GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GatB_Yqey - GatB domain
Pfam: PF02637 (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: CL0279
Length: 148
Sequences: 1776
Seq/Len: 12
HH_delta: -0.032 (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
99_E147_K1.086413.780
100_E130_E0.9163.187
97_L131_T0.742532.583
95_E147_K0.74012.575
100_E104_E0.732842.550
95_E146_E0.710842.473
51_L80_I0.698952.432
74_K82_E0.695382.419
119_A123_L0.691822.407
142_E146_E0.688612.396
6_V16_A0.679522.364
47_E77_E0.667682.323
81_E86_W0.636772.215
78_E82_E0.611872.129
68_E83_N0.560481.950
96_A100_E0.557751.940
47_E75_S0.557671.940
127_V140_V0.552921.924
57_I61_S0.539781.878
108_E119_A0.528961.840
99_E103_A0.500421.741
108_E111_D0.481771.676
124_V141_K0.472671.644
5_E43_E0.464051.614
68_E72_N0.442721.540
24_L38_S0.440611.533
104_E130_E0.436191.518
75_S78_E0.424651.477
108_E123_L0.423921.475
139_E142_E0.412531.435
106_P110_E0.408331.421
65_L79_I0.404041.406
110_E114_N0.39991.391
87_Q136_D0.39171.363
111_D119_A0.390891.360
31_K71_E0.390121.357
27_L67_R0.388841.353
120_I144_L0.379891.322
117_K145_K0.379641.321
91_E139_E0.374141.302
5_E8_K0.373611.300
120_I145_K0.370911.290
56_K86_W0.367861.280
123_L144_L0.358171.246
93_E96_A0.355811.238
48_L69_L0.35491.235
34_D37_D0.347281.208
77_E81_E0.345231.201
47_E76_P0.339851.182
51_L76_P0.336711.171
107_K111_D0.336531.171
128_M133_G0.33581.168
27_L70_L0.333531.160
91_E95_E0.33311.159
33_L37_D0.33181.154
69_L76_P0.330031.148
6_V49_I0.324861.130
98_V143_L0.323841.127
74_K78_E0.31941.111
19_W62_A0.319331.111
10_G16_A0.319311.111
23_E63_K0.313441.090
97_L101_V0.312571.087
14_K18_N0.309511.077
79_I83_N0.307961.071
50_N54_D0.307721.071
51_L77_E0.307151.069
15_L53_E0.307081.068
135_A140_V0.30681.067
27_L31_K0.304251.059
95_E143_L0.299691.043
7_V10_G0.299431.042
95_E99_E0.299111.041
98_V147_K0.296181.030
12_N53_E0.290661.011
41_S44_H0.288041.002
6_V42_P0.288011.002
122_F126_Q0.283650.987
141_K145_K0.281270.979
121_G124_V0.278540.969
112_Y145_K0.27660.962
58_S87_Q0.275920.960
44_H73_G0.275290.958
101_V127_V0.273280.951
47_E50_N0.271390.944
110_E113_R0.266370.927
94_L131_T0.261010.908
111_D123_L0.256720.893
22_N26_G0.256540.893
105_N126_Q0.256530.892
119_A122_F0.255710.890
121_G141_K0.253690.883
26_G30_K0.253080.880
94_L134_R0.250560.872
102_I109_V0.249560.868
117_K120_I0.249250.867
31_K70_L0.247330.860
107_K110_E0.247170.860
28_L38_S0.246060.856
39_P70_L0.244890.852
127_V131_T0.242260.843
116_K119_A0.240840.838
17_A21_L0.239720.834
105_N122_F0.238250.829
138_K142_E0.237970.828
90_D93_E0.237930.828
1_D5_E0.237620.827
60_K64_E0.237150.825
27_L30_K0.236980.824
6_V46_A0.235270.819
44_H76_P0.234760.817
