GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrome_C7 - Cytochrome c7
Pfam: PF14522 (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: CL0317
Length: 65
Sequences: 1108
Seq/Len: 17.05
HH_delta: 0.2 (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
14_N17_S0.335652.012
54_Q58_A0.300631.802
42_T46_D0.272731.635
13_V17_S0.268311.608
35_K39_V0.244441.465
50_A62_S0.228391.369
59_N62_S0.223111.337
60_C63_C0.220111.319
60_C64_H0.213511.280
32_M38_G0.211521.268
58_A62_S0.209561.256
46_D49_N0.202081.211
12_G25_A0.191651.149
54_Q59_N0.191251.146
49_N54_Q0.188851.132
38_G57_P0.181951.091
38_G62_S0.179211.074
39_V43_S0.176551.058
43_S61_A0.175051.049
23_E26_G0.173051.037
39_V42_T0.171751.030
38_G42_T0.169411.016
30_W40_A0.168791.012
28_A37_A0.166490.998
22_T40_A0.166360.997
16_A47_G0.166280.997
13_V54_Q0.16610.996
28_A62_S0.164360.985
25_A40_A0.162740.976
21_D47_G0.162710.975
40_A61_A0.159890.958
47_G58_A0.159830.958
13_V48_K0.15870.951
26_G57_P0.155130.930
32_M42_T0.154950.929
30_W35_K0.15450.926
13_V20_S0.153810.922
14_N42_T0.153730.922
22_T27_A0.153070.918
26_G34_P0.151950.911
20_S31_T0.151940.911
16_A30_W0.15130.907
34_P39_V0.151170.906
56_G61_A0.150070.900
57_P61_A0.149940.899
13_V42_T0.149090.894
33_P56_G0.146310.877
14_N25_A0.146280.877
34_P57_P0.144330.865
40_A49_N0.143230.859
48_K56_G0.143150.858
39_V46_D0.142870.856
32_M48_K0.141410.848
22_T37_A0.14120.846
20_S38_G0.138580.831
27_A35_K0.13820.828
17_S40_A0.136270.817
49_N58_A0.136150.816
12_G37_A0.135860.814
16_A22_T0.135670.813
55_P58_A0.135390.812
41_C63_C0.135360.811
35_K40_A0.135220.811
50_A54_Q0.133860.802
35_K38_G0.133650.801
32_M43_S0.133440.800
26_G55_P0.133290.799
14_N56_G0.13320.798
25_A46_D0.133070.798
24_P33_P0.131850.790
41_C64_H0.131610.789
39_V59_N0.13150.788
32_M35_K0.131130.786
16_A33_P0.130610.783
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
3oueA0.938598.70.2
3ouqA0.953898.70.202
3h4nA0.892398.60.222
1rwjA0.938598.50.251
3ov0A0.938598.50.253
3oueA0.938598.50.257
3ouqA0.984698.50.26
3ov0A0.953898.50.26
3h34A0.876998.50.261
3bxuA0.892398.40.279

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