GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Oxidored_q1_N - NADH-Ubiquinone oxidoreductase (complex I) chain 5 N-terminus
Pfam: PF00662 (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: 62
Sequences: 4981
Seq/Len: 80.34
HH_delta: 0.135 (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
52_N55_R1.116032.989
43_S56_F1.031732.763
6_E9_S0.719671.927
6_E14_N0.675011.808
40_H60_L0.636381.704
44_I53_Y0.564581.512
20_Y23_P0.560031.500
47_M50_D0.545131.460
6_E20_Y0.533171.428
22_D25_S0.526141.409
54_N58_S0.509661.365
37_S41_I0.506391.356
8_F11_G0.500551.340
6_E16_S0.495421.327
9_S14_N0.483981.296
40_H61_S0.481011.288
34_F38_L0.467931.253
23_P27_L0.46781.253
53_Y57_F0.457771.226
33_L37_S0.427841.146
39_V60_L0.427611.145
6_E11_G0.409431.096
32_V36_S0.407181.090
42_Y46_Y0.39671.062
36_S39_V0.393811.055
41_I45_G0.389421.043
30_L33_L0.389121.042
40_H57_F0.384191.029
49_H53_Y0.37811.013
6_E10_L0.377751.012
21_L33_L0.373921.001
8_F14_N0.370430.992
36_S59_Y0.367420.984
43_S57_F0.36290.972
39_V46_Y0.357070.956
36_S60_L0.356110.954
11_G14_N0.354150.948
8_F16_S0.348050.932
9_S12_S0.338520.907
41_I44_I0.33460.896
55_R59_Y0.33410.895
44_I48_S0.333040.892
36_S40_H0.331270.887
38_L42_Y0.323760.867
9_S16_S0.323310.866
43_S47_M0.320640.859
12_S16_S0.315680.845
40_H44_I0.312490.837
47_M57_F0.307480.823
21_L26_A0.30480.816
25_S29_L0.294660.789
21_L25_S0.293730.787
51_P54_N0.291420.780
13_L57_F0.289420.775
43_S60_L0.286420.767
50_D53_Y0.28550.765
40_H58_S0.283160.758
35_I47_M0.280990.752
42_Y55_R0.280290.751
35_I39_V0.279880.750
12_S15_I0.277490.743
33_L53_Y0.2760.739
55_R58_S0.273150.731
14_N23_P0.271860.728
38_L41_I0.271230.726
50_D58_S0.270390.724
32_V54_N0.270140.723
45_G48_S0.265390.711
9_S15_I0.263310.705
56_F59_Y0.262420.703
39_V61_S0.259760.696
23_P43_S0.251460.673
31_L54_N0.251260.673
50_D60_L0.247730.663
12_S17_F0.24530.657
54_N61_S0.23910.640
24_L28_F0.238790.639
26_A30_L0.238650.639
39_V55_R0.238450.639
23_P26_A0.235840.632
24_L34_F0.232890.624
8_F12_S0.231870.621
27_L31_L0.230290.617
32_V47_M0.229690.615
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
3rkoL198.60.135
4he8L0.935598.20.238
3rkoM0.967797.70.348
3rkoN0.9839970.432
4he8M0.887195.90.506
4he8N0.887185.40.639
1oedB0.72583.40.836
2bg9E0.70972.30.848
2bg9C0.72582.10.851
2l6wA0.6291.80.856

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