GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UPF0175 - Uncharacterised protein family (UPF0175)
Pfam: PF03683 (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: 76
Sequences: 374
Seq/Len: 4.92
HH_delta: 0.795 (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
26_A44_A0.389292.879
28_K31_E0.339412.510
24_E58_R0.28432.103
54_L57_E0.274662.032
35_I43_L0.267551.979
27_I55_L0.267531.979
35_I39_K0.228531.690
23_E54_L0.225041.664
72_D75_T0.224311.659
39_K42_E0.195041.443
28_K58_R0.193781.433
23_E44_A0.190071.406
11_R14_P0.181471.342
32_E58_R0.177421.312
37_L48_R0.176221.303
26_A35_I0.175781.300
28_K33_G0.173551.284
19_Q73_L0.171651.270
22_R45_G0.162391.201
47_S50_E0.159471.180
23_E73_L0.15161.121
54_L58_R0.151021.117
32_E59_G0.150591.114
21_L25_L0.150181.111
22_R26_A0.147391.090
30_Y33_G0.145941.079
28_K32_E0.143441.061
44_A51_F0.143361.060
27_I58_R0.142781.056
49_W72_D0.140961.043
22_R44_A0.141.036
7_L10_L0.138181.022
24_E60_I0.136471.009
35_I50_E0.134650.996
30_Y62_I0.132390.979
36_S59_G0.130010.962
29_L40_A0.129250.956
43_L62_I0.12810.947
29_L38_G0.127860.946
36_S39_K0.127180.941
24_E27_I0.125490.928
46_M54_L0.124760.923
30_Y60_I0.124460.921
11_R36_S0.123870.916
20_E42_E0.122570.907
45_G71_E0.122220.904
59_G74_E0.122020.903
37_L60_I0.12190.902
30_Y46_M0.121760.901
29_L51_F0.121240.897
2_I7_L0.121140.896
33_G67_E0.120880.894
37_L49_W0.120570.892
38_G48_R0.119490.884
7_L26_A0.11720.867
13_T34_K0.116890.865
37_L41_A0.116830.864
36_S52_L0.11650.862
68_E71_E0.116280.860
37_L61_P0.115740.856
22_R54_L0.115650.855
33_G66_E0.115040.851
24_E63_N0.1130.836
35_I44_A0.112420.832
35_I74_E0.112210.830
50_E69_L0.111390.824
37_L52_L0.111050.821
21_L24_E0.110580.818
39_K50_E0.110270.816
8_Q13_T0.10950.810
29_L54_L0.108840.805
19_Q70_E0.108560.803
63_N68_E0.107930.798
12_L56_K0.107040.792
40_A51_F0.106990.791
29_L37_L0.106970.791
2_I18_E0.106640.789
37_L53_E0.106170.785
27_I65_D0.1050.777
7_L22_R0.103740.767
8_Q72_D0.103530.766
40_A54_L0.102920.761
23_E46_M0.10280.760
22_R71_E0.102330.757
11_R21_L0.102150.756
26_A48_R0.101990.754
56_K60_I0.101850.753
25_L72_D0.101630.752
71_E74_E0.101370.750
6_I59_G0.1010.747
32_E42_E0.099470.736
6_I14_P0.0990.732
11_R57_E0.098850.731
36_S68_E0.098420.728
5_E13_T0.097690.723
5_E47_S0.097370.720
66_E69_L0.096920.717
49_W53_E0.096850.716
18_E29_L0.096450.713
36_S58_R0.096390.713
40_A44_A0.095270.705
21_L50_E0.094680.700
59_G67_E0.094530.699
66_E70_E0.094490.699
51_F62_I0.094030.695
19_Q23_E0.093940.695
5_E10_L0.093550.692
30_Y68_E0.092550.685
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
1ntcA0.7588.50.795
1umqA0.7587.60.797
1g2hA0.7586.70.8
2lvsA0.789586.60.8
1etoA0.7581.10.813
3e7lA0.802680.10.815
4fe7A0.960559.60.839
3oouA0.934259.10.84
1jkoC0.684257.20.842
2pjpA0.881657.20.842
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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