GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
T5orf172 - T5orf172 domain
Pfam: PF10544 (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: CL0418
Length: 100
Sequences: 1185
Seq/Len: 11.85
HH_delta: 0.585 (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
19_I64_I0.571052.992
24_N31_E0.549872.881
27_R31_E0.444072.326
24_N27_R0.406032.127
65_H85_F0.397572.083
59_K63_L0.388312.034
64_I68_L0.38392.011
28_R83_E0.330241.730
18_K83_E0.328631.722
21_Y58_R0.316881.660
18_K28_R0.305691.602
58_R62_R0.291791.529
26_E30_R0.284781.492
74_R80_G0.280221.468
7_T44_E0.280191.468
28_R61_E0.271181.421
70_D74_R0.269811.414
6_L29_L0.266051.394
21_Y57_A0.265061.389
23_T27_R0.256581.344
5_I47_Y0.255741.340
70_D73_Y0.248891.304
17_Y89_P0.244961.283
13_G20_G0.244921.283
63_L67_E0.241011.263
10_S13_G0.231591.213
52_V56_D0.230711.209
21_Y54_V0.230421.207
23_T31_E0.227381.191
3_I21_Y0.214691.125
36_S43_F0.212381.113
56_D59_K0.211031.106
63_L66_R0.193881.016
36_S39_S0.193061.011
2_Y54_V0.192651.009
62_R66_R0.192311.008
10_S44_E0.190941.000
19_I68_L0.18940.992
10_S37_T0.187930.985
20_G61_E0.187680.983
28_R31_E0.18710.980
7_T46_I0.182680.957
9_P14_Y0.181730.952
54_V61_E0.181050.949
23_T54_V0.17950.940
5_I19_I0.179440.940
57_A61_E0.178120.933
49_F60_V0.176980.927
20_G28_R0.176130.923
17_Y46_I0.175610.920
68_L83_E0.172050.901
36_S40_P0.17060.894
17_Y87_L0.163680.858
20_G83_E0.160830.843
19_I66_R0.159950.838
52_V55_P0.15750.825
6_L42_D0.157010.823
50_E56_D0.156370.819
3_I64_I0.155840.816
25_P32_L0.154760.811
26_E48_E0.153540.804
32_L65_H0.152770.800
6_L32_L0.151910.796
33_N42_D0.150940.791
33_N84_W0.150360.788
32_L61_E0.148770.779
29_L33_N0.148220.777
26_E45_V0.147220.771
28_R65_H0.147060.770
54_V60_V0.146760.769
22_T25_P0.146580.768
18_K85_F0.146090.765
21_Y62_R0.145390.762
53_P56_D0.1450.760
32_L84_W0.143550.752
26_E52_V0.143370.751
69_K75_I0.141880.743
73_Y88_D0.141690.742
61_E65_H0.141130.739
18_K68_L0.140760.737
80_G83_E0.140120.734
75_I84_W0.139230.729
22_T57_A0.139160.729
23_T58_R0.139140.729
25_P64_I0.139140.729
63_L68_L0.139140.729
56_D83_E0.138740.727
8_S42_D0.138710.727
55_P59_K0.138240.724
50_E83_E0.137820.722
62_R69_K0.137340.720
42_D80_G0.136810.717
30_R37_T0.136410.715
56_D85_F0.136260.714
30_R52_V0.135260.709
22_T49_F0.135010.707
19_I83_E0.134720.706
21_Y84_W0.134260.703
81_H87_L0.131650.690
62_R81_H0.131430.689
43_F84_W0.13130.688
14_Y17_Y0.131290.688
27_R53_P0.1310.686
64_I80_G0.130460.683
5_I11_N0.129820.680
59_K62_R0.129620.679
39_S50_E0.128450.673
30_R55_P0.12840.673
11_N73_Y0.128030.671
60_V63_L0.127680.669
48_E88_D0.127540.668
36_S80_G0.127520.668
23_T90_E0.126820.664
50_E54_V0.125430.657
8_S32_L0.124980.655
51_S57_A0.124850.654
18_K65_H0.124670.653
8_S40_P0.124260.651
39_S46_I0.124080.650
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
1zg2A0.998.20.585
1ywlA0.8398.10.597
3oqgA0.7875.10.82
1mk0A0.7771.50.825
2wshA0.7464.90.832
1yd0A0.74630.834
1yd6A0.77520.844
3fkrA0.713.20.883
2lwfA0.898.80.891
4flbA0.467.20.896
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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