GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF2202 - Uncharacterized protein domain (DUF2202)
Pfam: PF09968 (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: CL0044
Length: 162
Sequences: 3021
Seq/Len: 18.65
HH_delta: 0.336 (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_E91_K0.771452.825
44_A122_N0.763282.795
9_R49_L0.666682.441
38_E41_H0.582872.134
85_S88_D0.56782.079
49_L54_L0.541011.981
127_S130_H0.511531.873
87_E138_L0.485481.778
16_R39_Q0.475241.740
101_I105_E0.474331.737
12_E41_H0.463291.696
11_E103_D0.441451.616
94_A135_V0.432491.584
8_M104_L0.427781.566
5_L45_V0.424941.556
108_L124_R0.405081.483
36_R39_Q0.4031.476
94_A131_L0.384691.409
132_R136_R0.384031.406
106_E110_R0.382681.401
10_E14_L0.381051.395
29_P33_N0.379371.389
105_E124_R0.377341.382
99_L103_D0.375951.377
108_L121_E0.375871.376
95_L98_E0.375561.375
38_E130_H0.372491.364
102_A106_E0.36891.351
45_V123_L0.366591.342
13_K42_M0.359881.318
91_K95_L0.335081.227
4_G107_A0.334171.224
118_T121_E0.332961.219
9_R42_M0.326951.197
94_A98_E0.325191.191
41_H127_S0.324861.190
100_D127_S0.324621.189
12_E97_E0.323031.183
41_H130_H0.319821.171
84_K88_D0.31631.158
101_I131_L0.31421.151
41_H97_E0.314141.150
8_M103_D0.313021.146
101_I124_R0.312341.144
20_L39_Q0.311871.142
24_E46_K0.309891.135
92_V95_L0.307171.125
97_E130_H0.303641.112
104_L127_S0.301541.104
88_D91_K0.30121.103
7_Y103_D0.300271.100
48_L116_I0.300121.099
39_Q43_D0.297731.090
40_R44_A0.291581.068
121_E125_R0.291371.067
133_A136_R0.289961.062
30_I34_I0.288611.057
96_I104_L0.287581.053
30_I33_N0.284511.042
4_G110_R0.284471.042
43_D47_A0.282181.033
5_L49_L0.281791.032
118_T122_N0.279831.025
15_A18_V0.277861.017
24_E43_D0.271930.996
106_E109_A0.271860.995
99_L102_A0.268980.985
6_L54_L0.26830.982
117_K121_E0.268270.982
37_S41_H0.263110.963
37_S127_S0.262740.962
112_D117_K0.262570.961
31_F93_G0.261850.959
20_L35_A0.255050.934
113_N116_I0.254890.933
48_L119_V0.25380.929
23_Y32_N0.253410.928
38_E97_E0.252510.925
12_E127_S0.252180.923
111_T117_K0.25180.922
107_A120_Y0.251750.922
8_M120_Y0.250760.918
29_P40_R0.250020.916
45_V119_V0.249940.915
12_E38_E0.249630.914
36_R43_D0.247280.905
13_K17_D0.24690.904
23_Y35_A0.246250.902
30_I137_Q0.244430.895
12_E130_H0.243370.891
50_E54_L0.238350.873
32_N35_A0.23830.873
6_L49_L0.237930.871
118_T125_R0.23510.861
91_K138_L0.229820.842
43_D46_K0.229620.841
8_M45_V0.229610.841
51_K115_D0.227370.833
11_E100_D0.22720.832
31_F89_A0.224420.822
96_I99_L0.22430.821
94_A138_L0.221070.809
19_Y97_E0.219970.805
131_L134_F0.219690.804
44_A126_G0.219220.803
34_I130_H0.218530.800
15_A38_E0.216740.794
10_E89_A0.21520.788
35_A39_Q0.215090.788
95_L99_L0.213440.782
82_G88_D0.211850.776
100_D123_L0.211060.773
109_A112_D0.209990.769
103_D107_A0.209490.767
109_A117_K0.208830.765
114_E117_K0.208820.765
5_L48_L0.207870.761
25_K82_G0.206870.758
17_D58_V0.205310.752
133_A137_Q0.204880.750
20_L23_Y0.203620.746
28_L32_N0.20320.744
4_G103_D0.202670.742
33_N133_A0.202270.741
29_P32_N0.200990.736
22_L93_G0.200860.735
122_N125_R0.200060.733
34_I134_F0.196850.721
127_S131_L0.196350.719
44_A119_V0.195890.717
9_R14_L0.195870.717
16_R20_L0.195790.717
114_E118_T0.194230.711
98_E131_L0.192980.707
32_N36_R0.192370.704
48_L52_Y0.192360.704
84_K92_V0.188310.690
15_A126_G0.188130.689
27_G32_N0.187540.687
94_A134_F0.185720.680
4_G7_Y0.185030.678
90_L134_F0.184110.674
4_G8_M0.183360.671
11_E15_A0.182630.669
37_S40_R0.182580.669
27_G114_E0.180830.662
37_S126_G0.18080.662
9_R45_V0.180450.661
28_L34_I0.180430.661
101_I123_L0.178690.654
11_E99_L0.178340.653
12_E19_Y0.178070.652
30_I133_A0.177690.651
17_D21_T0.176950.648
8_M100_D0.17660.647
134_F137_Q0.174820.640
131_L135_V0.17420.638
25_K89_A0.173910.637
31_F90_L0.173150.634
107_A110_R0.172580.632
14_L18_V0.171950.630
103_D106_E0.171390.628
121_E124_R0.171170.627
26_W86_L0.170660.625
111_T135_V0.170560.625
104_L130_H0.169780.622
123_L130_H0.167680.614
115_D118_T0.16650.610
16_R35_A0.16590.607
33_N40_R0.16550.606
48_L51_K0.165460.606
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
3q4oA199.80.336
2oh3A0.944499.60.429
4am5A0.882799.60.455
2fzfA0.919899.50.462
1vjxA0.839599.50.474
3unoA0.907499.50.487
1eumA0.907499.50.491
1s3qA0.907499.40.493
1krqA0.907499.40.498
3qb9A0.901299.40.501

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