GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MUG113 - Meiotically up-regulated gene 113
Pfam: PF13455 (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: CL0418
Length: 83
Sequences: 655
Seq/Len: 7.89
HH_delta: 0.833 (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
52_K75_D0.534053.162
45_I49_L0.404952.397
1_L76_V0.336321.991
46_H69_F0.308521.826
37_H40_R0.293451.737
12_R67_E0.288981.711
1_L73_A0.286471.696
24_L68_W0.273061.617
72_E75_D0.27221.611
40_R44_L0.270221.600
8_N11_R0.265581.572
10_E14_N0.259891.539
49_L79_V0.254821.509
5_R39_H0.248691.472
5_R38_V0.235561.395
73_A76_V0.233151.380
43_R47_L0.228071.350
16_W20_C0.227081.344
12_R42_E0.224011.326
2_K67_E0.216061.279
50_A53_R0.211471.252
14_N23_E0.209981.243
44_L48_E0.207761.230
3_I49_L0.201221.191
74_E78_E0.197041.166
17_S23_E0.196041.161
2_K12_R0.181391.074
16_W19_Q0.179451.062
42_E67_E0.178881.059
4_G67_E0.177931.053
15_Q19_Q0.175431.039
30_Y77_K0.173421.027
4_G12_R0.172121.019
23_E48_E0.17081.011
6_T9_V0.169071.001
16_W68_W0.165090.977
6_T73_A0.164760.975
50_A79_V0.164330.973
69_F78_E0.16320.966
44_L47_L0.161650.957
43_R52_K0.160180.948
26_L29_Y0.156390.926
5_R68_W0.15620.925
7_T25_E0.154920.917
22_H25_E0.149940.888
30_Y71_V0.149750.887
4_G42_E0.146980.870
48_E79_V0.145590.862
6_T24_L0.144080.853
15_Q21_G0.137270.813
48_E78_E0.137110.812
44_L78_E0.136030.805
21_G58_E0.135790.804
28_R32_Y0.135770.804
10_E26_L0.135540.802
19_Q38_V0.134930.799
53_R72_E0.134920.799
7_T38_V0.134840.798
55_R58_E0.134610.797
13_L26_L0.134350.795
33_S77_K0.134250.795
72_E76_V0.134230.795
18_R47_L0.134140.794
21_G24_L0.133480.790
19_Q24_L0.131390.778
39_H43_R0.130350.772
18_R21_G0.13010.770
20_C38_V0.129780.768
12_R46_H0.12920.765
43_R51_D0.128660.762
14_N78_E0.128080.758
9_V13_L0.127860.757
33_S37_H0.127480.755
1_L71_V0.126360.748
16_W37_H0.125360.742
74_E77_K0.125070.740
10_E33_S0.125060.740
45_I76_V0.122050.723
25_E41_V0.121670.720
17_S68_W0.121530.719
53_R58_E0.121430.719
3_I41_V0.120620.714
17_S58_E0.119280.706
10_E76_V0.118630.702
16_W21_G0.117810.697
9_V45_I0.116990.693
31_P48_E0.116380.689
73_A77_K0.115480.684
33_S51_D0.115450.683
17_S47_L0.115080.681
38_V42_E0.115070.681
23_E77_K0.1150.681
43_R50_A0.114370.677
40_R47_L0.114360.677
37_H55_R0.114310.677
16_W24_L0.112910.668
31_P78_E0.111640.661
75_D78_E0.111260.659
15_Q70_E0.110160.652
7_T55_R0.110060.652
7_T15_Q0.110030.651
9_V29_Y0.109670.649
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
1ywlA0.807275.90.833
1zg2A0.927769.80.84
3fkrA0.843434.20.87
3l21A0.903624.40.879
1j5sA120.70.883
2k8sA0.602418.90.884
2pcqA0.710816.50.887
3b4uA0.783116.40.888
2q01A114.80.89
2nuwA0.734914.60.89
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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