GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HxxPF_rpt - HxxPF-repeated domain
Pfam: PF13745 (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. )
Length: 91
Sequences: 5474
Seq/Len: 60.15
HH_delta: 0.102 (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
65_V74_L1.231333.319
85_E89_E1.149283.098
76_L88_I0.961372.592
9_R13_A0.950212.562
63_L76_L0.935992.523
78_Y88_I0.9052.440
84_S87_T0.84612.281
5_Y13_A0.824292.222
30_F65_V0.796282.147
5_Y10_L0.783562.112
19_D22_R0.758622.045
83_F88_I0.751212.025
10_L14_L0.744672.008
62_T77_E0.728691.964
9_R12_E0.704641.900
42_L47_L0.669491.805
6_P9_R0.656841.771
7_F11_V0.647261.745
88_I91_M0.520391.403
29_M62_T0.520211.402
78_Y83_F0.493091.329
58_K62_T0.47921.292
63_L74_L0.478941.291
22_R27_Q0.476921.286
41_D46_R0.468311.262
57_A62_T0.468241.262
31_N62_T0.465991.256
83_F87_T0.444381.198
87_T90_R0.442591.193
26_F59_F0.422581.139
64_E75_Q0.403741.088
57_A77_E0.402811.086
68_D73_R0.399921.078
44_G47_L0.392581.058
27_Q60_D0.392021.057
5_Y27_Q0.391011.054
12_E15_G0.388351.047
23_N26_F0.387471.045
68_D71_G0.382271.031
11_V16_P0.375681.013
31_N64_E0.371731.002
64_E77_E0.371541.002
42_L45_L0.37070.999
80_T85_E0.362990.979
60_D82_L0.358760.967
29_M59_F0.352360.950
23_N59_F0.351550.948
23_N27_Q0.35020.944
11_V18_R0.348790.940
54_N77_E0.348530.940
57_A60_D0.347370.936
32_Y65_V0.347180.936
82_L87_T0.346410.934
81_D91_M0.345180.931
10_L13_A0.343230.925
33_Q66_R0.339520.915
43_G46_R0.339050.914
65_V72_L0.338240.912
1_E4_D0.334970.903
86_E89_E0.334870.903
34_N67_E0.334660.902
58_K77_E0.330560.891
2_H5_Y0.33040.891
45_L49_P0.328640.886
41_D44_G0.32520.877
35_F66_R0.320260.863
49_P52_L0.318130.858
35_F38_S0.314720.848
59_F62_T0.303790.819
30_F63_L0.299220.807
33_Q64_E0.298240.804
27_Q31_N0.298080.804
86_E90_R0.294150.793
6_P10_L0.291450.786
46_R49_P0.29130.785
87_T91_M0.28720.774
48_E52_L0.28490.768
37_Q40_L0.284620.767
53_E56_G0.282080.760
24_P27_Q0.278650.751
1_E5_Y0.275390.742
42_L46_R0.275380.742
7_F10_L0.274240.739
55_G77_E0.27410.739
37_Q73_R0.263990.712
5_Y9_R0.263250.710
31_N34_N0.262530.708
78_Y85_E0.262450.708
39_A73_R0.261650.705
24_P28_V0.260230.702
15_G18_R0.257820.695
12_E16_P0.25770.695
37_Q66_R0.253360.683
18_R21_S0.251610.678
55_G75_Q0.250870.676
50_I55_G0.243940.658
30_F33_Q0.243870.657
7_F24_P0.241850.652
40_L47_L0.240550.648
52_L55_G0.237680.641
28_V31_N0.237250.640
56_G77_E0.236110.637
2_H6_P0.22860.616
45_L50_I0.228390.616
18_R25_L0.228070.615
60_D83_F0.226310.610
22_R82_L0.225040.607
13_A16_P0.225020.607
7_F23_N0.224360.605
61_L88_I0.222730.600
35_F64_E0.220230.594
27_Q30_F0.218360.589
40_L49_P0.217950.588
43_G55_G0.217150.585
43_G47_L0.216870.585
66_R73_R0.215690.581
11_V14_L0.215570.581
34_N37_Q0.215080.580
36_S40_L0.214260.578
47_L51_P0.213480.576
18_R24_P0.211340.570
55_G58_K0.210560.568
50_I54_N0.210210.567
32_Y72_L0.208940.563
8_E11_V0.207880.560
54_N64_E0.207160.558
55_G64_E0.205960.555
46_R51_P0.205770.555
66_R75_Q0.204110.550
78_Y81_D0.203470.549
32_Y35_F0.203070.547
26_F29_M0.201550.543
4_D87_T0.201320.543
2_H61_L0.201060.542
51_P54_N0.200820.541
58_K64_E0.198370.535
44_G48_E0.197190.532
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
2jgpA198.80.102
1l5aA0.945198.30.241
2vsqA0.912198.30.253
4hvmA0.97897.90.334
4jn3A0.912197.80.345
2xhgA0.98997.50.403
1q9jA0.868195.60.541
3fotA126.50.769
2wu8A0.65932.60.852
3dobA0.9892.10.859

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