GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
IL8 - Small cytokines (intecrinechemokine) interleukin-8 like
Pfam: PF00048 (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: 64
Sequences: 1050
Seq/Len: 16.41
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
40_F50_A0.51072.377
24_Y40_F0.488192.272
55_P59_K0.42491.978
21_I60_L0.417781.945
7_C33_C0.338841.577
23_S41_T0.338321.575
11_Y36_P0.331321.542
41_T47_E0.312171.453
29_P36_P0.311981.452
38_V57_V0.30671.428
53_N63_K0.287021.336
18_P60_L0.28671.334
15_R19_K0.282261.314
24_Y50_A0.281081.308
38_V52_P0.273031.271
51_D54_A0.269411.254
27_Q39_I0.265881.238
28_P31_P0.250411.166
9_L29_P0.250351.165
30_S47_E0.239591.115
24_Y27_Q0.237051.103
27_Q35_R0.23381.088
24_Y37_A0.230351.072
27_Q37_A0.227691.060
12_S22_K0.225931.052
59_K62_K0.225041.047
37_A40_F0.224921.047
55_P63_K0.224431.045
11_Y51_D0.221631.032
21_I56_W0.216431.007
60_L64_L0.208080.968
38_V51_D0.206720.962
21_I63_K0.206460.961
32_S39_I0.204450.952
10_S22_K0.204050.950
9_L27_Q0.200090.931
13_T51_D0.199940.931
28_P53_N0.197670.920
40_F57_V0.197010.917
37_A50_A0.195660.911
33_C39_I0.192340.895
17_P42_T0.18580.865
57_V61_I0.184940.861
18_P63_K0.184480.859
28_P36_P0.183070.852
18_P59_K0.182720.850
20_N23_S0.181350.844
41_T45_G0.180490.840
43_K63_K0.178120.829
41_T62_K0.177420.826
20_N62_K0.17690.823
32_S60_L0.176190.820
27_Q30_S0.175250.816
11_Y37_A0.174120.810
23_S61_I0.172010.801
10_S55_P0.170440.793
48_V51_D0.169750.790
36_P53_N0.16850.784
12_S17_P0.168050.782
12_S45_G0.167510.780
22_K45_G0.165980.773
9_L35_R0.165430.770
20_N46_R0.165360.770
54_A61_I0.164240.764
54_A57_V0.16340.761
58_K62_K0.163060.759
42_T48_V0.161640.752
15_R34_P0.160530.747
46_R59_K0.159850.744
24_Y42_T0.159780.744
17_P20_N0.158050.736
12_S15_R0.157950.735
10_S19_K0.156370.728
19_K45_G0.154270.718
32_S61_I0.153380.714
43_K59_K0.153010.712
53_N58_K0.15130.704
22_K28_P0.149830.697
13_T44_K0.149180.694
13_T19_K0.147980.689
52_P57_V0.147930.689
24_Y57_V0.147090.685
11_Y29_P0.144780.674
29_P37_A0.143580.668
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
1ha6A0.984499.60.028
2l4nA199.60.033
1m8aA0.984499.60.034
1icwA199.60.039
3tn2A0.968899.60.043
1eotA0.984499.60.045
1dokA0.984499.60.046
1eigA0.984499.60.059
1esrA0.984499.60.059
1zxtA0.968899.60.062

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