GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_C - Cytochrome c
Pfam: PF00034 (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: CL0318
Length: 91
Sequences: 14069
Seq/Len: 154.6
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_R82_D2.476433.599
76_S79_E2.336573.395
7_L83_L1.563512.272
78_E82_D1.465162.129
2_A5_K1.285621.868
8_F87_L1.272941.850
79_E82_D1.256591.826
3_R6_E1.240481.803
84_A88_R1.238031.799
5_K9_Q1.217791.770
65_M69_M1.047131.522
8_F83_L1.022341.486
7_L79_E1.01931.481
47_I50_P1.01221.471
63_M69_M0.980331.425
3_R79_E0.971621.412
77_D81_A0.945991.375
34_I37_R0.889081.292
43_I46_Y0.88741.290
7_L11_N0.864661.257
82_D85_A0.860531.251
85_A88_R0.839141.219
75_L80_I0.831411.208
59_M63_M0.8291.205
11_N14_A0.824931.199
59_M62_A0.820481.192
80_I84_A0.814471.184
41_D45_R0.79471.155
47_I51_E0.788571.146
33_G36_K0.786321.143
81_A85_A0.769631.118
66_F69_M0.768731.117
42_W46_Y0.768461.117
3_R7_L0.740141.076
45_R49_N0.73841.073
49_N52_A0.734161.067
4_G8_F0.729741.060
34_I38_Y0.712781.036
6_E9_Q0.711361.034
40_Y44_G0.705851.026
9_Q13_A0.697861.014
38_Y42_W0.690311.003
46_Y50_P0.672210.977
8_F31_L0.664210.965
78_E81_A0.66250.963
48_T51_E0.650840.946
7_L82_D0.63540.923
31_L87_L0.630530.916
75_L79_E0.62690.911
6_E10_A0.626050.910
43_I47_I0.613630.892
4_G82_D0.612540.890
77_D80_I0.611860.889
17_G20_G0.606680.882
21_N30_D0.602470.875
84_A87_L0.598190.869
44_G48_T0.589450.857
8_F20_G0.585120.850
46_Y49_N0.580220.843
2_A6_E0.563980.820
31_L34_I0.562750.818
18_A21_N0.562740.818
44_G81_A0.552140.802
63_M66_F0.55150.801
62_A65_M0.545940.793
19_D22_G0.533940.776
60_P63_M0.533610.775
4_G86_Y0.533060.775
17_G21_N0.532820.774
45_R48_T0.518120.753
17_G22_G0.512560.745
32_T36_K0.511970.744
7_L75_L0.50970.741
35_G39_S0.500030.727
4_G83_L0.498430.724
40_Y43_I0.49730.723
52_A59_M0.495740.720
41_D44_G0.492830.716
30_D33_G0.488170.709
85_A89_S0.484390.704
21_N32_T0.48090.699
3_R78_E0.477960.695
23_D26_G0.477890.694
37_R40_Y0.474980.690
75_L83_L0.473430.688
11_N79_E0.465550.677
8_F13_A0.464750.675
64_P67_P0.46440.675
5_K86_Y0.461910.671
65_M68_M0.452650.658
35_G38_Y0.448380.652
12_C15_C0.445820.648
19_D24_G0.443590.645
36_K39_S0.443390.644
39_S42_W0.442940.644
43_I49_N0.441160.641
44_G47_I0.43920.638
40_Y81_A0.439080.638
63_M67_P0.437040.635
59_M65_M0.433670.630
4_G85_A0.433580.630
48_T52_A0.433180.629
46_Y51_E0.429390.624
79_E83_L0.428720.623
7_L10_A0.42860.623
4_G7_L0.427840.622
12_C16_H0.422520.614
36_K40_Y0.417320.606
13_A17_G0.412690.600
35_G88_R0.410790.597
64_P69_M0.404530.588
21_N24_G0.401070.583
83_L87_L0.395360.575
82_D86_Y0.393960.572
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
2yevB0.890199.10.163
1kb0A0.8462990.193
2l4dA0.989990.195
1yiqA0.8242990.195
3ziyA0.956990.205
2c1dB1990.207
2zooA0.9231990.207
2w9kA0.8791990.21
1kv9A0.8352990.213
1m70A0.890198.90.216

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