GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_B_N_2 - Cytochrome b(N-terminal)b6petB
Pfam: PF13631 (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: CL0328
Length: 168
Sequences: 3329
Seq/Len: 19.82
HH_delta: -0.052 (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
136_H140_T0.913244.015
7_M38_V0.865053.803
73_D77_E0.729453.207
37_L107_L0.721823.174
38_V104_I0.609872.681
36_L40_A0.56482.483
40_A65_L0.54342.389
105_L108_I0.506392.226
44_T96_L0.504262.217
30_S110_L0.496192.182
24_R29_I0.47732.098
65_L79_L0.474792.087
11_M35_L0.472162.076
41_T100_L0.470592.069
40_A100_L0.470392.068
2_L150_F0.466912.053
22_K118_H0.465832.048
155_I158_A0.443741.951
161_F164_P0.433511.906
29_I33_V0.43251.902
14_G19_S0.405641.783
27_N118_H0.377471.660
74_W77_E0.370121.627
152_F156_L0.368251.619
24_R117_K0.365551.607
96_L100_L0.354131.557
150_F154_F0.347231.527
65_L75_L0.34211.504
154_F158_A0.334771.472
52_Q56_W0.315171.386
21_K108_I0.313221.377
91_T95_V0.313141.377
156_L161_F0.310121.363
27_N120_S0.309951.363
29_I32_V0.309791.362
34_L108_I0.305131.342
151_L155_I0.297661.309
33_V107_L0.297261.307
30_S108_I0.296941.306
49_P57_A0.294761.296
18_G21_K0.287911.266
148_L152_F0.282711.243
33_V36_L0.281761.239
87_N95_V0.280021.231
109_I113_L0.276941.218
124_L130_S0.276721.217
66_S76_V0.271831.195
152_F155_I0.270061.187
71_I74_W0.269861.186
50_W55_Y0.268861.182
30_S114_L0.263661.159
141_L144_L0.262291.153
127_D130_S0.260681.146
129_N132_K0.258661.137
22_K108_I0.258631.137
50_W78_W0.258091.135
79_L96_L0.254251.118
23_P29_I0.253221.113
2_L153_L0.253151.113
115_L120_S0.251841.107
37_L100_L0.248291.092
51_D57_A0.247541.088
156_L160_F0.247281.087
76_V80_W0.246281.083
13_R92_R0.244231.074
7_M108_I0.24391.072
147_F150_F0.243411.070
148_L155_I0.243321.070
160_F163_Y0.240491.057
24_R30_S0.238581.049
157_L161_F0.235741.036
50_W56_W0.235431.035
106_A109_I0.235131.034
27_N115_L0.231141.016
32_V36_L0.229131.007
41_T104_I0.227941.002
50_W90_L0.22620.995
30_S107_L0.224630.988
34_L104_I0.223820.984
98_V102_F0.221130.972
4_F8_Y0.221020.972
40_A79_L0.218310.960
163_Y166_G0.21830.960
8_Y11_M0.217690.957
7_M35_L0.216880.954
149_L152_F0.215130.946
103_I148_L0.214530.943
6_L150_F0.21210.933
148_L153_L0.210210.924
36_L113_L0.208550.917
105_L112_L0.208220.915
23_P44_T0.20730.911
53_M56_W0.20710.911
9_L30_S0.205030.901
7_M104_I0.204820.901
147_F151_L0.204460.899
153_L156_L0.202070.888
155_I159_F0.201920.888
51_D78_W0.200940.883
70_F78_W0.199720.878
85_V89_T0.198710.874
82_G86_G0.19870.874
63_N76_V0.196390.863
23_P74_W0.195880.861
24_R160_F0.195230.858
39_M57_A0.194690.856
127_D132_K0.194340.854
103_I106_A0.194330.854
46_Y49_P0.193760.852
2_L5_I0.192820.848
1_S4_F0.191120.840
44_T79_L0.190850.839
69_P72_G0.190850.839
47_V76_V0.190420.837
136_H139_F0.190340.837
22_K27_N0.1870.822
6_L12_F0.186850.822
21_K127_D0.186650.821
51_D54_S0.186570.820
103_I112_L0.186440.820
52_Q55_Y0.186420.820
87_N91_T0.18520.814
157_L165_L0.184730.812
150_F153_L0.184580.812
110_L148_L0.184060.809
