GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SPOR - Sporulation related domain
Pfam: PF05036 (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: 76
Sequences: 3352
Seq/Len: 44.11
HH_delta: 0.084 (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
15_E19_E1.33093.349
51_F60_A1.277013.213
61_L72_A1.074962.705
53_S56_E0.986422.482
54_R58_E0.962762.423
11_S43_W0.829032.086
6_Y50_P0.776331.954
18_A46_V0.773751.947
21_L24_K0.772191.943
22_L26_K0.769281.936
14_S17_N0.706571.778
8_Q11_S0.640541.612
17_N20_R0.608381.531
61_L65_K0.607031.528
11_S45_R0.591871.489
13_S43_W0.568341.430
8_Q47_R0.561551.413
12_F21_L0.557921.404
5_Y54_R0.556221.400
56_E59_A0.549011.382
24_K28_K0.537971.354
19_E22_L0.522251.314
52_S56_E0.514671.295
20_R24_K0.498681.255
7_V61_L0.496951.251
60_A63_K0.484551.219
12_F46_V0.456131.148
15_E44_Y0.44691.125
55_E59_A0.444711.119
63_K68_A0.435611.096
35_V42_P0.43191.087
7_V57_A0.421191.060
51_F57_A0.409841.031
6_Y47_R0.402711.013
19_E23_A0.401131.009
9_V25_L0.399161.004
8_Q73_F0.391770.986
37_V42_P0.382720.963
16_E20_R0.368130.926
22_L46_V0.361570.910
37_V40_G0.361130.909
23_A27_K0.357080.899
63_K67_A0.356620.897
59_A63_K0.348390.877
8_Q45_R0.347170.874
29_G32_A0.343260.864
25_L46_V0.340310.856
56_E60_A0.332590.837
5_Y74_V0.330830.832
47_R73_F0.329260.829
21_L46_V0.327990.825
58_E62_R0.325720.820
7_V60_A0.320210.806
68_A71_D0.317610.799
39_K42_P0.305450.769
22_L61_L0.304620.767
65_K72_A0.294950.742
65_K71_D0.293980.740
59_A62_R0.293180.738
8_Q43_W0.280870.707
6_Y49_G0.279030.702
20_R23_A0.278880.702
21_L67_A0.274590.691
16_E19_E0.27370.689
5_Y57_A0.269340.678
55_E58_E0.267220.672
4_G50_P0.263780.664
48_V60_A0.262160.660
28_K68_A0.260950.657
58_E61_L0.259910.654
7_V72_A0.258760.651
36_Q45_R0.258720.651
17_N21_L0.258380.650
69_G72_A0.25630.645
14_S20_R0.254820.641
12_F17_N0.253780.639
22_L32_A0.253670.638
58_E65_K0.252390.635
29_G46_V0.250790.631
23_A26_K0.250480.630
13_S41_G0.250290.630
44_Y47_R0.249770.629
6_Y45_R0.248510.625
27_K55_E0.245780.618
62_R65_K0.243420.613
25_L29_G0.242250.610
5_Y51_F0.236020.594
30_P63_K0.233820.588
10_G45_R0.231130.582
9_V46_V0.230090.579
57_A73_F0.229190.577
3_S52_S0.229030.576
58_E74_V0.228010.574
54_R74_V0.2230.561
30_P70_P0.21890.551
14_S48_V0.217270.547
11_S42_P0.215960.543
36_Q43_W0.21430.539
15_E35_V0.214150.539
30_P44_Y0.213920.538
31_D74_V0.212240.534
36_Q40_G0.212060.534
5_Y50_P0.210660.530
36_Q50_P0.209940.528
14_S67_A0.209720.528
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
1x60A0.947499.30.084
1utaA0.947499.30.097
2lfvA0.986898.30.386
1utaA0.539590.40.698
1x60A0.539590.30.698
3ffrA0.881639.50.797
4iw7A0.9868380.799
4hddA0.815829.40.81
3f0hA0.947428.80.81
2gqcA0.907927.60.812

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