GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SBF - Sodium Bile acid symporter family
Pfam: PF01758 (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: CL0064
Length: 187
Sequences: 3051
Seq/Len: 16.32
HH_delta: 0.097 (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
9_F144_L0.949255.512
79_T84_G0.534013.101
9_F140_L0.427582.483
37_Q71_G0.407552.366
68_A107_L0.397342.307
38_F103_L0.353622.053
19_D22_R0.347952.020
21_R25_R0.347172.016
35_L39_L0.341091.980
79_T89_S0.332491.931
142_M146_K0.329761.915
22_R25_R0.313391.820
125_D128_K0.299031.736
18_E21_R0.286861.666
16_T19_D0.270711.572
31_L35_L0.270481.570
143_L147_Y0.26281.526
124_W128_K0.25671.490
45_A67_A0.255061.481
34_L99_L0.253851.474
148_L153_F0.250921.457
139_L143_L0.250091.452
49_A60_A0.238961.387
144_L157_L0.238551.385
116_V119_D0.238381.384
72_G75_S0.23551.367
103_L107_L0.235421.367
47_G51_L0.234831.363
71_G93_T0.232951.353
76_N93_T0.232631.351
38_F96_S0.231381.343
26_R85_D0.230761.340
107_L111_L0.228841.329
100_A104_M0.22741.320
8_M12_G0.225721.311
18_E22_R0.219621.275
156_R160_F0.21931.273
143_L146_K0.218161.267
131_L136_L0.217761.264
154_A158_K0.214761.247
12_G141_G0.213671.241
80_Y83_G0.213191.238
71_G75_S0.212061.231
33_G92_L0.210011.219
91_S94_L0.209861.219
27_P31_L0.209361.216
145_R155_R0.208031.208
61_L112_S0.207571.205
46_F51_L0.204341.186
103_L106_L0.200821.166
169_L180_N0.200471.164
43_L47_G0.198281.151
36_A40_I0.196571.141
37_Q93_T0.194981.132
39_L43_L0.194241.128
34_L95_I0.193951.126
61_L108_L0.19361.124
132_L136_L0.193361.123
149_P153_F0.193181.122
90_V134_V0.193121.121
153_F156_R0.191181.110
73_P78_F0.190191.104
140_L144_L0.188761.096
164_L168_L0.18831.093
4_L8_M0.188021.092
62_G137_P0.188011.092
155_R158_K0.187661.090
49_A52_L0.186241.081
71_G97_T0.185971.080
149_P154_A0.183791.067
54_P57_P0.183121.063
6_L164_L0.182761.061
87_A90_V0.182621.060
119_D125_D0.181241.052
13_L134_V0.180151.046
127_I131_L0.178741.038
41_M67_A0.177991.033
15_L87_A0.177621.031
71_G92_L0.177511.031
124_W131_L0.17751.031
65_L104_M0.177451.030
3_L171_L0.174661.014
13_L99_L0.173791.009
80_Y86_V0.17341.007
64_L69_C0.172271.000
144_L148_L0.1720.999
8_M11_M0.171670.997
21_R24_L0.171150.994
109_Y115_S0.17110.993
33_G37_Q0.171030.993
32_I36_A0.170960.993
35_L40_I0.17050.990
70_P105_P0.170140.988
152_K156_R0.169220.983
72_G97_T0.169080.982
169_L176_I0.168990.981
106_L109_Y0.168160.976
72_G76_N0.16570.962
123_P127_I0.165550.961
152_K157_L0.165260.960
60_A63_L0.165240.959
105_P137_P0.163290.948
99_L103_L0.162250.942
104_M107_L0.16210.941
84_G137_P0.161830.940
49_A59_L0.160470.932
105_P113_G0.159860.928
37_Q75_S0.159840.928
11_M77_V0.158350.919
29_L88_L0.158120.918
16_T145_R0.157780.916
49_A64_L0.157730.916
6_L168_L0.156340.908
37_Q96_S0.155930.905
78_F176_I0.155340.902
165_S172_I0.155180.901
46_F49_A0.155150.901
78_F81_L0.155090.900
65_L131_L0.155030.900
37_Q76_N0.154290.896
173_I176_I0.154210.895
22_R26_R0.153760.893
159_P163_P0.153050.889
111_L115_S0.152440.885
7_M78_F0.151960.882
153_F157_L0.150760.875
83_G86_V0.150550.874
37_Q92_L0.150440.873
80_Y166_F0.150210.872
56_S59_L0.149830.870
