GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1906 - Domain of unknown function (DUF1906)
Pfam: PF08924 (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: 136
Sequences: 1593
Seq/Len: 11.71
HH_delta: 0.232 (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
80_R124_A1.016194.620
98_Y133_G0.634192.883
24_Y27_G0.572922.605
83_V128_S0.50772.308
75_G120_G0.497792.263
22_G133_G0.457882.082
124_A127_A0.413691.881
46_D49_A0.412451.875
41_A45_Q0.40731.852
97_I125_L0.382251.738
76_V120_G0.372331.693
39_L42_G0.367841.672
99_F118_F0.364621.658
119_R123_S0.356661.622
23_R43_E0.353761.608
22_G98_Y0.351241.597
26_S59_Q0.341241.551
75_G79_A0.339771.545
76_V124_A0.334051.519
60_G103_Y0.333491.516
12_A16_A0.332011.509
14_K19_R0.32951.498
11_Q15_A0.328371.493
21_V52_L0.32631.484
101_V118_F0.313871.427
13_L16_A0.304151.383
31_G38_N0.301241.370
9_S12_A0.293741.335
44_V54_I0.293461.334
13_L18_Y0.291311.324
40_T57_I0.286571.303
40_T44_V0.283821.290
42_G46_D0.281951.282
76_V80_R0.279111.269
124_A128_S0.269151.224
47_I50_A0.268431.220
44_V89_L0.266591.212
47_I54_I0.265681.208
86_A97_I0.264361.202
10_A21_V0.262911.195
80_R128_S0.260031.182
29_R77_A0.255381.161
121_W125_L0.255081.160
46_D50_A0.253241.151
74_Q77_A0.252051.146
28_S59_Q0.247021.123
25_L82_A0.240121.092
112_S116_P0.239051.087
10_A46_D0.238171.083
22_G56_P0.23481.068
83_V125_L0.234551.066
126_G131_R0.234031.064
110_C113_A0.233271.061
17_G21_V0.231371.052
23_R47_I0.230721.049
11_Q50_A0.227571.035
8_A13_L0.226211.028
66_S117_Y0.223261.015
121_W132_P0.222821.013
66_S99_F0.221871.009
48_R54_I0.220831.004
25_L59_Q0.216460.984
82_A97_I0.216180.983
68_F117_Y0.214750.976
27_G60_G0.205490.934
109_E113_A0.205280.933
23_R54_I0.202670.921
83_V124_A0.201370.916
24_Y59_Q0.200320.911
11_Q45_Q0.199850.909
120_G124_A0.199570.907
75_G117_Y0.198730.904
111_D115_L0.198040.900
80_R84_A0.19790.900
45_Q49_A0.196170.892
79_A83_V0.192320.874
57_I82_A0.19230.874
26_S85_A0.192150.874
44_V57_I0.190920.868
20_A96_P0.188890.859
42_G49_A0.188780.858
44_V48_R0.188650.858
76_V123_S0.187080.851
79_A121_W0.182530.830
14_K50_A0.181860.827
82_A86_A0.180410.820
27_G31_G0.179590.816
22_G53_R0.178240.810
13_L52_L0.17790.809
60_G100_A0.176950.804
77_A80_R0.176880.804
23_R40_T0.176050.800
59_Q102_D0.1760.800
27_G59_Q0.173010.787
14_K17_G0.171910.782
84_A128_S0.171620.780
100_A135_Y0.171070.778
99_F121_W0.169080.769
12_A15_A0.168760.767
41_A89_L0.167950.764
79_A125_L0.16780.763
18_Y52_L0.167210.760
125_L132_P0.166250.756
81_D85_A0.164890.750
25_L86_A0.16430.747
74_Q78_D0.163450.743
113_A116_P0.160870.731
28_S78_D0.160630.730
43_E46_D0.160460.730
118_F121_W0.159120.723
101_V121_W0.158830.722
122_N126_G0.158760.722
28_S31_G0.158690.721
13_L43_E0.158310.720
129_G132_P0.158280.720
122_N132_P0.157460.716
58_Y135_Y0.156550.712
39_L43_E0.154020.700
59_Q82_A0.153820.699
50_A112_S0.153730.699
15_A115_L0.153290.697
87_R130_Y0.152010.691
93_A130_Y0.151650.689
113_A123_S0.15110.687
10_A13_L0.15010.682
77_A81_D0.14790.672
86_A89_L0.14750.671
27_G67_D0.147150.669
25_L40_T0.146890.668
95_T131_R0.145950.664
20_A132_P0.144950.659
99_F122_N0.143950.654
24_Y58_Y0.143640.653
30_G81_D0.143640.653
10_A43_E0.143220.651
14_K51_G0.141970.645
45_Q48_R0.141520.643
19_R52_L0.140940.641
115_L119_R0.140780.640
28_S67_D0.140540.639
67_D78_D0.140430.638
58_Y100_A0.139490.634
123_S127_A0.138680.631
25_L121_W0.138660.630
60_G102_D0.136710.622
104_D107_D0.136580.621
24_Y43_E0.136110.619
43_E56_P0.135770.617
15_A116_P0.135660.617
132_P135_Y0.135410.616
68_F99_F0.134960.614
69_T74_Q0.134950.614
31_G105_A0.134490.611
14_K52_L0.133960.609
56_P59_Q0.133310.606
57_I97_I0.133150.605
83_V87_R0.132450.602
23_R44_V0.132120.601
11_Q49_A0.132110.601
79_A124_A0.132090.601
82_A99_F0.131620.598
15_A19_R0.131050.596
41_A84_A0.129890.591
59_Q100_A0.129640.589
28_S60_G0.128960.586
40_T54_I0.128850.586
102_D135_Y0.127760.581
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
2x8rA0.911899.90.232
2wagA0.889799.90.239
2ww5A0.911899.90.241
1jfxA0.911899.90.243
3hmcA0.845699.90.29
2j8gA0.852999.90.294
1sfsA0.882499.70.434
3ianA0.948585.30.866
4hmeA0.948583.20.869
4do4A0.625820.871

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