GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ROK - ROK family
Pfam: PF00480 (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: CL0108
Length: 179
Sequences: 6375
Seq/Len: 35.61
HH_delta: 0.035 (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
98_E141_R1.206573.287
15_D19_E1.190113.242
40_A90_R1.111653.028
82_P85_E1.08422.954
105_A132_G1.014592.764
104_A122_Y0.95842.611
164_C169_C0.956172.605
98_E103_A0.889652.424
105_A134_I0.826162.251
85_E89_E0.799042.177
98_E102_N0.795222.166
24_E45_R0.786292.142
114_A120_F0.785922.141
84_K88_E0.775612.113
135_I140_Y0.766762.089
11_I42_L0.755832.059
162_C169_C0.743792.026
64_D67_K0.68821.875
37_D90_R0.674021.836
81_I86_E0.665621.813
58_S103_A0.646511.761
161_P167_R0.63851.739
86_E89_E0.621561.693
109_Y120_F0.614681.674
162_C165_G0.606561.652
129_I174_A0.593111.616
8_S176_G0.583431.589
55_I91_F0.574151.564
1_G56_G0.572551.560
118_D136_N0.565731.541
152_H164_C0.56541.540
142_G147_A0.556521.516
22_Y46_L0.537251.464
2_I11_I0.534771.457
108_E112_G0.527221.436
121_L133_I0.526411.434
55_I93_V0.526291.434
152_H169_C0.525451.431
31_S34_E0.52191.422
160_E173_Y0.515771.405
99_N149_E0.512591.396
12_A20_I0.508061.384
101_A124_Y0.507391.382
6_G127_T0.503561.372
29_P38_A0.501371.366
120_F134_I0.500091.362
119_N135_I0.49271.342
44_E90_R0.492441.341
8_S25_S0.491961.340
11_I46_L0.491461.339
82_P86_E0.488131.330
40_A91_F0.482571.315
14_V20_I0.473951.291
5_G127_T0.472851.288
119_N140_Y0.471681.285
152_H162_C0.468551.276
44_E91_F0.466731.271
36_L86_E0.466081.270
131_A150_I0.463771.263
24_E49_D0.462881.261
22_Y49_D0.457851.247
40_A44_E0.457541.246
24_E42_L0.456191.243
117_C120_F0.45571.241
169_C172_T0.453511.235
88_E95_V0.431141.174
87_L95_V0.42821.166
133_I148_G0.420361.145
109_Y134_I0.41861.140
86_E90_R0.417231.137
112_G116_D0.416171.134
105_A120_F0.416151.134
3_D7_T0.415521.132
62_I73_S0.411521.121
10_R176_G0.408291.112
57_I87_L0.407371.110
2_I43_I0.404231.101
54_G94_P0.404191.101
102_N139_I0.403861.100
156_D159_G0.403441.099
13_L46_L0.403021.098
121_L131_A0.401991.095
38_A41_E0.385661.051
7_T127_T0.376751.026
1_G12_A0.375341.022
37_D41_E0.373241.017
101_A132_G0.372291.014
56_G103_A0.3721.013
112_G115_K0.370211.009
64_D71_I0.369981.008
9_I28_T0.369681.007
26_I41_E0.369031.005
128_G149_E0.368041.003
119_N143_S0.366030.997
11_I24_E0.362550.988
155_V170_L0.362120.986
6_G100_D0.35730.973
36_L90_R0.357170.973
105_A122_Y0.357090.973
26_I45_R0.355160.968
26_I38_A0.352440.960
129_I170_L0.351340.957
2_I55_I0.349180.951
41_E45_R0.348980.951
165_G169_C0.34830.949
10_R25_S0.346080.943
102_N149_E0.343830.937
122_Y126_G0.342940.934
100_D127_T0.342640.933
88_E92_G0.337930.921
26_I42_L0.33470.912
3_D6_G0.334250.911
30_T34_E0.32850.895
69_R82_P0.327650.893
3_D127_T0.326470.889
142_G148_G0.323580.881
34_E37_D0.32340.881
2_I39_L0.323160.880
171_E175_S0.320160.872
87_L91_F0.318690.868
4_I9_I0.317680.865
109_Y137_G0.316710.863
160_E172_T0.316570.862
99_N128_G0.315980.861
133_I140_Y0.315970.861
15_D21_I0.315280.859
32_P78_W0.314270.856
104_A124_Y0.314030.855
4_I59_V0.312640.852
4_I39_L0.312190.850
35_L78_W0.311940.850
45_R49_D0.308730.841
60_P75_N0.307170.837
78_W81_I0.307070.837
