GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
C1-set - Immunoglobulin C1-set domain
Pfam: PF07654 (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: CL0011
Length: 83
Sequences: 18977
Seq/Len: 228.64
HH_delta: -0.016 (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
30_L72_R2.034343.705
15_C71_C1.37472.503
28_T74_T1.347412.454
30_L70_S1.282112.335
31_K67_D1.27252.317
32_N36_V1.165312.122
28_T72_R1.095581.995
17_V73_V1.082891.972
17_V27_V1.051431.915
19_G24_D1.039321.893
31_K69_Y0.909351.656
7_L63_W0.886821.615
39_G42_T0.886111.614
28_T35_E0.839271.528
10_S60_T0.78161.423
26_T74_T0.757671.380
56_T59_L0.748391.363
19_G22_P0.736171.341
42_T45_P0.73531.339
53_Y56_T0.732681.334
48_N52_T0.729671.329
30_L35_E0.711391.296
32_N35_E0.699611.274
24_D75_H0.690731.258
33_G36_V0.676671.232
56_T60_T0.656371.195
63_W66_G0.640271.166
13_L69_Y0.639741.165
11_V61_V0.601781.096
24_D73_V0.59461.083
37_T40_V0.571651.041
21_Y24_D0.570461.039
32_N70_S0.551581.004
17_V22_P0.550651.003
38_E41_E0.522820.952
17_V71_C0.509210.927
41_E47_P0.4820.878
47_P50_D0.473510.862
12_T54_S0.472240.860
10_S59_L0.463040.843
55_V59_L0.459540.837
56_T61_V0.458260.835
27_V73_V0.455860.830
64_N67_D0.450510.820
72_R76_E0.447030.814
22_P26_T0.442070.805
32_N68_E0.421920.768
24_D27_V0.418850.763
18_S21_Y0.415520.757
19_G73_V0.405810.739
22_P27_V0.403790.735
48_N51_G0.401450.731
50_D53_Y0.400760.730
61_V71_C0.400030.728
23_K26_T0.399110.727
47_P54_S0.397520.724
16_L19_G0.396160.721
8_G60_T0.389820.710
34_K37_T0.38650.704
70_S73_V0.38240.696
46_P51_G0.3770.687
7_L66_G0.370180.674
37_T41_E0.369310.673
59_L62_T0.368960.672
45_P56_T0.366440.667
42_T47_P0.366090.667
49_S54_S0.365850.666
19_G75_H0.364690.664
30_L33_G0.363180.661
26_T29_W0.358610.653
51_G56_T0.35470.646
22_P73_V0.346710.631
23_K73_V0.344470.627
11_V14_T0.337720.615
33_G68_E0.330280.601
31_K34_K0.328950.599
65_S69_Y0.327720.597
51_G55_V0.326480.595
49_S52_T0.324480.591
49_S53_Y0.319870.583
46_P54_S0.3160.575
13_L31_K0.311450.567
65_S76_E0.310360.565
27_V70_S0.307970.561
31_K64_N0.305810.557
19_G23_K0.303630.553
35_E38_E0.30150.549
62_T65_S0.300930.548
63_W68_E0.300360.547
8_G65_S0.299720.546
16_L51_G0.293470.534
11_V67_D0.293120.534
39_G48_N0.292210.532
47_P51_G0.290550.529
19_G66_G0.290430.529
12_T60_T0.286640.522
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
3usaC198.6-0.016
3usaD198.6-0.003
4gupA198.50.022
1uvqA198.50.026
3c5jA198.50.026
3c5jB198.50.03
2p24A198.50.035
1uvqB198.50.037
1iakA198.40.038
1iaoB198.40.042

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