GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0004 - Uncharacterized protein family UPF0004
Pfam: PF00919 (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: 98
Sequences: 3020
Seq/Len: 30.82
HH_delta: 0.019 (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
6_T16_S0.948172.735
1_K29_E0.805032.322
19_I75_T0.764942.207
79_A96_V0.756662.183
4_I16_S0.749342.162
73_V95_L0.739982.135
2_V30_I0.726522.096
75_T97_V0.678591.958
33_D36_E0.643431.856
84_E88_K0.6411.849
80_Q98_G0.639161.844
49_E53_Q0.614031.771
5_E58_R0.577781.667
41_I73_V0.572081.650
82_Y85_E0.568541.640
46_T52_E0.564671.629
17_E21_S0.539531.556
83_G87_K0.516781.491
7_L58_R0.51081.474
1_K36_E0.501391.446
46_T81_R0.494711.427
44_T74_V0.48691.405
63_K72_I0.456431.317
44_T55_S0.456271.316
6_T43_N0.450351.299
1_K31_V0.435331.256
50_S53_Q0.433031.249
28_Y39_V0.43031.241
16_S43_N0.430091.241
53_Q57_N0.428461.236
7_L55_S0.426421.230
6_T13_Q0.423061.220
42_I62_L0.41831.207
3_Y34_P0.414051.194
54_K57_N0.407811.176
85_E88_K0.406321.172
20_A30_I0.405531.170
40_I62_L0.401431.158
52_E81_R0.400021.154
2_V20_A0.397981.148
59_I74_V0.391631.130
2_V24_Q0.386861.116
56_R60_R0.386441.115
11_M14_Y0.385931.113
73_V97_V0.380541.098
57_N60_R0.37691.087
66_K94_D0.376081.085
10_Q48_R0.368081.062
71_K95_L0.36441.051
58_R62_L0.360541.040
20_A24_Q0.356061.027
7_L42_I0.354391.022
24_Q29_E0.350241.010
80_Q83_G0.34851.005
4_I20_A0.341620.986
18_R22_I0.327020.943
93_V96_V0.325560.939
36_E65_L0.3250.938
39_V73_V0.3220.929
58_R61_K0.321060.926
52_E82_Y0.320860.926
66_K70_A0.318340.918
11_M54_K0.317660.916
63_K94_D0.314150.906
50_S54_K0.311590.899
23_L41_I0.308770.891
79_A90_F0.306790.885
61_K64_K0.304860.879
11_M48_R0.303760.876
3_Y32_D0.303360.875
42_I59_I0.303110.874
42_I55_S0.301490.870
39_V71_K0.299930.865
38_D70_A0.293210.846
15_D21_S0.293140.846
86_L93_V0.292190.843
74_V93_V0.287770.830
87_K96_V0.285790.824
2_V28_Y0.285740.824
55_S59_I0.285260.823
31_V36_E0.285050.822
65_L70_A0.283710.818
52_E78_M0.281380.812
71_K94_D0.281360.812
16_S20_A0.280780.810
85_E89_E0.280720.810
14_Y18_R0.278050.802
4_I41_I0.273280.788
13_Q17_E0.273070.788
63_K90_F0.272220.785
17_E20_A0.271850.784
31_V37_A0.266560.769
18_R21_S0.264750.764
65_L69_G0.262680.758
21_S25_A0.260490.751
59_I92_E0.260330.751
40_I69_G0.260250.751
56_R78_M0.259220.748
24_Q30_I0.258750.746
22_I26_A0.257980.744
3_Y37_A0.253960.733
22_I25_A0.253760.732
34_P40_I0.253020.730
84_E87_K0.251410.725
41_I95_L0.251330.725
11_M51_A0.24780.715
11_M15_D0.245280.708
1_K38_D0.244260.705
2_V23_L0.243790.703
34_P62_L0.24090.695
40_I70_A0.238770.689
48_R54_K0.238450.688
7_L52_E0.238270.687
18_R98_G0.236080.681
3_Y40_I0.236010.681
47_V54_K0.235970.681
34_P65_L0.23470.677
35_E88_K0.234140.675
19_I43_N0.231970.669
32_D36_E0.226030.652
7_L63_K0.225950.652
11_M47_V0.225520.651
86_L96_V0.225310.650
19_I97_V0.225150.650
62_L72_I0.223660.645
42_I58_R0.220750.637
35_E69_G0.220390.636
52_E56_R0.215950.623
29_E32_D0.215630.622
78_M81_R0.214160.618
12_N43_N0.213520.616
56_R89_E0.212880.614
48_R78_M0.210270.607
3_Y31_V0.209120.603
64_K88_K0.20770.599
24_Q27_G0.207250.598
35_E68_P0.206860.597
2_V26_A0.205910.594
3_Y30_I0.204270.589
69_G72_I0.203880.588
12_N85_E0.203690.588
6_T12_N0.203280.586
26_A87_K0.203270.586
8_G12_N0.202880.585
55_S74_V0.202550.584
52_E85_E0.202060.583
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
4jc0A11000.019
1reqA0.959293.70.841
1reqB0.918492.90.846
2xijA0.959292.70.846
2yxbA0.959287.20.864
3aekB0.877682.80.871
3pdiA0.908278.10.877
3u7qA0.918477.30.878
1mioB0.89873.90.881
1mioA0.918468.30.886

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