GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trigger_C - Bacterial trigger factor protein (TF) C-terminus
Pfam: PF05698 (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: CL0262
Length: 162
Sequences: 1792
Seq/Len: 11.06
HH_delta: 0.122 (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
32_A35_E0.63953.001
115_E155_K0.627062.942
102_A106_K0.610052.863
102_A105_K0.59222.779
14_E18_K0.569812.674
91_E95_K0.554232.601
31_D92_K0.516012.421
7_E11_E0.50652.377
87_R91_E0.502112.356
43_E47_E0.499052.342
8_K11_E0.46412.178
31_D35_E0.463272.174
10_R14_E0.456852.144
3_E7_E0.439822.064
4_E7_E0.419641.969
107_E159_F0.407871.914
24_Q28_A0.402571.889
119_E122_K0.398671.871
51_E83_R0.393081.844
81_E84_E0.388761.824
121_E125_Q0.386481.813
78_T81_E0.386241.812
49_E93_R0.365751.716
37_S99_I0.365181.714
32_A36_N0.363351.705
133_E136_E0.35261.654
11_E14_E0.347961.633
11_E15_K0.342891.609
130_N133_E0.342831.609
117_E135_K0.342591.608
1_T4_E0.339571.593
112_S115_E0.320211.503
2_L6_K0.306491.438
113_D148_R0.305931.436
104_A156_V0.302851.421
117_E121_E0.302071.417
158_D162_E0.300491.410
55_E58_E0.300071.408
15_K19_Q0.297421.396
84_E87_R0.296571.392
115_E118_E0.294351.381
43_E87_R0.292131.371
33_L99_I0.289941.360
113_D117_E0.289411.358
8_K12_E0.286861.346
118_E121_E0.284941.337
7_E10_R0.282691.326
3_E6_K0.279251.310
51_E55_E0.275661.293
27_E31_D0.275591.293
136_E140_K0.270931.271
119_E154_D0.264661.242
59_Q62_K0.258591.213
114_E117_E0.258061.211
39_V95_K0.257721.209
120_I131_P0.252361.184
18_K22_E0.251261.179
109_I159_F0.247171.160
103_I156_V0.24661.157
55_E59_Q0.238331.118
118_E122_K0.237491.114
114_E118_E0.237311.114
49_E52_R0.235431.105
7_E14_E0.234111.099
60_Q64_Q0.232141.089
53_L56_Q0.231981.089
103_I107_E0.229081.075
30_L96_Q0.227121.066
41_L46_V0.226161.061
50_I87_R0.223961.051
88_E92_K0.222841.046
111_V152_L0.222431.044
47_E87_R0.222221.043
22_E161_L0.219571.030
47_E83_R0.218021.023
25_K28_A0.2151.009
34_I37_S0.214931.009
111_V151_L0.214131.005
29_V160_L0.209790.984
80_E84_E0.208640.979
25_K161_L0.207770.975
13_L17_K0.207250.972
156_V159_F0.20710.972
104_A152_L0.206970.971
53_L90_A0.204970.962
3_E10_R0.204520.960
16_Q20_Q0.204310.959
159_F162_E0.204050.957
82_F85_E0.200580.941
9_I12_E0.199980.938
26_R158_D0.199590.937
120_I134_L0.199580.936
46_V94_L0.199070.934
20_Q24_Q0.195830.919
56_Q60_Q0.194990.915
133_E137_Q0.193240.907
89_E92_K0.193230.907
94_L98_L0.19290.905
124_A128_G0.186980.877
33_L36_N0.1830.859
156_V160_L0.182990.859
88_E91_E0.182750.858
100_L156_V0.182710.857
61_L64_Q0.181380.851
47_E51_E0.180730.848
105_K152_L0.179040.840
124_A134_L0.176950.830
147_L151_L0.176610.829
97_Q153_E0.176290.827
22_E154_D0.175950.826
17_K20_Q0.175780.825
101_D153_E0.17570.824
38_E95_K0.172730.810
60_Q63_Q0.172130.808
2_L5_L0.170870.802
15_K18_K0.170390.800
