GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fer4_17 - 4Fe-4S dicluster domain
Pfam: PF13534 (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: 61
Sequences: 15063
Seq/Len: 246.93
HH_delta: 0.163 (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
3_T58_Q2.038023.586
11_A51_L1.194352.101
50_G53_E1.085371.910
11_A55_V1.00881.775
42_A45_L0.977051.719
51_L54_S0.906171.594
6_G9_V0.885751.558
33_K36_E0.853851.502
2_C5_C0.845261.487
7_Y10_P0.83541.470
51_L55_V0.821481.445
14_S47_I0.814731.434
40_S43_A0.809631.425
49_C52_C0.780691.374
12_C52_C0.777411.368
3_T7_Y0.755891.330
46_C52_C0.745121.311
7_Y55_V0.714811.258
6_G19_P0.702031.235
34_I37_I0.684031.204
44_S48_G0.673421.185
7_Y57_P0.656161.155
12_C46_C0.607061.068
16_I45_L0.607051.068
2_C8_C0.60591.066
35_D39_E0.598761.054
34_I38_S0.59721.051
23_R26_M0.59521.047
6_G10_P0.593291.044
13_P17_A0.590421.039
5_C8_C0.588591.036
3_T57_P0.587621.034
1_A58_Q0.579541.020
22_P25_P0.554150.975
41_H44_S0.546090.961
21_E26_M0.542410.954
8_C12_C0.537220.945
8_C56_C0.520580.916
33_K38_S0.497230.875
50_G54_S0.493920.869
33_K37_I0.493380.868
12_C49_C0.488520.860
1_A59_G0.477390.840
9_V17_A0.471970.830
18_T22_P0.449820.791
18_T24_S0.444090.781
7_Y11_A0.443070.780
45_L48_G0.440270.775
47_I51_L0.435460.766
43_A48_G0.430560.758
9_V19_P0.429480.756
20_D23_R0.425940.749
13_P47_I0.422660.744
9_V15_Y0.416740.733
25_P34_I0.416090.732
20_D26_M0.41230.725
13_P49_C0.408050.718
26_M34_I0.397130.699
52_C56_C0.387540.682
35_D38_S0.383510.675
15_Y19_P0.380960.670
6_G58_Q0.370240.651
4_Q58_Q0.370220.651
53_E59_G0.369080.649
26_M36_E0.367530.647
37_I40_S0.360990.635
4_Q9_V0.360410.634
2_C12_C0.356260.627
25_P35_D0.351510.618
3_T6_G0.348310.613
1_A4_Q0.348210.613
5_C12_C0.347310.611
14_S54_S0.344010.605
34_I40_S0.341050.600
48_G51_L0.334780.589
16_I51_L0.332240.585
7_Y14_S0.328670.578
13_P45_L0.32790.577
7_Y58_Q0.323340.569
18_T40_S0.32330.569
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
2bs2B198.30.163
2wdqB198.20.165
1kf6B198.20.169
2h88B198.20.17
3vr8B198.20.183
2c42A198.10.192
3i9v9198.10.196
3cf4A0.901698.10.199
1hfeL0.7705980.221
3c8yA0.918980.235

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