GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
NLPC_P60 - NlpCP60 family
Pfam: PF00877 (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: CL0125
Length: 105
Sequences: 4422
Seq/Len: 42.11
HH_delta: -0.035 (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
73_L88_V1.669693.340
14_F22_W1.292592.585
8_G13_G1.171822.344
32_P41_V1.147982.296
80_H89_S1.136672.274
84_G87_S1.021382.043
16_C68_H1.008422.017
20_V71_I0.985391.971
49_I52_L0.96611.932
72_Y76_G0.881041.762
19_L23_V0.849641.699
20_V57_L0.832851.666
57_L69_V0.802611.605
34_T37_D0.79811.596
22_W26_Q0.791611.583
77_K90_S0.780191.561
70_G78_F0.753041.506
20_V38_Q0.723081.446
25_R30_N0.722371.445
60_F70_G0.714021.428
24_Y31_L0.710591.421
82_S87_S0.702331.405
48_P51_E0.68551.371
20_V31_L0.673841.348
23_V27_A0.668491.337
60_F78_F0.665651.331
35_S39_Y0.651361.303
61_K67_S0.650931.302
62_G67_S0.650351.301
59_F69_V0.62861.257
21_R25_R0.620291.241
2_T10_S0.616731.234
10_S13_G0.615631.231
11_P22_W0.610061.220
39_Y66_I0.586741.174
68_H80_H0.581141.162
52_L72_Y0.581081.162
9_R21_R0.575121.150
59_F66_I0.564781.130
77_K88_V0.563491.127
3_P13_G0.560781.122
82_S85_G0.55321.107
2_T13_G0.551671.103
79_I88_V0.547151.094
2_T86_V0.546561.093
73_L79_I0.545871.092
5_V13_G0.544091.088
9_R33_R0.538931.078
72_Y75_D0.529281.059
24_Y71_I0.525441.051
33_R37_D0.523491.047
10_S14_F0.50791.016
78_F91_L0.506611.013
53_Q56_D0.502641.005
21_R33_R0.485540.971
70_G80_H0.476420.953
20_V69_V0.476030.952
39_Y42_G0.472230.945
35_S38_Q0.458190.916
21_R38_Q0.456770.914
47_V51_E0.453220.907
86_V91_L0.452690.905
58_I72_Y0.452460.905
61_K66_I0.446420.893
15_D18_G0.446070.892
32_P37_D0.440050.880
2_T14_F0.437720.876
9_R22_W0.428690.857
4_Y16_C0.427270.855
52_L58_I0.420770.842
84_G89_S0.416050.832
82_S89_S0.412130.824
11_P14_F0.411320.823
76_G92_S0.40780.816
35_S66_I0.402180.804
36_A39_Y0.401480.803
61_K65_G0.389020.778
89_S93_G0.382740.766
4_Y81_A0.377120.754
54_P74_G0.376750.754
37_D40_S0.374460.749
58_I70_G0.373850.748
47_V52_L0.372960.746
14_F18_G0.370330.741
80_H87_S0.363330.727
2_T8_G0.360330.721
60_F67_S0.359680.719
20_V24_Y0.358370.717
23_V71_I0.35430.709
34_T38_Q0.354020.708
24_Y29_I0.349620.699
44_Q47_V0.348030.696
74_G77_K0.342240.685
86_V90_S0.337730.676
36_A40_S0.337520.675
5_V8_G0.337340.675
2_T11_P0.335590.671
7_G17_S0.333530.667
73_L77_K0.32630.653
90_S93_G0.324760.650
52_L91_L0.321180.642
31_L41_V0.320790.642
19_L79_I0.320170.640
33_R38_Q0.316560.633
4_Y17_S0.310670.621
21_R30_N0.309160.618
62_G66_I0.305340.611
54_P73_L0.296720.593
30_N50_S0.29440.589
71_I79_I0.292610.585
78_F92_S0.289220.578
39_Y61_K0.289160.578
14_F86_V0.288850.578
38_Q59_F0.288080.576
50_S75_D0.281520.563
7_G15_D0.280710.561
62_G93_G0.280150.560
78_F89_S0.278030.556
35_S69_V0.276110.552
9_R14_F0.274610.549
72_Y77_K0.274030.548
22_W25_R0.272270.545
62_G65_G0.270780.542
80_H92_S0.270690.541
18_G22_W0.270060.540
12_D25_R0.26870.537
49_I92_S0.265790.532
36_A66_I0.262490.525
36_A65_G0.261810.524
48_P52_L0.261580.523
8_G14_F0.26140.523
83_G87_S0.261350.523
30_N40_S0.261130.522
16_C35_S0.261030.522
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
2k1gA0.98199.9-0.035
3h41A0.98199.90.002
4hpeA0.971499.90.008
3npfA0.971499.90.009
4fdyA0.971499.90.014
2jyxA0.98199.90.02
2hbwA0.98199.90.021
3ne0A0.971499.90.101
3pbiA0.971499.80.103
3gt2A0.961999.80.129

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