GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MMS19_C - RNAPII transcription regulator C-terminal
Pfam: PF12460 (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: CL0020
Length: 415
Sequences: 1916
Seq/Len: 4.62
HH_delta: 0.525 (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
60_C106_S0.169063.048
333_K372_Q0.133422.405
138_D142_S0.131522.371
286_G334_E0.113042.038
281_S330_E0.110731.996
321_F362_E0.105831.908
290_A343_Y0.104911.891
194_L213_L0.10371.870
280_L292_A0.102031.840
370_L388_T0.099561.795
393_L400_I0.097131.751
270_T319_R0.095081.714
22_I25_A0.091541.650
139_E144_F0.091151.643
286_G339_I0.08481.529
138_D145_L0.084021.515
405_S409_P0.083231.501
60_C63_I0.083061.498
47_L67_L0.082821.493
334_E339_I0.081051.461
23_L32_S0.080651.454
250_A254_L0.080261.447
119_R195_L0.080161.445
380_D389_L0.079931.441
406_S409_P0.07931.430
114_L117_L0.078011.406
124_I178_L0.078011.406
340_K376_L0.077581.399
20_E24_E0.075651.364
267_P277_L0.074831.349
189_E192_Q0.074631.346
259_K295_I0.073751.330
253_I256_W0.073731.329
323_Q327_K0.07341.323
389_L393_L0.072931.315
347_L351_L0.072731.311
188_E192_Q0.072691.311
238_I252_E0.072671.310
287_Q342_N0.072531.308
398_E401_S0.072441.306
215_A218_V0.072411.305
375_S410_R0.072371.305
25_A28_A0.071961.297
333_K365_T0.071311.286
273_L293_F0.070871.278
370_L404_L0.070871.278
195_L270_T0.070851.277
175_L217_L0.070591.273
319_R323_Q0.070271.267
190_L357_S0.070141.265
56_S59_Y0.070121.264
140_L144_F0.06991.260
213_L288_Q0.069891.260
61_H110_D0.069831.259
27_A113_V0.06961.255
323_Q326_P0.069471.252
281_S328_L0.069461.252
45_N142_S0.069081.245
328_L350_L0.068931.243
62_A209_A0.068881.242
142_S145_L0.06881.240
32_S44_L0.068551.236
114_L144_F0.068541.236
330_E333_K0.068471.234
272_L276_L0.068321.232
405_S408_I0.068081.227
56_S65_S0.067661.220
192_Q196_N0.067641.219
395_E400_I0.067461.216
119_R130_P0.067291.213
177_S194_L0.066791.204
344_L348_S0.066661.202
368_P404_L0.066591.201
267_P271_E0.066481.199
332_F403_H0.066431.198
356_K359_L0.065371.179
128_L132_K0.065231.176
246_L250_A0.065121.174
107_S110_D0.065061.173
376_L381_V0.065031.172
297_L350_L0.064981.172
367_L393_L0.064651.166
389_L400_I0.064491.163
138_D143_L0.06431.159
36_L39_L0.063871.152
254_L259_K0.063661.148
327_K330_E0.063641.147
47_L66_T0.063581.146
364_P370_L0.063061.137
105_Q111_D0.0631.136
235_L275_K0.062811.132
371_L385_S0.06281.132
192_Q214_L0.062071.119
105_Q322_T0.061881.116
267_P297_L0.06171.112
293_F297_L0.061561.110
382_L385_S0.061411.107
229_E232_D0.061361.106
358_V392_I0.061241.104
325_L358_V0.061081.101
218_V236_Q0.060611.093
367_L403_H0.060591.092
374_L385_S0.060321.088
384_S389_L0.059921.080
196_N200_S0.059891.080
27_A32_S0.059881.080
186_D196_N0.059651.075
47_L234_L0.059561.074
36_L43_L0.059541.073
48_S67_L0.05911.066
361_P365_T0.059031.064
350_L353_N0.058881.062
361_P364_P0.058831.061
46_K121_I0.058621.057
271_E274_D0.058471.054
22_I43_L0.058211.049
297_L301_D0.058131.048
355_P395_E0.058131.048
238_I241_S0.057911.044
