DUF3440 - PFAM28P - GREMLIN Contacts

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DUF3440 - Domain of unknown function (DUF3440)

PFAM:	PF11922	Sequences: GVPIDQMRVASPFNDEAKSSLNLYRVIDPETWGKLVGRVNGANFGAIYGGTKAMGYRSIKLPEGHTWKSYTKFLLDTLPEETRENYLKKFNTSIKFWREKGGGLSEETIQELEEAGIKIEVNGKTNYKTDKRPVRMKEYPDDLDIKSFKDIPSWKRMCICILKNDHTCKYMGFSLTKEQQER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	182 (181)
Sequences:	676 (368)
Seq/√Len:	27.4
META:	0.885

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_H	69_S	5.235	1.00
2_V	6_Q	4.497	1.00
83_R	87_L	4.203	1.00
28_D	31_T	3.819	1.00
3_P	6_Q	3.231	1.00
61_L	64_G	3.229	1.00
61_L	65_H	3.162	1.00
106_E	132_R	3.068	1.00
61_L	69_S	3.065	1.00
95_K	99_E	3.026	1.00
18_K	45_G	2.816	1.00
28_D	35_L	2.744	1.00
178_E	181_E	2.650	0.99
177_K	181_E	2.512	0.99
110_Q	114_E	2.279	0.98
140_P	153_S	2.258	0.98
68_K	72_K	2.248	0.98
64_G	69_S	2.176	0.98
72_K	76_D	2.112	0.97
80_E	84_E	1.980	0.96
68_K	154_W	1.965	0.96
17_A	20_S	1.910	0.95
139_Y	152_P	1.879	0.94
42_A	46_A	1.847	0.94
14_N	17_A	1.817	0.93
22_N	50_G	1.784	0.93
52_K	162_L	1.740	0.92
28_D	167_T	1.727	0.91
71_T	154_W	1.681	0.90
2_V	23_L	1.659	0.90
56_Y	163_K	1.611	0.88
111_E	147_S	1.610	0.88
84_E	88_K	1.548	0.86
98_R	138_E	1.528	0.85
85_N	166_H	1.525	0.85
147_S	150_D	1.505	0.85
71_T	90_F	1.490	0.84
109_I	134_V	1.467	0.83
113_E	119_I	1.448	0.82
121_V	132_R	1.431	0.81
71_T	158_C	1.430	0.81
105_S	130_D	1.399	0.80
72_K	154_W	1.375	0.79
26_V	46_A	1.364	0.78
110_Q	113_E	1.331	0.76
10_A	17_A	1.316	0.75
76_D	113_E	1.315	0.75
31_T	35_L	1.315	0.75
103_G	133_P	1.304	0.75
68_K	91_N	1.297	0.74
55_G	70_Y	1.278	0.73
128_K	131_K	1.271	0.73
148_F	171_M	1.270	0.73
25_R	47_I	1.249	0.72
157_M	160_C	1.243	0.71
115_A	143_L	1.241	0.71
92_T	103_G	1.222	0.70
104_L	109_I	1.216	0.69
93_S	102_G	1.216	0.69
133_P	136_M	1.195	0.68
70_Y	178_E	1.183	0.67
121_V	134_V	1.176	0.67
46_A	52_K	1.175	0.67
61_L	66_T	1.167	0.66
7_M	14_N	1.143	0.65
51_T	55_G	1.131	0.64
111_E	146_K	1.122	0.63
154_W	157_M	1.121	0.63
111_E	145_I	1.111	0.62
111_E	150_D	1.101	0.62
103_G	109_I	1.086	0.61
112_L	117_I	1.085	0.60
56_Y	162_L	1.072	0.59
174_S	180_Q	1.049	0.58
54_M	162_L	1.045	0.58
14_N	18_K	1.044	0.57
11_S	14_N	1.043	0.57
99_E	138_E	1.042	0.57
63_E	69_S	1.035	0.57
156_R	168_C	1.010	0.55
40_N	82_T	1.007	0.55
14_N	20_S	1.001	0.54
154_W	179_Q	0.992	0.54
