GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
COG5 - Golgi transport complex subunit 5
Pfam: PF10392 (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: CL0295
Length: 132
Sequences: 795
Seq/Len: 6.02
HH_delta: 0.844 (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
57_H60_L0.198732.072
106_T109_L0.194712.030
10_P14_A0.190471.986
8_F13_F0.1721.793
105_L108_Q0.166621.737
30_D33_T0.150991.574
10_P16_D0.148041.543
105_L109_L0.138671.446
120_R123_S0.135971.418
88_Y92_R0.135741.415
32_S36_K0.126671.321
7_D62_S0.125651.310
121_S124_R0.125321.307
6_P10_P0.124521.298
47_K58_E0.121811.270
52_Q60_L0.121461.266
7_D12_Q0.120741.259
7_D15_N0.120461.256
101_K110_E0.120031.251
9_D12_Q0.119971.251
84_L92_R0.118141.232
54_T63_Q0.116451.214
50_R53_V0.115651.206
95_V129_V0.114981.199
88_Y91_L0.113691.185
83_S90_R0.113131.180
12_Q16_D0.112721.175
30_D36_K0.112131.169
30_D34_P0.111881.166
33_T40_F0.111761.165
96_I100_E0.110511.152
113_H116_S0.110391.151
79_S82_E0.108951.136
103_Q107_S0.108581.132
42_I46_D0.106971.115
86_S89_E0.106881.114
83_S86_S0.106591.111
98_P101_K0.106081.106
32_S35_L0.105561.101
14_A19_K0.105051.095
77_V94_E0.105031.095
102_I111_R0.105011.095
54_T60_L0.10371.081
126_L129_V0.103321.077
83_S125_F0.103191.076
48_R86_S0.102981.074
103_Q119_L0.10271.071
86_S97_E0.102451.068
112_L119_L0.102391.068
81_V93_S0.102111.065
76_A81_V0.102041.064
51_S62_S0.101741.061
110_E114_Q0.101741.061
13_F17_L0.101731.061
47_K51_S0.101661.060
102_I106_T0.101441.058
30_D37_K0.101321.056
75_Q86_S0.101141.055
84_L91_L0.09971.039
109_L113_H0.099251.035
43_Q46_D0.098891.031
6_P16_D0.098771.030
72_S89_E0.098641.028
38_L42_I0.09831.025
54_T59_D0.098151.023
51_S59_D0.097981.022
67_I125_F0.097411.016
75_Q79_S0.097281.014
70_L95_V0.096031.001
65_S72_S0.09580.999
81_V112_L0.095590.997
10_P18_L0.095430.995
35_L42_I0.094840.989
55_S66_S0.094590.986
44_E90_R0.09380.978
54_T64_A0.092260.962
93_S111_R0.091850.958
65_S68_E0.091440.953
9_D48_R0.091090.950
7_D104_K0.090930.948
98_P119_L0.089740.936
111_R116_S0.089690.935
44_E75_Q0.08920.930
42_I115_T0.088250.920
55_S93_S0.088020.918
50_R63_Q0.087990.917
109_L116_S0.087870.916
40_F72_S0.087650.914
124_R128_L0.087630.914
95_V98_P0.08760.913
29_L33_T0.087440.912
33_T44_E0.087330.911
96_I118_L0.08720.909
97_E100_E0.087020.907
33_T91_L0.0870.907
60_L63_Q0.086850.906
123_S127_Q0.086670.904
75_Q97_E0.086650.903
53_V56_N0.086640.903
111_R118_L0.086620.903
9_D122_V0.085880.895
53_V67_I0.085850.895
76_A83_S0.085390.890
112_L122_V0.0850.886
122_V125_F0.084760.884
82_E101_K0.084350.879
92_R109_L0.084350.879
48_R60_L0.084280.879
109_L117_D0.084190.878
80_S86_S0.084020.876
75_Q107_S0.08370.873
80_S92_R0.08360.872
6_P17_L0.083540.871
31_I57_H0.083180.867
124_R127_Q0.083070.866
51_S58_E0.082860.864
48_R73_V0.082380.859
76_A80_S0.082350.859
33_T43_Q0.082260.858
31_I42_I0.082250.858
99_Y109_L0.082080.856
85_Q123_S0.081880.854
16_D127_Q0.081760.852
83_S120_R0.081710.852
15_N18_L0.081370.848
105_L124_R0.081020.845
72_S90_R0.080630.841
98_P109_L0.080630.841
72_S86_S0.08060.840
16_D93_S0.080510.839
41_D46_D0.080480.839
74_L80_S0.080340.838
19_K111_R0.080240.837
13_F50_R0.080030.834
102_I109_L0.079730.831
53_V129_V0.079560.830
32_S44_E0.079420.828
28_E36_K0.079260.826
63_Q68_E0.079260.826
65_S92_R0.079240.826
49_I105_L0.079220.826
77_V125_F0.079050.824
48_R65_S0.078960.823
108_Q115_T0.078930.823
18_L60_L0.078830.822
62_S77_V0.078580.819
89_E93_S0.078550.819
14_A28_E0.078520.819
91_L99_Y0.078260.816
80_S93_S0.078130.815
7_D11_V0.077950.813
12_Q18_L0.077940.813
78_R107_S0.077710.810
18_L109_L0.077460.808
53_V66_S0.077350.806
77_V84_L0.076760.800
75_Q82_E0.076740.800
28_E111_R0.076710.800
99_Y106_T0.076680.799
7_D16_D0.076510.798
63_Q106_T0.076380.796
72_S120_R0.076280.795
35_L71_E0.076250.795
49_I53_V0.076110.794
93_S100_E0.075960.792
47_K97_E0.075950.792
36_K93_S0.075940.792
18_L29_L0.075830.791
72_S93_S0.075790.790
50_R54_T0.075620.788
17_L31_I0.075570.788
99_Y116_S0.075390.786
69_E75_Q0.075330.785
63_Q87_S0.075040.782
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
3vkgA0.969760.30.844
4hpqC0.969757.90.847
3ghgA0.939457.30.847
4etpB0.5303550.849
2jqqA0.7554.60.85
1jcdA0.393949.60.854
3ghgA0.969748.40.855
1deqA0.893947.20.856
4etpA0.530343.90.858
1ez3A0.780340.80.861
If you are interested in a protein containing this domain,
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