32_P86_E0.306440.835
100_D130_G0.305250.832
54_G96_I0.30440.829
44_E48_A0.303740.827
12_A23_S0.303430.827
59_V63_V0.303040.826
128_G151_G0.302260.823
33_E86_E0.301060.820
42_L45_R0.299470.816
59_V70_I0.296830.809
5_G126_G0.296730.808
84_K95_V0.296660.808
10_R23_S0.294370.802
84_K97_I0.292750.797
11_I26_I0.292490.797
33_E37_D0.291980.795
42_L46_L0.291210.793
89_E92_G0.291190.793
41_E44_E0.289770.789
175_S178_A0.289460.789
156_D173_Y0.28860.786
162_C172_T0.286870.781
63_V70_I0.286760.781
123_L131_A0.285110.777
62_I146_F0.282280.769
20_I23_S0.281550.767
125_I175_S0.280920.765
47_L93_V0.279840.762
156_D160_E0.278960.760
166_N169_C0.276010.752
159_G173_Y0.275930.752
1_G58_S0.275920.752
3_D176_G0.274510.748
6_G124_Y0.274220.747
3_D99_N0.273550.745
164_C168_G0.272590.743
4_I35_L0.271390.739
85_E88_E0.271270.739
165_G168_G0.269570.734
3_D10_R0.268530.732
6_G126_G0.267460.729
47_L50_Y0.266440.726
106_L109_Y0.265890.724
153_M170_L0.265670.724
154_P157_P0.265550.723
34_E38_A0.261480.712
125_I176_G0.261010.711
118_D137_G0.259010.706
99_N124_Y0.255940.697
101_A130_G0.255650.696
44_E47_L0.255190.695
159_G168_G0.254990.695
5_G8_S0.254750.694
102_N147_A0.252070.687
164_C172_T0.251870.686
3_D58_S0.251040.684
162_C166_N0.250150.681
128_G171_E0.250.681
100_D124_Y0.248120.676
119_N133_I0.244350.666
123_L150_I0.244160.665
154_P166_N0.243550.663
7_T176_G0.240940.656
150_I170_L0.23990.654
114_A117_C0.239510.652
39_L87_L0.239380.652
113_A116_D0.238790.651
13_L50_Y0.238310.649
5_G176_G0.237660.647
100_D128_G0.236030.643
3_D124_Y0.235540.642
14_V18_G0.234950.640
170_L174_A0.234770.640
172_T177_R0.233730.637
132_G135_I0.233370.636
43_I55_I0.233060.635
99_N130_G0.232870.634
40_A86_E0.231470.631
162_C168_G0.231280.630
160_E167_R0.229040.624
72_S79_E0.228420.622
32_P57_I0.226970.618
135_I138_K0.226780.618
165_G172_T0.225840.615
130_G149_E0.225580.615
102_N148_G0.224970.613
170_L179_L0.224110.611
54_G93_V0.221660.604
105_A109_Y0.221520.603
19_E45_R0.221270.603
5_G10_R0.220230.600
45_R48_A0.21970.598
13_L21_I0.218420.595
22_Y50_Y0.21810.594
106_L110_W0.21640.590
28_T35_L0.215560.587
159_G167_R0.215160.586
100_D176_G0.213110.581
2_I9_I0.212360.579
63_V97_I0.212090.578
18_G110_W0.211880.577
92_G95_V0.2110.575
69_R80_N0.210760.574
65_S141_R0.210580.574
134_I139_I0.209770.571
38_A42_L0.208490.568
41_E161_P0.20680.563
107_A169_C0.206340.562
104_A107_A0.205920.561
9_I26_I0.205770.561
57_I83_L0.205360.559
149_E152_H0.204430.557
36_L40_A0.2040.556
102_N130_G0.202810.552
5_G100_D0.202720.552
111_F115_K0.202360.551
126_G176_G0.201780.550
102_N141_R0.201280.548
106_L134_I0.201260.548
152_H165_G0.200320.546
109_Y117_C0.199680.544
159_G162_C0.19870.541
32_P81_I0.19680.536
98_E106_L0.19650.535
158_N161_P0.196420.535
3_D8_S0.196280.535
144_N147_A0.196280.535
116_D137_G0.195140.532
3_D122_Y0.195090.531
60_P100_D0.194890.531
55_I95_V0.194650.530
101_A131_A0.194650.530
88_E94_P0.194580.530
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
3vglA11000.035
1z05A11000.063
4db3A11000.072
1z6rA11000.079
3htvA0.99441000.084
3vovA0.99441000.087
2yhwA11000.091
2hoeA0.98321000.094
2qm1A11000.099
3epqA0.95531000.104

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