41_I45_N0.057851.043
265_G299_D0.057671.040
393_L396_A0.057371.034
141_Y235_L0.057361.034
57_S398_E0.057261.032
141_Y190_L0.057151.030
248_P252_E0.057021.028
349_H353_N0.057021.028
290_A294_G0.056991.027
236_Q255_I0.056951.027
114_L118_S0.056831.025
228_D232_D0.056791.024
69_S293_F0.05671.022
191_L282_S0.056611.021
259_K265_G0.05661.020
199_L239_S0.056521.019
268_L273_L0.05651.019
384_S391_M0.056391.017
248_P254_L0.056321.015
145_L194_L0.056221.014
366_L392_I0.056191.013
45_N245_E0.056171.013
293_F369_L0.056111.012
187_L194_L0.0561.010
184_L226_D0.055971.009
118_S347_L0.055961.009
236_Q243_D0.055881.007
75_Q117_L0.055761.005
296_L412_L0.055731.005
96_F199_L0.055721.005
385_S396_A0.055711.004
21_R25_A0.05551.001
331_G339_I0.055491.000
328_L338_E0.055461.000
400_I404_L0.055451.000
26_L206_S0.055260.996
321_F324_V0.055230.996
345_T355_P0.05510.993
124_I128_L0.054940.991
107_S145_L0.054920.990
337_D348_S0.05490.990
116_L119_R0.054870.989
250_A255_I0.054870.989
72_E123_L0.054860.989
402_E405_S0.054810.988
42_R113_V0.054790.988
37_E88_H0.054720.987
276_L292_A0.054640.985
366_L385_S0.054510.983
176_C391_M0.054440.982
248_P251_L0.054420.981
296_L397_P0.054360.980
382_L411_L0.054350.980
68_Q121_I0.054330.980
43_L55_S0.054240.978
388_T391_M0.054190.977
333_K377_P0.054160.976
23_L38_T0.054120.976
214_L218_V0.054110.976
374_L389_L0.05410.975
75_Q128_L0.054080.975
136_I347_L0.0540.974
265_G390_K0.053990.973
82_D87_F0.053930.972
210_A214_L0.053920.972
364_P368_P0.053860.971
382_L397_P0.053850.971
138_D196_N0.053830.971
27_A62_A0.053790.970
265_G303_V0.053790.970
266_H281_S0.053770.969
358_V361_P0.053760.969
183_S210_A0.05370.968
54_E59_Y0.053640.967
344_L385_S0.053570.966
35_I39_L0.053390.963
113_V116_L0.053370.962
130_P134_Q0.053370.962
135_E142_S0.053260.960
345_T353_N0.053250.960
338_E403_H0.053190.959
269_A301_D0.053150.958
276_L279_L0.053140.958
217_L223_D0.053130.958
83_N86_Y0.053040.956
242_E275_K0.053020.956
175_L368_P0.052990.955
42_R75_Q0.05290.954
75_Q124_I0.052880.953
223_D227_L0.052870.953
225_D261_L0.052770.951
361_P368_P0.052770.951
329_L392_I0.052760.951
320_F354_V0.052710.950
67_L249_Q0.052690.950
42_R45_N0.052680.950
381_V400_I0.052680.950
374_L386_L0.052670.950
325_L352_K0.052650.949
194_L199_L0.05260.948
233_S282_S0.05260.948
106_S110_D0.052560.948
85_W88_H0.052520.947
269_A276_L0.052490.946
42_R46_K0.052430.945
30_S33_P0.052370.944
142_S278_E0.052370.944
348_S355_P0.052250.942
58_D61_H0.052190.941
60_C286_G0.052140.940
71_L128_L0.052130.940
362_E392_I0.052120.940
226_D232_D0.052110.940
346_A353_N0.052020.938
139_E142_S0.051920.936
230_F407_L0.051910.936
320_F339_I0.051780.934
85_W107_S0.051740.933
106_S147_P0.051740.933
339_I342_N0.051720.932
163_Q166_R0.051710.932
402_E412_L0.051610.930
182_V301_D0.051560.930
332_F344_L0.051490.928
110_D113_V0.051480.928
371_L401_S0.051470.928
116_L213_L0.051440.927
243_D248_P0.051410.927
243_D255_I0.051410.927
351_L395_E0.051320.925
60_C113_V0.051290.925
389_L411_L0.051230.924
