GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fungal_trans - Fungal specific transcription factor domain
Pfam: PF04082 (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: CL0507
Length: 260
Sequences: 5982
Seq/Len: 23.01
HH_delta: 0.675 (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_E254_Q0.824423.986
17_R21_L0.771213.728
5_F17_R0.713043.447
16_H19_T0.662273.202
122_A150_W0.545432.637
112_W116_G0.517442.501
116_G120_R0.499052.413
122_A153_I0.495722.396
158_R223_S0.492872.383
214_F217_R0.47132.278
37_A94_A0.449322.172
144_E148_R0.446212.157
5_F20_F0.444552.149
130_E147_R0.423662.048
147_R179_P0.423612.048
93_Q145_L0.403221.949
139_D142_E0.396051.915
150_W176_I0.379551.835
3_L46_G0.376691.821
4_Y9_H0.372211.799
130_E179_P0.369121.784
96_L153_I0.366831.773
90_E93_Q0.366261.771
112_W166_R0.366131.770
2_D6_E0.358621.734
150_W171_I0.355881.720
2_D21_L0.355061.716
38_L41_A0.352271.703
41_A94_A0.350051.692
212_F216_I0.347831.682
9_H13_P0.345621.671
158_R168_P0.343281.660
252_D256_D0.337411.631
115_I119_I0.336881.629
129_R177_D0.335141.620
16_H141_E0.329311.592
151_W154_Y0.314581.521
115_I153_I0.303131.465
89_L93_Q0.30291.464
213_S217_R0.301041.455
144_E147_R0.29451.424
70_Y74_A0.293461.419
124_S166_R0.293311.418
157_D161_S0.292961.416
95_L114_L0.291261.408
172_S227_S0.290261.403
92_L149_L0.286671.386
73_R76_S0.285211.379
250_E254_Q0.284531.376
118_A153_I0.28441.375
171_I175_D0.281961.363
127_L146_R0.280111.354
20_F24_Y0.278181.345
20_F42_I0.27581.333
145_L149_L0.272081.315
253_Q257_Q0.270111.306
15_L42_I0.269061.301
122_A127_L0.265681.284
215_L219_S0.265621.284
154_Y173_D0.265491.283
40_L73_R0.265291.282
184_D187_E0.264811.280
71_F75_R0.261161.263
100_I156_L0.260551.260
126_G165_G0.259131.253
128_H150_W0.256791.241
155_I215_L0.256251.239
138_L142_E0.255341.234
138_L146_R0.253021.223
39_L43_L0.251541.216
174_E227_S0.247851.198
3_L7_N0.246951.194
36_P40_L0.246651.192
75_R78_I0.246131.190
98_L102_L0.245821.188
99_S118_A0.245331.186
15_L38_L0.245221.185
119_I153_I0.242971.175
155_I216_I0.242811.174
128_H167_P0.241721.169
41_A97_L0.240851.164
120_R123_Q0.238621.154
20_F35_S0.238461.153
173_D223_S0.237341.147
154_Y158_R0.236831.145
120_R157_D0.236771.145
74_A78_I0.236431.143
138_L143_Q0.235951.141
16_H144_E0.235221.137
173_D220_R0.233741.130
69_E73_R0.231751.120
19_T141_E0.229921.112
188_W192_S0.228691.106
2_D17_R0.226741.096
249_R252_D0.224951.087
92_L125_L0.223571.081
7_N10_P0.222071.074
172_S175_D0.221771.072
130_E146_R0.221261.070
20_F23_D0.21741.051
141_E145_L0.21681.048
113_M124_S0.215611.042
158_R173_D0.215491.042
185_D189_E0.213881.034
161_S165_G0.212461.027
150_W154_Y0.211761.024
114_L118_A0.207951.005
89_L127_L0.207941.005
123_Q167_P0.207921.005
126_G129_R0.207781.004
95_L118_A0.207631.004
23_D35_S0.206951.000
102_L110_A0.206410.998
14_I149_L0.205940.996
154_Y220_R0.205790.995
71_F74_A0.204290.988
41_A98_L0.204280.988
119_I123_Q0.204120.987
95_L117_M0.203670.985
254_Q257_Q0.202860.981
50_S53_P0.202710.980
8_V45_L0.202410.979
99_S115_I0.202330.978
173_D176_I0.202290.978
130_E134_S0.201990.976
168_P223_S0.20130.973
213_S216_I0.20090.971
4_Y13_P0.200840.971
120_R170_I0.199760.966
32_E35_S0.199690.965
102_L106_G0.198020.957
37_A40_L0.196980.952
250_E253_Q0.196430.950
92_L122_A0.195910.947
23_D90_E0.195510.945
14_I97_L0.194570.941
151_W181_P0.194510.940
45_L97_L0.193770.937
16_H145_L0.193130.934
144_E182_S0.19220.929
217_R220_R0.191680.927
93_Q149_L0.191410.925
88_S91_S0.189420.916
14_I152_C0.188920.913
5_F21_L0.188820.913
119_I170_I0.188150.910
184_D189_E0.188120.909
70_Y75_R0.186490.902
114_L117_M0.186140.900
210_S214_F0.184140.890
73_R77_L0.182250.881
188_W191_L0.182050.880
92_L99_S0.181380.877
185_D188_W0.179890.870
209_R213_S0.179730.869
35_S39_L0.179280.867
142_E146_R0.177620.859
229_L232_P0.176890.855
58_N61_S0.176420.853
28_S31_S0.175210.847
219_S223_S0.174230.842
38_L94_A0.174180.842
40_L43_L0.172640.835
119_I150_W0.172530.834
20_F39_L0.169580.820
108_P111_A0.169170.818
171_I176_I0.168750.816
