GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
XPG_N - XPG N-terminal domain
Pfam: PF00752 (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: CL0280
Length: 101
Sequences: 1214
Seq/Len: 12.02
HH_delta: 0.092 (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
33_A79_F0.341972.226
28_R74_K0.262731.710
65_L77_F0.249531.624
40_F60_G0.245721.599
89_E92_Q0.24381.587
93_K96_K0.242521.579
80_D87_K0.241261.570
33_A77_F0.240511.565
47_E50_Q0.235171.531
39_Q60_G0.23341.519
1_M6_L0.230731.502
19_V24_L0.229271.492
87_K94_R0.226441.474
47_E52_V0.21981.431
51_G54_T0.218841.424
29_V89_E0.214591.397
3_I6_L0.212261.382
89_E96_K0.205391.337
38_H44_C0.203141.322
34_S91_I0.200581.306
36_W64_R0.200451.305
31_I77_F0.199551.299
31_I75_P0.195691.274
88_R92_Q0.192261.251
92_Q96_K0.188911.230
49_G52_V0.1881.224
46_E52_V0.187381.220
61_L77_F0.185121.205
46_E50_Q0.183821.196
7_W36_W0.183251.193
90_T94_R0.180741.176
8_Q11_K0.176911.152
6_L10_L0.173871.132
22_S71_H0.173541.130
33_A40_F0.173541.130
11_K23_E0.171921.119
92_Q95_R0.171891.119
60_G66_C0.170221.108
62_F66_C0.169421.103
5_G18_K0.169351.102
25_R28_R0.16861.097
48_L54_T0.166921.086
22_S74_K0.166181.082
42_F45_R0.165141.075
46_E49_G0.163751.066
9_L64_R0.162561.058
4_K8_Q0.162131.055
50_Q53_G0.161891.054
48_L52_V0.161121.049
93_K97_R0.160791.047
89_E93_K0.160551.045
48_L51_G0.157751.027
23_E29_V0.154921.008
51_G85_P0.152870.995
2_G87_K0.152490.993
17_R20_S0.15220.991
36_W77_F0.150080.977
49_G54_T0.149880.976
80_D94_R0.149570.974
5_G29_V0.148660.968
58_L65_L0.148350.966
30_A64_R0.14710.957
46_E51_G0.14690.956
58_L62_F0.146770.955
90_T93_K0.146710.955
61_L71_H0.146340.953
67_R70_E0.14630.952
12_P88_R0.142890.930
66_C70_E0.142410.927
19_V25_R0.141480.921
34_S64_R0.141390.920
47_E51_G0.140890.917
2_G5_G0.14050.915
10_L14_A0.140420.914
17_R23_E0.138880.904
31_I36_W0.138120.899
41_L66_C0.138110.899
84_P91_I0.137180.893
20_S96_K0.136910.891
5_G67_R0.135970.885
44_C59_R0.135530.882
24_L57_H0.133580.869
30_A36_W0.133210.867
34_S37_L0.132710.864
2_G6_L0.131790.858
33_A61_L0.131510.856
71_H88_R0.130560.850
2_G7_W0.130550.850
85_P89_E0.130410.849
21_L68_L0.130140.847
37_L43_S0.129730.844
86_L96_K0.129710.844
71_H82_K0.129650.844
18_K89_E0.128090.834
45_R56_S0.128090.834
14_A74_K0.127410.829
62_F69_L0.127350.829
14_A90_T0.127320.829
40_F61_L0.126750.825
28_R92_Q0.126270.822
23_E61_L0.126110.821
81_G87_K0.125540.817
35_C60_G0.125460.817
76_I93_K0.125440.816
59_R63_S0.125150.815
92_Q97_R0.12480.812
11_K26_G0.124480.810
2_G80_D0.124460.810
2_G94_R0.123950.807
42_F97_R0.12370.805
34_S84_P0.123140.802
25_R72_G0.122540.798
75_P78_V0.122210.795
40_F43_S0.12210.795
67_R75_P0.121660.792
37_L61_L0.121030.788
39_Q42_F0.11990.780
43_S57_H0.119810.780
75_P79_F0.119660.779
18_K53_G0.118320.770
72_G94_R0.117110.762
26_G89_E0.116990.761
30_A33_A0.116270.757
65_L69_L0.115660.753
10_L37_L0.11490.748
31_I89_E0.114830.747
29_V70_E0.114420.745
12_P19_V0.114150.743
69_L74_K0.113750.740
26_G72_G0.11280.734
91_I94_R0.111370.725
4_K13_A0.110630.720
24_L90_T0.11010.717
37_L41_L0.10970.714
30_A86_L0.109690.714
22_S30_A0.108920.709
41_L92_Q0.108810.708
21_L73_I0.108290.705
61_L65_L0.10790.702
19_V97_R0.107370.699
7_W12_P0.107360.699
26_G88_R0.107020.697
44_C54_T0.106610.694
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
3qe9Y0.980299.90.092
1b43A0.950599.80.233
3oryA0.980299.70.248
1a76A0.950599.70.261
3q8kA0.990199.70.264
1rxwA0.950599.70.264
1ul1X0.990199.70.272
2izoA0.920899.50.383
1bgxT0.8614990.518
1exnA0.841698.40.624

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