GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Big_5 - Bacterial Ig-like domain
Pfam: PF13205 (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: 107
Sequences: 2540
Seq/Len: 23.74
HH_delta: 0.479 (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
7_V27_I0.936163.911
88_D92_N0.767663.207
28_T63_T0.598232.499
33_V86_I0.58942.462
54_V66_I0.537092.244
26_V65_T0.491442.053
24_P67_T0.471091.968
56_F66_I0.452211.889
7_V10_T0.420781.758
9_S28_T0.418391.748
73_K78_Y0.414471.731
31_E92_N0.414331.731
72_L78_Y0.397141.659
44_I80_V0.383951.604
55_S69_S0.350071.462
43_T81_T0.333871.395
73_K76_T0.324671.356
27_I80_V0.320681.340
81_T97_P0.309461.293
26_V63_T0.297941.245
49_G52_V0.29091.215
34_D37_S0.288231.204
67_T71_P0.286371.196
80_V98_F0.285181.191
10_T14_D0.270071.128
31_E88_D0.268261.121
29_F64_L0.267791.119
51_G54_V0.265971.111
24_P65_T0.264491.105
10_T98_F0.262331.096
8_V30_S0.257211.074
21_P74_P0.257151.074
60_D63_T0.257121.074
41_A83_D0.256831.073
12_P16_A0.256821.073
12_P25_I0.254011.061
59_W62_N0.253071.057
68_P72_L0.252491.055
13_A16_A0.251621.051
82_I94_L0.249811.044
31_E90_A0.249531.042
48_N52_V0.247591.034
89_L93_P0.244661.022
79_T97_P0.238390.996
54_V68_P0.23520.983
20_P74_P0.232980.973
18_N22_D0.232370.971
34_D87_K0.232320.971
31_E89_L0.232110.970
41_A44_I0.222870.931
50_S70_Q0.222830.931
22_D88_D0.219330.916
21_P75_G0.218630.913
11_S18_N0.217770.910
60_D65_T0.216750.905
42_I80_V0.2160.902
32_P62_N0.21570.901
48_N79_T0.211090.882
82_I90_A0.206460.862
69_S73_K0.204670.855
34_D38_V0.203810.851
16_A19_V0.202820.847
52_V55_S0.202080.844
49_G76_T0.20110.840
7_V12_P0.199330.833
39_S83_D0.195390.816
21_P71_P0.191890.802
88_D94_L0.191520.800
17_T69_S0.189330.791
51_G56_F0.188810.789
48_N76_T0.186150.778
20_P23_S0.184520.771
57_S67_T0.184030.769
88_D91_G0.180670.755
72_L76_T0.180030.752
33_V38_V0.178790.747
82_I92_N0.17680.739
10_T27_I0.176640.738
8_V28_T0.176020.735
15_G93_P0.175730.734
11_S16_A0.175040.731
42_I66_I0.175010.731
87_K90_A0.174720.730
20_P69_S0.172850.722
50_S76_T0.172750.722
48_N51_G0.171860.718
44_I56_F0.171760.718
11_S26_V0.170110.711
38_V42_I0.169520.708
57_S69_S0.168760.705
42_I56_F0.167270.699
25_I72_L0.16610.694
38_V86_I0.161830.676
27_I42_I0.161090.673
8_V57_S0.159830.668
12_P15_G0.159620.667
39_S43_T0.159230.665
25_I66_I0.158060.660
54_V57_S0.157710.659
69_S89_L0.157310.657
87_K93_P0.157220.657
39_S42_I0.157190.657
32_P89_L0.155930.651
64_L88_D0.155110.648
35_P70_Q0.154910.647
41_A86_I0.154880.647
48_N54_V0.154740.646
57_S87_K0.154370.645
24_P55_S0.153880.643
44_I48_N0.153640.642
89_L92_N0.153610.642
22_D67_T0.153380.641
50_S54_V0.153310.640
12_P80_V0.152790.638
82_I86_I0.152580.637
59_W63_T0.152350.636
15_G28_T0.151950.635
38_V64_L0.151770.634
94_L97_P0.149990.627
32_P63_T0.1460.610
23_S26_V0.14420.602
81_T87_K0.1430.597
24_P68_P0.142770.596
43_T79_T0.142730.596
11_S23_S0.142280.594
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
4hu2A0.943998.60.479
2c9rA0.869298.60.481
1lyqA0.878598.60.482
3vynA0.943998.50.505
3vypA0.943998.20.553
3turA0.943998.20.554
4hu2A0.850598.10.57
4k73A0.8224980.578
3vynA0.8505980.578
2ra1A0.878597.40.64

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