73_D79_L0.184010.809
95_V99_I0.184010.809
24_R148_L0.182430.802
137_P159_F0.1820.800
2_L73_D0.181420.798
113_L117_K0.181030.796
47_V80_W0.180180.792
9_L12_F0.180110.792
62_T76_V0.179890.791
147_F155_I0.179540.789
54_S57_A0.179230.788
35_L38_V0.178530.785
153_L161_F0.177810.782
47_V67_A0.177660.781
59_T62_T0.177040.778
145_F149_L0.176520.776
147_F164_P0.176490.776
3_M38_V0.175890.773
106_A110_L0.174930.769
22_K30_S0.174760.768
135_F143_D0.174260.766
94_F131_D0.173630.763
59_T63_N0.172520.759
152_F158_A0.171790.755
28_W78_W0.171690.755
116_H120_S0.171640.755
122_N125_G0.170270.749
148_L156_L0.169610.746
35_L168_P0.168720.742
2_L137_P0.168610.741
58_A85_V0.168340.740
65_L113_L0.16830.740
62_T66_S0.167980.739
62_T80_W0.167640.737
27_N30_S0.166690.733
151_L160_F0.166610.733
63_N80_W0.165880.729
120_S139_F0.165110.726
18_G75_L0.164210.722
37_L105_L0.163870.720
145_F154_F0.163720.720
148_L168_P0.163710.720
71_I104_I0.16370.720
83_F90_L0.163470.719
156_L164_P0.163470.719
2_L147_F0.162590.715
109_I112_L0.162480.714
117_K147_F0.162450.714
149_L153_L0.162030.712
105_L109_I0.161970.712
38_V88_A0.161790.711
60_V143_D0.161710.711
68_I159_F0.161680.711
116_H143_D0.161450.710
64_L98_V0.161230.709
19_S22_K0.161050.708
149_L155_I0.160980.708
19_S118_H0.16070.707
24_R33_V0.159950.703
7_M11_M0.159770.702
41_T52_Q0.159470.701
164_P167_D0.159270.700
37_L104_I0.159250.700
76_V96_L0.159060.699
21_K161_F0.158810.698
28_W39_M0.158650.698
158_A163_Y0.158210.696
59_T85_V0.15780.694
139_F143_D0.15710.691
13_R16_F0.1570.690
73_D156_L0.15610.686
139_F142_K0.156060.686
61_I64_L0.155720.685
99_I128_S0.155670.684
158_A164_P0.155540.684
28_W56_W0.155070.682
40_A68_I0.154770.680
71_I107_L0.154610.680
28_W50_W0.154280.678
105_L158_A0.153660.676
34_L38_V0.153630.675
21_K24_R0.153590.675
66_S88_A0.153530.675
111_H116_H0.153440.675
27_N117_K0.153140.673
131_D157_L0.152870.672
82_G89_T0.152810.672
18_G95_V0.152510.671
144_L147_F0.151960.668
107_L130_S0.151810.667
10_H31_G0.15170.667
119_G123_P0.151420.666
39_M53_M0.15140.666
56_W60_V0.151250.665
110_L113_L0.151130.664
121_S159_F0.150710.663
107_L153_L0.15060.662
13_R69_P0.150570.662
36_L153_L0.149850.659
67_A93_F0.149830.659
154_F159_F0.14970.658
133_I137_P0.149690.658
21_K29_I0.149540.657
71_I75_L0.149310.656
107_L127_D0.149150.656
15_F160_F0.148970.655
29_I71_I0.148350.652
91_T131_D0.148210.652
38_V106_A0.148120.651
73_D153_L0.148020.651
131_D137_P0.147690.649
7_M34_L0.147120.647
103_I107_L0.147050.647
130_S153_L0.146980.646
44_T158_A0.146670.645
9_L71_I0.146340.643
68_I121_S0.146180.643
97_H111_H0.146180.643
41_T98_V0.145570.640
68_I75_L0.145270.639
146_G150_F0.145150.638
55_Y84_S0.145140.638
112_L115_L0.14460.636
18_G134_P0.144510.635
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
2qjyA1100-0.052
3cx5C1100-0.051
1pp9C0.9881100-0.025
1vf5A0.73811000.161
4h44A0.73811000.24
4h44B0.333398.20.837
1vf5B0.315597.20.874
4gd3A0.720210.60.957
1jb0X0.07743.10.966
4he8J0.6312.60.967

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