GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
5TM-5TMR_LYT - 5TMR of 5TMR-LYT
Pfam: PF07694 (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: CL0315
Length: 169
Sequences: 1076
Seq/Len: 6.37
HH_delta: 0.64 (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
47_R74_R0.308912.813
26_G66_A0.303542.764
67_G71_G0.268582.446
22_G26_G0.217761.983
59_G63_G0.216351.970
36_P124_I0.205491.871
51_I70_I0.188121.713
33_M74_R0.176581.608
96_A100_S0.172521.571
54_A63_G0.159171.449
33_M45_D0.157651.436
54_A58_G0.154991.411
29_G70_I0.153491.398
48_F92_I0.152621.390
30_I73_Y0.152391.388
81_T85_A0.1511.375
26_G69_I0.150461.370
22_G66_A0.150311.369
22_G62_S0.15031.369
55_G93_G0.148521.352
101_R105_R0.148011.348
34_Y73_Y0.147931.347
31_L35_F0.144891.319
59_G62_S0.144511.316
22_G65_I0.142981.302
85_A89_I0.14161.289
99_I118_L0.141261.286
95_L99_I0.138561.262
74_R78_G0.137911.256
51_I96_A0.137011.248
123_S152_I0.135021.230
40_G149_L0.13441.224
115_L163_G0.134171.222
45_D126_S0.133591.217
119_S148_L0.133141.212
127_M151_Y0.132541.207
75_F86_F0.131861.201
47_R70_I0.131071.194
56_L115_L0.129721.181
54_A59_G0.128541.171
48_F126_S0.128321.169
16_K20_L0.128121.167
26_G30_I0.127091.157
119_S156_V0.127031.157
45_D123_S0.12671.154
29_G66_A0.126361.151
58_G62_S0.12451.134
127_M144_V0.123981.129
75_F78_G0.122721.118
54_A66_A0.121671.108
50_P155_N0.120481.097
57_Y150_P0.118991.084
121_V124_I0.118331.078
101_R104_R0.117251.068
34_Y78_G0.117071.066
84_P133_L0.116631.062
45_D48_F0.115861.055
19_I23_L0.115041.048
23_L27_I0.114981.047
148_L152_I0.114641.044
54_A62_S0.114591.044
88_I92_I0.114251.040
36_P125_I0.114021.038
132_L136_P0.113951.038
129_I136_P0.113581.034
55_G97_G0.113531.034
45_D78_G0.113531.034
70_I123_S0.113331.032
126_S143_L0.113291.032
34_Y77_L0.112311.023
156_V160_L0.112251.022
32_L50_P0.111711.017
26_G29_G0.111661.017
71_G165_I0.111381.014
87_I133_L0.111061.011
128_L132_L0.110081.002
155_N158_G0.109841.000
51_I66_A0.10981.000
20_L27_I0.109440.997
48_F160_L0.108930.992
91_L95_L0.107620.980
152_I156_V0.107170.976
55_G63_G0.106980.974
36_P123_S0.106790.972
111_K114_Y0.106650.971
131_L166_I0.10610.966
123_S126_S0.105960.965
20_L161_L0.105580.961
41_G148_L0.105410.960
71_G93_G0.105120.957
65_I103_F0.104510.952
72_I91_L0.104250.949
30_I74_R0.104030.947
41_G143_L0.104020.947
64_L104_R0.103770.945
92_I126_S0.103710.944
120_L156_V0.103560.943
16_K19_I0.103270.940
104_R121_V0.103120.939
29_G46_L0.10280.936
20_L49_I0.102570.934
85_A88_I0.102370.932
67_G93_G0.101680.926
119_S159_I0.101430.924
33_M47_R0.10110.921
56_L60_P0.100480.915
63_G93_G0.100380.914
45_D151_Y0.100130.912
28_L50_P0.099960.910
136_P155_N0.099510.906
18_K94_I0.099040.902
