GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lipocalin - Lipocalin cytosolic fatty-acid binding protein family
Pfam: PF00061 (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: CL0116
Length: 144
Sequences: 2113
Seq/Len: 14.67
HH_delta: 0.054 (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
31_K39_P0.466182.941
6_E9_L0.450132.840
33_L37_N0.397562.508
126_F129_S0.377212.380
126_F130_L0.376832.377
120_L139_R0.360122.272
108_L115_L0.337672.130
7_V110_S0.314381.983
3_K29_V0.30651.934
108_L123_F0.305851.930
125_K129_S0.299021.887
117_P121_E0.276411.744
86_Y90_A0.27411.729
65_K80_W0.261951.653
133_D136_N0.259531.637
28_V42_F0.258521.631
86_Y92_V0.257941.627
23_L44_S0.257261.623
85_D88_N0.249631.575
123_F126_F0.241341.523
37_N56_T0.240041.514
4_W108_L0.233091.471
83_D122_K0.231281.459
106_A137_I0.228751.443
125_K128_K0.22851.442
3_K27_P0.227921.438
50_C53_I0.224441.416
121_E125_K0.217081.370
120_L124_K0.215771.361
134_E137_I0.205861.299
121_E124_K0.20181.273
110_S115_L0.201541.272
29_V43_T0.197991.249
106_A127_A0.196351.239
123_F127_A0.195661.234
118_E122_K0.195551.234
18_E21_K0.195061.231
5_Y113_P0.19291.217
24_K141_F0.188631.190
124_K134_E0.188341.188
1_A32_P0.186711.178
65_K68_V0.183551.158
95_C132_I0.18181.147
31_K41_T0.180881.141
81_V92_V0.177021.117
77_N81_V0.173821.097
53_I74_P0.173111.092
9_L107_W0.171971.085
17_E138_V0.171191.080
46_R49_Q0.17091.078
122_K126_F0.168031.060
128_K134_E0.166581.051
33_L39_P0.165461.044
90_A94_S0.163511.032
25_C95_C0.163491.031
117_P120_L0.16341.031
25_C123_F0.163131.029
89_Y119_A0.160521.013
9_L26_F0.160511.013
37_N54_T0.160231.011
122_K125_K0.158681.001
78_D81_V0.158380.999
91_I123_F0.158010.997
28_V68_V0.157540.994
83_D123_F0.157090.991
73_Y77_N0.15660.988
119_A122_K0.156350.986
26_F29_V0.155110.979
134_E139_R0.154880.977
116_S119_A0.154790.977
16_F20_K0.153530.969
6_E107_W0.151680.957
83_D89_Y0.151380.955
124_K137_I0.151190.954
88_N92_V0.149940.946
102_H106_A0.149640.944
122_K129_S0.14790.933
84_T90_A0.147760.932
65_K78_D0.147080.928
125_K141_F0.146530.924
49_Q91_I0.145440.918
42_F68_V0.145270.917
57_F60_T0.143970.908
4_W111_R0.143370.905
71_S80_W0.143010.902
124_K127_A0.140430.886
115_L123_F0.139920.883
20_K107_W0.139770.882
112_T116_S0.139250.879
2_G111_R0.13850.874
124_K139_R0.138210.872
50_C54_T0.138180.872
1_A38_L0.137520.868
59_K63_P0.136850.863
118_E131_G0.136280.860
59_K65_K0.13580.857
44_S66_F0.135760.857
40_V92_V0.135290.854
43_T52_T0.135180.853
68_V86_Y0.134960.851
10_A136_N0.134730.850
62_E117_P0.133960.845
88_N93_Y0.133770.844
106_A132_I0.133750.844
78_D82_L0.132850.838
100_G103_T0.131820.832
46_R135_E0.130720.825
69_E72_E0.13040.823
88_N119_A0.130310.822
18_E124_K0.129970.820
86_Y94_S0.129860.819
7_V115_L0.129180.815
66_F70_F0.128150.809
30_I107_W0.127890.807
62_E118_E0.127810.806
17_E21_K0.127750.806
52_T61_E0.127590.805
89_Y95_C0.127530.805
9_L20_K0.126480.798
28_V32_P0.126430.798
111_R131_G0.125990.795
86_Y89_Y0.125680.793
134_E140_T0.125620.793
124_K128_K0.125320.791
91_I126_F0.124960.788
81_V94_S0.124830.788
103_T130_L0.124640.786
22_E26_F0.12440.785
111_R114_E0.124170.783
70_F74_P0.124070.783
127_A130_L0.123830.781
47_G121_E0.123090.777
52_T59_K0.12280.775
41_T136_N0.12160.767
41_T117_P0.121510.767
41_T52_T0.121330.765
124_K130_L0.121170.764
30_I42_F0.120990.763
102_H125_K0.120810.762
115_L130_L0.120690.761
19_E42_F0.120520.760
122_K130_L0.120460.760
52_T56_T0.120080.758
84_T89_Y0.11960.755
83_D86_Y0.119410.753
19_E22_E0.119340.753
46_R130_L0.119250.752
10_A137_I0.119220.752
6_E23_L0.119210.752
122_K128_K0.118770.749
82_L126_F0.118540.748
39_P130_L0.117950.744
55_V68_V0.117230.740
56_T69_E0.117030.738
81_V84_T0.115050.726
119_A126_F0.114880.725
57_F86_Y0.114730.724
86_Y111_R0.11470.724
39_P48_G0.114640.723
72_E75_G0.113440.716
120_L134_E0.113140.714
51_V54_T0.112550.710
19_E66_F0.112460.710
16_F80_W0.112220.708
127_A134_E0.112090.707
116_S136_N0.111870.706
24_K47_G0.111470.703
62_E65_K0.111380.703
6_E140_T0.111350.703
51_V55_V0.111310.702
8_A137_I0.111190.702
55_V94_S0.110970.700
135_E139_R0.110850.699
29_V39_P0.110440.697
35_N138_V0.110370.696
93_Y132_I0.109160.689
79_F105_V0.108830.687
127_A131_G0.108080.682
17_E105_V0.107860.680
6_E42_F0.107590.679
21_K47_G0.107490.678
105_V131_G0.107470.678
3_K38_L0.107020.675
4_W86_Y0.106960.675
39_P52_T0.106790.674
83_D91_I0.106150.670
114_E122_K0.10610.669
6_E19_E0.105930.668
118_E125_K0.105860.668
74_P79_F0.105530.666
67_T76_G0.105440.665
31_K141_F0.105310.664
26_F42_F0.105210.664
81_V93_Y0.104880.662
30_I77_N0.104690.660
24_K64_G0.104540.660
88_N111_R0.104220.658
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
3saoA0.979299.90.054
3l4rA0.972299.90.06
4es7A199.90.078
3kffA0.972299.90.079
2xstA0.979299.90.081
3qkgA199.90.082
3o22A199.90.084
3cbcA0.993199.90.086
1gm6A0.972299.90.087
1ew3A0.979299.90.089

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