GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CheW - CheW-like domain
Pfam: PF01584 (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: 138
Sequences: 5033
Seq/Len: 36.47
HH_delta: 0.058 (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
21_E45_R1.156814.125
6_R87_Q0.987923.522
2_Y13_A0.90783.237
71_V82_G0.852963.041
20_V75_R0.792422.825
47_E80_R0.767732.737
40_G53_D0.765312.729
11_R123_Q0.698342.490
43_N46_G0.676752.413
100_Q118_I0.663182.365
51_V71_V0.604862.157
49_I73_I0.60172.145
6_R89_P0.597882.132
95_E98_D0.587132.093
18_D131_E0.586742.092
20_V80_R0.567572.024
94_V117_V0.552551.970
13_A125_V0.501581.788
55_A86_D0.475651.696
43_N48_I0.461951.647
6_R9_G0.429481.531
129_D132_A0.420491.499
8_G55_A0.406421.449
42_I71_V0.391541.396
53_D56_R0.384971.373
74_L83_L0.384951.373
114_S129_D0.380261.356
22_I88_V0.378551.350
2_Y94_V0.375051.337
75_R80_R0.371441.324
113_I126_L0.353971.262
111_P132_A0.353231.259
15_P18_D0.351131.252
3_L22_I0.350771.251
4_L13_A0.350411.249
66_S69_S0.34891.244
49_I82_G0.336221.199
54_L133_L0.334421.192
56_R62_P0.330461.178
5_F72_L0.328031.170
4_L11_R0.325561.161
63_Q66_S0.322481.150
11_R89_P0.321891.148
49_I80_R0.320461.143
21_E44_Y0.319831.140
13_A117_V0.315371.124
24_P70_R0.313281.117
81_I134_L0.312631.115
26_P30_P0.307541.097
99_I115_G0.304431.085
74_L130_V0.302611.079
72_L85_V0.29931.067
119_L123_Q0.296961.059
25_V84_L0.295441.053
118_I124_L0.291351.039
2_Y127_I0.287311.024
117_V127_I0.286171.020
36_P56_R0.284951.016
4_L90_G0.283761.012
32_P40_G0.282771.008
53_D84_L0.281361.003
55_A58_L0.272420.971
4_L119_L0.272320.971
69_S84_L0.271590.968
15_P114_S0.271530.968
4_L125_V0.268550.957
2_Y92_V0.267810.955
51_V82_G0.265480.947
20_V47_E0.265310.946
54_L83_L0.261250.931
99_I127_I0.258130.920
32_P46_G0.254290.907
26_P29_T0.254020.906
65_P69_S0.244770.873
119_L125_V0.242790.866
29_T32_P0.240320.857
19_V72_L0.238890.852
25_V71_V0.237560.847
35_P40_G0.234930.838
14_I130_V0.23490.838
41_V48_I0.232560.829
4_L92_V0.232510.829
32_P43_N0.231750.826
4_L89_P0.229350.818
23_L44_Y0.227360.811
44_Y85_V0.226520.808
73_I82_G0.222850.795
58_L128_L0.222760.794
7_L55_A0.222660.794
5_F14_I0.220710.787
27_P30_P0.219450.782
115_G127_I0.219430.782
33_G36_P0.218990.781
45_R73_I0.218720.780
18_D130_V0.218650.780
24_P124_L0.218110.778
2_Y117_V0.217940.777
3_L70_R0.216890.773
14_I72_L0.216820.773
23_L73_I0.21680.773
31_I41_V0.215180.767
92_V119_L0.213240.760
102_P113_I0.213220.760
2_Y96_V0.212440.757
13_A127_I0.210880.752
36_P78_G0.21020.749
44_Y73_I0.209680.748
76_H79_Q0.208290.743
31_I34_A0.20790.741
32_P35_P0.207340.739
108_R111_P0.206680.737
54_L128_L0.206570.737
70_R85_V0.205830.734
37_W57_L0.204820.730
24_P68_A0.203620.726
71_V84_L0.203580.726
100_Q103_L0.202320.721
45_R48_I0.20190.720
12_F60_L0.198670.708
97_K117_V0.197030.702
95_E122_G0.1970.702
128_L133_L0.195360.697
34_A41_V0.193540.690
23_L88_V0.191970.684
41_V50_P0.191920.684
10_E60_L0.191840.684
5_F85_V0.188690.673
3_L116_V0.188530.672
70_R100_Q0.188030.670
98_D121_D0.187870.670
3_L88_V0.187090.667
16_L127_I0.186980.667
98_D122_G0.185780.662
12_F58_L0.185770.662
23_L71_V0.18540.661
93_E97_K0.184070.656
52_I57_L0.183370.654
56_R68_A0.183050.653
42_I51_V0.183010.653
23_L42_I0.182960.652
50_P74_L0.182070.649
104_A110_P0.181790.648
16_L90_G0.181610.648
53_D62_P0.180980.645
74_L91_I0.180730.644
6_R11_R0.180040.642
65_P68_A0.179720.641
116_V124_L0.179080.638
55_A60_L0.178640.637
22_I32_P0.178390.636
76_H131_E0.177520.633
119_L124_L0.17690.631
56_R65_P0.176140.628
118_I122_G0.175280.625
29_T48_I0.174310.621
95_E103_L0.173780.620
40_G43_N0.173610.619
61_P64_P0.172950.617
69_S86_D0.172450.615
75_R78_G0.171520.612
33_G83_L0.171270.611
3_L90_G0.171130.610
34_A70_R0.170810.609
126_L129_D0.170620.608
16_L91_I0.170060.606
26_P71_V0.169310.604
70_R87_Q0.167530.597
12_F86_D0.166620.594
44_Y49_I0.165950.592
8_G60_L0.165190.589
42_I87_Q0.165060.589
21_E73_I0.164360.586
55_A63_Q0.163610.583
98_D119_L0.163480.583
64_P81_I0.16290.581
42_I49_I0.162540.580
18_D129_D0.162510.579
92_V117_V0.162350.579
18_D123_Q0.161530.576
115_G129_D0.158620.566
74_L133_L0.158540.565
15_P96_V0.158150.564
3_L19_V0.157930.563
12_F19_V0.157490.562
63_Q86_D0.157280.561
37_W56_R0.156840.559
32_P125_V0.15640.558
12_F113_I0.155840.556
95_E117_V0.155470.554
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
2ho9A0.992899.90.058
2qdlA0.992899.90.062
3ur1B0.978399.90.076
1b3qA0.920399.70.303
3ur1B0.463895.10.787
2ho9A0.565294.80.791
2qdlA0.536294.20.797
1b3qA0.41377.50.847
1sg5A0.253614.30.901
2zodA0.34785.20.918

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