GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAS_6 - YheO-like PAS domain
Pfam: PF08348 (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: CL0183
Length: 118
Sequences: 1263
Seq/Len: 10.7
HH_delta: 0.659 (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
19_N101_C0.653493.684
91_D95_K0.560523.160
80_K105_D0.399612.253
46_K49_D0.379042.137
9_V24_L0.36192.040
39_N44_G0.356722.011
10_D45_R0.336391.896
90_R96_L0.32681.842
62_K90_R0.304571.717
76_T79_G0.302521.705
26_D50_P0.294691.661
88_F96_L0.273171.540
34_I49_D0.269591.520
57_E61_E0.268631.514
56_L60_K0.26851.514
6_I31_E0.263471.485
21_E103_N0.262281.479
51_I99_A0.261941.477
89_I98_G0.257151.450
45_R103_N0.250231.411
23_V86_T0.245581.384
91_D97_I0.244831.380
45_R72_Y0.235171.326
51_I55_A0.232951.313
13_A19_N0.224411.265
20_C104_F0.220041.240
21_E101_C0.217041.223
23_V49_D0.215821.217
60_K96_L0.214171.207
76_T80_K0.211351.191
10_D38_A0.211071.190
59_L64_Y0.20421.151
36_A39_N0.202281.140
61_E64_Y0.199541.125
18_P104_F0.196661.109
23_V103_N0.194881.099
21_E45_R0.192741.087
80_K107_S0.190821.076
21_E49_D0.189051.066
86_T99_A0.188211.061
30_P33_S0.188161.061
17_G39_N0.18431.039
62_K95_K0.184211.038
57_E63_Q0.17981.014
64_Y87_F0.178471.006
23_V101_C0.175970.992
72_Y101_C0.175410.989
16_L83_R0.174070.981
35_V40_G0.171110.965
83_R106_I0.171060.964
84_S103_N0.170890.963
9_V38_A0.169610.956
76_T81_I0.167790.946
87_F100_L0.16460.928
52_T56_L0.162640.917
62_K96_L0.162610.917
12_L55_A0.161240.909
16_L20_C0.161110.908
13_A104_F0.16070.906
12_L16_L0.160270.903
87_F90_R0.16020.903
11_F87_F0.159340.898
76_T82_L0.156590.883
9_V100_L0.154680.872
5_Y98_G0.153520.865
32_H40_G0.153070.863
27_L54_L0.152680.861
59_L62_K0.15210.857
5_Y89_I0.151450.854
45_R101_C0.151060.852
10_D40_G0.151050.851
22_V35_V0.150470.848
38_A47_V0.148710.838
73_K85_S0.1480.834
17_G98_G0.147440.831
13_A35_V0.147160.830
51_I78_D0.146040.823
74_T88_F0.145950.823
34_I77_K0.14530.819
19_N108_A0.145080.818
62_K88_F0.144880.817
77_K103_N0.143210.807
25_H56_L0.142860.805
19_N106_I0.142750.805
90_R94_G0.141980.800
83_R100_L0.141030.795
23_V46_K0.139840.788
20_C83_R0.137880.777
108_A111_Q0.137540.775
45_R86_T0.137160.773
25_H28_S0.136910.772
85_S102_I0.136610.770
28_S32_H0.134980.761
91_D94_G0.134940.761
14_A92_E0.134920.761
26_D48_G0.134470.758
57_E60_K0.133540.753
36_A40_G0.133150.751
106_I109_L0.132410.746
84_S101_C0.132120.745
53_D59_L0.13210.745
10_D14_A0.131790.743
20_C100_L0.131760.743
56_L61_E0.131610.742
40_G89_I0.130850.738
13_A36_A0.13030.735
51_I77_K0.130080.733
74_T84_S0.129620.731
75_K84_S0.129270.729
92_E95_K0.12890.727
81_I106_I0.12870.726
11_F83_R0.128550.725
14_A60_K0.126940.716
74_T82_L0.126150.711
24_L98_G0.125860.709
33_S40_G0.125460.707
8_L19_N0.124960.704
54_L58_L0.124960.704
78_D81_I0.124750.703
5_Y10_D0.124120.700
34_I37_I0.124110.700
6_I93_N0.12410.700
6_I97_I0.124070.699
25_H103_N0.123090.694
9_V102_I0.123070.694
58_L63_Q0.122550.691
19_N73_K0.122490.690
21_E83_R0.122450.690
28_S54_L0.122310.689
53_D58_L0.121720.686
10_D98_G0.121520.685
62_K94_G0.121330.684
12_L24_L0.121130.683
24_L52_T0.12090.682
13_A55_A0.120110.677
34_I101_C0.119430.673
39_N84_S0.118610.669
40_G72_Y0.118560.668
5_Y12_L0.118050.665
21_E72_Y0.118040.665
74_T78_D0.118040.665
58_L98_G0.117770.664
28_S50_P0.117680.663
86_T103_N0.117660.663
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
1p0zA0.82297.90.659
3by8A0.872997.80.667
3caxA0.889896.70.738
2qkpA0.906896.40.745
4dahA0.915396.20.752
2w1rA0.889895.70.764
3lifA0.915395.60.766
2ykfA0.932295.40.769
3e4oA0.915393.50.79
3volA0.915392.50.797
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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