GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAS_9 - PAS domain
Pfam: PF13426 (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: CL0183
Length: 104
Sequences: 45850
Seq/Len: 440.87
HH_delta: -0.214 (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
2_D100_R3.227232.936
70_R74_E2.786232.535
67_R77_W2.70022.456
19_A22_R2.375412.161
5_F97_G2.196991.998
67_R75_T2.190461.993
16_V20_F2.131781.939
70_R76_F2.055481.870
21_E28_R2.052811.867
69_R75_T1.951631.775
12_R35_S1.944281.769
80_V99_F1.937321.762
63_S79_E1.934661.760
8_D12_R1.930831.756
34_K38_D1.929441.755
3_G99_F1.921071.748
3_G23_L1.901581.730
26_Y71_K1.886811.716
79_E100_R1.866711.698
16_V21_E1.708211.554
18_P22_R1.682511.531
6_I15_Y1.669221.518
66_V80_V1.662961.513
6_I94_G1.660331.510
86_R92_I1.648121.499
28_R32_I1.614111.468
5_F13_I1.511971.375
14_L94_G1.506281.370
5_F20_F1.499921.364
84_P92_I1.480441.347
54_R58_E1.470011.337
6_I96_I1.469071.336
27_S30_E1.446581.316
18_P21_E1.434511.305
16_V31_L1.401461.275
41_P44_D1.399211.273
87_D91_E1.378141.254
8_D14_L1.371261.247
9_P92_I1.355391.233
7_L97_G1.322891.203
21_E27_S1.298131.181
63_S81_S1.291341.175
35_S38_D1.269011.154
68_L78_V1.26491.151
20_F24_F1.250981.138
53_E57_E1.204771.096
81_S100_R1.200981.092
78_V99_F1.20061.092
49_E53_E1.188811.081
15_Y28_R1.184341.077
65_E79_E1.182571.076
76_F101_D1.169381.064
2_D98_I1.136161.034
26_Y30_E1.13271.030
87_D93_T1.126121.024
6_I14_L1.124431.023
44_D48_F1.113251.013
85_I96_I1.110271.010
83_S96_I1.107631.008
5_F99_F1.099761.000
9_P93_T1.096680.998
82_A97_G1.073040.976
30_E71_K1.036340.943
18_P28_R1.031590.938
24_F68_L1.02770.935
25_G72_D1.012690.921
50_E54_R1.008980.918
21_E31_L0.999680.909
37_S49_E0.989480.900
77_W103_T0.987350.898
51_Q54_R0.984010.895
6_I85_I0.96740.880
19_A23_L0.964770.878
44_D67_R0.955910.870
3_G20_F0.952010.866
82_A95_I0.949470.864
85_I94_G0.928920.845
24_F99_F0.921710.838
45_R49_E0.918480.835
2_D19_A0.917140.834
37_S45_R0.91660.834
55_A58_E0.910310.828
20_F31_L0.90820.826
41_P75_T0.899650.818
7_L13_I0.899640.818
4_I96_I0.889860.809
86_R93_T0.882630.803
4_I98_I0.880520.801
47_E51_Q0.879140.800
7_L36_I0.873420.795
26_Y31_L0.860540.783
3_G19_A0.836450.761
34_K39_F0.83290.758
9_P91_E0.830760.756
68_L76_F0.82670.752
42_E45_R0.819520.745
46_P50_E0.818310.744
17_N20_F0.814120.741
86_R90_G0.803450.731
46_P49_E0.793420.722
2_D81_S0.793010.721
55_A60_G0.792450.721
48_F51_Q0.787920.717
40_F43_E0.787910.717
9_P12_R0.782460.712
23_L78_V0.777950.708
53_E56_L0.776590.706
7_L95_I0.772880.703
16_V24_F0.753980.686
44_D47_E0.75250.685
13_I16_V0.730980.665
7_L52_I0.730470.664
51_Q55_A0.728720.663
79_E102_I0.727530.662
55_A59_G0.727230.662
65_E102_I0.725260.660
25_G70_R0.722250.657
45_R48_F0.718350.653
7_L11_G0.703770.640
16_V28_R0.69820.635
77_W102_I0.692130.630
47_E50_E0.687210.625
48_F66_V0.684420.623
32_I35_S0.672380.612
87_D90_G0.670510.610
84_P95_I0.669120.609
23_L76_F0.664610.605
21_E24_F0.663790.604
36_I40_F0.662280.602
87_D94_G0.652780.594
3_G17_N0.645360.587
4_I17_N0.645070.587
7_L82_A0.642020.584
61_S83_S0.639350.582
54_R57_E0.634580.577
40_F66_V0.632840.576
12_R32_I0.632630.575
51_Q62_W0.628760.572
36_I97_G0.62860.572
30_E34_K0.624530.568
86_R89_D0.622560.566
87_D92_I0.620980.565
49_E52_I0.619330.563
20_F99_F0.618050.562
52_I82_A0.617970.562
92_I95_I0.615010.559
26_Y39_F0.611410.556
84_P93_T0.609010.554
55_A62_W0.605820.551
11_G53_E0.605770.551
29_E32_I0.605710.551
80_V97_G0.60480.550
65_E68_L0.604110.550
54_R60_G0.60270.548
86_R91_E0.598930.545
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
2wkqA199-0.214
3p7nA199-0.214
3f1pA199-0.212
3f1pB199-0.203
2gj3A199-0.196
4hiaA199-0.196
1n9lA199-0.187
4ehoA0.990499-0.185
4f3lA199-0.184
3ewkA0.980898.9-0.167

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