GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0254 - Uncharacterised protein family (UPF0254)
Pfam: PF06787 (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: 160
Sequences: 1916
Seq/Len: 11.97
HH_delta: 0.362 (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
86_A106_T1.263143.446
2_I101_I1.051582.869
15_I105_T1.011442.759
70_V88_L0.996822.720
63_E88_L0.904082.467
70_V85_V0.902342.462
83_L87_K0.830372.265
64_P72_K0.803892.193
5_A99_C0.786982.147
12_H20_H0.786732.146
57_E64_P0.751252.050
18_E148_I0.706631.928
139_N142_E0.682121.861
17_R21_K0.680651.857
14_K148_I0.678551.851
74_I84_E0.669721.827
2_I100_D0.665381.815
116_I154_L0.646231.763
16_G45_V0.62731.711
53_I76_A0.617941.686
94_K117_V0.617361.684
153_K157_E0.610471.665
87_K131_A0.602471.644
36_D97_L0.58831.605
36_D58_S0.579341.581
71_I76_A0.576831.574
114_I134_R0.538091.468
90_A117_V0.535311.460
14_K17_R0.534681.459
46_A89_M0.534611.459
59_L96_K0.533571.456
91_K129_V0.532641.453
7_A93_V0.52791.440
36_D55_G0.510821.394
17_R144_Q0.510061.392
21_K144_Q0.504461.376
14_K144_Q0.498291.359
7_A60_L0.49681.355
87_K91_K0.492741.344
46_A55_G0.48691.328
105_T147_G0.486141.326
63_E70_V0.475231.297
93_V102_G0.469071.280
134_R150_K0.467931.277
23_A110_G0.467821.276
83_L133_L0.463661.265
104_G115_C0.461651.259
4_V19_I0.451411.232
58_S98_N0.451141.231
44_V97_L0.449891.227
153_K156_E0.44791.222
4_V155_F0.445021.214
6_T37_E0.439941.200
3_T35_Y0.437931.195
6_T15_I0.436271.190
10_F111_R0.428681.170
63_E69_Y0.424931.159
17_R148_I0.423511.155
35_Y99_C0.404771.104
100_D119_D0.401771.096
69_Y73_Y0.399711.090
55_G97_L0.393181.073
5_A97_L0.385631.052
15_I151_A0.384731.050
101_I118_T0.380811.039
3_T100_D0.374541.022
62_I92_A0.372881.017
101_I155_F0.3721.015
5_A93_V0.368461.005
94_K119_D0.368161.004
114_I150_K0.36661.000
61_N96_K0.359170.980
6_T16_G0.35790.976
36_D59_L0.356860.974
44_V93_V0.351940.960
120_K128_D0.349850.954
57_E71_I0.348970.952
141_L144_Q0.348410.951
16_G37_E0.344510.940
116_I158_I0.344290.939
136_S150_K0.341870.933
10_F105_T0.335790.916
53_I75_K0.332370.907
21_K141_L0.330270.901
25_G110_G0.326730.891
35_Y54_S0.326530.891
130_Y158_I0.325660.888
19_I22_I0.325260.887
149_E153_K0.322990.881
74_I82_D0.320490.874
6_T19_I0.31470.859
105_T151_A0.307330.838
60_L89_M0.305540.834
94_K102_G0.304180.830
2_I118_T0.295210.805
146_S153_K0.291930.796
138_E143_R0.291910.796
83_L131_A0.290560.793
24_S140_I0.287280.784
91_K117_V0.282020.769
10_F76_A0.278510.760
132_D150_K0.275910.753
55_G59_L0.275330.751
46_A97_L0.275230.751
70_V84_E0.274170.748
146_S149_E0.271640.741
44_V59_L0.268980.734
138_E146_S0.267230.729
141_L145_K0.266190.726
132_D154_L0.262740.717
36_D44_V0.262240.715
14_K18_E0.262070.715
135_K139_N0.254030.693
143_R147_G0.252850.690
44_V96_K0.252520.689
91_K95_N0.251590.686
4_V103_I0.250730.684
6_T103_I0.250150.682
62_I85_V0.249910.682
54_S58_S0.248340.678
15_I147_G0.246730.673
103_I116_I0.246480.672
90_A115_C0.242970.663
58_S96_K0.23490.641
4_V26_Y0.23260.635
53_I111_R0.232230.634
87_K129_V0.2310.630
90_A102_G0.230780.630
51_P56_A0.230030.628
15_I148_I0.228930.625
142_E146_S0.227320.620
71_I88_L0.226170.617
9_C56_A0.222820.608
90_A131_A0.22140.604
3_T99_C0.220960.603
150_K153_K0.220410.601
15_I152_L0.21970.599
24_S108_G0.219460.599
5_A44_V0.218570.596
20_H144_Q0.216090.590
101_I119_D0.214660.586
90_A94_K0.213220.582
75_K144_Q0.212940.581
64_P69_Y0.21280.581
10_F53_I0.212390.579
88_L92_A0.211630.577
22_I26_Y0.210440.574
51_P140_I0.20980.572
52_S75_K0.209720.572
17_R141_L0.209040.570
44_V55_G0.208790.570
103_I155_F0.207690.567
71_I85_V0.207310.566
18_E149_E0.207150.565
12_H17_R0.206920.565
115_C131_A0.206580.564
92_A96_K0.206110.562
35_Y98_N0.206010.562
61_N95_N0.205930.562
137_D146_S0.204830.559
107_A140_I0.204190.557
25_G145_K0.203950.556
69_Y72_K0.203950.556
62_I88_L0.203360.555
26_Y154_L0.203010.554
91_K94_K0.202940.554
60_L93_V0.202290.552
145_K149_E0.201810.551
136_S143_R0.200810.548
82_D111_R0.200190.546
10_F82_D0.199670.545
117_V129_V0.198830.542
82_D88_L0.198240.541
94_K116_I0.197650.539
15_I19_I0.197160.538
63_E71_I0.196740.537
86_A104_G0.196010.535
24_S51_P0.194990.532
118_T158_I0.194870.532
7_A92_A0.194780.531
53_I113_A0.193570.528
82_D85_V0.191510.522
18_E145_K0.189690.518
101_I116_I0.189130.516
51_P62_I0.1880.513
98_N119_D0.187960.513
70_V74_I0.187820.512
93_V97_L0.186010.507
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
2a9sA0.80631000.362
2d5uA0.281213.80.95
1nwzA0.643813.80.95
1vfgA0.681312.10.951
1pzxA0.668711.20.952
3dbiA0.62510.50.952
3hwwA0.76889.90.953
1surA0.63759.40.953
2vk8A0.74388.20.954
1zc6A0.40627.90.955

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