GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SecD-TM1 - SecD export protein N-terminal TM region
Pfam: PF13721 (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: 101
Sequences: 853
Seq/Len: 8.45
HH_delta: 0.723 (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
78_S81_Q0.362872.495
38_A41_A0.294022.021
52_E56_K0.282511.942
53_Q57_A0.280691.930
6_L10_L0.239611.647
35_Q39_S0.229511.578
31_D63_K0.22741.563
55_L85_A0.206321.418
54_A92_A0.204981.409
4_Y8_K0.202271.391
19_G26_N0.200491.378
61_A77_D0.197831.360
56_K59_G0.195071.341
34_V89_L0.19371.332
86_K90_S0.193361.329
76_F79_T0.192021.320
3_R6_L0.19191.319
19_G23_A0.191671.318
54_A89_L0.189551.303
49_F52_E0.189541.303
23_A27_L0.188521.296
13_L91_K0.187041.286
38_A42_G0.185691.277
14_V18_L0.185361.274
36_I93_L0.183011.258
62_V65_I0.182911.257
81_Q84_K0.174791.202
60_I85_A0.170661.173
72_L89_L0.16861.159
24_L27_L0.168041.155
83_L87_D0.167061.149
16_L75_R0.165861.140
15_V18_L0.164511.131
64_S74_I0.162451.117
5_P8_K0.158711.091
51_V72_L0.156411.075
2_N9_Y0.156351.075
88_V91_K0.156271.074
44_Q47_D0.156041.073
54_A88_V0.155411.068
7_W22_Y0.154051.059
31_D75_R0.151721.043
19_G22_Y0.151651.043
63_K73_L0.1511.038
39_S42_G0.15071.036
15_V19_G0.149081.025
34_V39_S0.149071.025
10_L57_A0.148471.021
18_L61_A0.147831.016
59_G62_V0.147121.011
58_A88_V0.14651.007
60_I76_F0.145831.003
21_L27_L0.144780.995
13_L16_L0.143580.987
4_Y9_Y0.143180.984
26_N75_R0.142960.983
18_L67_Q0.142030.976
5_P9_Y0.141480.973
54_A58_A0.141330.972
76_F82_Q0.141160.970
60_I86_K0.14040.965
65_I74_I0.140370.965
50_Q78_S0.139770.961
31_D36_I0.139640.960
54_A91_K0.138880.955
41_A48_A0.137660.946
15_V44_Q0.137610.946
2_N8_K0.13670.940
52_E59_G0.136130.936
21_L42_G0.136010.935
67_Q71_S0.13540.931
31_D73_L0.134640.926
33_A75_R0.134170.922
16_L29_G0.133230.916
69_G87_D0.132280.909
9_Y82_Q0.131560.904
2_N6_L0.131360.903
46_P84_K0.130890.900
6_L9_Y0.130210.895
27_L73_L0.127880.879
20_A70_D0.127450.876
26_N62_V0.127350.876
51_V85_A0.127330.875
50_Q92_A0.127210.875
60_I79_T0.126980.873
56_K62_V0.126530.870
88_V92_A0.125290.861
9_Y36_I0.124560.856
43_V86_K0.124230.854
51_V68_E0.124090.853
10_L91_K0.123970.852
22_Y33_A0.123280.848
76_F85_A0.121910.838
86_K91_K0.121440.835
8_K82_Q0.119220.820
41_A44_Q0.117940.811
32_P79_T0.117510.808
30_E90_S0.116730.803
21_L65_I0.11670.802
57_A62_V0.11660.802
77_D92_A0.116030.798
18_L65_I0.115450.794
19_G24_L0.11540.793
16_L61_A0.114760.789
9_Y12_I0.114410.787
23_A28_Y0.11410.784
17_L69_G0.113970.784
49_F60_I0.113480.780
76_F81_Q0.113410.780
25_P28_Y0.113290.779
49_F53_Q0.112860.776
20_A28_Y0.112710.775
80_D87_D0.112630.774
60_I63_K0.111890.769
23_A68_E0.11170.768
43_V47_D0.11170.768
29_G33_A0.111450.766
59_G94_G0.111210.765
40_S49_F0.11080.762
65_I89_L0.110630.761
28_Y75_R0.110320.758
80_D88_V0.110110.757
62_V74_I0.110040.757
16_L48_A0.109220.751
82_Q86_K0.109050.750
10_L14_V0.108630.747
51_V92_A0.108350.745
39_S43_V0.108060.743
34_V37_S0.107760.741
43_V48_A0.107460.739
8_K12_I0.107120.736
62_V69_G0.107010.736
21_L74_I0.106660.733
53_Q59_G0.106590.733
29_G35_Q0.106490.732
45_L66_E0.106280.731
15_V72_L0.106220.730
24_L72_L0.105220.723
58_A92_A0.103920.714
47_D81_Q0.103740.713
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
3aqpA0.970397.30.723
2y9jY0.633763.40.862
3ur8A0.693137.50.881
2v50A0.990134.50.883
3ucpA0.920829.60.887
3cxjA0.5545270.889
3cprA0.891126.10.89
4dx5A0.980225.60.89
1xmxA0.811925.50.891
3w9iA0.980224.20.892
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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