GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UQ_con - Ubiquitin-conjugating enzyme
Pfam: PF00179 (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: CL0208
Length: 140
Sequences: 3532
Seq/Len: 25.23
HH_delta: -0.033 (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
56_D60_S1.166244.263
1_R5_E0.786412.875
71_F124_L0.752182.749
118_N121_A0.751242.746
31_H48_K0.62562.287
29_E52_S0.584762.137
29_E50_R0.584382.136
36_G40_T0.568332.077
53_F97_I0.564432.063
50_R67_L0.544291.990
36_G43_E0.53091.941
26_N29_E0.5191.897
114_E126_K0.475671.739
64_V104_I0.472481.727
2_L53_F0.443761.622
116_P122_A0.440991.612
35_F46_I0.438971.605
50_R65_R0.431271.576
51_I64_V0.428311.566
119_E123_E0.423251.547
22_S29_E0.420551.537
22_S31_H0.419591.534
106_S110_E0.417931.528
7_K10_Q0.412011.506
113_P125_Y0.385861.410
30_W53_F0.383811.403
32_V51_I0.380151.390
48_K67_L0.37921.386
112_N115_D0.378851.385
84_D87_N0.376581.376
3_Q7_K0.370111.353
4_K8_E0.366831.341
76_D80_R0.361291.321
64_V100_I0.35011.280
72_H75_I0.344481.259
38_P43_E0.341271.247
92_S95_Y0.339831.242
65_R80_R0.337781.235
16_G105_Q0.33581.227
49_F64_V0.328681.201
74_N107_L0.328331.200
103_S106_S0.327961.199
79_G86_L0.32761.197
14_P17_I0.32531.189
120_E123_E0.316791.158
40_T43_E0.311641.139
95_Y103_S0.31131.138
59_F94_S0.31121.138
18_S33_T0.309021.130
71_F121_A0.307321.123
18_S21_P0.305961.118
76_D117_L0.304531.113
8_E12_N0.302281.105
58_P62_P0.297021.086
49_F66_F0.289871.060
123_E126_K0.285411.043
31_H50_R0.28371.037
4_K7_K0.279681.022
42_Y47_F0.278581.018
3_Q27_L0.27721.013
98_E102_L0.274751.004
101_L105_Q0.274191.002
32_V101_L0.274141.002
119_E122_A0.268240.980
96_T99_S0.264740.968
119_E126_K0.262840.961
32_V49_F0.262440.959
8_E96_T0.257710.942
112_N117_L0.254280.929
51_I101_L0.253810.928
33_T46_I0.249220.911
42_Y45_G0.248210.907
28_F55_P0.246730.902
49_F104_I0.246290.900
20_Q31_H0.244790.895
63_K80_R0.244280.893
31_H67_L0.243680.891
40_T109_S0.243130.889
19_V22_S0.240020.877
37_P42_Y0.238460.872
52_S65_R0.237850.869
117_L121_A0.236840.866
2_L5_E0.234790.858
7_K11_K0.234250.856
1_R58_P0.234080.856
81_I107_L0.233960.855
22_S26_N0.233710.854
65_R78_N0.231720.847
30_W97_I0.229860.840
22_S50_R0.22940.839
115_D118_N0.228140.834
84_D95_Y0.22810.834
2_L30_W0.22790.833
82_C116_P0.226220.827
84_D92_S0.225140.823
19_V97_I0.223430.817
82_C85_I0.22320.816
12_N98_E0.221220.809
68_T71_F0.21860.799
53_F78_N0.214730.785
85_I103_S0.214250.783
6_L10_Q0.214240.783
10_Q22_S0.212180.776
115_D122_A0.212080.775
99_S102_L0.212060.775
39_G43_E0.210320.769
113_P122_A0.209990.768
120_E124_L0.209910.767
52_S63_K0.209420.765
52_S55_P0.209230.765
36_G39_G0.208510.762
94_S110_E0.207920.760
21_P30_W0.20710.757
8_E98_E0.206010.753
10_Q20_Q0.205420.751
103_S107_L0.204110.746
74_N111_P0.204080.746
21_P24_D0.203880.745
102_L106_S0.20360.744
17_I101_L0.202910.742
59_F92_S0.202570.740
121_A124_L0.202120.739
3_Q59_F0.200910.734
17_I105_Q0.200870.734
23_E26_N0.200740.734
108_L111_P0.199640.730
81_I84_D0.198630.726
2_L6_L0.19690.720
4_K11_K0.196040.717
6_L27_L0.195260.714
112_N118_N0.194420.711
35_F44_G0.193740.708
91_W100_I0.192450.703
114_E119_E0.192250.703
35_F38_P0.192150.702
118_N122_A0.190470.696
1_R4_K0.190330.696
51_I97_I0.189850.694
13_P16_G0.189770.694
115_D121_A0.189680.693
6_L30_W0.187830.687
10_Q13_P0.18760.686
73_P121_A0.187550.686
95_Y99_S0.186870.683
39_G44_G0.186450.682
54_P60_S0.185830.679
3_Q10_Q0.184830.676
57_Y99_S0.182770.668
83_L87_N0.181070.662
66_F75_I0.179620.657
41_P46_I0.179480.656
3_Q55_P0.179190.655
94_S102_L0.179070.655
1_R21_P0.178810.654
16_G20_Q0.178270.652
83_L103_S0.176610.646
8_E18_S0.175890.643
49_F87_N0.174990.640
92_S99_S0.173890.636
26_N30_W0.173670.635
37_P40_T0.173550.634
47_F66_F0.172080.629
42_Y58_P0.171630.627
5_E96_T0.171620.627
9_L19_V0.17130.626
49_F75_I0.171160.626
18_S35_F0.170880.625
62_P100_I0.170730.624
74_N82_C0.17060.624
72_H76_D0.170120.622
45_G68_T0.169110.618
74_N86_L0.168730.617
73_P111_P0.168670.617
23_E31_H0.168570.616
12_N15_P0.168430.616
83_L107_L0.168070.614
28_F52_S0.167570.613
8_E24_D0.166260.608
117_L122_A0.165880.606
87_N115_D0.164880.603
81_I117_L0.164840.603
99_S105_Q0.164550.601
97_I101_L0.163840.599
94_S106_S0.162330.593
58_P61_P0.161850.592
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
4ddgA0.9857100-0.033
4jquA1100-0.028
2pwqA0.9857100-0.027
2uczA1100-0.024
1tteA0.9929100-0.023
3h8kA1100-0.022
1ayzA0.9857100-0.02
2ayvA0.9857100-0.019
2c2vB0.9857100-0.017
2awfA0.9929100-0.017

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