GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rhomboid - Rhomboid family
Pfam: PF01694 (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: CL0207
Length: 145
Sequences: 4558
Seq/Len: 31.43
HH_delta: 0.119 (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
52_S79_G1.424884.718
13_P53_G1.419994.702
5_Q8_R1.384724.585
55_L132_A0.951423.151
17_A71_V0.901532.985
82_G130_F0.851052.818
12_S57_S0.799242.647
53_G76_A0.746132.471
59_L128_G0.697582.310
60_S122_S0.667612.211
60_S70_Y0.660922.189
16_H21_H0.64242.127
33_G45_F0.625512.071
19_F23_L0.578511.916
49_Y76_A0.577041.911
70_Y122_S0.57411.901
7_W11_T0.556031.841
74_S126_H0.527361.746
48_L52_S0.489191.620
86_F134_L0.477971.583
21_H25_N0.466811.546
103_V107_I0.464181.537
21_H126_H0.456981.513
25_N126_H0.438051.451
56_G75_G0.436061.444
29_L33_G0.432261.431
37_E41_G0.431851.430
25_N74_S0.431581.429
48_L83_A0.419141.388
13_P76_A0.416051.378
86_F137_G0.412551.366
21_H74_S0.410781.360
132_A136_Y0.403141.335
12_S70_Y0.393231.302
15_V71_V0.392481.300
100_L103_V0.389911.291
75_G125_G0.381361.263
24_F28_A0.379961.258
34_S38_R0.376631.247
116_G123_F0.373981.238
37_E42_S0.370091.226
9_L61_L0.367431.217
93_K96_R0.366281.213
49_Y80_L0.360931.195
49_Y73_A0.360591.194
29_L77_V0.359111.189
16_H25_N0.3591.189
124_L128_G0.356771.181
82_G137_G0.354361.173
73_A76_A0.349421.157
89_P93_K0.344531.141
56_G128_G0.337631.118
16_H126_H0.33151.098
108_V112_I0.330281.094
27_L31_F0.32361.072
106_I110_V0.314421.041
9_L57_S0.313221.037
41_G44_R0.3131.036
26_L29_L0.311961.033
107_I110_V0.309761.026
122_S125_G0.30751.018
40_L48_L0.300980.997
83_A137_G0.299710.992
128_G132_A0.299330.991
99_Y103_V0.298210.987
20_L23_L0.292020.967
57_S70_Y0.290130.961
16_H74_S0.289660.959
38_R42_S0.285450.945
101_A105_P0.284470.942
6_W10_F0.279940.927
49_Y53_G0.277130.918
43_R47_A0.274970.911
56_G76_A0.273590.906
107_I111_I0.273520.906
52_S132_A0.271830.900
10_F54_L0.269810.893
70_Y124_L0.269790.893
89_P96_R0.266650.883
28_A31_F0.265060.878
28_A77_V0.261930.867
51_L55_L0.256980.851
13_P57_S0.256270.849
40_L83_A0.255190.845
119_P123_F0.25510.845
135_L139_L0.252290.835
20_L24_F0.250330.829
101_A104_V0.25030.829
25_N73_A0.249790.827
42_S46_L0.247340.819
128_G131_L0.247340.819
55_L128_G0.244660.810
8_R11_T0.243970.808
25_N75_G0.241920.801
46_L50_L0.240490.796
20_L27_L0.239280.792
109_L112_I0.23910.792
39_R88_Y0.237940.788
84_F88_Y0.23770.787
33_G37_E0.237020.785
47_A51_L0.236930.785
23_L27_L0.236660.784
18_N71_V0.236180.782
52_S56_G0.235190.779
25_N129_G0.234970.778
34_S42_S0.234510.777
110_V115_L0.2340.775
73_A77_V0.233050.772
45_F49_Y0.231030.765
54_L58_L0.230020.762
83_A87_L0.227650.754
56_G79_G0.22640.750
136_Y140_I0.224650.744
75_G126_H0.223870.741
10_F50_L0.221940.735
57_S75_G0.221590.734
8_R37_E0.220420.730
20_L118_I0.220080.729
107_I112_I0.219790.728
63_F124_L0.219560.727
108_V111_I0.219310.726
51_L136_Y0.218260.723
86_F138_F0.21550.714
125_G133_G0.213270.706
113_L116_G0.212450.704
29_L73_A0.211540.700
29_L49_Y0.211120.699
134_L138_F0.210440.697
112_I115_L0.210290.696
43_R48_L0.208810.691
24_F31_F0.208120.689
105_P108_V0.207480.687
74_S129_G0.206990.685
22_L26_L0.206590.684
30_W96_R0.206050.682
121_I126_H0.205280.680
116_G122_S0.20480.678
83_A88_Y0.204330.677
41_G46_L0.203710.675
40_L87_L0.199180.660
64_S69_P0.198280.657
131_L135_L0.19820.656
6_W9_L0.197770.655
60_S64_S0.197550.654
103_V106_I0.195090.646
48_L136_Y0.194610.644
112_I116_G0.194060.643
89_P92_K0.192560.638
16_H72_G0.191780.635
52_S128_G0.191420.634
133_G137_G0.191210.633
87_L90_Q0.190510.631
100_L116_G0.190430.631
102_L106_I0.189930.629
48_L140_I0.189750.628
110_V114_L0.18690.619
135_L138_F0.186870.619
44_R47_A0.185830.615
53_G56_G0.184850.612
110_V116_G0.184770.612
111_I114_L0.184410.611
32_F89_P0.184350.610
88_Y92_K0.183910.609
119_P122_S0.183720.608
100_L105_P0.183590.608
112_I123_F0.182630.605
16_H75_G0.182180.603
35_L88_Y0.181310.600
61_L64_S0.181110.600
16_H22_L0.179570.595
28_A78_F0.178910.592
127_L131_L0.177840.589
9_L54_L0.17630.584
108_V113_L0.176180.583
78_F112_I0.175690.582
27_L30_W0.175430.581
99_Y104_V0.175370.581
36_L83_A0.174140.577
47_A139_L0.174070.576
113_L127_L0.1730.573
26_L76_A0.172560.571
62_L65_P0.171230.567
20_L106_I0.170770.565
7_W137_G0.169850.562
7_W38_R0.168740.559
30_W34_S0.16870.559
104_V112_I0.168580.558
136_Y139_L0.168450.558
87_L91_N0.168370.558
82_G86_F0.167240.554
89_P105_P0.166190.550
51_L69_P0.166110.550
15_V18_N0.165580.548
26_L99_Y0.165250.547
35_L84_F0.165180.547
59_L124_L0.165040.547
21_H75_G0.163970.543
28_A108_V0.163440.541
62_L67_N0.162810.539
63_F67_N0.162420.538
50_L66_P0.162330.538
52_S137_G0.162130.537
19_F22_L0.161960.536
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
2nr9A0.979399.80.119
2xovA0.965599.80.142
4g1uA0.6696.90.909
2qi9A0.63456.50.91
2auhB0.13792.30.927
2nq2A0.6692.30.927
2wjnL0.85522.10.928
1rzhL0.855220.929
3rceA0.903420.929
2lojA0.14481.90.93

Page generated in 0.015 seconds.