142_D	148_F	0.987	0.53
122_N	135_R	0.985	0.53
149_K	160_C	0.974	0.52
11_S	17_A	0.972	0.52
90_F	140_P	0.965	0.51
102_G	173_F	0.963	0.51
30_E	138_E	0.962	0.51
50_G	56_Y	0.953	0.51
42_A	45_G	0.951	0.50
34_K	40_N	0.944	0.50
124_K	132_R	0.941	0.50
2_V	7_M	0.912	0.47
10_A	13_F	0.912	0.47
160_C	171_M	0.906	0.47
104_L	112_L	0.898	0.46
52_K	60_K	0.891	0.46
36_V	47_I	0.888	0.46
27_I	134_V	0.886	0.46
108_T	151_I	0.883	0.45
22_N	30_E	0.882	0.45
160_C	167_T	0.870	0.44
96_F	104_L	0.867	0.44
176_T	179_Q	0.860	0.44
38_R	41_G	0.853	0.43
126_N	129_T	0.853	0.43
70_Y	163_K	0.848	0.43
51_T	57_R	0.846	0.43
16_E	70_Y	0.846	0.43
108_T	111_E	0.844	0.42
143_L	153_S	0.835	0.42
167_T	175_L	0.830	0.41
27_I	83_R	0.822	0.41
160_C	166_H	0.821	0.41
90_F	157_M	0.820	0.41
122_N	133_P	0.819	0.41
113_E	121_V	0.819	0.41
9_V	24_Y	0.816	0.40
109_I	115_A	0.806	0.40
125_T	150_D	0.804	0.39
86_Y	173_F	0.801	0.39
16_E	45_G	0.800	0.39
58_S	110_Q	0.799	0.39
160_C	170_Y	0.794	0.39
11_S	18_K	0.789	0.38
123_G	132_R	0.787	0.38
94_I	139_Y	0.783	0.38
126_N	130_D	0.782	0.38
46_A	54_M	0.776	0.37
30_E	34_K	0.772	0.37
1_G	8_R	0.771	0.37
121_V	124_K	0.762	0.36
106_E	110_Q	0.761	0.36
125_T	160_C	0.760	0.36
7_M	111_E	0.751	0.36
76_D	80_E	0.751	0.36
86_Y	156_R	0.750	0.36
120_E	135_R	0.738	0.35
86_Y	102_G	0.737	0.35
46_A	162_L	0.737	0.35
111_E	143_L	0.737	0.35
112_L	129_T	0.734	0.35
111_E	140_P	0.724	0.34
133_P	158_C	0.723	0.34
75_L	156_R	0.717	0.33
40_N	159_I	0.716	0.33
144_D	169_K	0.715	0.33
96_F	126_N	0.715	0.33
22_N	94_I	0.713	0.33
168_C	171_M	0.713	0.33
169_K	174_S	0.708	0.33
3_P	87_L	0.706	0.33
26_V	110_Q	0.706	0.33
102_G	139_Y	0.705	0.33
78_L	161_I	0.703	0.32
72_K	99_E	0.701	0.32
93_S	172_G	0.697	0.32
63_E	95_K	0.697	0.32
113_E	116_G	0.696	0.32
86_Y	93_S	0.695	0.32
72_K	87_L	0.692	0.32
119_I	125_T	0.687	0.31
98_R	137_K	0.685	0.31
148_F	170_Y	0.683	0.31
105_S	108_T	0.677	0.31
75_L	86_Y	0.672	0.30
26_V	33_G	0.672	0.30
13_F	35_L	0.667	0.30
34_K	118_K	0.664	0.30
80_E	109_I	0.660	0.30
4_I	120_E	0.658	0.29
159_I	170_Y	0.657	0.29
103_G	139_Y	0.655	0.29
114_E	119_I	0.654	0.29
90_F	136_M	0.653	0.29
85_N	160_C	0.650	0.29
10_A	14_N	0.648	0.29
33_G	40_N	0.647	0.29
107_E	110_Q	0.644	0.29
115_A	119_I	0.641	0.28
122_N	125_T	0.639	0.28
52_K	153_S	0.639	0.28
111_E	115_A	0.637	0.28
55_G	139_Y	0.636	0.28
125_T	174_S	0.636	0.28
24_Y	170_Y	0.634	0.28
