GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Miro - Miro-like protein
Pfam: PF08477 (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: CL0023
Length: 119
Sequences: 30129
Seq/Len: 253.18
HH_delta: 0.054 (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
83_L115_G2.003313.072
7_D91_Y1.763752.705
80_V116_N1.669012.560
15_L80_V1.627122.495
78_I114_V1.624032.491
3_V74_A1.533622.352
95_L98_W1.504292.307
83_L118_S1.187041.821
98_W101_N1.177571.806
4_V16_I1.13361.739
81_Y115_G1.069891.641
82_D85_D1.058111.623
63_F66_Q1.054751.618
71_L74_A1.019081.563
82_D117_K1.008341.546
4_V78_I1.004661.541
96_L111_I0.98041.504
2_I76_A0.966661.483
81_Y113_L0.966391.482
64_Y67_H0.961311.474
97_K101_N0.955231.465
76_A112_I0.935371.435
96_L100_K0.907261.391
17_R21_G0.902321.384
99_L103_R0.895021.373
97_K100_K0.883061.354
85_D88_S0.86111.321
66_Q69_F0.833521.278
77_V109_I0.828751.271
30_P33_T0.794211.218
61_E64_Y0.794181.218
78_I112_I0.791161.213
98_W102_I0.785371.204
64_Y68_Q0.783851.202
63_F67_H0.781831.199
44_V51_S0.774311.188
47_G50_Q0.749261.149
44_V53_Q0.74771.147
8_S60_Q0.74711.146
88_S91_Y0.746461.145
35_E38_I0.740921.136
15_L114_V0.730391.120
56_D59_G0.726661.114
6_G11_G0.720061.104
94_Q97_K0.716971.100
79_L92_L0.71421.095
42_V53_Q0.71051.090
66_Q70_F0.70631.083
93_S97_K0.703811.079
63_F68_Q0.700291.074
94_Q98_W0.693711.064
3_V57_F0.690121.058
67_H70_F0.678291.040
79_L96_L0.676631.038
63_F70_F0.674611.035
15_L19_L0.673341.033
65_S69_F0.6681.024
20_C24_F0.664031.018
115_G118_S0.65971.012
30_P34_S0.649740.996
46_D49_R0.649530.996
46_D51_S0.648550.995
90_E94_Q0.648540.995
95_L102_I0.637370.978
2_I52_L0.636980.977
32_E39_G0.63360.972
61_E65_S0.616170.945
33_T37_T0.60810.933
65_S68_Q0.607050.931
44_V47_G0.605410.928
76_A110_P0.594080.911
87_E90_E0.593580.910
99_L102_I0.592270.908
6_G12_K0.592070.908
74_A77_V0.587250.901
17_R30_P0.586790.900
7_D85_D0.586740.900
33_T36_I0.585030.897
17_R23_E0.583070.894
34_S38_I0.58140.892
31_E36_I0.579150.888
30_P35_E0.569670.874
16_I54_F0.568660.872
82_D116_N0.565870.868
89_L93_S0.562560.863
89_L92_L0.56150.861
79_L95_L0.558610.857
7_D10_V0.554140.850
45_V54_F0.550950.845
2_I54_F0.547780.840
95_L103_R0.544840.836
18_R24_F0.544770.835
79_L113_L0.540860.829
38_I41_D0.533140.818
61_E67_H0.531330.815
30_P37_T0.52840.810
63_F69_F0.528380.810
87_E91_Y0.519770.797
98_W103_R0.516170.792
18_R22_G0.512240.786
31_E34_S0.511470.784
46_D50_Q0.504240.773
4_V15_L0.502340.770
32_E37_T0.502280.770
34_S37_T0.501610.769
100_K103_R0.50030.767
42_V55_W0.495110.759
13_T17_R0.491850.754
90_E93_S0.488360.749
17_R25_P0.487220.747
34_S41_D0.482790.740
79_L111_I0.474650.728
62_E66_Q0.473850.727
30_P38_I0.469810.721
61_E68_Q0.469610.720
17_R24_F0.468270.718
9_G32_E0.468180.718
31_E37_T0.467950.718
96_L102_I0.467570.717
3_V77_V0.466650.716
31_E35_E0.461430.708
33_T41_D0.458370.703
64_Y70_F0.458170.703
91_Y94_Q0.456850.701
96_L99_L0.455860.699
35_E39_G0.455290.698
37_T40_V0.453790.696
36_I39_G0.452480.694
6_G10_V0.451250.692
13_T56_D0.449340.689
37_T43_I0.442140.678
33_T38_I0.439010.673
16_I43_I0.436220.669
14_S17_R0.435190.667
92_L96_L0.4280.656
62_E67_H0.427280.655
20_C43_I0.425690.653
17_R20_C0.425040.652
32_E35_E0.425040.652
3_V6_G0.4220.647
79_L99_L0.420470.645
45_V52_L0.419670.644
55_W58_G0.417160.640
62_E65_S0.41180.632
37_T41_D0.407110.624
85_D89_L0.406390.623
95_L100_K0.402620.617
95_L99_L0.401460.616
92_L95_L0.400170.614
44_V49_R0.400150.614
10_V80_V0.399070.612
81_Y89_L0.397260.609
45_V48_D0.396990.609
14_S18_R0.395020.606
57_F60_Q0.394480.605
86_P89_L0.394390.605
34_S39_G0.393250.603
22_G25_P0.392370.602
42_V51_S0.392080.601
19_L54_F0.388550.596
33_T43_I0.388270.595
10_V13_T0.388170.595
20_C23_E0.388040.595
35_E43_I0.386060.592
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
3r7wA0.974899.70.054
3r7wB0.95899.70.076
3dz8A0.966499.70.087
3l0iB0.966499.70.087
2hupA0.966499.70.088
2p5sA0.966499.70.089
2ew1A0.966499.70.089
4dkxA0.966499.70.091
3lvqE0.932899.70.092
2bcgY0.966499.70.094

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