GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Germane - Sporulation and spore germination
Pfam: PF10646 (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: 117
Sequences: 952
Seq/Len: 8.14
HH_delta: 0.876 (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
29_A93_T0.566743.593
56_N69_D0.465162.949
5_Y18_R0.431342.734
5_Y36_G0.375842.383
47_S89_Q0.347732.204
105_Q112_P0.318562.019
32_A35_K0.310721.970
72_S109_D0.297081.883
30_V90_I0.281451.784
65_T103_K0.280791.780
69_D107_L0.278361.765
66_L101_V0.266461.689
93_T98_F0.263141.668
7_D11_T0.257081.630
60_V66_L0.251191.592
68_V94_L0.25091.591
5_Y37_P0.242161.535
69_D110_G0.240681.526
65_T105_Q0.23861.513
48_A89_Q0.23811.509
30_V34_L0.234161.484
90_I106_I0.229831.457
26_A94_L0.225191.428
56_N109_D0.223291.416
70_F74_F0.220111.395
27_E31_N0.218721.387
2_T15_P0.210911.337
58_V68_V0.204441.296
3_V18_R0.202561.284
67_T107_L0.201131.275
26_A66_L0.200851.273
95_T104_V0.196861.248
53_T70_F0.196671.247
94_L101_V0.194291.232
58_V66_L0.193921.229
91_V104_V0.193681.228
68_V104_V0.191031.211
91_V95_T0.187361.188
16_V41_E0.187271.187
53_T74_F0.186451.182
16_V45_L0.183871.166
2_T17_T0.177821.127
30_V55_L0.175841.115
49_L86_L0.174981.109
98_F101_V0.173281.098
54_K71_S0.17281.095
83_E89_Q0.169941.077
12_K15_P0.168921.071
59_T67_T0.166091.053
29_A98_F0.163371.036
75_L108_V0.161661.025
33_L36_G0.15931.010
79_G82_Q0.158561.005
26_A100_G0.157640.999
88_A92_N0.156840.994
7_D12_K0.156240.990
74_F87_L0.156070.989
89_Q92_N0.153970.976
2_T97_Q0.153030.970
50_P53_T0.152480.967
6_P85_L0.152070.964
3_V7_D0.146880.931
10_G20_I0.145810.924
26_A58_V0.144450.916
18_R32_A0.143580.910
33_L93_T0.143080.907
97_Q101_V0.141540.897
78_L86_L0.138290.877
80_S83_E0.137830.874
6_P48_A0.136430.865
33_L37_P0.13630.864
85_L92_N0.135960.862
8_D11_T0.13570.860
87_L113_L0.134420.852
55_L68_V0.134220.851
35_K65_T0.134040.850
39_D46_R0.133660.847
74_F106_I0.13220.838
74_F86_L0.130790.829
13_L92_N0.12970.822
78_L83_E0.12960.822
33_L49_L0.128220.813
39_D45_L0.126360.801
48_A109_D0.126250.800
99_P102_K0.12580.797
10_G81_S0.125560.796
20_I28_A0.125240.794
101_V104_V0.125230.794
34_L55_L0.122610.777
16_V19_W0.122430.776
27_E55_L0.121830.772
18_R74_F0.121630.771
25_D97_Q0.120070.761
18_R36_G0.119630.758
88_A113_L0.118140.749
7_D10_G0.117970.748
65_T101_V0.117870.747
81_S84_A0.117560.745
27_E54_K0.117450.745
36_G48_A0.117340.744
3_V37_P0.117260.743
19_W41_E0.116220.737
6_P47_S0.115230.730
86_L107_L0.115180.730
60_V101_V0.113410.719
22_E113_L0.113360.719
55_L71_S0.113270.718
87_L91_V0.113170.717
4_Y97_Q0.112760.715
30_V56_N0.111390.706
66_L99_P0.111120.704
13_L88_A0.110930.703
56_N108_V0.110640.701
90_I113_L0.110620.701
66_L94_L0.10910.692
93_T105_Q0.108760.689
70_F97_Q0.108660.689
8_D65_T0.107880.684
29_A103_K0.107720.683
13_L21_S0.106920.678
80_S85_L0.106620.676
67_T105_Q0.106410.675
23_E26_A0.106350.674
30_V58_V0.105460.669
49_L83_E0.104670.664
23_E35_K0.104560.663
108_V113_L0.104530.663
69_D72_S0.104030.659
35_K72_S0.103830.658
70_F106_I0.103410.656
41_E45_L0.103250.655
18_R37_P0.102890.652
24_D99_P0.102590.650
23_E28_A0.102310.649
5_Y16_V0.101480.643
30_V94_L0.101050.641
92_N95_T0.100520.637
61_D67_T0.098680.626
57_S106_I0.098380.624
20_I32_A0.098340.623
87_L92_N0.098020.621
9_D50_P0.096960.615
75_L93_T0.096330.611
12_K20_I0.095810.607
22_E28_A0.094810.601
55_L104_V0.094780.601
48_A86_L0.094740.601
67_T71_S0.094230.597
59_T102_K0.093910.595
5_Y49_L0.093290.591
10_G13_L0.092860.589
79_G110_G0.092720.588
49_L74_F0.092710.588
25_D30_V0.092330.585
67_T103_K0.092180.584
90_I104_V0.092170.584
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
3lnoA0.743636.70.876
3cq1A0.743624.60.886
1vd2A0.367519.30.891
1uwdA0.752117.70.893
3ny5A0.692316.80.894
4b0mA0.401714.90.896
3bwuD0.410312.20.9
2z51A0.752111.90.9
2l05A0.649611.80.901
2vupA0.333310.20.903
If you are interested in a protein containing this domain,
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