GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RadC - RadC-like JAB domain
Pfam: PF04002 (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: CL0366
Length: 123
Sequences: 1878
Seq/Len: 15.27
HH_delta: -0.028 (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
70_L103_L0.843092.721
57_F96_A0.832682.687
39_E59_R0.782.517
115_F120_N0.736772.378
30_D34_R0.725452.341
12_L71_A0.719612.322
86_I117_F0.698372.254
89_T106_H0.607771.962
46_I66_S0.595991.924
86_I122_L0.580781.874
16_L19_L0.576051.859
2_I35_L0.56941.838
21_Q43_E0.557361.799
83_D87_A0.548511.770
70_L92_L0.547571.767
25_R38_D0.542661.751
90_R94_K0.533131.721
3_N7_D0.531171.714
93_K103_L0.504931.630
58_R64_N0.493421.592
27_L35_L0.488471.577
40_V43_E0.487241.573
31_S47_D0.482011.556
28_Y59_R0.481481.554
56_I92_L0.476691.538
37_G63_L0.474711.532
25_R40_V0.470691.519
23_Q40_V0.46771.509
17_Q111_D0.45291.462
28_Y63_L0.451991.459
42_S49_A0.448041.446
16_L25_R0.444071.433
20_D58_R0.438281.415
59_R62_R0.437051.411
5_P119_E0.430841.391
60_A68_V0.427951.381
83_D86_I0.418211.350
57_F99_L0.416921.346
51_V88_L0.416241.343
6_E10_D0.415771.342
59_R63_L0.406261.311
79_P113_G0.400811.294
94_K97_R0.397851.284
79_P115_F0.392681.267
24_F51_V0.385531.244
21_Q42_S0.384531.241
107_I114_Y0.382981.236
28_Y60_A0.381771.232
19_L23_Q0.381591.232
15_K38_D0.381521.231
33_N67_S0.37791.220
23_Q43_E0.376451.215
24_F103_L0.375851.213
60_A101_I0.37041.195
32_K78_D0.364721.177
93_K97_R0.359361.160
117_F123_L0.358981.159
117_F122_L0.353261.140
2_I8_V0.346791.119
80_E120_N0.346431.118
108_I115_F0.344731.113
28_Y39_E0.342421.105
2_I7_D0.334391.079
9_A107_I0.326171.053
19_L40_V0.325531.051
115_F122_L0.323591.044
45_T52_D0.323221.043
12_L27_L0.315651.019
17_Q110_G0.315481.018
93_K123_L0.312391.008
68_V96_A0.310921.003
10_D13_R0.308160.995
13_R112_G0.307460.992
27_L38_D0.302750.977
95_A99_L0.30250.976
96_A99_L0.300480.970
45_T55_E0.292070.943
21_Q39_E0.291510.941
4_S7_D0.285590.922
11_Y38_D0.282230.911
39_E63_L0.282020.910
9_A114_Y0.280330.905
25_R71_A0.280250.904
8_V69_I0.278610.899
6_E119_E0.277080.894
9_A119_E0.276280.892
13_R17_Q0.275910.890
95_A98_L0.272530.880
33_N104_L0.271050.875
90_R93_K0.265750.858
58_R62_R0.265710.858
9_A13_R0.26570.858
55_E58_R0.26550.857
2_I11_Y0.261660.844
28_Y41_V0.260960.842
8_V71_A0.260510.841
96_A103_L0.25760.831
117_F120_N0.257460.831
21_Q55_E0.256420.828
79_P108_I0.253490.818
26_V70_L0.249980.807
29_L67_S0.244160.788
5_P9_A0.242850.784
87_A90_R0.24280.784
8_V107_I0.241720.780
67_S104_L0.239890.774
52_D55_E0.239280.772
45_T50_P0.233750.754
94_K98_L0.233580.754
44_G85_D0.232710.751
74_H85_D0.232690.751
13_R111_D0.23230.750
49_A88_L0.231920.749
26_V41_V0.225390.727
97_R102_E0.223930.723
28_Y37_G0.22210.717
105_D116_S0.21920.707
22_E74_H0.216730.699
46_I54_R0.215050.694
20_D62_R0.21390.690
79_P110_G0.213360.689
37_G59_R0.212940.687
47_D66_S0.211420.682
109_V114_Y0.211030.681
24_F49_A0.208380.673
7_D35_L0.205320.663
24_F117_F0.204640.660
5_P8_V0.20440.660
96_A101_I0.204310.659
91_R100_G0.202630.654
29_L69_I0.201940.652
31_S66_S0.198680.641
68_V103_L0.19780.638
14_P17_Q0.196730.635
114_Y119_E0.196580.634
36_I65_A0.195430.631
81_P115_F0.192770.622
28_Y42_S0.191930.619
72_H75_P0.190250.614
24_F88_L0.189330.611
74_H82_S0.189270.611
28_Y65_A0.188650.609
24_F70_L0.187840.606
91_R94_K0.186340.601
42_S50_P0.185820.600
22_E75_P0.184030.594
57_F98_L0.183350.592
51_V56_I0.182770.590
82_S85_D0.18160.586
19_L38_D0.178770.577
22_E72_H0.177990.574
41_V56_I0.177670.573
14_P111_D0.177450.573
91_R95_A0.177190.572
88_L91_R0.176780.571
61_L95_A0.176280.569
54_R66_S0.176070.568
108_I120_N0.175660.567
3_N90_R0.174790.564
22_E85_D0.171840.555
44_G74_H0.171450.553
5_P118_R0.168590.544
91_R98_L0.166990.539
45_T53_P0.166410.537
14_P19_L0.165960.536
3_N83_D0.165760.535
20_D64_N0.165640.535
35_L71_A0.16520.533
97_R100_G0.164190.530
11_Y40_V0.163960.529
31_S41_V0.16340.527
86_I90_R0.162420.524
31_S46_I0.1620.523
78_D81_P0.16140.521
5_P23_Q0.16120.520
31_S62_R0.159640.515
15_K25_R0.158950.513
20_D43_E0.15790.510
67_S102_E0.157880.510
13_R16_L0.157450.508
22_E82_S0.157440.508
24_F56_I0.157330.508
113_G120_N0.156470.505
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
2qlcA1100-0.028
2kksA0.910695.50.861
2kcqA0.910694.30.87
1oi0A0.87893.60.874
4h17A0.918782.20.898
3k13A0.983778.80.901
3oqpA0.796777.60.902
1f6yA0.959372.10.906
2znrA0.959371.70.907
3lqyA0.804968.60.909

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