GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Chorein_N - N-terminal region of Chorein a TM vesicle-mediated sorter
Pfam: PF12624 (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: 118
Sequences: 557
Seq/Len: 4.72
HH_delta: 0.905 (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
61_G83_D0.471633.882
18_E40_E0.348522.869
60_I84_V0.269972.222
62_K82_E0.265232.183
36_L39_L0.237571.956
34_V65_I0.222021.828
56_K89_K0.221981.827
69_W72_L0.201411.658
69_W77_V0.200371.649
78_V86_L0.197841.629
19_N24_Q0.169661.397
71_S75_K0.155011.276
54_E89_K0.154521.272
6_S10_N0.151791.250
18_E44_D0.149611.232
5_V27_V0.14891.226
18_E42_K0.148881.226
52_P58_G0.147741.216
20_L32_G0.145761.200
54_E57_S0.142681.175
10_N24_Q0.142181.170
35_E62_K0.137761.134
72_L77_V0.136671.125
40_E48_N0.136041.120
35_E64_R0.134861.110
13_L24_Q0.131961.086
20_L23_D0.130421.074
53_I88_L0.127511.050
30_W77_V0.126971.045
74_S95_E0.126831.044
74_S93_Q0.126691.043
24_Q29_L0.126641.043
60_I89_K0.126441.041
45_A88_L0.126051.038
41_L60_I0.125791.036
24_Q28_S0.125451.033
8_L12_Y0.124871.028
28_S31_N0.124571.025
9_L25_L0.124071.021
2_E30_W0.123971.021
3_S18_E0.123911.020
5_V13_L0.121581.001
26_S94_D0.121360.999
5_V79_I0.120080.988
13_L36_L0.119840.987
75_K78_V0.118630.977
29_L34_V0.118610.976
30_W69_W0.118370.974
16_Y30_W0.11810.972
13_L16_Y0.11770.969
51_L76_P0.116750.961
14_G25_L0.116350.958
30_W33_E0.115850.954
67_I92_D0.115690.952
33_E54_E0.115580.951
37_R62_K0.11420.940
61_G90_P0.113880.937
14_G21_D0.113850.937
27_V31_N0.113530.935
31_N75_K0.113380.933
15_R92_D0.113090.931
21_D63_L0.112830.929
17_I39_L0.110030.906
6_S46_L0.109920.905
79_I89_K0.109630.902
33_E66_K0.109580.902
63_L74_S0.109380.900
46_L55_V0.108980.897
61_G82_E0.108380.892
50_G91_K0.108350.892
2_E20_L0.108030.889
42_K47_N0.107940.889
16_Y41_L0.10730.883
4_L8_L0.10690.880
38_N60_I0.106080.873
49_L81_I0.105940.872
15_R48_N0.105850.871
14_G17_I0.105680.870
42_K58_G0.105570.869
28_S84_V0.105520.869
9_L13_L0.105230.866
2_E61_G0.104980.864
19_N76_P0.104890.863
16_Y34_V0.104540.861
7_S27_V0.104230.858
5_V56_K0.103730.854
55_V88_L0.10320.850
17_I41_L0.10310.849
7_S18_E0.103040.848
25_L29_L0.102310.842
17_I75_K0.102210.841
19_N43_K0.101650.837
8_L47_N0.101150.833
52_P76_P0.101080.832
2_E5_V0.100960.831
43_K81_I0.100480.827
68_P87_V0.099870.822
2_E9_L0.098850.814
28_S90_P0.098520.811
66_K78_V0.098120.808
67_I71_S0.09810.808
2_E24_Q0.098070.807
5_V8_L0.097970.806
17_I29_L0.09780.805
86_L89_K0.097630.804
48_N91_K0.097310.801
56_K95_E0.097060.799
41_L88_L0.096840.797
38_N61_G0.096770.797
20_L90_P0.096550.795
44_D63_L0.096550.795
75_K91_K0.096410.794
35_E78_V0.096310.793
26_S35_E0.096140.791
16_Y28_S0.096020.790
5_V30_W0.094710.780
4_L10_N0.093780.772
48_N63_L0.093570.770
15_R71_S0.093040.766
32_G69_W0.092840.764
31_N59_S0.092790.764
57_S81_I0.092770.764
16_Y49_L0.092720.763
21_D53_I0.092640.763
65_I90_P0.092470.761
51_L81_I0.092360.760
11_K28_S0.092210.759
91_K94_D0.0920.757
36_L76_P0.091970.757
32_G53_I0.091590.754
64_R80_E0.091520.753
19_N49_L0.091260.751
2_E26_S0.090840.748
28_S79_I0.089930.740
14_G31_N0.089880.740
25_L58_G0.089840.740
21_D30_W0.089570.737
19_N25_L0.089540.737
43_K73_W0.089390.736
55_V66_K0.089320.735
30_W70_T0.088990.733
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
1deqA0.881431.40.905
3ghgA0.9068290.906
4e45A0.813619.30.913
1m1jA0.915317.70.915
2z06A0.47466.60.929
3r9jC0.43226.10.93
3aabA0.6615.30.932
4eldA0.68644.90.932
2m3vA0.44074.80.933
3hzhB0.60174.70.933
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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