GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NIF - NLI interacting factor-like phosphatase
Pfam: PF03031 (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: CL0137
Length: 159
Sequences: 7869
Seq/Len: 49.49
HH_delta: 0.187 (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
113_D118_K1.267153.155
62_E66_E1.016382.531
122_Q129_V0.947522.360
97_K101_K0.947152.359
58_T65_A0.919482.290
2_T104_R0.883892.201
42_D46_E0.856682.133
99_L109_V0.828982.064
3_L48_L0.812542.023
37_L42_D0.772841.925
99_L106_L0.770341.918
105_D108_N0.706081.758
47_E50_K0.702731.750
5_L54_V0.700531.744
97_K100_S0.698981.741
4_V57_W0.648341.615
119_W129_V0.637461.587
11_L41_L0.631331.572
55_V81_R0.630561.570
6_D10_T0.627511.563
4_V111_I0.624171.554
111_I122_Q0.618561.540
3_L52_Y0.61771.538
67_P70_D0.584361.455
4_V109_V0.583481.453
53_E80_S0.579441.443
7_L12_V0.578531.441
5_L44_F0.566781.411
7_L56_I0.550751.371
46_E49_S0.542731.352
6_D114_D0.534981.332
7_L65_A0.52891.317
66_E70_D0.522331.301
46_E78_L0.514221.281
111_I121_L0.512591.276
23_D27_I0.503881.255
2_T55_V0.50221.251
54_V79_F0.501551.249
57_W94_S0.501051.248
40_G43_E0.499321.243
99_L127_I0.486861.212
62_E87_D0.484491.206
5_L112_V0.484411.206
92_K96_I0.483861.205
4_V55_V0.482341.201
8_D14_S0.482121.201
43_E46_E0.475141.183
24_F27_I0.474951.183
3_L112_V0.471591.174
70_D76_G0.469931.170
8_D114_D0.465171.158
48_L52_Y0.464211.156
38_R41_L0.460661.147
120_A124_D0.457011.138
21_P24_F0.452851.128
91_D94_S0.452611.127
53_E104_R0.451741.125
44_F48_L0.446781.113
45_L54_V0.446191.111
98_D102_L0.444431.107
21_P26_I0.444351.107
22_Y26_I0.44161.100
13_H38_R0.436531.087
106_L109_V0.436051.086
69_L74_P0.435581.085
83_L101_K0.434671.082
90_F93_G0.428961.068
90_F94_S0.428561.067
65_A68_V0.423361.054
117_R120_A0.421771.050
55_V102_L0.420281.047
115_S118_K0.417621.040
95_Y121_L0.413131.029
56_I79_F0.408131.016
10_T114_D0.405071.009
13_H36_K0.40261.003
37_L41_L0.402411.002
48_L54_V0.399560.995
22_Y27_I0.398460.992
116_P120_A0.391510.975
119_W123_P0.389190.969
104_R109_V0.388790.968
40_G44_F0.38760.965
84_Y88_C0.384840.958
29_Q33_Y0.382770.953
9_G114_D0.377830.941
119_W126_G0.377250.939
85_R88_C0.376920.939
11_L56_I0.375680.936
90_F95_Y0.373710.931
2_T53_E0.36970.921
59_S115_S0.363480.905
21_P25_K0.359130.894
120_A123_P0.353420.880
43_E47_E0.35190.876
65_A69_L0.349330.870
81_R102_L0.347170.865
63_E66_E0.342930.854
118_K126_G0.341860.851
2_T102_L0.341430.850
109_V127_I0.338040.842
2_T109_V0.336830.839
74_P77_K0.334580.833
8_D58_T0.329630.821
96_I100_S0.326630.813
81_R101_K0.320620.798
9_G14_S0.31930.795
67_P71_A0.318420.793
83_L86_D0.314030.782
4_V98_D0.310620.774
104_R108_N0.310080.772
10_T112_V0.307570.766
10_T118_K0.303860.757
41_L45_L0.303860.757
99_L102_L0.303070.755
93_G96_I0.301040.750
111_I127_I0.299530.746
12_V68_V0.297170.740
7_L68_V0.295670.736
3_L54_V0.295340.735
60_A64_Y0.294880.734
118_K121_L0.293360.731
31_G34_Y0.293110.730
68_V72_L0.292960.730
5_L79_F0.292660.729
23_D26_I0.291370.726
60_A65_A0.291330.725
111_I118_K0.289770.722
64_Y68_V0.289380.721
53_E77_K0.287720.716
38_R44_F0.287640.716
18_S60_A0.286030.712
14_S35_V0.284760.709
9_G12_V0.28220.703
62_E86_D0.281410.701
57_W98_D0.280750.699
42_D71_A0.280210.698
84_Y87_D0.278320.693
19_P22_Y0.27650.689
81_R85_R0.276410.688
6_D9_G0.275830.687
62_E65_A0.272670.679
41_L44_F0.269740.672
63_E67_P0.268960.670
55_V98_D0.266260.663
15_S18_S0.265560.661
21_P27_I0.25960.646
47_E51_H0.259480.646
79_F82_R0.259280.646
99_L104_R0.257620.642
45_L79_F0.257580.641
48_L112_V0.255550.636
30_R33_Y0.254520.634
83_L98_D0.254180.633
8_D113_D0.254180.633
59_S117_R0.253830.632
94_S98_D0.253690.632
7_L60_A0.253440.631
53_E103_G0.253390.631
46_E77_K0.251740.627
20_L23_D0.251280.626
15_S117_R0.2510.625
22_Y25_K0.250430.624
52_Y110_V0.250010.623
66_E82_R0.249210.621
92_K95_Y0.249160.620
3_L110_V0.248270.618
30_R34_Y0.246760.614
119_W128_P0.245820.612
91_D95_Y0.244840.610
5_L11_L0.244580.609
83_L94_S0.244190.608
37_L68_V0.244110.608
15_S115_S0.243630.607
122_Q128_P0.243480.606
111_I125_N0.240980.600
93_G97_K0.240490.599
122_Q127_I0.239180.596
99_L105_D0.239010.595
111_I115_S0.238990.595
54_V78_L0.237110.590
14_S17_K0.235320.586
10_T60_A0.235190.586
12_V35_V0.234360.584
105_D109_V0.234070.583
9_G115_S0.233620.582
18_S58_T0.23340.581
119_W122_Q0.232030.578
5_L48_L0.230740.575
62_E84_Y0.229830.572
121_L125_N0.228630.569
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
2ghtA0.987499.80.187
2hhlA0.987499.80.219
3qleA0.918299.80.271
2ah5A0.95699.70.292
3kbbA0.95699.70.293
3ib6A0.962399.70.293
2gfhA0.993799.70.297
1qq5A0.987499.70.298
3kzxA0.987499.70.302
4eekA0.993799.70.308

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