22_N25_L0.234250.815
11_K16_A0.2310.804
101_V123_L0.230970.804
127_V135_A0.230660.802
101_V126_Q0.230420.802
59_K63_K0.229790.799
102_I106_P0.228930.796
2_Y35_I0.228230.794
74_K79_I0.227250.791
112_Y122_F0.227250.791
65_L80_I0.223990.779
69_L74_K0.222550.774
78_E81_E0.222190.773
54_D77_E0.220620.768
96_A99_E0.220060.766
23_E27_L0.220060.766
112_Y117_K0.21920.763
40_I70_L0.217610.757
112_Y148_L0.217530.757
126_Q129_K0.217310.756
112_Y120_I0.21720.756
76_P80_I0.216640.754
19_W63_K0.215190.749
9_K43_E0.2140.745
109_V112_Y0.213360.742
109_V113_R0.213180.742
88_I131_T0.213130.742
48_L66_L0.213030.741
44_H75_S0.212930.741
102_I148_L0.212850.741
80_I86_W0.212250.738
22_N29_N0.208010.724
23_E26_G0.203990.710
21_L25_L0.203760.709
52_L57_I0.20330.707
111_D116_K0.203220.707
61_S85_L0.201030.699
109_V123_L0.20.696
108_E122_F0.199620.694
97_L127_V0.198290.690
6_V20_I0.197380.687
102_I147_K0.196740.684
51_L56_K0.196150.682
131_T135_A0.195420.680
67_R71_E0.195040.679
64_E83_N0.19450.677
92_E96_A0.194130.675
24_L40_I0.194010.675
4_E8_K0.193030.672
68_E71_E0.192640.670
2_Y24_L0.191520.666
94_L143_L0.190710.664
93_E97_L0.18960.660
10_G49_I0.18850.656
105_N108_E0.188070.654
69_L79_I0.187580.653
108_E116_K0.187210.651
18_N23_E0.187040.651
69_L72_N0.186740.650
5_E42_P0.18610.647
45_L49_I0.185370.645
143_L146_E0.185220.644
89_S94_L0.185210.644
7_V16_A0.184670.642
61_S83_N0.183920.640
2_Y6_V0.181220.630
3_F20_I0.180740.629
7_V13_P0.180030.626
109_V148_L0.179760.625
101_V130_E0.178560.621
60_K88_I0.177320.617
94_L135_A0.176860.615
68_E79_I0.176210.613
24_L35_I0.175840.612
35_I38_S0.175810.612
137_P141_K0.175470.610
26_G59_K0.174660.608
49_I59_K0.174360.607
89_S136_D0.174190.606
52_L59_K0.173230.603
22_N58_S0.173050.602
98_V127_V0.172990.602
5_E9_K0.172580.600
49_I53_E0.172560.600
79_I82_E0.172470.600
57_I80_I0.171520.597
58_S61_S0.171440.596
48_L65_L0.170920.595
27_L66_L0.168670.587
33_L39_P0.168020.585
125_G128_M0.166640.580
139_E146_E0.164940.574
94_L127_V0.164580.573
72_N83_N0.164580.573
49_I52_L0.164040.571
97_L100_E0.16330.568
55_G136_D0.162620.566
30_K67_R0.161570.562
23_E66_L0.161450.562
11_K46_A0.1610.560
50_N77_E0.160980.560
33_L70_L0.160890.560
92_E95_E0.160320.558
88_I94_L0.160080.557
109_V119_A0.159170.554
127_V144_L0.158720.552
55_G132_K0.158160.550
126_Q130_E0.157810.549
29_N35_I0.157140.547
112_Y119_A0.156820.546
46_A49_I0.156270.544
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
3ip4B1100-0.032
3h0lB1100-0.006
2hz7A0.9595100-0.003
3al0B11000.028
2d6fC0.95271000.191
1zq1C0.94591000.219
3kfuF0.993299.80.445
1ng6A0.885199.70.506
4h3sA0.912296.70.832
3tl4X0.912296.60.834

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