GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FERM_M - FERM central domain
Pfam: PF00373 (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: 126
Sequences: 1335
Seq/Len: 10.6
HH_delta: 0.1 (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
22_V111_F0.522083.505
48_D101_G0.385712.590
21_D26_R0.367562.468
15_Y41_Q0.356752.395
39_A99_L0.32222.163
12_H108_K0.305552.051
17_Q21_D0.294591.978
36_K39_A0.292811.966
43_Q48_D0.292321.963
20_R24_Q0.276821.858
33_D36_K0.248281.667
102_M110_Q0.235991.584
88_W92_I0.23411.572
95_Q98_K0.231451.554
52_E55_H0.230711.549
50_N55_H0.222551.494
43_Q96_H0.210891.416
40_L107_A0.20671.388
73_I88_W0.201051.350
118_L123_S0.196851.322
93_L96_H0.196441.319
103_S106_E0.194631.307
118_L121_Y0.188721.267
18_A115_C0.188641.266
43_Q47_G0.180191.210
18_A112_L0.178331.197
95_Q99_L0.172941.161
116_Q125_F0.171161.149
7_D10_T0.170271.143
102_M107_A0.170161.142
81_K98_K0.166451.117
35_I92_I0.164821.107
6_D14_L0.16161.085
47_G96_H0.161531.084
10_T16_L0.160941.080
5_I10_T0.160721.079
41_Q111_F0.157781.059
43_Q101_G0.155371.043
73_I92_I0.155091.041
23_L111_F0.155031.041
18_A111_F0.154951.040
15_Y108_K0.154761.039
93_L97_K0.150511.010
36_K99_L0.150341.009
10_T14_L0.149431.003
94_E97_K0.148740.999
16_L19_R0.146760.985
22_V74_P0.145540.977
17_Q40_L0.14540.976
22_V43_Q0.144370.969
110_Q113_Q0.144360.969
49_Y96_H0.14420.968
104_P108_K0.143820.966
50_N53_Q0.143730.965
49_Y55_H0.143440.963
50_N54_E0.143380.963
83_M87_E0.142810.959
113_Q117_S0.141880.953
38_A111_F0.140770.945
116_Q120_T0.140220.941
6_D23_L0.137690.924
13_L17_Q0.137420.923
54_E100_R0.136750.918
87_E91_R0.135230.908
102_M106_E0.13490.906
20_R27_L0.134260.901
99_L102_M0.132740.891
8_P38_A0.132520.890
9_I30_S0.132290.888
8_P11_R0.131550.883
80_I84_K0.129370.869
12_H16_L0.129330.868
14_L109_L0.128970.866
17_Q20_R0.127240.854
6_D106_E0.126390.849
99_L124_T0.1260.846
46_Y53_Q0.125820.845
28_P125_F0.125050.840
112_L120_T0.124910.839
45_E63_E0.124840.838
13_L26_R0.123790.831
35_I95_Q0.123530.829
24_Q62_P0.12350.829
15_Y90_K0.122960.826
22_V31_E0.122520.823
120_T124_T0.121940.819
120_T125_F0.12190.818
44_A107_A0.12150.816
91_R94_E0.121420.815
5_I14_L0.121130.813
55_H61_D0.1210.812
44_A108_K0.119650.803
19_R45_E0.119560.803
86_K119_P0.119390.802
74_P80_I0.119140.800
114_I120_T0.118960.799
10_T121_Y0.118380.795
26_R46_Y0.118290.794
103_S110_Q0.117430.788
114_I117_S0.117060.786
42_L72_F0.116920.785
13_L98_K0.116810.784
120_T123_S0.116510.782
19_R29_C0.116390.781
28_P113_Q0.116360.781
23_L73_I0.116290.781
15_Y44_A0.115910.778
32_E95_Q0.115460.775
28_P110_Q0.115250.774
36_K40_L0.115250.774
107_A115_C0.115250.774
21_D27_L0.11420.767
31_E36_K0.11420.767
46_Y55_H0.113830.764
10_T13_L0.113750.764
88_W125_F0.113680.763
99_L106_E0.113460.762
62_P72_F0.113350.761
12_H21_D0.112980.759
35_I98_K0.112950.758
19_R34_A0.112830.758
19_R118_L0.112770.757
19_R73_I0.112630.756
94_E98_K0.112230.753
83_M93_L0.111830.751
48_D96_H0.111810.751
52_E82_K0.111390.748
25_G53_Q0.111170.746
94_E103_S0.111030.745
30_S39_A0.110880.744
26_R82_K0.110870.744
26_R88_W0.110670.743
22_V38_A0.110390.741
94_E117_S0.110370.741
15_Y19_R0.110230.740
31_E91_R0.110060.739
92_I112_L0.109670.736
46_Y52_E0.109610.736
72_F82_K0.108380.728
37_L111_F0.108010.725
123_S126_F0.107670.723
11_R15_Y0.107530.722
52_E103_S0.107370.721
33_D114_I0.107090.719
7_D36_K0.106580.716
54_E97_K0.106460.715
105_E112_L0.105960.711
13_L108_K0.10470.703
98_K123_S0.104540.702
24_Q32_E0.104020.698
82_K102_M0.10390.698
120_T126_F0.103840.697
22_V28_P0.103590.695
23_L38_A0.103530.695
37_L100_R0.103390.694
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
2i1jA0.920699.90.1
1ef1A0.920699.90.107
1h4rA0.920699.90.114
3qijA0.87399.90.122
4dxaB0.928699.90.138
1mixA0.888999.90.152
2al6A0.960399.90.165
3ivfA0.888999.80.172
3pvlA0.904899.80.186
4f7gA0.888999.80.187

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