37_I153_V0.09880.900
29_G51_I0.098750.899
63_G97_G0.09870.899
116_F160_L0.098230.895
80_P143_L0.097680.890
72_I90_I0.097580.889
124_I152_I0.097470.888
151_Y155_N0.097160.885
72_I76_L0.097060.884
21_I58_G0.096630.880
15_F94_I0.096140.875
45_D74_R0.096030.874
57_Y161_L0.095840.873
18_K129_I0.095740.872
154_I166_I0.095610.871
98_L146_T0.095170.867
89_I92_I0.095060.866
45_D85_A0.095060.866
19_I61_I0.094460.860
49_I116_F0.094180.858
28_L147_I0.094130.857
32_L46_L0.093670.853
56_L112_L0.093660.853
50_P89_I0.093660.853
33_M85_A0.093550.852
29_G76_L0.092970.847
84_P129_I0.092510.842
32_L37_I0.092240.840
53_L109_K0.092190.840
89_I93_G0.092060.838
52_I111_K0.092040.838
50_P123_S0.0920.838
22_G162_F0.091840.836
45_D89_I0.091730.835
52_I92_I0.09170.835
24_L119_S0.091630.834
108_K121_V0.091530.834
48_F51_I0.091510.833
105_R120_L0.091190.830
65_I90_I0.091170.830
95_L152_I0.091090.830
89_I126_S0.090940.828
19_I53_L0.090810.827
42_F155_N0.090690.826
67_G97_G0.090530.824
16_K65_I0.090420.823
45_D81_T0.09040.823
25_F32_L0.090230.822
32_L154_I0.090220.822
54_A73_Y0.090170.821
52_I159_I0.090130.821
34_Y75_F0.090020.820
56_L154_I0.089760.817
25_F54_A0.089570.816
53_L103_F0.089220.812
123_S155_N0.089060.811
50_P81_T0.08890.810
59_G97_G0.088770.808
127_M130_I0.088320.804
124_I148_L0.08830.804
127_M158_G0.088260.804
91_L128_L0.088210.803
14_R17_R0.088090.802
42_F73_Y0.08790.800
123_S151_Y0.087790.799
22_G69_I0.087680.798
15_F22_G0.08760.798
45_D88_I0.087390.796
35_F51_I0.087340.795
74_R143_L0.087330.795
39_I110_I0.087250.795
111_K121_V0.087150.794
27_I40_G0.08690.791
47_R78_G0.08690.791
63_G162_F0.086860.791
59_G94_I0.086840.791
110_I149_L0.08670.790
41_G81_T0.086460.787
30_I33_M0.086310.786
75_F85_A0.086270.786
92_I96_A0.085960.783
24_L132_L0.085830.782
64_L94_I0.085720.781
99_I124_I0.085690.780
49_I57_Y0.085390.778
46_L164_Y0.085310.777
50_P84_P0.085240.776
94_I110_I0.085150.775
56_L158_G0.084680.771
76_L160_L0.084660.771
131_L137_F0.08460.770
60_P72_I0.084510.770
37_I78_G0.084510.770
41_G79_G0.084440.769
20_L86_F0.084420.769
33_M36_P0.084390.768
50_P54_A0.084290.768
52_I122_I0.084170.766
95_L125_I0.083920.764
35_F130_I0.08390.764
49_I159_I0.083730.762
63_G67_G0.083630.762
56_L118_L0.083380.759
29_G33_M0.083250.758
72_I157_L0.083170.757
121_V128_L0.083140.757
53_L115_L0.083020.756
36_P45_D0.082960.755
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
3p5nA0.958698.50.64
4hzuS0.899498.40.648
4huqS0.940898.20.669
3rlbA0.976397.90.699
4dveA0.9822930.819
2ksfA0.532515.80.906
2zjsY0.9293.40.929
3dl8G0.91723.30.93
3hd7B0.23672.80.932
2losA0.71012.90.932
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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