GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ThiW - Thiamine-precursor transporter protein (ThiW)
Pfam: PF09512 (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: 150
Sequences: 2872
Seq/Len: 19.15
HH_delta: 0.233 (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
14_L34_I0.797583.511
43_G47_A0.766843.375
43_G80_G0.754453.321
38_A50_M0.644692.838
4_A46_Y0.640472.819
44_P84_R0.60752.674
11_G51_A0.57972.552
55_S69_F0.507262.233
48_V77_L0.45211.990
7_L38_A0.43061.895
63_T66_L0.416591.834
44_P77_L0.391791.724
29_P32_H0.390481.719
75_G108_S0.377651.662
63_T68_A0.366021.611
15_S54_T0.354571.561
47_A80_G0.349861.540
71_G75_G0.346651.526
128_P131_I0.344671.517
48_V73_M0.340671.499
51_A76_A0.335851.478
64_G68_A0.335351.476
77_L81_L0.335041.475
120_A124_F0.32711.440
38_A42_L0.320141.409
141_Y145_K0.308781.359
108_S112_A0.304751.341
45_W48_V0.301811.328
109_Y112_A0.30151.327
8_I50_M0.301071.325
65_T68_A0.297511.309
40_V144_L0.296241.304
2_T5_A0.289311.273
109_Y133_T0.287821.267
74_F111_V0.287271.264
65_T69_F0.284591.253
88_K91_A0.284331.251
71_G111_V0.282211.242
95_G99_G0.277281.220
55_S73_M0.276231.216
4_A50_M0.274511.208
52_F73_M0.273131.202
122_L127_P0.270741.192
37_I41_L0.267771.179
42_L46_Y0.263191.158
15_S58_R0.262631.156
134_L138_I0.262041.153
5_A9_A0.25991.144
123_F127_P0.259451.142
106_L110_P0.258571.138
10_L34_I0.25651.129
115_F125_F0.254651.121
3_L7_L0.254491.120
58_R61_L0.253481.116
11_G54_T0.252831.113
12_V15_S0.249051.096
30_M33_M0.248061.092
32_H35_N0.244541.076
29_P72_S0.244321.075
49_A52_F0.241911.065
54_T58_R0.241561.063
45_W84_R0.237791.047
8_I12_V0.236271.040
93_A138_I0.236091.039
11_G34_I0.228851.007
36_V39_A0.228511.006
142_I146_A0.227561.002
74_F77_L0.227371.001
2_T6_M0.226390.996
28_F132_S0.225970.995
138_I142_I0.225280.992
2_T10_L0.224350.987
8_I53_I0.2210.973
51_A55_S0.218350.961
15_S31_Q0.217780.959
39_A47_A0.217080.955
11_G38_A0.216480.953
111_V114_L0.216360.952
82_L95_G0.215180.947
96_E137_A0.212670.936
31_Q58_R0.212050.933
55_S72_S0.211470.931
36_V79_A0.210680.927
62_G66_L0.209440.922
112_A115_F0.205360.904
40_V96_E0.203410.895
8_I11_G0.202690.892
33_M139_I0.200950.884
48_V51_A0.200780.884
61_L65_T0.200670.883
44_P81_L0.199140.877
63_T117_G0.198750.875
129_F132_S0.198430.873
44_P80_G0.197940.871
61_L66_L0.196930.867
132_S136_G0.196420.865
4_A49_A0.195170.859
137_A141_Y0.194790.857
85_K97_V0.194320.855
16_P19_S0.193570.852
29_P54_T0.192950.849
12_V57_I0.192870.849
129_F136_G0.191910.845
42_L50_M0.190460.838
107_L111_V0.190070.837
82_L98_I0.189730.835
70_P74_F0.189460.834
43_G46_Y0.189180.833
36_V75_G0.188350.829
143_L146_A0.188240.829
11_G35_N0.187180.824
90_W94_L0.186530.821
39_A44_P0.185570.817
69_F72_S0.184580.812
4_A8_I0.183010.806
79_A99_G0.182930.805
74_F78_L0.182470.803
81_L85_K0.182040.801
78_L107_L0.181090.797
96_E99_G0.179920.792
113_K116_M0.179770.791
35_N51_A0.179560.790
36_V140_G0.177940.783
107_L112_A0.17710.780
109_Y126_V0.176860.778
100_T137_A0.176840.778
28_F32_H0.176720.778
37_I147_L0.17570.773
32_H132_S0.173560.764
54_T61_L0.173360.763
7_L41_L0.173040.762
5_A13_V0.172920.761
130_L134_L0.171890.757
108_S132_S0.170780.752
54_T72_S0.169540.746
136_G140_G0.16930.745
26_K29_P0.169190.745
127_P131_I0.169050.744
4_A42_L0.16880.743
87_K90_W0.167290.736
118_K121_A0.166780.734
58_R72_S0.165030.726
94_L142_I0.164620.725
40_V83_Y0.164410.724
12_V16_P0.164340.723
135_I138_I0.163960.722
93_A97_V0.163510.720
33_M140_G0.163220.718
125_F129_F0.162710.716
55_S58_R0.162520.715
28_F75_G0.161410.710
92_A96_E0.161110.709
26_K129_F0.160380.706
91_A94_L0.160290.706
119_E123_F0.160280.705
15_S29_P0.15980.703
31_Q72_S0.159180.701
131_I134_L0.158830.699
32_H136_G0.158330.697
76_A80_G0.158150.696
89_L92_A0.157410.693
79_A83_Y0.156780.690
73_M78_L0.156650.689
36_V137_A0.15560.685
33_M143_L0.155530.685
2_T136_G0.155410.684
59_N66_L0.15520.683
92_A145_K0.155140.683
93_A117_G0.154660.681
124_F128_P0.154330.679
77_L84_R0.153930.678
8_I57_I0.153180.674
25_A129_F0.152980.673
127_P130_L0.152680.672
17_F20_I0.152460.671
89_L139_I0.152390.671
97_V106_L0.152020.669
35_N55_S0.151760.668
32_H100_T0.151350.666
110_P123_F0.151270.666
54_T59_N0.150940.664
31_Q55_S0.150770.664
52_F69_F0.150370.662
19_S29_P0.149910.660
37_I144_L0.149290.657
56_L59_N0.148880.655
86_T91_A0.148270.653
54_T69_F0.147940.651
118_K122_L0.14790.651
90_W93_A0.147550.649
33_M41_L0.146550.645
35_N39_A0.146310.644
19_S116_M0.145620.641
15_S32_H0.14430.635
23_G129_F0.143980.634
46_Y49_A0.143920.633
107_L114_L0.143620.632
60_L93_A0.143580.632
23_G113_K0.143440.631
97_V100_T0.143230.630
84_R139_I0.142540.627
79_A96_E0.142450.627
93_A96_E0.142430.627
71_G74_F0.142320.626
14_L28_F0.142090.625
125_F128_P0.142040.625
46_Y50_M0.142020.625
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
4huqS0.973399.80.233
4hzuS0.986799.70.263
3p5nA0.993399.70.274
4dveA0.986799.60.354
3rlbA0.9899.30.467
2ksfA0.586718.90.897
4gc0A0.87332.20.931
2v50A0.822.10.932
3w9iA0.81.80.934
4g1uA0.921.60.937

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