GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ERGIC_N - Endoplasmic Reticulum-Golgi Intermediate Compartment (ERGIC)
Pfam: PF13850 (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: 96
Sequences: 468
Seq/Len: 4.88
HH_delta: 0.611 (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
33_I37_F0.247872.291
74_M79_L0.245242.267
12_P15_L0.205591.901
10_K23_G0.190931.765
6_D10_K0.18981.755
70_T82_D0.186551.725
9_P15_L0.180791.671
19_T22_G0.161671.495
8_F58_S0.153361.418
68_D77_D0.151411.400
31_V48_E0.149311.380
27_I44_Y0.146911.358
38_I69_I0.136741.264
55_V85_D0.134681.245
29_T33_I0.132621.226
34_V48_E0.132261.223
42_Y46_S0.132071.221
11_V16_R0.131121.212
5_F10_K0.129251.195
75_P78_F0.128391.187
35_I42_Y0.12751.179
8_F15_L0.126631.171
7_A11_V0.12651.169
37_F41_L0.12521.157
5_F23_G0.125041.156
82_D88_G0.124961.155
5_F66_N0.124521.151
28_I38_I0.123671.143
25_I87_S0.123481.142
26_S49_I0.122121.129
44_Y56_D0.121781.126
31_V35_I0.121281.121
62_K83_V0.121281.121
25_I30_I0.120111.110
41_L45_L0.118691.097
75_P79_L0.11861.096
68_D92_L0.116421.076
38_I46_S0.115751.070
3_K20_S0.114481.058
19_T25_I0.114421.058
78_F81_V0.113781.052
13_E16_R0.113441.049
52_Q60_D0.111611.032
28_I48_E0.111131.027
55_V60_D0.10931.010
53_L90_H0.108511.003
16_R54_V0.108341.002
18_K23_G0.1070.989
9_P65_I0.106990.989
9_P16_R0.106590.985
37_F54_V0.105210.973
53_L71_F0.104980.970
42_Y45_L0.104440.965
13_E87_S0.104430.965
17_E91_Q0.103880.960
34_V50_K0.103630.958
53_L81_V0.103430.956
2_L38_I0.103240.954
18_K65_I0.103060.953
34_V42_Y0.10240.947
26_S89_D0.102150.944
4_R31_V0.101960.943
29_T39_S0.101450.938
15_L23_G0.100810.932
18_K26_S0.100750.931
8_F41_L0.099280.918
67_F82_D0.099140.916
9_P12_P0.098610.912
36_L39_S0.098460.910
80_S88_G0.097980.906
23_G27_I0.097120.898
49_I63_L0.096540.892
31_V64_Q0.096080.888
33_I56_D0.096050.888
2_L20_S0.095920.887
58_S61_E0.095920.887
64_Q77_D0.095880.886
5_F52_Q0.095090.879
19_T30_I0.09460.875
25_I53_L0.094020.869
50_K75_P0.093640.866
50_K64_Q0.093550.865
38_I42_Y0.093270.862
39_S69_I0.093210.862
37_F50_K0.093170.861
81_V89_D0.093010.860
84_Q89_D0.09210.851
8_F20_S0.092050.851
2_L49_I0.091740.848
4_R52_Q0.091510.846
28_I42_Y0.091260.844
82_D85_D0.0910.841
19_T62_K0.09090.840
16_R43_S0.090890.840
31_V42_Y0.090820.840
47_G81_V0.090450.836
11_V65_I0.089970.832
67_F79_L0.089310.826
7_A89_D0.089030.823
27_I90_H0.088940.822
20_S24_I0.08880.821
12_P16_R0.088060.814
68_D79_L0.087880.812
62_K65_I0.087630.810
7_A59_R0.087580.810
55_V89_D0.087450.808
2_L11_V0.087440.808
24_I50_K0.087420.808
18_K36_L0.087280.807
2_L6_D0.086870.803
3_K30_I0.086550.800
21_S70_T0.086540.800
71_F78_F0.086370.798
66_N89_D0.086340.798
59_R89_D0.086220.797
2_L33_I0.086120.796
10_K35_I0.086010.795
58_S63_L0.085820.793
12_P83_V0.08580.793
7_A68_D0.085750.793
28_I32_L0.085330.789
62_K84_Q0.084990.786
14_D82_D0.084930.785
62_K92_L0.084440.781
24_I28_I0.083920.776
65_I74_M0.083350.771
44_Y92_L0.082550.763
38_I41_L0.082530.763
17_E51_Y0.082240.760
24_I35_I0.082170.760
16_R35_I0.082070.759
22_G55_V0.081450.753
64_Q67_F0.081430.753
32_L69_I0.081140.750
44_Y52_Q0.080820.747
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
3zlcA0.541798.90.611
2qtsA0.5208190.909
4gtwA0.333310.90.919
4e3yA0.33336.80.925
4iqgC0.58335.90.927
4hp8A0.61463.90.933
1g8tA0.33333.80.933
3zfsC0.97923.50.934
4fs3A0.6253.40.934
4ah6A0.59383.20.935
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0149 seconds.