63_I106_S0.051170.923
224_D303_V0.051150.922
261_L268_L0.051130.922
286_G289_A0.051110.921
54_E106_S0.051060.921
136_I139_E0.051060.921
363_L393_L0.051050.920
392_I400_I0.051030.920
193_S196_N0.0510.919
344_L355_P0.050990.919
342_N348_S0.050980.919
231_L252_E0.050910.918
27_A42_R0.05090.918
348_S394_E0.050880.917
331_G334_E0.050870.917
64_L172_S0.050810.916
88_H367_L0.050730.915
237_S289_A0.050720.914
362_E367_L0.05070.914
376_L383_L0.050690.914
134_Q138_D0.050630.913
166_R208_L0.050580.912
191_L274_D0.050560.912
370_L400_I0.050430.909
265_G354_V0.050340.908
328_L346_A0.050230.906
351_L362_E0.050180.905
262_V373_S0.050150.904
135_E146_S0.050130.904
295_I299_D0.050130.904
75_Q386_L0.050080.903
401_S405_S0.050080.903
293_F407_L0.050050.902
292_A296_L0.050040.902
66_T120_L0.050020.902
67_L75_Q0.049990.901
122_N127_S0.049990.901
43_L276_L0.049970.901
294_G353_N0.049960.901
386_L400_I0.049910.900
373_S380_D0.049820.898
408_I412_L0.049810.898
255_I265_G0.049780.897
207_R210_A0.049760.897
21_R30_S0.049720.896
291_K342_N0.049660.895
291_K299_D0.049640.895
178_L214_L0.049630.895
192_Q235_L0.049630.895
96_F408_I0.049570.894
141_Y367_L0.049560.894
113_V139_E0.049540.893
168_V260_A0.04950.892
217_L244_S0.04940.891
35_I165_S0.049380.890
97_E139_E0.049360.890
21_R24_E0.049350.890
212_Q370_L0.049350.890
129_S194_L0.049310.889
267_P302_D0.049280.888
242_E324_V0.049230.888
277_L392_I0.049190.887
27_A31_T0.049180.887
340_K343_Y0.049180.887
342_N349_H0.049160.886
195_L273_L0.049150.886
350_L366_L0.049150.886
202_E214_L0.049130.886
362_E376_L0.049090.885
248_P336_D0.049050.884
270_T303_V0.049020.884
201_S206_S0.049010.884
395_E401_S0.048950.883
251_L290_A0.048930.882
60_C332_F0.048920.882
385_S400_I0.048920.882
277_L357_S0.048870.881
207_R367_L0.048830.880
381_V387_E0.048830.880
194_L284_E0.048810.880
237_S240_S0.048790.880
165_S366_L0.048750.879
384_S388_T0.048720.878
133_Q141_Y0.048680.878
399_L407_L0.048680.878
273_L277_L0.048660.877
59_Y351_L0.048590.876
234_L256_W0.048580.876
298_S353_N0.048540.875
320_F324_V0.048510.875
327_K332_F0.048450.874
386_L395_E0.048440.873
343_Y351_L0.048430.873
294_G297_L0.048390.872
82_D85_W0.048370.872
19_Y27_A0.048270.870
365_T369_L0.048260.870
363_L399_L0.048250.870
275_K279_L0.048240.870
404_L407_L0.048240.870
207_R248_P0.048230.870
252_E391_M0.048230.870
71_L218_V0.048220.869
107_S116_L0.048210.869
291_K393_L0.048170.868
369_L380_D0.048150.868
123_L126_R0.04810.867
175_L185_P0.048080.867
223_D264_R0.048030.866
371_L399_L0.0480.865
175_L282_S0.047990.865
291_K297_L0.047990.865
321_F325_L0.047990.865
26_L128_L0.047930.864
130_P225_D0.047930.864
121_I330_E0.047840.863
254_L272_L0.047820.862
220_K346_A0.047790.862
224_D276_L0.047770.861
318_Q326_P0.047760.861
330_E337_D0.047750.861
31_T213_L0.047730.861
56_S400_I0.047720.860
292_A295_I0.047680.860
227_L230_F0.047670.859
182_V190_L0.047640.859
147_P274_D0.047630.859
24_E28_A0.047610.858
284_E287_Q0.047560.857
253_I337_D0.047530.857
369_L411_L0.047520.857
82_D374_L0.047510.857
