GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SH2 - SH2 domain
Pfam: PF00017 (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: CL0541
Length: 77
Sequences: 3158
Seq/Len: 41.01
HH_delta: -0.119 (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
39_S48_H0.776122.655
69_S72_D0.713112.440
7_S10_E0.64642.211
2_F28_P0.615912.107
15_L39_S0.59932.050
1_W26_V0.56651.938
40_V49_F0.550361.883
21_D42_F0.531161.817
21_D43_D0.493921.690
38_L51_I0.484641.658
4_G28_P0.436011.492
19_K23_T0.43251.480
10_E13_R0.416991.427
21_D44_G0.416071.423
67_F76_H0.415231.420
68_P72_D0.409911.402
26_V74_V0.409431.401
29_S37_V0.408931.399
3_H6_I0.406241.390
67_F77_Y0.387061.324
6_I14_L0.366861.255
59_Y62_S0.360681.234
1_W24_F0.356531.220
37_V50_R0.350271.198
20_P23_T0.347521.189
8_R27_R0.347461.189
28_P34_G0.345811.183
54_T57_G0.337411.154
26_V36_Y0.336851.152
5_F28_P0.333881.142
23_T41_R0.330031.129
71_S75_E0.324821.111
53_R57_G0.323991.108
42_F47_K0.323811.108
13_R16_M0.308731.056
32_K50_R0.307621.052
53_R56_N0.301641.032
60_F64_G0.301521.031
1_W5_F0.299511.025
62_S65_K0.298911.023
35_K50_R0.29881.022
3_H28_P0.291080.996
9_Q12_E0.285240.976
21_D45_K0.280720.960
12_E48_H0.2790.954
3_H14_L0.273880.937
17_Q20_P0.273730.936
62_S66_K0.272340.932
22_G27_R0.27140.928
11_A15_L0.270950.927
37_V48_H0.266430.911
6_I10_E0.264840.906
73_L76_H0.25230.863
52_N55_E0.250260.856
9_Q52_N0.246360.843
49_F64_G0.245580.840
70_L74_V0.241390.826
65_K77_Y0.241320.826
10_E14_L0.240610.823
47_K50_R0.238410.816
59_Y69_S0.237510.813
24_F27_R0.231870.793
68_P71_S0.231540.792
41_R46_V0.231230.791
27_R39_S0.228530.782
45_K63_D0.226370.774
42_F45_K0.226160.774
67_F70_L0.226160.774
56_N66_K0.225730.772
25_L28_P0.225520.771
60_F63_D0.224630.768
40_V62_S0.223820.766
54_T66_K0.223280.764
11_A39_S0.223070.763
1_W8_R0.221560.758
9_Q13_R0.219180.750
14_L17_Q0.217380.744
19_K72_D0.216960.742
49_F70_L0.215390.737
17_Q75_E0.212240.726
6_I11_A0.209310.716
28_P31_S0.209250.716
49_F77_Y0.208980.715
39_S46_V0.208110.712
49_F62_S0.207890.711
31_S36_Y0.207770.711
30_S50_R0.207520.710
2_F6_I0.206940.708
24_F74_V0.206930.708
25_L39_S0.206120.705
12_E46_V0.20430.699
49_F61_L0.202980.694
54_T68_P0.201980.691
30_S37_V0.201250.688
16_M46_V0.20050.686
71_S74_V0.198730.680
35_K46_V0.198220.678
17_Q41_R0.196850.673
51_I67_F0.195690.669
26_V51_I0.195560.669
13_R44_G0.195510.669
57_G68_P0.194320.665
2_F26_V0.193930.663
61_L67_F0.192450.658
62_S73_L0.192140.657
16_M42_F0.191640.656
7_S30_S0.190440.651
47_K60_F0.186550.638
70_L73_L0.186060.637
53_R71_S0.18580.636
15_L25_L0.185570.635
9_Q14_L0.185080.633
72_D76_H0.184730.632
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
2ozoA199.6-0.119
4fl3A199.6-0.117
4fl3A0.98799.6-0.101
2ecdA0.98799.6-0.1
2lqnA0.97499.6-0.099
1ka6A199.6-0.095
1a81A199.6-0.095
3k2mA0.98799.6-0.094
3ps5A0.98799.6-0.094
4fbnA199.6-0.094

Page generated in 0.0181 seconds.