GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MRP-S35 - Mitochondrial ribosomal protein MRP-S35
Pfam: PF10246 (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: 104
Sequences: 1895
Seq/Len: 18.22
HH_delta: 0.192 (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
72_K93_D0.709182.878
69_L89_L0.680112.760
23_E73_D0.610952.480
71_L87_T0.589182.391
49_C89_L0.575352.335
55_A72_K0.568912.309
28_I68_R0.536142.176
62_V65_S0.525512.133
29_G41_I0.488721.983
34_V39_L0.395261.604
41_I89_L0.392311.592
18_Q46_K0.373711.517
22_P25_K0.373381.515
26_I68_R0.368341.495
13_N76_L0.366031.486
16_F20_G0.35951.459
38_D50_V0.35941.459
30_K66_R0.346261.405
13_N17_I0.345431.402
51_C61_Y0.342081.388
16_F74_L0.33671.366
28_I66_R0.32871.334
34_V63_R0.317761.290
32_F42_D0.3171.287
56_V61_Y0.316151.283
39_L61_Y0.313241.271
63_R69_L0.29041.179
51_C69_L0.276491.122
61_Y67_V0.27611.121
52_K55_A0.270861.099
33_H63_R0.265391.077
52_K88_T0.257381.045
18_Q87_T0.257181.044
31_I61_Y0.253221.028
48_H65_S0.248881.010
39_L56_V0.244840.994
27_V89_L0.240560.976
72_K88_T0.235220.955
59_E91_E0.224530.911
41_I67_V0.222480.903
51_C91_E0.220140.893
57_N92_A0.217980.885
72_K92_A0.217780.884
32_F56_V0.216750.880
90_L93_D0.213410.866
17_I76_L0.211430.858
16_F77_S0.211290.858
19_L23_E0.20930.849
38_D42_D0.209220.849
73_D88_T0.20880.847
55_A93_D0.20520.833
70_R90_L0.205010.832
43_F70_R0.202660.822
23_E74_L0.200830.815
29_G43_F0.200250.813
24_G63_R0.198830.807
12_R17_I0.198810.807
14_S17_I0.198640.806
22_P71_L0.197140.800
47_F58_G0.193630.786
35_V40_Y0.191070.775
76_L79_H0.189570.769
17_I20_G0.188770.766
49_C86_D0.187220.760
78_A86_D0.186760.758
31_I91_E0.185570.753
71_L77_S0.184410.748
70_R93_D0.183280.744
70_R79_H0.183080.743
37_D53_R0.183010.743
55_A88_T0.182930.742
74_L91_E0.182510.741
32_F63_R0.181890.738
51_C89_L0.181640.737
40_Y50_V0.181530.737
61_Y65_S0.180920.734
77_S87_T0.177670.721
48_H91_E0.177090.719
12_R33_H0.176280.715
16_F76_L0.175770.713
56_V72_K0.173440.704
15_P87_T0.172390.700
56_V62_V0.172110.699
33_H36_D0.171290.695
20_G24_G0.170570.692
33_H66_R0.170270.691
27_V71_L0.170020.690
51_C56_V0.168770.685
24_G60_K0.167990.682
15_P20_G0.16670.677
42_D46_K0.166280.675
47_F87_T0.165450.671
23_E26_I0.164170.666
28_I53_R0.16410.666
58_G62_V0.163870.665
29_G44_G0.163220.662
26_I50_V0.161870.657
26_I94_A0.161470.655
34_V64_G0.158470.643
17_I88_T0.158310.643
24_G72_K0.158220.642
34_V67_V0.15710.638
64_G89_L0.156220.634
60_K65_S0.156010.633
33_H40_Y0.155870.633
21_D34_V0.155030.629
77_S86_D0.154450.627
12_R32_F0.154130.626
90_L94_A0.154110.625
55_A92_A0.153980.625
46_K77_S0.151930.617
42_D48_H0.151680.616
57_N61_Y0.151550.615
34_V38_D0.151290.614
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
1k0rA0.961599.80.192
1hh2P0.951999.80.225
2asbA0.807799.80.241
3psfA0.942398.80.578
3psiA0.942398.80.581
1wi5A0.923198.80.588
2khjA0.903898.60.605
1q8kA0.846298.60.609
2k52A0.711598.60.611
3cw2C0.826998.60.616

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