2_V	20_S	0.634	0.28
157_M	168_C	0.625	0.27
46_A	56_Y	0.624	0.27
166_H	169_K	0.622	0.27
28_D	58_S	0.618	0.27
107_E	124_K	0.615	0.27
12_P	24_Y	0.610	0.27
15_D	37_G	0.610	0.27
93_S	156_R	0.609	0.26
95_K	118_K	0.608	0.26
98_R	136_M	0.606	0.26
2_V	31_T	0.601	0.26
173_F	177_K	0.601	0.26
52_K	99_E	0.600	0.26
29_P	63_E	0.599	0.26
31_T	47_I	0.598	0.26
76_D	104_L	0.593	0.26
13_F	21_L	0.593	0.26
42_A	90_F	0.591	0.25
16_E	19_S	0.590	0.25
65_H	167_T	0.586	0.25
114_E	174_S	0.583	0.25
125_T	167_T	0.581	0.25
9_V	13_F	0.568	0.24
91_N	99_E	0.563	0.24
8_R	12_P	0.562	0.24
86_Y	157_M	0.562	0.24
121_V	125_T	0.560	0.24
129_T	133_P	0.560	0.24
46_A	58_S	0.560	0.24
32_W	39_V	0.560	0.24
76_D	118_K	0.558	0.24
156_R	173_F	0.557	0.24
94_I	119_I	0.555	0.23
35_L	92_T	0.555	0.23
10_A	49_G	0.555	0.23
10_A	24_Y	0.554	0.23
109_I	132_R	0.553	0.23
49_G	73_F	0.553	0.23
107_E	113_E	0.552	0.23
118_K	123_G	0.551	0.23
11_S	24_Y	0.550	0.23
40_N	171_M	0.549	0.23
47_I	52_K	0.548	0.23
52_K	70_Y	0.548	0.23
124_K	174_S	0.548	0.23
80_E	169_K	0.546	0.23
76_D	83_R	0.546	0.23
73_F	77_T	0.545	0.23
87_L	92_T	0.544	0.23
56_Y	90_F	0.541	0.23
93_S	155_K	0.541	0.23
78_L	112_L	0.538	0.23
86_Y	89_K	0.536	0.22
72_K	91_N	0.532	0.22
36_V	70_Y	0.531	0.22
103_G	166_H	0.531	0.22
89_K	169_K	0.531	0.22
37_G	49_G	0.531	0.22
83_R	145_I	0.530	0.22
139_Y	154_W	0.527	0.22
95_K	135_R	0.526	0.22
81_E	85_N	0.525	0.22
53_A	70_Y	0.520	0.22
88_K	178_E	0.520	0.22
119_I	126_N	0.519	0.22
5_D	57_R	0.519	0.22
167_T	179_Q	0.517	0.21
13_F	17_A	0.516	0.21
88_K	118_K	0.514	0.21
15_D	20_S	0.512	0.21
50_G	163_K	0.512	0.21
42_A	52_K	0.511	0.21
34_K	69_S	0.509	0.21
120_E	145_I	0.508	0.21
92_T	169_K	0.506	0.21
96_F	125_T	0.505	0.21
11_S	16_E	0.504	0.21
54_M	179_Q	0.503	0.21
25_R	58_S	0.502	0.21
24_Y	93_S	0.502	0.21
1_G	7_M	0.502	0.21
81_E	114_E	0.501	0.21
69_S	72_K	0.500	0.21

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1xo0A	3	0.6593	21	0.964	Contact Map
4n4uA	1	0.8352	9.2	0.97	Contact Map
4nx1A	1	0.7637	9.1	0.97	Contact Map
4bolA	2	0.7967	8.4	0.97	Contact Map
4pf6A	1	0.8022	8.4	0.97	Contact Map
3iwfA	2	0.2582	7.9	0.97	Contact Map
2pfyA	1	0.7912	7.1	0.971	Contact Map
2pfzA	1	0.7967	6.6	0.972	Contact Map
1ujsA	1	0.3901	6.4	0.972	Contact Map
4bxjA	4	0.8187	6.4	0.972	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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