GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pentaxin - Pentaxin family
Pfam: PF00354 (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: CL0004
Length: 195
Sequences: 2533
Seq/Len: 12.99
HH_delta: 0.072 (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
87_H105_D0.877325.145
157_R163_E0.705224.136
83_D87_H0.628793.688
30_C90_C0.610353.579
101_Q108_R0.520653.053
30_C167_L0.515323.022
32_W88_H0.476952.797
160_S163_E0.450312.641
34_K148_E0.392972.305
155_W159_L0.389022.281
82_R87_H0.386212.265
34_K86_W0.354572.079
33_V89_I0.344322.019
33_V44_I0.33691.976
30_C153_N0.335021.965
31_F152_F0.331981.947
35_T83_D0.32641.914
92_T158_V0.32041.879
32_W150_S0.305371.791
31_F44_I0.291751.711
26_A94_D0.28881.694
30_C159_L0.286361.679
32_W151_D0.276871.624
108_R111_S0.27591.618
35_T82_R0.270711.588
35_T87_H0.263481.545
29_V154_I0.260931.530
35_T145_F0.260131.526
128_L152_F0.254271.491
93_W98_G0.248541.458
150_S155_W0.240051.408
161_P164_I0.239691.406
30_C88_H0.238951.401
32_W86_W0.238381.398
159_L167_L0.237921.395
101_Q111_S0.237461.393
127_V130_Q0.228711.341
153_N167_L0.226881.331
34_K84_G0.225951.325
92_T103_Y0.224421.316
30_C155_W0.217231.274
91_V100_W0.216751.271
155_W167_L0.209881.231
145_F149_I0.20971.230
153_N159_L0.204851.201
33_V87_H0.203911.196
36_D146_V0.203891.196
45_F152_F0.199861.172
85_Q105_D0.199531.170
128_L149_I0.198011.161
90_C164_I0.191111.121
162_E165_R0.185591.088
83_D105_D0.183421.076
159_L163_E0.182161.068
28_T158_V0.177941.044
61_S64_G0.176311.034
16_L128_L0.174811.025
66_L89_I0.174651.024
28_T92_T0.173771.019
43_T46_S0.173141.015
159_L164_I0.172051.009
81_I87_H0.168390.988
103_Y106_G0.166640.977
86_W149_I0.1660.974
14_V18_P0.163780.960
90_C155_W0.162090.951
161_P165_R0.160020.938
91_V102_L0.160.938
29_V45_F0.156280.917
92_T101_Q0.153850.902
29_V91_V0.15360.901
86_W150_S0.153050.898
103_Y161_P0.152280.893
156_D163_E0.152170.892
155_W164_I0.151850.891
148_E155_W0.150950.885
28_T90_C0.15050.883
35_T38_S0.147480.865
148_E165_R0.14620.857
68_L91_V0.145980.856
79_G89_I0.145940.856
26_A95_S0.145310.852
15_R125_T0.14470.849
27_F93_W0.144650.848
127_V132_Q0.144280.846
86_W102_L0.142630.836
18_P47_Y0.141430.829
14_V128_L0.140580.824
19_S23_P0.140020.821
157_R160_S0.138790.814
103_Y108_R0.137260.805
89_I104_V0.137190.805
43_T155_W0.136720.802
31_F128_L0.136330.800
47_Y125_T0.136210.799
31_F89_I0.136160.799
77_F109_L0.135210.793
107_V165_R0.134310.788
32_W90_C0.133470.783
163_E166_A0.133470.783
30_C151_D0.133010.780
88_H103_Y0.132140.775
88_H105_D0.131860.773
89_I166_A0.131570.772
28_T155_W0.131050.769
118_H156_D0.130810.767
64_G77_F0.130760.767
28_T164_I0.130540.766
43_T59_F0.130280.764
88_H151_D0.130130.763
45_F56_L0.129590.760
111_S124_G0.129350.759
79_G94_D0.128220.752
28_T106_G0.128170.752
19_S22_L0.128120.751
61_S133_D0.127820.750
126_L164_I0.127480.748
48_A143_Q0.127260.746
82_R85_Q0.127210.746
90_C153_N0.127030.745
24_L27_F0.125760.738
85_Q110_S0.125510.736
32_W155_W0.125080.734
119_S122_G0.124710.731
26_A93_W0.124430.730
25_S119_S0.123740.726
90_C103_Y0.123390.724
94_D99_R0.123090.722
42_G46_S0.122510.718
78_S109_L0.122120.716
65_S74_S0.121610.713
44_I66_L0.12130.711
24_L95_S0.121050.710
54_N131_E0.120950.709
158_V164_I0.118640.696
60_G64_G0.118350.694
49_T52_Q0.117580.690
37_D42_G0.117540.689
16_L47_Y0.117470.689
52_Q119_S0.117260.688
109_L160_S0.116870.685
38_S149_I0.116840.685
28_T103_Y0.116250.682
90_C106_G0.116150.681
37_D45_F0.115910.680
48_A122_G0.115510.677
99_R111_S0.115490.677
160_S164_I0.115430.677
88_H106_G0.115320.676
51_S121_P0.114030.669
94_D98_G0.113530.666
47_Y54_N0.113490.666
13_Y127_V0.113010.663
29_V152_F0.112820.662
85_Q156_D0.112170.658
162_E166_A0.111920.656
46_S132_Q0.111480.654
45_F48_A0.110720.649
25_S153_N0.110540.648
91_V152_F0.11030.647
87_H104_V0.109810.644
17_K115_A0.109620.643
55_E143_Q0.109430.642
77_F100_W0.109170.640
120_I123_G0.109070.640
35_T68_L0.109040.639
92_T100_W0.108720.638
162_E167_L0.108690.637
79_G125_T0.107520.631
60_G111_S0.107380.630
36_D77_F0.107270.629
93_W100_W0.107010.628
29_V117_G0.106160.623
56_L130_Q0.10610.622
55_E72_G0.10560.619
90_C159_L0.105450.618
77_F102_L0.105270.617
99_R162_E0.105250.617
95_S98_G0.105160.617
34_K85_Q0.105080.616
151_D155_W0.105020.616
146_V149_I0.1050.616
15_R127_V0.104620.614
22_L44_I0.104570.613
18_P23_P0.104380.612
98_G149_I0.104380.612
55_E61_S0.104360.612
146_V154_I0.104150.611
67_R74_S0.104090.610
50_S62_S0.104090.610
121_P127_V0.103580.607
56_L61_S0.103150.605
80_P104_V0.103140.605
45_F58_L0.103070.604
60_G154_I0.1030.604
45_F154_I0.102770.603
94_D158_V0.102740.603
36_D84_G0.102490.601
109_L144_A0.102320.600
67_R78_S0.102260.600
32_W103_Y0.102250.600
24_L124_G0.101810.597
33_V145_F0.101740.597
155_W161_P0.101480.595
31_F134_S0.101320.594
122_G149_I0.100940.592
33_V81_I0.100630.590
24_L51_S0.100570.590
52_Q115_A0.100380.589
46_S126_L0.100270.588
129_G145_F0.100110.587
12_D42_G0.099880.586
119_S141_E0.099860.586
31_F149_I0.099860.586
24_L120_I0.099770.585
37_D128_L0.099650.584
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
4avsA0.99491000.072
3kqrA0.99491000.072
3pvnA11000.073
3flpA0.99491000.113
4dqaA0.928299.90.38
2sliA0.953899.60.54
2jkbA0.948799.60.541
1a8dA0.948799.50.551
3v64A0.851399.50.552
3pveA0.856499.50.56

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