GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_8 - 4Fe-4S dicluster domain
Pfam: PF13183 (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: CL0344
Length: 57
Sequences: 21613
Seq/Len: 379.18
HH_delta: -0.001 (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
6_I55_V2.814953.483
17_V44_T1.875042.320
14_V48_A1.499421.855
5_C11_C1.40781.742
46_C49_C1.388321.718
9_G12_T1.300921.610
47_G50_S1.300361.609
43_C49_C1.213221.501
48_A51_E1.197141.481
14_V52_V1.19161.474
9_G22_G1.079081.335
48_A52_V1.077621.333
26_H30_D0.959811.188
15_C46_C0.959171.187
19_R42_S0.954181.181
31_R34_A0.932811.154
47_G51_E0.92981.151
5_C8_C0.90581.121
30_D33_S0.90031.114
6_I10_A0.878541.087
10_A54_P0.850651.053
5_C53_C0.84441.045
45_T48_A0.844061.044
9_G13_S0.843011.043
30_D34_A0.8341.032
10_A13_S0.8191.013
41_W45_T0.800270.990
8_C11_C0.797390.987
10_A52_V0.793720.982
4_K55_V0.792530.981
43_C46_C0.790780.979
23_R26_H0.788660.976
15_C43_C0.783010.969
25_S31_R0.769080.952
10_A14_V0.747810.925
18_Y22_G0.717840.888
8_C53_C0.717250.888
25_S30_D0.6820.844
16_P48_A0.675110.835
15_C49_C0.659670.816
7_R22_G0.654110.809
11_C53_C0.65290.808
6_I54_P0.638570.790
24_F30_D0.635060.786
41_W44_T0.620680.768
10_A55_V0.599360.742
26_H33_S0.597220.739
44_T48_A0.590030.730
16_P20_N0.565640.700
39_E42_S0.565110.699
50_S56_G0.562060.695
25_S34_A0.553260.685
22_G26_H0.553260.685
17_V42_S0.550730.681
22_G25_S0.546730.677
12_T22_G0.538320.666
42_S45_T0.538180.666
12_T20_N0.525730.651
23_R30_D0.521460.645
44_T47_G0.499790.618
13_S52_V0.481070.595
16_P46_C0.451480.559
23_R33_S0.447340.554
16_P44_T0.441230.546
4_K56_G0.43750.541
34_A39_E0.432220.535
17_V45_T0.421420.521
17_V21_T0.415460.514
18_Y21_T0.410540.508
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
2c42A198.5-0.001
3c8yA198.50.016
3i9v9198.50.017
3i9v3198.40.035
1xerA198.40.037
1hfeL0.859698.40.039
3cf4A198.30.073
3gyxB0.894798.30.077
1gteA0.859698.30.08
2wdqB198.30.081

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