19_T23_D0.168670.815
19_T145_L0.16840.814
43_L47_A0.168220.813
150_W178_V0.16650.805
18_P22_R0.166030.803
159_F215_L0.165760.801
183_D187_E0.165760.801
70_Y78_I0.164920.797
231_S234_K0.164370.795
144_E181_P0.1640.793
249_R253_Q0.1640.793
149_L153_I0.16270.787
147_R178_V0.162270.784
237_S241_S0.161960.783
96_L159_F0.161560.781
9_H17_R0.161410.780
154_Y176_I0.160550.776
110_A113_M0.160460.776
207_S210_S0.160060.774
141_E144_E0.159840.773
216_I220_R0.159380.770
3_L50_S0.158690.767
115_I118_A0.158310.765
16_H189_E0.15820.765
4_Y97_L0.158150.765
92_L121_L0.158150.765
116_G157_D0.157970.764
15_L20_F0.157050.759
151_W216_I0.156580.757
209_R212_F0.156410.756
84_S87_P0.15610.755
81_D84_S0.156050.754
171_I174_E0.155680.753
46_G49_F0.154960.749
38_L93_Q0.154260.746
140_A144_E0.154130.745
86_S91_S0.154050.745
183_D210_S0.153410.742
9_H14_I0.153240.741
210_S213_S0.153060.740
224_E228_S0.152870.739
5_F24_Y0.152740.738
112_W124_S0.152580.738
165_G230_Y0.152490.737
253_Q256_D0.150750.729
41_A45_L0.150740.729
5_F9_H0.15060.728
121_L125_L0.150530.728
113_M117_M0.15040.727
74_A98_L0.149960.725
181_P185_D0.149770.724
59_S62_L0.148720.719
14_I96_L0.148450.718
72_L78_I0.147120.711
157_D223_S0.147020.711
149_L157_D0.146780.710
16_H20_F0.146470.708
159_F222_L0.146240.707
17_R20_F0.1460.706
83_S87_P0.145250.702
43_L46_G0.14510.701
103_F106_G0.144780.700
123_Q128_H0.144330.698
42_I46_G0.14410.697
40_L70_Y0.143850.695
122_A146_R0.143810.695
183_D188_W0.143380.693
235_D238_S0.143330.693
112_W120_R0.143130.692
7_N49_F0.142880.691
41_A46_G0.142720.690
119_I171_I0.142690.690
103_F160_L0.142550.689
219_S222_L0.142540.689
215_L218_L0.141670.685
96_L152_C0.141140.682
189_E192_S0.141120.682
236_T240_D0.140950.681
238_S241_S0.140920.681
187_E190_S0.140830.681
151_W219_S0.140690.680
182_S187_E0.140610.680
211_I215_L0.140550.679
13_P152_C0.140490.679
8_V46_G0.140480.679
118_A122_A0.140150.678
229_L248_V0.139860.676
96_L118_A0.139840.676
41_A44_A0.139710.675
102_L107_N0.139670.675
128_H177_D0.139410.674
122_A171_I0.139270.673
232_P236_T0.138810.671
18_P141_E0.138770.671
115_I156_L0.138470.669
167_P171_I0.138350.669
96_L103_F0.138210.668
157_D168_P0.13810.668
126_G166_R0.137630.665
35_S38_L0.137250.664
99_S111_A0.136940.662
120_R124_S0.136620.660
119_I157_D0.13660.660
239_E249_R0.136560.660
43_L70_Y0.136320.659
91_S94_A0.13610.658
102_L111_A0.135830.657
141_E189_E0.135130.653
13_P212_F0.134590.651
55_S59_S0.134490.650
48_R101_Y0.134110.648
225_I255_L0.133840.647
237_S240_D0.133640.646
227_S231_S0.133290.644
119_I122_A0.133240.644
163_S166_R0.133010.643
38_L97_L0.132780.642
34_A91_S0.132730.642
34_A88_S0.132140.639
92_L95_L0.132040.638
37_A98_L0.132010.638
159_F163_S0.13170.637
208_S211_I0.131550.636
143_Q147_R0.131410.635
34_A37_A0.131370.635
159_F162_L0.131330.635
224_E251_L0.131130.634
82_L86_S0.130980.633
144_E180_L0.130760.632
103_F111_A0.130710.632
151_W180_L0.13070.632
115_I120_R0.13030.630
122_A128_H0.13010.629
228_S236_T0.129940.628
58_N62_L0.12980.627
161_S170_I0.129640.627
24_Y35_S0.129540.626
42_I97_L0.129240.625
74_A77_L0.128380.621
34_A38_L0.1280.619
92_L153_I0.127030.614
249_R257_Q0.126920.614
108_P163_S0.126910.614
180_L220_R0.126770.613
145_L148_R0.126660.612
5_F15_L0.126470.611
93_Q96_L0.126120.610
109_S124_S0.126090.610
49_F83_S0.126060.609
89_L149_L0.126060.609
250_E255_L0.126040.609
116_G170_I0.125550.607
217_R254_Q0.125530.607
118_A149_L0.125050.605
13_P106_G0.125040.604
150_W158_R0.124350.601
41_A114_L0.123450.597
32_E36_P0.123440.597
92_L127_L0.122890.594
87_P124_S0.122630.593
12_F152_C0.122090.590
110_A161_S0.122040.590
41_A101_Y0.1220.590
113_M120_R0.1220.590
103_F156_L0.121760.589
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
2veqA0.8808990.675
3ajfA0.28855.20.945
3lphA0.25774.80.946
1b5lA0.37694.30.947
1wu3I0.36924.20.947
1xn7A0.161530.95
2k02A0.161530.951
3m6jA0.22.80.951
2hfiA0.21152.80.951
2x7lM0.42312.70.951
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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