279_A287_E0.082010.737
210_E214_A0.081990.737
197_L205_E0.081960.736
25_Q42_G0.081910.736
161_Q165_S0.081770.735
71_A78_D0.081690.734
218_L286_Q0.081650.734
219_K252_R0.08160.733
135_F139_N0.081560.733
122_L126_I0.081520.732
258_E294_A0.081370.731
170_A176_A0.081360.731
82_E85_E0.081360.731
223_R275_R0.081320.731
237_A241_S0.081220.730
263_E276_E0.080940.727
193_Y196_K0.080930.727
164_S170_A0.080920.727
180_E183_Q0.080760.726
155_V160_D0.080690.725
86_D89_R0.080590.724
120_V123_E0.080550.724
293_L300_A0.080480.723
297_A301_T0.080470.723
19_K27_N0.080420.722
184_K194_Q0.080330.722
175_R185_N0.080290.721
220_E234_S0.080240.721
238_K241_S0.08020.720
230_A233_E0.080020.719
265_A287_E0.079990.719
60_R64_D0.079960.718
21_R25_Q0.079960.718
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
3tnuA0.419999.50.54
3tnuB0.413599.50.544
1gk4A0.266990.654
1x8yA0.2724990.659
3s4rA0.282198.90.663
1i84S0.919998.90.665
3movA0.301398.80.68
1i84S0.903898.80.681
3ol1A0.381498.80.687
2xv5A0.198798.40.726
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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