GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1298 - Protein of unknown function (DUF1298)
Pfam: PF06974 (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: 153
Sequences: 960
Seq/Len: 6.27
HH_delta: 0.783 (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
146_A149_E0.304992.940
34_K38_D0.229122.209
141_D145_E0.224962.169
81_S114_T0.221032.131
81_S112_N0.200471.933
144_E148_E0.200381.932
57_P61_G0.180491.740
9_N41_K0.177211.708
102_P125_G0.171961.658
113_I139_L0.16781.618
85_G117_S0.166121.601
89_P96_R0.164291.584
91_Y96_R0.162481.566
138_R142_C0.159541.538
30_L150_L0.158141.524
126_I139_L0.15811.524
41_K82_N0.154191.486
110_A132_A0.150691.453
78_L113_I0.150041.446
9_N83_V0.148161.428
86_P117_S0.146741.415
39_R96_R0.143981.388
128_A136_P0.141661.366
21_A32_A0.138481.335
83_V112_N0.137061.321
82_N117_S0.136061.312
29_R146_A0.134761.299
61_G105_L0.134381.295
83_V86_P0.134251.294
37_M41_K0.13331.285
53_L69_S0.127341.228
41_K83_V0.126841.223
28_E31_R0.126831.223
89_P119_A0.125881.214
67_A73_S0.124911.204
24_A148_E0.122531.181
25_D31_R0.121261.169
46_A58_P0.120911.166
137_Q141_D0.119281.150
115_V122_L0.119221.149
135_D151_K0.118761.145
18_L128_A0.118631.144
87_Q120_G0.118481.142
59_L68_L0.117961.137
13_F106_G0.11721.130
52_L55_L0.115751.116
82_N85_G0.115571.114
71_R74_P0.114991.109
126_I140_A0.114671.105
66_R69_S0.114571.104
50_Y69_S0.114411.103
117_S122_L0.114231.101
12_G41_K0.113961.099
48_L68_L0.113561.095
21_A35_R0.112811.088
31_R38_D0.111951.079
19_P33_A0.110841.069
24_A28_E0.110691.067
28_E32_A0.110461.065
73_S108_G0.109991.060
76_A109_Q0.109831.059
16_L37_M0.10981.058
86_P118_Y0.108521.046
54_A67_A0.108491.046
111_L126_I0.108481.046
55_L97_V0.108381.045
32_A35_R0.10821.043
12_G92_F0.108151.043
110_A125_G0.10731.034
138_R151_K0.107221.034
14_V40_K0.107081.032
126_I143_F0.106261.024
91_Y95_A0.105481.017
87_Q119_A0.105391.016
96_R119_A0.105071.013
55_L66_R0.105031.013
19_P129_D0.104441.007
38_D42_R0.104041.003
85_G118_Y0.103771.000
77_N91_Y0.103751.000
37_M109_Q0.103350.996
58_P61_G0.102430.987
135_D141_D0.102130.985
97_V119_A0.101510.979
29_R95_A0.101440.978
114_T125_G0.101250.976
145_E149_E0.101040.974
20_T107_D0.10030.967
30_L33_A0.099510.959
106_G115_V0.099350.958
105_L125_G0.099270.957
104_P125_G0.098950.954
140_A147_L0.098920.954
51_A59_L0.098840.953
6_R92_F0.098840.953
50_Y64_A0.098780.952
31_R35_R0.098760.952
67_A71_R0.098480.949
144_E147_L0.098440.949
124_F136_P0.098240.947
14_V37_M0.09760.941
111_L139_L0.097420.939
85_G125_G0.097050.936
102_P114_T0.096630.932
87_Q96_R0.096190.927
122_L137_Q0.095890.924
85_G102_P0.095340.919
24_A32_A0.095320.919
8_G76_A0.094740.913
77_N95_A0.094350.910
114_T127_V0.09410.907
72_L75_K0.093490.901
37_M115_V0.093290.899
43_S123_D0.093190.898
78_L110_A0.092740.894
67_A145_E0.092460.891
13_F115_V0.092380.891
7_W16_L0.092320.890
41_K112_N0.092080.888
38_D128_A0.091830.885
8_G12_G0.091340.881
51_A54_A0.091210.879
57_P122_L0.091050.878
80_I115_V0.090720.875
39_R44_L0.090430.872
48_L104_P0.089880.866
77_N80_I0.089830.866
31_R119_A0.089680.865
84_P87_Q0.089440.862
47_M59_L0.088970.858
57_P60_L0.088870.857
14_V71_R0.088470.853
42_R127_V0.088110.849
51_A66_R0.087750.846
99_Y132_A0.08750.844
111_L133_V0.087060.839
11_F111_L0.086860.837
75_K97_V0.086570.835
12_G106_G0.08630.832
25_D41_K0.086230.831
86_P90_L0.086150.831
33_A36_S0.08560.825
97_V100_I0.085430.824
8_G37_M0.085370.823
65_A143_F0.085080.820
70_N75_K0.084960.819
110_A136_P0.084840.818
44_L48_L0.084810.818
7_W101_Y0.084570.815
65_A92_F0.084390.814
51_A79_V0.084270.812
91_Y94_G0.084240.812
80_I113_I0.083920.809
66_R72_L0.083760.807
113_I143_F0.083450.804
12_G45_E0.083170.802
53_L65_A0.083170.802
35_R98_E0.082890.799
64_A142_C0.082750.798
68_L148_E0.082470.795
11_F127_V0.082370.794
12_G44_L0.082280.793
17_P21_A0.08220.792
84_P117_S0.082120.792
16_L40_K0.082060.791
5_A115_V0.082010.791
147_L151_K0.081750.788
12_G147_L0.081670.787
32_A36_S0.081330.784
28_E70_N0.081180.783
117_S135_D0.081020.781
39_R94_G0.080930.780
75_K104_P0.08090.780
51_A70_N0.080880.780
29_R33_A0.080830.779
98_E143_F0.080480.776
133_V139_L0.080440.775
141_D144_E0.080250.774
33_A106_G0.080240.774
21_A139_L0.079940.771
64_A69_S0.079740.769
25_D28_E0.079740.769
37_M40_K0.079520.767
70_N73_S0.079440.766
126_I136_P0.07940.765
78_L109_Q0.079390.765
126_I148_E0.079250.764
15_L79_V0.079220.764
11_F14_V0.079130.763
115_V151_K0.078730.759
11_F85_G0.07870.759
86_P120_G0.078590.758
27_L108_G0.078550.757
107_D112_N0.078420.756
17_P133_V0.077980.752
133_V151_K0.077880.751
130_R133_V0.077810.750
20_T106_G0.077770.750
17_P80_I0.077660.749
9_N28_E0.077540.747
79_V126_I0.077490.747
133_V149_E0.077240.745
55_L61_G0.077130.744
142_C151_K0.077120.743
18_L105_L0.076970.742
49_S56_V0.076760.740
61_G66_R0.076680.739
116_F127_V0.076640.739
60_L70_N0.076540.738
51_A55_L0.076440.737
27_L96_R0.076210.735
34_K37_M0.076150.734
57_P68_L0.076010.733
111_L117_S0.075580.729
54_A66_R0.075570.729
62_A72_L0.075480.728
50_Y53_L0.075310.726
80_I111_L0.075250.725
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
1q9jA0.908597.60.783
2jgpA0.941297.10.807
1l5aA0.9085970.812
3fotA0.967396.60.823
4hvmA0.954295.20.844
4jn3A0.888993.90.855
2xhgA0.9477900.87
2vsqA0.90289.90.87
2debA0.91587.30.876
1nm8A0.9281850.88
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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