GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MacB_PCD - MacB-like periplasmic core domain
Pfam: PF12704 (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: 232
Sequences: 12699
Seq/Len: 54.74
HH_delta: 0.368 (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
163_T172_T1.251663.192
147_E178_E1.191123.038
143_I192_I1.091932.785
147_E151_K1.079382.753
142_E174_V1.032762.634
163_T170_P0.963642.457
144_V175_G0.93332.380
165_T170_P0.906932.313
129_R174_V0.880222.245
150_A176_I0.876182.234
221_D224_A0.863532.202
86_E217_K0.841892.147
142_E172_T0.835442.131
84_G228_E0.799482.039
84_G217_K0.791952.020
124_K178_E0.782621.996
145_I173_V0.77561.978
72_T75_D0.764471.950
194_I199_A0.759971.938
145_I192_I0.744371.898
143_I194_I0.740131.887
76_I80_R0.739261.885
16_I20_A0.734561.873
6_R9_K0.732341.868
216_L225_V0.720951.839
86_E215_R0.715511.825
143_I171_F0.692831.767
145_I149_L0.692231.765
226_K230_K0.687931.754
77_E80_R0.687641.754
145_I150_A0.680551.736
144_V177_V0.668891.706
84_G225_V0.663851.693
141_N198_T0.645611.646
171_F198_T0.631241.610
143_I164_I0.626981.599
223_E226_K0.623991.591
222_I226_K0.605711.545
118_F130_W0.6051.543
224_A228_E0.592071.510
144_V174_V0.588671.501
149_L153_L0.578691.476
126_I147_E0.577791.473
146_S177_V0.574961.466
227_E230_K0.566441.445
146_S149_L0.565921.443
91_S211_Q0.562911.436
87_A215_R0.562721.435
82_I228_E0.55881.425
130_W144_V0.553951.413
131_F174_V0.55061.404
78_K81_K0.548431.399
148_S179_D0.546341.393
218_D221_D0.54621.393
126_I178_E0.543951.387
196_L200_Q0.543551.386
129_R142_E0.538051.372
34_N38_S0.534931.364
31_S35_G0.534841.364
148_S151_K0.530921.354
20_A24_A0.529431.350
74_E78_K0.522451.332
125_L130_W0.522151.332
3_R6_R0.520011.326
156_S162_D0.51931.324
125_L175_G0.515191.314
155_L162_D0.512661.307
112_G199_A0.507081.293
10_G13_I0.504121.286
146_S190_P0.498691.272
15_T18_G0.49741.268
13_I17_L0.497341.268
110_I192_I0.493831.259
195_P198_T0.486171.240
113_V117_Y0.483741.234
160_I174_V0.476461.215
131_F144_V0.475821.213
116_D119_D0.475411.212
82_I225_V0.474621.210
129_R132_S0.474011.209
145_I164_I0.473571.208
223_E227_E0.466051.189
92_L199_A0.457011.165
85_V88_V0.456811.165
160_I176_I0.455391.161
19_I23_V0.454711.160
194_I198_T0.452941.155
5_L12_S0.452141.153
197_S200_Q0.452051.153
127_E160_I0.447231.141
73_E77_E0.439521.121
225_V228_E0.439111.120
88_V214_V0.435661.111
34_N37_Q0.43471.109
80_R88_V0.431081.099
154_G162_D0.430781.099
131_F142_E0.430011.097
85_V214_V0.420071.071
177_V193_F0.419071.069
75_D78_K0.418081.066
39_S43_S0.417251.064
18_G22_G0.415171.059
2_W6_R0.414091.056
148_S152_K0.405871.035
110_I194_I0.405581.034
142_E195_P0.403511.029
87_A120_V0.400411.021
145_I176_I0.399891.020
161_G172_T0.399541.019
11_R15_T0.385480.983
38_S42_R0.385240.982
24_A28_A0.384480.981
76_I88_V0.382620.976
147_E179_D0.382250.975
91_S213_Y0.380780.971
217_K221_D0.375290.957
48_G215_R0.367150.936
89_S114_D0.365310.932
30_L34_N0.361140.921
224_A227_E0.360630.920
20_A23_V0.360150.918
125_L144_V0.359330.916
10_G14_L0.357270.911
8_N11_R0.356120.908
9_K13_I0.355310.906
79_L88_V0.35180.897
79_L229_I0.350850.895
39_S42_R0.350070.893
74_E77_E0.348230.888
88_V212_I0.347710.887
37_Q41_E0.34770.887
143_I173_V0.346650.884
52_I226_K0.343650.876
89_S117_Y0.343380.876
216_L222_I0.343320.876
76_I90_P0.339280.865
87_A119_D0.337430.861
15_T29_I0.337160.860
73_E76_I0.336660.859
114_D117_Y0.336590.858
166_L171_F0.334610.853
155_L173_V0.332850.849
146_S191_S0.329280.840
9_K12_S0.329160.839
53_V56_P0.327110.834
123_I177_V0.326930.834
95_G110_I0.326840.834
147_E150_A0.324390.827
126_I177_V0.319970.816
90_P212_I0.319690.815
113_V193_F0.319120.814
199_A203_F0.318990.813
214_V229_I0.317110.809
