GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
XPG_I - XPG I-region
Pfam: PF00867 (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: CL0464
Length: 94
Sequences: 3147
Seq/Len: 33.48
HH_delta: 0.053 (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
69_D72_D1.501394.779
80_T83_Q1.182343.764
1_R7_Y1.125063.581
74_L80_T0.873052.779
87_L91_C0.856822.727
71_D75_K0.777212.474
32_T37_L0.603341.920
70_L74_L0.60121.914
71_D74_L0.599311.908
84_F88_C0.571371.819
20_Y24_N0.527921.680
43_P70_L0.524041.668
18_C30_V0.516911.645
79_L83_Q0.49291.569
70_L82_E0.490221.560
35_S88_C0.490021.560
72_D75_K0.479461.526
13_E34_D0.471491.501
10_A17_Q0.461141.468
72_D76_E0.423721.349
18_C37_L0.415291.322
29_A67_V0.404131.286
15_E34_D0.393871.254
84_F87_L0.388211.236
73_I79_L0.358781.142
83_Q86_D0.352961.124
19_A88_C0.351931.120
32_T48_K0.344261.096
66_E72_D0.335551.068
79_L87_L0.333841.063
38_L68_I0.333671.062
22_E28_D0.331961.057
85_I89_I0.331091.054
50_S53_S0.327481.042
12_Y31_I0.327311.042
17_Q21_L0.321381.023
17_Q20_Y0.319081.016
22_E43_P0.318021.012
44_K67_V0.317181.010
44_K69_D0.314081.000
49_L52_K0.311630.992
39_L88_C0.310850.989
30_V37_L0.308210.981
41_G73_I0.300260.956
68_I72_D0.291520.928
85_I88_C0.287280.914
23_R42_A0.286460.912
13_E36_D0.28380.903
65_V68_I0.27680.881
19_A85_I0.275320.876
38_L41_G0.273940.872
15_E36_D0.270470.861
49_L62_E0.269610.858
8_I17_Q0.267730.852
15_E37_L0.265670.846
39_L86_D0.262050.834
8_I21_L0.257830.821
16_A40_F0.252180.803
74_L78_G0.25050.797
38_L84_F0.250060.796
35_S84_F0.248950.792
15_E18_C0.245420.781
32_T36_D0.241730.769
69_D76_E0.239550.763
19_A37_L0.239480.762
23_R82_E0.236560.753
79_L84_F0.235950.751
18_C22_E0.235740.750
1_R6_P0.2350.748
53_S64_E0.233550.743
1_R9_V0.232470.740
46_I67_V0.231470.737
13_E32_T0.229890.732
18_C27_V0.224890.716
41_G70_L0.224780.715
27_V44_K0.223240.711
22_E27_V0.220850.703
73_I76_E0.216670.690
50_S65_V0.216250.688
66_E76_E0.215010.684
70_L80_T0.212990.678
16_A19_A0.211270.672
53_S63_K0.211260.672
81_R85_I0.208650.664
71_D76_E0.207630.661
48_K68_I0.206190.656
63_K66_E0.202640.645
3_M8_I0.20210.643
38_L73_I0.20120.640
63_K68_I0.200990.640
70_L81_R0.200750.639
23_R27_V0.200610.639
35_S91_C0.19970.636
73_I77_L0.198320.631
16_A39_L0.197730.629
38_L87_L0.196970.627
12_Y20_Y0.196710.626
22_E86_D0.195640.623
53_S62_E0.195260.622
32_T88_C0.192810.614
50_S62_E0.190150.605
12_Y18_C0.189940.605
38_L88_C0.189290.603
25_G43_P0.187720.598
15_E32_T0.187610.597
77_L91_C0.187570.597
10_A27_V0.186240.593
25_G45_V0.185530.591
33_E50_S0.184320.587
14_A37_L0.183550.584
21_L24_N0.182930.582
77_L84_F0.182280.580
52_K63_K0.18050.575
35_S39_L0.18020.574
23_R43_P0.180150.573
29_A44_K0.180030.573
8_I65_V0.179510.571
15_E89_I0.179450.571
19_A23_R0.179430.571
38_L45_V0.178980.570
39_L84_F0.178860.569
11_P17_Q0.178190.567
25_G66_E0.178180.567
88_C91_C0.175780.560
50_S63_K0.175470.559
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
1b43A0.978799.80.053
1a76A0.904399.80.054
1ul1X0.936299.80.065
2izoA0.978799.80.07
3q8kA0.936299.80.076
3oryA0.978799.80.076
3qe9Y0.893699.80.093
1rxwA0.978799.80.116
1bgxT0.861799.70.19
1exnA0.872399.60.248

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