60_A64_L0.149580.869
162_K178_A0.149550.868
7_M12_G0.148810.864
43_L111_L0.148610.863
41_M72_G0.14720.855
9_F13_L0.146570.851
75_S89_S0.146120.848
99_L153_F0.145960.847
152_K155_R0.144970.842
11_M90_V0.144780.841
8_M71_G0.144560.839
40_I44_L0.144390.838
63_L66_V0.144130.837
41_M45_A0.143520.833
161_L164_L0.14350.833
9_F12_G0.143150.831
162_K165_S0.142770.829
70_P84_G0.142720.829
157_L161_L0.14250.827
17_F146_K0.14180.823
149_P156_R0.141310.820
128_K132_L0.141060.819
175_L179_S0.140830.818
126_I130_L0.140620.816
7_M74_A0.140580.816
27_P142_M0.139110.808
7_M73_P0.138290.803
54_P60_A0.137890.801
56_S60_A0.137550.799
71_G78_F0.137280.797
136_L140_L0.137050.796
20_L91_S0.136740.794
140_L155_R0.136580.793
66_V180_N0.136160.791
19_D87_A0.135460.787
143_L167_I0.135450.786
147_Y152_K0.135010.784
76_N89_S0.134960.784
172_I176_I0.134930.783
96_S100_A0.134890.783
31_L103_L0.134770.783
148_L152_K0.133970.778
170_L175_L0.13390.777
136_L159_P0.133820.777
138_L144_L0.133240.774
63_L161_L0.132540.770
128_K131_L0.132540.770
47_G52_L0.13230.768
90_V93_T0.132290.768
100_A134_V0.131720.765
17_F20_L0.131520.764
157_L160_F0.131330.763
160_F163_P0.130930.760
63_L173_I0.130880.760
69_C73_P0.130760.759
69_C104_M0.130750.759
75_S96_S0.130620.758
29_L32_I0.130450.757
59_L62_G0.130370.757
46_F135_I0.130260.756
169_L172_I0.130240.756
34_L91_S0.129890.754
73_P169_L0.129560.752
12_G74_A0.129480.752
130_L135_I0.129470.752
15_L83_G0.129260.751
153_F158_K0.129130.750
59_L79_T0.128830.748
56_S99_L0.128770.748
57_P117_D0.128620.747
24_L98_L0.128560.746
149_P152_K0.128490.746
44_L47_G0.128440.746
11_M134_V0.128240.745
134_V166_F0.12810.744
45_A93_T0.127750.742
22_R87_A0.127510.740
21_R119_D0.127220.739
4_L11_M0.12720.739
17_F21_R0.126850.737
69_C100_A0.126820.736
8_M97_T0.126720.736
82_A104_M0.126580.735
26_R29_L0.126560.735
86_V90_V0.126460.734
143_L148_L0.126160.733
110_L113_G0.126080.732
171_L174_V0.125680.730
91_S95_I0.1250.726
5_F136_L0.124930.725
77_V165_S0.124870.725
174_V178_A0.124850.725
163_P171_L0.124710.724
119_D146_K0.12470.724
78_F170_L0.124690.724
55_L107_L0.124670.724
167_I171_L0.124510.723
49_A53_L0.124320.722
48_L53_L0.124290.722
147_Y167_I0.12380.719
155_R159_P0.123730.718
10_S71_G0.123660.718
22_R27_P0.123490.717
20_L158_K0.123180.715
23_V91_S0.123160.715
58_A62_G0.123030.714
74_A169_L0.122790.713
169_L173_I0.122430.711
6_L23_V0.122370.711
134_V138_L0.122110.709
160_F164_L0.121990.708
69_C75_S0.121110.703
71_G89_S0.121090.703
15_L90_V0.120440.699
7_M10_S0.120310.699
14_S158_K0.12020.698
41_M70_P0.119990.697
51_L155_R0.119920.696
9_F143_L0.119750.695
155_R160_F0.119680.695
25_R31_L0.119670.695
6_L163_P0.119620.695
21_R54_P0.119530.694
99_L133_I0.119080.691
101_P127_I0.118950.691
65_L91_S0.118260.687
119_D123_P0.118080.686
11_M135_I0.118050.685
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
3zuxA0.96791000.097
2kv5A0.176514.30.928
2fyuK0.23539.60.933
3w9iA0.80218.50.934
3ne5A0.74876.50.938
4b19A0.160440.943
4dx5A0.844930.946
1zcdA0.75941.90.951
4huqS0.80211.70.953
1iijA0.18721.60.953

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