165_S201_S0.047510.857
380_D383_L0.04750.856
361_P389_L0.047490.856
376_L385_S0.047480.856
44_L392_I0.047390.854
293_F349_H0.047340.854
363_L369_L0.047280.852
277_L327_K0.047260.852
126_R195_L0.047230.852
140_L146_S0.047230.852
345_T348_S0.047150.850
135_E196_N0.047130.850
169_I172_S0.047110.849
328_L340_K0.04710.849
196_N364_P0.047070.849
129_S133_Q0.047020.848
135_E293_F0.047010.848
110_D368_P0.046980.847
130_P224_D0.046960.847
319_R330_E0.046950.846
263_M296_L0.046830.844
364_P406_S0.046790.844
67_L197_L0.046770.843
246_L251_L0.046770.843
298_S352_K0.046750.843
375_S406_S0.046740.843
294_G328_L0.046730.843
22_I28_A0.046720.842
199_L210_A0.046710.842
388_T392_I0.04670.842
381_V384_S0.046690.842
215_A219_N0.046680.842
269_A297_L0.046680.842
251_L344_L0.046660.841
26_L30_S0.046640.841
328_L348_S0.046520.839
298_S342_N0.04650.838
131_E227_L0.046470.838
66_T114_L0.046440.837
354_V390_K0.046430.837
248_P287_Q0.046420.837
192_Q233_S0.046410.837
364_P375_S0.046410.837
294_G345_T0.04640.837
23_L73_K0.046310.835
97_E146_S0.046310.835
368_P382_L0.04630.835
290_A331_G0.046290.835
192_Q330_E0.046270.834
281_S366_L0.046240.834
251_L291_K0.046220.833
341_S350_L0.046190.833
320_F343_Y0.046170.832
361_P396_A0.046170.832
219_N295_I0.046160.832
189_E325_L0.046120.832
67_L375_S0.04610.831
342_N366_L0.046080.831
42_R374_L0.046060.830
34_Q38_T0.046010.830
301_D354_V0.0460.829
163_Q203_D0.045990.829
26_L274_D0.045950.828
263_M389_L0.045950.828
105_Q135_E0.045940.828
138_D185_P0.045940.828
339_I354_V0.045940.828
344_L382_L0.045930.828
351_L355_P0.045920.828
33_P37_E0.045910.828
273_L279_L0.045870.827
56_S384_S0.045850.827
254_L325_L0.04580.826
216_S296_L0.045790.826
224_D238_I0.045790.826
379_A382_L0.045720.824
127_S140_L0.045710.824
112_R120_L0.045680.824
297_L341_S0.045670.823
293_F318_Q0.045660.823
293_F324_V0.045620.822
297_L321_F0.045610.822
243_D246_L0.04560.822
208_L235_L0.045550.821
125_V173_A0.045510.821
121_I395_E0.045490.820
218_V346_A0.045450.819
225_D333_K0.045450.819
218_V301_D0.045370.818
217_L276_L0.045360.818
273_L365_T0.045320.817
294_G366_L0.045320.817
86_Y97_E0.045310.817
408_I411_L0.04530.817
318_Q322_T0.045290.817
84_S367_L0.045270.816
23_L227_L0.045260.816
185_P189_E0.045220.815
342_N345_T0.045210.815
328_L351_L0.045190.815
128_L136_I0.045180.815
87_F194_L0.045160.814
345_T349_H0.045160.814
343_Y350_L0.045140.814
44_L244_S0.045090.813
73_K276_L0.045090.813
172_S332_F0.045020.812
195_L280_L0.044990.811
185_P192_Q0.044970.811
344_L370_L0.044930.810
404_L411_L0.044890.809
142_S214_L0.044830.808
96_F371_L0.044790.808
203_D206_S0.044750.807
231_L274_D0.044740.807
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
4fddA0.90121000.525
3w3wA0.88671000.543
3w3wA0.91571000.56
1u6gC0.89161000.566
2bptA0.89641000.574
1u6gC0.901299.90.575
4fddA0.889299.90.576
1qgrA0.896499.90.583
2bptA0.925399.90.585
1qgrA0.896499.90.6
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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