GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RF-1 - RF-1 domain
Pfam: PF00472 (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: CL0337
Length: 113
Sequences: 3155
Seq/Len: 27.92
HH_delta: 0.028 (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
74_Y77_K1.495133.347
72_E76_E1.235522.766
20_R33_N1.123792.516
28_N32_T1.053092.357
76_E80_E1.049372.349
51_E61_D1.033482.313
19_S48_K0.934752.092
73_A77_K0.930272.082
52_S57_Q0.892431.998
16_I38_L0.867641.942
15_E41_I0.848711.900
79_R83_R0.828691.855
21_S28_N0.815611.826
79_R82_T0.796731.783
18_F36_V0.795671.781
24_P28_N0.776781.739
52_S61_D0.7691.721
16_I63_L0.756131.693
39_R46_V0.755561.691
14_L63_L0.754991.690
18_F33_N0.754541.689
67_R71_D0.747981.674
85_I88_S0.720291.612
77_K81_K0.710521.590
28_N53_R0.705931.580
75_R79_R0.704391.577
28_N31_K0.665951.491
78_R82_T0.658121.473
74_Y78_R0.656961.471
14_L38_L0.624281.397
75_R78_R0.620731.389
56_H60_E0.62031.389
24_P53_R0.616621.380
16_I59_R0.611961.370
61_D64_E0.611661.369
71_D75_R0.598351.339
40_H43_T0.587981.316
65_K69_K0.587611.315
38_L63_L0.581381.301
90_V97_K0.570391.277
60_E64_E0.567331.270
17_S39_R0.565221.265
106_R109_V0.548871.229
19_S35_K0.526591.179
40_H44_G0.516851.157
34_S55_Q0.512321.147
35_K50_Q0.511361.145
28_N54_S0.504241.129
19_S37_R0.502211.124
101_T112_H0.51.119
83_R87_K0.495771.110
15_E39_R0.49431.106
90_V94_E0.49131.100
91_K94_E0.490421.098
86_R89_Q0.485631.087
81_K84_E0.484831.085
76_E79_R0.467771.047
49_C61_D0.463211.037
57_Q60_E0.458771.027
86_R90_V0.452041.012
5_K71_D0.449711.007
17_S37_R0.440950.987
14_L41_I0.431950.967
105_P108_R0.417330.934
77_K80_E0.415780.931
51_E65_K0.410740.919
49_C62_A0.410260.918
28_N56_H0.408230.914
41_I44_G0.406550.910
87_K91_K0.405530.908
45_I73_A0.396730.888
10_P13_D0.396340.887
21_S31_K0.395460.885
93_L97_K0.387270.867
90_V93_L0.385410.863
19_S33_N0.382320.856
48_K51_E0.37360.836
32_T54_S0.371530.832
94_E98_K0.371150.831
49_C65_K0.3710.830
57_Q61_D0.368010.824
13_D40_H0.364590.816
80_E84_E0.364320.816
84_E88_S0.364040.815
28_N33_N0.362690.812
34_S54_S0.354250.793
104_F107_S0.352220.788
6_E67_R0.348740.781
11_E14_L0.348520.780
91_K97_K0.343380.769
22_S50_Q0.342410.766
14_L42_P0.336670.754
72_E75_R0.329260.737
63_L67_R0.328390.735
70_L73_A0.32790.734
38_L62_A0.323250.724
73_A76_E0.319080.714
95_R98_K0.314960.705
21_S35_K0.314370.704
38_L47_V0.313070.701
98_K110_K0.312570.700
85_I89_Q0.310190.694
19_S50_Q0.309930.694
49_C52_S0.309040.692
7_I67_R0.308590.691
101_T108_R0.308460.690
56_H59_R0.307820.689
106_R110_K0.304250.681
83_R86_R0.299890.671
110_K113_R0.299080.669
53_R64_E0.298710.669
57_Q64_E0.296830.664
13_D42_P0.296010.663
42_P45_I0.292590.655
87_K90_V0.291860.653
22_S48_K0.291560.653
23_G30_N0.286140.641
21_S50_Q0.285780.640
48_K65_K0.285490.639
89_Q93_L0.285450.639
4_E64_E0.282720.633
4_E67_R0.279720.626
107_S110_K0.279340.625
78_R81_K0.277720.622
18_F28_N0.275830.617
108_R111_D0.272760.611
16_I36_V0.271980.609
62_A112_H0.267540.599
46_V50_Q0.264810.593
9_I63_L0.263240.589
89_Q104_F0.262810.588
59_R63_L0.261680.586
28_N34_S0.260940.584
82_T85_I0.259570.581
109_V112_H0.257410.576
82_T86_R0.255890.573
108_R112_H0.255760.573
11_E63_L0.251550.563
97_K108_R0.250880.562
96_K103_N0.25060.561
37_R48_K0.249510.559
64_E68_E0.247850.555
103_N108_R0.245970.551
94_E107_S0.245140.549
18_F24_P0.242770.543
60_E109_V0.242330.542
43_T70_L0.240920.539
22_S29_V0.238270.533
79_R88_S0.236380.529
23_G27_Q0.236180.529
29_V50_Q0.235970.528
9_I67_R0.233870.524
68_E71_D0.233020.522
97_K106_R0.232260.520
79_R85_I0.231990.519
64_E71_D0.231570.518
79_R84_E0.228930.512
47_V62_A0.226650.507
31_K36_V0.226180.506
95_R103_N0.225880.506
36_V55_Q0.22450.503
106_R112_H0.224390.502
68_E72_E0.222950.499
51_E57_Q0.222450.498
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
3d5aX0.99121000.028
1zbtA0.99121000.029
1rq0A0.99121000.038
2b3tB11000.039
2ihr10.99121000.039
1gqeA0.99121000.041
4dh9Y0.93811000.201
2rsmA0.716899.90.245
2jvaA0.734599.90.293
1j26A0.699199.90.302

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