81_E85_E0.169560.796
115_E151_L0.168960.793
132_E135_K0.167670.787
59_Q63_Q0.166560.782
29_V157_I0.166180.780
12_E15_K0.166090.779
132_E136_E0.166040.779
51_E54_I0.164440.772
116_V148_R0.164110.770
90_A94_L0.163490.767
131_P135_K0.163350.766
28_A32_A0.162180.761
49_E97_Q0.161940.760
43_E91_E0.16170.759
145_E148_R0.161330.757
89_E93_R0.160820.755
134_L138_Y0.160360.752
29_V161_L0.160280.752
153_E156_V0.159650.749
26_R153_E0.158710.745
154_D158_D0.157950.741
53_L93_R0.157720.740
1_T5_L0.157360.738
42_P98_L0.156610.735
109_I156_V0.155960.732
22_E158_D0.155850.731
124_A129_M0.155620.730
1_T150_D0.155610.730
117_E139_E0.153220.719
68_L79_E0.152570.716
144_L148_R0.150780.707
136_E139_E0.149940.704
123_L127_Y0.149660.702
109_I152_L0.148640.697
45_L98_L0.148390.696
39_V99_I0.148280.696
100_L153_E0.14820.695
93_R98_L0.148150.695
20_Q23_Q0.147770.693
119_E123_L0.145350.682
63_Q69_E0.144860.680
52_R56_Q0.144750.679
153_E157_I0.144730.679
34_I99_I0.144720.679
62_K65_G0.144010.676
110_E148_R0.143910.675
28_A31_D0.143580.674
103_I160_L0.141660.665
58_E62_K0.140770.661
46_V91_E0.140410.659
63_Q66_M0.139170.653
79_E83_R0.137950.647
94_L97_Q0.137760.646
19_Q23_Q0.137540.645
152_L156_V0.137270.644
58_E68_L0.137250.644
111_V155_K0.137160.644
24_Q50_I0.136910.642
139_E142_K0.136730.642
14_E17_K0.135750.637
54_I79_E0.135460.636
23_Q27_E0.135370.635
119_E151_L0.134790.632
121_E131_P0.134240.630
59_Q160_L0.134170.630
46_V49_E0.133910.628
50_I89_E0.13340.626
56_Q93_R0.131950.619
26_R161_L0.131520.617
22_E26_R0.130790.614
117_E120_I0.130260.611
117_E158_D0.130230.611
41_L94_L0.128410.603
1_T7_E0.126990.596
140_K143_Q0.126120.592
90_A93_R0.125880.591
54_I83_R0.125340.588
125_Q128_G0.125220.588
137_Q142_K0.124770.585
41_L45_L0.124450.584
50_I83_R0.124370.584
82_F134_L0.123570.580
57_M61_L0.123250.578
45_L49_E0.123110.578
11_E18_K0.122860.576
120_I140_K0.122720.576
155_K159_F0.122450.575
56_Q59_Q0.12240.574
147_L150_D0.121730.571
26_R94_L0.12150.570
42_P45_L0.121410.570
85_E89_E0.120850.567
26_R154_D0.120840.567
34_I96_Q0.120690.566
112_S155_K0.120590.566
34_I38_E0.120040.563
116_V121_E0.119970.563
103_I159_F0.119910.563
9_I146_Q0.119380.560
149_D153_E0.118770.557
111_V149_D0.118740.557
33_L96_Q0.118570.556
48_E52_R0.118480.556
99_I103_I0.118460.556
52_R55_E0.118380.555
108_K112_S0.118370.555
39_V150_D0.117830.553
66_M99_I0.117810.553
117_E131_P0.117580.552
29_V105_K0.116470.547
65_G69_E0.116390.546
93_R97_Q0.116130.545
97_Q149_D0.115360.541
124_A127_Y0.114250.536
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
3gtyX0.96399.90.122
1w26A0.932199.90.159
2nsaA0.96399.90.167
1zxjA0.851999.90.253
1t11A0.790199.80.28
1m5yA0.746996.60.792
3rgcA0.635895.60.811
3rgcA0.827295.20.816
3nrkA0.790193.50.832
3nrkA0.919892.80.836

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