GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Big_2 - Bacterial Ig-like domain (group 2)
Pfam: PF02368 (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: CL0159
Length: 79
Sequences: 2096
Seq/Len: 26.53
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
28_P31_G1.160193.084
14_L57_A1.113692.961
12_V20_Q1.018532.708
47_T58_L0.925172.460
41_S63_A0.886512.357
21_Q54_K0.843962.244
39_S68_T0.714631.900
46_A55_V0.714171.899
9_P20_Q0.672481.788
49_D54_K0.669031.779
46_A63_A0.611031.624
15_K18_Q0.602891.603
49_D52_T0.600751.597
48_V55_V0.584081.553
38_W67_A0.57741.535
24_A38_W0.560851.491
40_S43_P0.547821.456
22_L55_V0.544221.447
28_P69_S0.543381.445
35_K70_G0.534361.421
19_T54_K0.533381.418
36_V67_A0.517691.376
40_S65_I0.515171.370
41_S66_T0.513721.366
43_P47_T0.497681.323
48_V53_G0.495941.318
6_T27_T0.485291.290
69_S73_K0.466211.239
45_I63_A0.455361.211
42_N45_I0.453791.206
49_D53_G0.45111.199
9_P12_V0.415391.104
26_V69_S0.403981.074
41_S64_T0.399031.061
16_V60_A0.395491.051
38_W53_G0.389711.036
28_P32_S0.386921.029
22_L48_V0.382671.017
14_L20_Q0.376531.001
8_T23_T0.372260.990
26_V31_G0.370930.986
40_S48_V0.365570.972
40_S63_A0.349290.929
45_I59_K0.345190.918
4_S27_T0.343180.912
15_K60_A0.332520.884
36_V69_S0.326960.869
16_V59_K0.31760.844
47_T56_T0.312740.831
13_T16_V0.30080.800
19_T56_T0.29990.797
21_Q53_G0.294190.782
41_S44_S0.288370.767
4_S73_K0.285180.758
37_T68_T0.281460.748
5_I24_A0.280870.747
69_S72_N0.277640.738
28_P33_N0.276680.736
12_V63_A0.276120.734
70_G73_K0.273250.726
24_A67_A0.273160.726
44_S59_K0.265620.706
26_V34_S0.264020.702
7_I67_A0.262370.698
64_T74_S0.260760.693
19_T57_A0.258430.687
6_T25_T0.255030.678
22_L67_A0.254890.678
40_S45_I0.254320.676
5_I69_S0.251650.669
22_L38_W0.249450.663
7_I24_A0.246710.656
25_T64_T0.245660.653
8_T20_Q0.243890.648
26_V36_V0.240720.640
14_L18_Q0.238130.633
21_Q52_T0.237030.630
9_P22_L0.236120.628
33_N70_G0.233550.621
12_V55_V0.227220.604
53_G65_I0.219140.583
5_I73_K0.217020.577
48_V65_I0.216620.576
31_G34_S0.214730.571
33_N71_D0.211770.563
28_P36_V0.209280.556
7_I22_L0.206930.550
29_S43_P0.205870.547
46_A65_I0.204120.543
6_T60_A0.202590.539
13_T35_K0.200120.532
61_G65_I0.199340.530
68_T72_N0.198470.528
39_S44_S0.196950.524
8_T25_T0.196660.523
7_I10_T0.196440.522
7_I65_I0.194870.518
26_V71_D0.191270.508
5_I26_V0.185440.493
38_W48_V0.185240.492
20_Q23_T0.184920.492
13_T39_S0.184740.491
57_A61_G0.184290.490
21_Q60_A0.180040.479
63_A67_A0.179950.478
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
2l04A0.987399.40.053
3ncxA0.911498.40.384
1f1sA0.898797.10.566
1f00I0.936796.80.591
4aq1A0.987392.20.693
1cwvA0.96289.90.71
3pe9A0.974755.10.785
3zyiA0.949453.40.787
3pddA0.987350.90.79
2l7yA0.898750.70.79

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