GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Rieske - Rieske 2Fe-2S domain
Pfam: PF00355 (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: CL0516
Length: 97
Sequences: 6519
Seq/Len: 67.21
HH_delta: 0.022 (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
44_P71_F1.725373.381
61_V70_R1.273512.496
48_C66_C1.200172.352
8_S36_I1.102862.161
41_N51_S1.066622.090
7_R10_E0.986641.934
69_W83_A0.949641.861
26_L30_R0.943421.849
74_D77_E0.932871.828
31_R37_Y0.929771.822
41_N49_P0.917991.799
70_R80_G0.914981.793
72_D79_V0.883071.731
40_S88_P0.88271.730
61_V79_V0.880091.725
63_V70_R0.856771.679
39_F87_L0.850291.666
72_D77_E0.829421.625
4_P7_R0.810441.588
48_C65_P0.802311.572
45_H67_H0.801751.571
26_L29_V0.718721.409
6_C11_L0.713441.398
31_R35_E0.711741.395
37_Y73_L0.707671.387
6_C10_E0.700711.373
28_L38_A0.669141.311
17_V28_L0.653111.280
46_Q66_C0.643881.262
43_C64_C0.643011.260
43_C67_H0.630491.236
10_E18_K0.622961.221
12_P16_D0.614521.204
13_E31_R0.595691.167
26_L38_A0.591221.159
21_D25_K0.556761.091
69_W81_G0.547731.073
64_C67_H0.53921.057
78_C86_P0.5331.045
58_D63_V0.523161.025
45_H64_C0.5221.023
44_P78_C0.496240.973
42_R47_G0.492140.964
35_E74_D0.484520.950
13_E16_D0.479040.939
16_D21_D0.472520.926
77_E86_P0.472290.926
46_Q69_W0.448860.880
69_W78_C0.448060.878
25_K40_S0.446780.876
18_K21_D0.445770.874
34_G37_Y0.438750.860
63_V68_G0.437290.857
49_P66_C0.436510.855
31_R34_G0.434440.851
17_V62_I0.434240.851
21_D24_G0.431340.845
61_V72_D0.428080.839
16_D58_D0.425890.835
19_R41_N0.415030.813
30_R62_I0.412580.809
12_P15_G0.411070.806
71_F78_C0.409120.802
46_Q67_H0.407430.798
24_G40_S0.404830.793
29_V73_L0.403110.790
60_G74_D0.400090.784
21_D26_L0.388070.761
16_D19_R0.386820.758
13_E33_D0.385670.756
44_P86_P0.381940.749
3_V22_V0.379360.743
19_R51_S0.376360.738
17_V30_R0.374250.733
78_C81_G0.362310.710
17_V57_E0.358630.703
66_C81_G0.355950.698
81_G84_P0.355570.697
50_L53_G0.352110.690
8_S30_R0.351460.689
45_H71_F0.35120.688
32_S73_L0.350810.688
26_L41_N0.348520.683
3_V7_R0.344410.675
52_E65_P0.339690.666
51_S62_I0.338690.664
60_G72_D0.338170.663
41_N87_L0.337290.661
37_Y74_D0.332370.651
19_R49_P0.325570.638
41_N68_G0.325420.638
30_R36_I0.32410.635
6_C18_K0.32390.635
27_V30_R0.32220.631
5_V20_V0.321590.630
50_L87_L0.32110.629
29_V38_A0.320870.629
29_V39_F0.317810.623
25_K49_P0.316960.621
69_W82_P0.313410.614
63_V80_G0.312730.613
44_P69_W0.311680.611
32_S60_G0.311510.610
19_R26_L0.3060.600
48_C52_E0.305760.599
11_L36_I0.305290.598
17_V20_V0.303050.594
12_P17_V0.302010.592
44_P83_A0.30160.591
71_F76_G0.298990.586
48_C53_G0.298090.584
29_V37_Y0.291470.571
42_R49_P0.289680.568
71_F87_L0.288560.566
13_E35_E0.282640.554
69_W86_P0.281350.551
50_L62_I0.280460.550
5_V38_A0.276140.541
44_P87_L0.274020.537
58_D70_R0.273040.535
31_R36_I0.271750.533
46_Q84_P0.269230.528
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
3dqyA0.969199.90.022
3gceA0.989799.90.027
2qpzA0.969199.90.041
2i7fA0.969199.90.043
2de6D0.969199.90.044
1fqtA0.979499.90.047
3gcfA0.989799.90.052
3gkqA0.989799.90.055
1vm9A0.958899.90.058
4aivA0.979499.90.063

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