GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Usp - Universal stress protein family
Pfam: PF00582 (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: CL0039
Length: 140
Sequences: 13610
Seq/Len: 97.21
HH_delta: 0.008 (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
4_R34_T1.909813.203
6_L103_A1.772472.973
91_A127_K1.612362.704
4_R32_E1.576392.644
105_L137_L1.53082.567
34_T103_A1.340392.248
97_F101_H1.297332.176
108_M128_L1.296912.175
34_T84_V1.255612.106
32_E82_E1.234292.070
8_A94_I1.227152.058
98_A106_I1.201842.016
34_T101_H1.173871.969
8_A108_M1.105771.855
21_F137_L1.074741.803
110_S140_P1.045711.754
34_T97_F1.036811.739
88_G93_A1.020351.711
36_L97_F1.009341.693
7_V22_A1.004471.685
126_E130_R0.990191.661
106_I134_C0.980481.644
127_K131_H0.961031.612
86_E93_A0.959911.610
93_A96_E0.959771.610
84_V97_F0.956041.603
95_I131_H0.933741.566
38_V93_A0.911831.529
22_A26_A0.893131.498
106_I132_A0.890481.494
99_E133_P0.875261.468
6_L36_L0.844591.417
7_V19_L0.822051.379
98_A134_C0.820771.377
4_R104_D0.818341.373
97_F100_E0.791061.327
21_F139_V0.786711.319
25_L29_S0.782961.313
22_A107_V0.770061.292
110_S138_V0.753721.264
36_L94_I0.753021.263
98_A103_A0.73961.240
26_A31_A0.729531.224
32_E80_V0.724751.216
34_T82_E0.721791.211
5_I105_L0.716451.202
87_S93_A0.695581.167
72_E76_E0.69181.160
11_G37_H0.687921.154
95_I132_A0.684891.149
97_F103_A0.682411.145
59_A63_E0.674591.131
78_G81_I0.671351.126
98_A133_P0.661241.109
90_V124_V0.661181.109
31_A104_D0.656971.102
21_F24_E0.648321.087
95_I128_L0.637881.070
60_E64_Q0.632081.060
21_F25_L0.63091.058
106_I128_L0.628491.054
21_F135_P0.626031.050
116_L120_L0.616681.034
95_I98_A0.612521.027
96_E100_E0.611561.026
4_R103_A0.608021.020
38_V90_V0.600231.007
3_K31_A0.597541.002
9_I19_L0.590190.990
108_M138_V0.590030.990
22_A33_I0.582150.976
7_V18_A0.581690.976
107_V137_L0.577460.969
115_G118_R0.56530.948
118_R126_E0.562290.943
6_L106_I0.561450.942
113_R117_E0.557910.936
129_L138_V0.554390.930
6_L97_F0.554340.930
89_D92_D0.5530.928
15_S18_A0.548980.921
19_L35_L0.545050.914
24_E28_R0.543470.912
8_A109_G0.543340.911
7_V33_I0.540230.906
23_L27_K0.539580.905
94_I128_L0.536850.900
86_E97_F0.535260.898
3_K104_D0.532030.892
108_M125_A0.530940.891
74_E77_G0.529840.889
132_A136_V0.529670.888
9_I15_S0.526020.882
9_I18_A0.511960.859
110_S125_A0.507890.852
17_R20_R0.504550.846
16_R20_R0.501740.842
57_E61_E0.499620.838
84_V101_H0.495290.831
26_A33_I0.492860.827
72_E75_A0.492450.826
125_A138_V0.491180.824
9_I35_L0.490650.823
73_A77_G0.487570.818
24_E27_K0.486470.816
109_G139_V0.485810.815
4_R101_H0.485570.814
25_L107_V0.485510.814
22_A31_A0.480920.807
73_A76_E0.478240.802
13_E16_R0.475280.797
12_S15_S0.475010.797
5_I26_A0.469770.788
5_I107_V0.467430.784
116_L119_L0.454350.762
91_A131_H0.453440.761
80_V88_G0.446490.749
48_S51_E0.445740.748
102_N134_C0.443420.744
91_A124_V0.442590.742
57_E60_E0.435980.731
19_L23_L0.434640.729
52_D56_E0.43250.725
58_E62_E0.432080.725
6_L98_A0.431350.723
20_R23_L0.43120.723
10_D15_S0.428950.719
76_E79_I0.428490.719
107_V139_V0.426720.716
9_I16_R0.424970.713
39_I87_S0.423230.710
59_A62_E0.422320.708
29_S104_D0.416870.699
81_I84_V0.416110.698
92_D96_E0.414670.695
53_E56_E0.414190.695
60_E63_E0.413460.693
115_G119_L0.412730.692
57_E64_Q0.411940.691
105_L135_P0.411180.690
94_I124_V0.408060.684
55_S59_A0.403440.677
91_A128_L0.396570.665
26_A29_S0.396520.665
111_R125_A0.395730.664
18_A107_V0.393030.659
23_L79_I0.392470.658
45_Y48_S0.392470.658
55_S63_E0.392010.657
93_A97_F0.391070.656
95_I127_K0.387740.650
129_L136_V0.386990.649
36_L86_E0.381980.641
32_E81_I0.379820.637
118_R130_R0.379480.636
50_A53_E0.379050.636
27_K77_G0.374290.628
52_D55_S0.374210.628
74_E78_G0.371020.622
121_F125_A0.370430.621
124_V128_L0.366870.615
109_G122_G0.366710.615
8_A106_I0.365910.614
49_A52_D0.364020.611
25_L105_L0.363930.610
51_E54_E0.363730.610
103_A134_C0.361520.606
90_V93_A0.357620.600
26_A30_G0.353930.594
20_R24_E0.351370.589
7_V35_L0.349910.587
119_L123_S0.349280.586
81_I88_G0.3480.584
46_S50_A0.347980.584
114_S119_L0.345690.580
89_D93_A0.345550.580
128_L136_V0.344680.578
4_R102_N0.341510.573
20_R72_E0.340570.571
23_L77_G0.339580.570
5_I31_A0.336240.564
34_T83_V0.333810.560
9_I37_H0.333540.559
50_A62_E0.332850.558
17_R21_F0.33230.557
56_E59_A0.330910.555
73_A78_G0.330330.554
90_V95_I0.330290.554
25_L28_R0.330250.554
48_S52_D0.328170.550
122_G125_A0.32780.550
72_E79_I0.32720.549
58_E61_E0.323990.543
61_E64_Q0.321740.540
35_L74_E0.321570.539
50_A54_E0.321370.539
11_G15_S0.320810.538
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
3s3tA199.80.008
3hgmA0.992999.80.024
3tnjA0.992999.80.026
3fg9A0.992999.80.03
1mjhA0.992999.70.037
2dumA0.992999.70.04
2z08A0.978699.70.046
3dloA0.935799.70.046
1tq8A0.992999.70.048
3idfA0.971499.70.063

Page generated in 0.0376 seconds.