GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
COG2 - COG (conserved oligomeric Golgi) complex component COG2
Pfam: PF06148 (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: 133
Sequences: 813
Seq/Len: 6.11
HH_delta: 0.769 (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
13_F18_F0.191572.094
103_L106_R0.18332.004
54_Y57_F0.177381.939
15_V19_L0.154661.690
14_D17_E0.151311.654
85_V89_R0.150781.648
60_L103_L0.133971.464
27_S30_D0.1321.443
47_I50_I0.130221.423
102_K106_R0.130031.421
46_L68_D0.127921.398
83_E86_E0.12681.386
102_K105_E0.122541.339
107_K111_E0.121141.324
17_E21_S0.120551.318
29_E32_R0.119651.308
82_R86_E0.119591.307
98_E107_K0.117191.281
81_F88_V0.114381.250
73_E78_L0.113491.240
81_F89_R0.112271.227
83_E94_N0.111941.224
61_S67_M0.111111.214
18_F92_L0.111021.213
54_Y126_L0.110661.210
80_Q87_S0.110361.206
17_E52_D0.110041.203
93_D97_E0.109821.200
40_K43_K0.109551.197
84_E87_S0.107121.171
39_S43_K0.107021.170
121_D129_L0.105861.157
58_V68_D0.10571.155
87_S95_T0.103991.137
85_V93_D0.103561.132
48_E88_V0.103471.131
73_E116_L0.103161.128
114_A127_E0.102231.117
19_L25_Y0.101961.114
86_E90_D0.101361.108
105_E112_E0.100761.101
45_E83_E0.100561.099
57_F60_L0.09931.085
119_L122_I0.098661.078
16_D21_S0.098491.077
21_S35_L0.098231.074
28_L34_D0.098231.074
75_R99_I0.098071.072
50_I58_V0.095951.049
51_N57_F0.095591.045
118_L123_S0.094151.029
44_N55_A0.093451.021
40_K73_E0.093431.021
108_E113_K0.093041.017
63_N72_E0.092791.014
109_L112_E0.092741.014
35_L64_L0.092191.008
80_Q83_E0.092171.007
21_S101_D0.0921.006
16_D20_S0.091891.004
108_E115_L0.091471.000
22_N28_L0.091440.999
42_L111_E0.090090.985
88_V92_L0.089680.980
80_Q122_I0.089420.977
62_T65_V0.089340.977
87_S94_N0.089210.975
118_L121_D0.089210.975
47_I60_L0.089050.973
46_L64_L0.08860.968
18_F26_V0.088460.967
72_E79_S0.088390.966
76_K79_S0.088370.966
114_A117_K0.088220.964
45_E62_T0.087230.953
72_E83_E0.086670.947
103_L109_L0.086540.946
17_E22_N0.086440.945
119_L123_S0.086310.943
43_K92_L0.085690.937
15_V97_E0.085650.936
85_V122_I0.085290.932
110_R129_L0.085180.931
22_N29_E0.084930.928
87_S90_D0.084730.926
77_P89_R0.084390.922
31_L106_R0.084120.919
100_E104_E0.084120.919
46_L108_E0.08410.919
110_R113_K0.084030.918
82_R93_D0.08390.917
17_E20_S0.083250.910
63_N68_D0.083210.910
77_P90_D0.08320.909
81_F107_K0.082940.907
73_E76_K0.08260.903
104_E114_A0.082470.901
102_K121_D0.082450.901
73_E94_N0.082430.901
72_E76_K0.082420.901
29_E76_K0.082210.899
37_S41_E0.08210.897
126_L130_E0.082070.897
15_V22_N0.082050.897
49_L56_D0.081940.896
27_S31_L0.081560.891
96_Q117_K0.081450.890
50_I61_S0.081430.890
27_S50_I0.081150.887
15_V99_I0.081140.887
50_I54_Y0.080890.884
41_E76_K0.080830.883
53_D57_F0.080610.881
51_N60_L0.080310.878
50_I67_M0.080270.877
18_F22_N0.080030.875
49_L66_G0.080020.875
53_D56_D0.079990.874
91_E94_N0.079890.873
106_R114_A0.079750.872
21_S24_R0.079380.868
62_T89_R0.079280.867
95_T113_K0.079180.865
59_S65_V0.079150.865
121_D125_S0.079120.865
78_L90_D0.078750.861
117_K125_S0.078350.856
23_R57_F0.078170.854
13_F32_R0.07810.854
74_L91_E0.078080.853
40_K65_V0.078070.853
61_S81_F0.078050.853
52_D63_N0.078020.853
87_S104_E0.077810.850
87_S111_E0.077740.850
57_F95_T0.07760.848
20_S92_L0.077470.847
31_L60_L0.077430.846
48_E56_D0.077060.842
29_E33_K0.077010.842
54_Y58_V0.076930.841
66_G86_E0.076480.836
22_N26_V0.076410.835
50_I126_L0.076370.835
34_D101_D0.076330.834
124_E127_E0.076050.831
74_L122_I0.076030.831
99_I106_R0.075910.830
22_N44_N0.075770.828
32_R36_R0.075730.828
85_V126_L0.075730.828
81_F84_E0.075640.827
79_S98_E0.07540.824
101_D127_E0.075330.823
100_E105_E0.075070.821
42_L124_E0.075060.820
96_Q113_K0.075010.820
69_E83_E0.074910.819
46_L82_R0.07490.819
24_R82_R0.07480.818
84_E127_E0.074690.816
79_S107_K0.074680.816
49_L57_F0.074640.816
77_P128_K0.074620.816
85_V128_K0.074550.815
46_L50_I0.074550.815
50_I55_A0.07450.814
32_R39_S0.074370.813
84_E111_E0.074320.812
110_R117_K0.074010.809
74_L98_E0.073690.805
65_V115_L0.073680.805
64_L74_L0.073570.804
26_V30_D0.073410.802
37_S73_E0.073220.800
42_L112_E0.073110.799
75_R89_R0.073060.799
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
2jqqA0.804595.30.769
1tohA0.661764.50.85
4etpA0.533858.40.855
1jcdA0.39156.60.857
1ez3A0.804553.60.859
2dfsA0.969953.60.859
4etpB0.548951.50.861
3u06A0.533846.20.865
2v71A0.9774330.875
2ffhA0.962432.90.875
If you are interested in a protein containing this domain,
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