92_L200_Q0.316060.806
220_A225_V0.315940.806
12_S16_I0.315130.804
144_V193_F0.314820.803
125_L128_G0.314440.802
90_P209_Y0.314290.802
87_A116_D0.314070.801
50_D215_R0.313570.800
85_V217_K0.313140.799
198_T201_Q0.31310.798
196_L209_Y0.312860.798
27_I31_S0.310680.792
140_E195_P0.309870.790
128_G175_G0.30940.789
76_I212_I0.307910.785
145_I155_L0.307330.784
53_V213_Y0.307230.784
77_E81_K0.307210.783
70_Q73_E0.305750.780
82_I229_I0.305740.780
30_L33_I0.305470.779
225_V229_I0.305010.778
112_G196_L0.304120.776
141_N171_F0.302870.772
173_V176_I0.302820.772
216_L220_A0.301630.769
125_L129_R0.301520.769
99_Y102_Q0.300380.766
38_S41_E0.29970.764
141_N169_Q0.297920.760
95_G167_N0.297460.759
146_S179_D0.296710.757
146_S189_D0.294170.750
71_L75_D0.293970.750
22_G25_L0.290940.742
82_I85_V0.290260.740
151_K179_D0.289620.739
92_L205_N0.287880.734
121_F213_Y0.287850.734
148_S190_P0.287650.734
15_T19_I0.286730.731
181_G189_D0.285760.729
156_S160_I0.285730.729
15_T23_V0.284590.726
147_E176_I0.284150.725
97_V106_I0.280690.716
89_S113_V0.279350.712
150_A160_I0.278290.710
48_G51_I0.277840.709
127_E176_I0.27710.707
25_L33_I0.276280.705
21_L25_L0.274160.699
51_I54_V0.274070.699
85_V225_V0.273560.698
29_I35_G0.273270.697
19_I22_G0.272340.695
37_Q40_I0.27220.694
32_L36_L0.270250.689
4_N7_R0.269820.688
128_G160_I0.269760.688
80_R87_A0.268920.686
4_N15_T0.268520.685
79_L214_V0.267990.683
117_Y121_F0.267740.683
54_V214_V0.267690.683
79_L212_I0.266290.679
120_V215_R0.265620.677
33_I37_Q0.263190.671
40_I44_I0.261690.667
22_G33_I0.2610.666
128_G176_I0.259970.663
104_E152_K0.259340.661
89_S120_V0.258930.660
111_I191_S0.258850.660
116_D120_V0.258390.659
129_R175_G0.25790.658
18_G35_G0.25410.648
114_D196_L0.254020.648
4_N11_R0.253260.646
171_F194_I0.251480.641
75_D79_L0.250940.640
14_L25_L0.250490.639
131_F175_G0.24990.637
36_L39_S0.249590.637
217_K220_A0.247580.631
127_E156_S0.247360.631
140_E172_T0.243740.622
14_L18_G0.24340.621
18_G27_I0.24320.620
142_E198_T0.241930.617
145_I154_G0.240940.614
26_L30_L0.240830.614
18_G44_I0.239480.611
84_G221_D0.238080.607
42_R45_S0.237830.607
125_L177_V0.237560.606
164_I171_F0.237540.606
97_V166_L0.23690.604
160_I175_G0.236580.603
98_S165_T0.236190.602
41_E45_S0.23590.602
12_S24_A0.235490.601
72_T76_I0.234990.599
17_L20_A0.234660.598
149_L192_I0.234120.597
90_P114_D0.232530.593
109_N191_S0.232420.593
198_T202_L0.23240.593
71_L212_I0.232070.592
177_V190_P0.23160.591
219_G222_I0.231120.589
150_A156_S0.228990.584
193_F196_L0.228990.584
127_E150_A0.227690.581
125_L178_E0.225810.576
91_S111_I0.225740.576
117_Y120_V0.225610.575
87_A90_P0.225440.575
29_I33_I0.224830.573
202_L205_N0.224060.571
11_R25_L0.222180.567
155_L164_I0.221840.566
23_V29_I0.220820.563
4_N12_S0.21940.560
23_V27_I0.217980.556
220_A224_A0.216990.553
15_T22_G0.216880.553
79_L82_I0.216580.552
96_T103_S0.216290.552
161_G164_I0.215440.549
99_Y162_D0.21440.547
196_L199_A0.214220.546
172_T175_G0.213620.545
96_T99_Y0.212950.543
205_N208_G0.212790.543
78_K82_I0.211890.540
8_N29_I0.211310.539
50_D53_V0.211210.539
51_I55_S0.211210.539
132_S174_V0.210650.537
164_I173_V0.210310.536
92_L112_G0.209950.535
106_I192_I0.209690.535
171_F202_L0.209580.534
94_F109_N0.208960.533
106_I152_K0.208640.532
151_K156_S0.208610.532
150_A173_V0.207930.530
140_E198_T0.207750.530
102_Q105_S0.207630.530
119_D130_W0.2070.528
125_L131_F0.206720.527
140_E197_S0.206190.526
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
3ftjA0.836299.70.368
3is6A0.797499.40.509
4ga6A0.418127.70.905
1zq1A0.271610.40.921
3ne5A0.95268.10.924
2j5lA0.349170.926
3keoA0.72416.70.927
3vupA0.33196.20.928
3nklA0.37936.10.928
4dx5A0.952660.928

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