DUF4241 - PFAM28P - GREMLIN Contacts

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DUF4241 - Protein of unknown function (DUF4241)

PFAM:	PF14025	Sequences: ELVLPSGRIVACDPLVTLDPDAEPFTRTVPPGRYPVELAVADVDDEDGERVAAARLRFSDEPPVRWELALTPGQDLEELGEGEFFGYGVDAGTGCFMDAEAARALDAFEEEWYEENPDGNIYDDLFADLFEESYKANPKYQRDGGDWLNWPLPGTGANVVAFSSGWGDGFYPSYWGYDADGEVVCLVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (178)
Sequences:	1585 (1306)
Seq/√Len:	97.9
META:	0.734

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_P	34_Y	4.319	1.00
87_Y	94_G	4.198	1.00
37_E	55_R	3.291	1.00
63_P	184_V	3.193	1.00
54_A	162_F	3.191	1.00
90_D	168_D	2.971	1.00
87_Y	188_T	2.954	1.00
27_R	177_Y	2.810	1.00
9_I	186_L	2.758	1.00
6_S	100_E	2.710	1.00
178_D	182_E	2.682	1.00
27_R	175_W	2.655	1.00
38_L	54_A	2.486	1.00
61_E	178_D	2.355	1.00
11_A	25_F	2.338	1.00
3_V	33_R	2.310	1.00
29_V	58_F	2.284	1.00
39_A	55_R	2.276	1.00
86_G	170_F	2.129	1.00
173_S	188_T	2.113	1.00
34_Y	58_F	2.112	1.00
8_R	28_T	2.112	1.00
167_G	171_Y	2.048	1.00
4_L	29_V	1.961	1.00
29_V	34_Y	1.937	1.00
175_W	186_L	1.875	1.00
50_R	166_W	1.830	1.00
5_P	100_E	1.813	1.00
88_G	168_D	1.794	1.00
177_Y	183_V	1.750	1.00
149_N	160_V	1.747	1.00
54_A	96_F	1.701	1.00
173_S	186_L	1.692	1.00
37_E	57_R	1.645	1.00
43_V	48_G	1.587	1.00
65_R	177_Y	1.554	1.00
9_I	56_L	1.533	1.00
84_F	172_P	1.530	1.00
8_R	99_A	1.517	1.00
59_S	182_E	1.496	1.00
43_V	166_W	1.482	1.00
69_A	175_W	1.423	1.00
59_S	184_V	1.417	1.00
2_L	56_L	1.403	0.99
129_L	132_E	1.400	0.99
30_P	34_Y	1.396	0.99
127_A	131_E	1.344	0.99
48_G	166_W	1.328	0.99
38_L	51_V	1.323	0.99
4_L	9_I	1.315	0.99
94_G	162_F	1.304	0.99
89_V	171_Y	1.303	0.99
125_L	129_L	1.291	0.99
13_D	91_A	1.287	0.99
116_N	119_G	1.279	0.99
27_R	67_E	1.277	0.99
97_M	102_A	1.212	0.99
92_G	167_G	1.203	0.98
92_G	164_S	1.199	0.98
123_D	127_A	1.197	0.98
4_L	31_P	1.193	0.98
94_G	188_T	1.188	0.98
121_I	125_L	1.185	0.98
80_G	83_E	1.184	0.98
101_A	157_A	1.181	0.98
70_L	74_Q	1.163	0.98
178_D	184_V	1.161	0.98
67_E	177_Y	1.142	0.98
71_T	74_Q	1.135	0.98
68_L	79_L	1.114	0.97
95_C	162_F	1.106	0.97
40_V	51_V	1.106	0.97
79_L	83_E	1.081	0.97
79_L	85_F	1.076	0.97
66_W	176_G	1.070	0.97
89_V	168_D	1.063	0.97
149_N	152_L	1.058	0.96
57_R	60_D	1.053	0.96
176_G	187_V	1.047	0.96
127_A	130_F	1.029	0.96
131_E	134_Y	1.012	0.95
87_Y	173_S	1.010	0.95
89_V	167_G	1.005	0.95
27_R	183_V	0.994	0.95
75_D	78_E	0.977	0.95
13_D	89_V	0.973	0.94
176_G	185_C	0.972	0.94
122_Y	126_F	0.970	0.94
70_L	76_L	0.962	0.94
165_G	171_Y	0.953	0.94
157_A	160_V	0.949	0.94
96_F	188_T	0.946	0.94
66_W	187_V	0.944	0.93
58_F	186_L	0.938	0.93
126_F	129_L	0.937	0.93
16_V	91_A	0.921	0.93
165_G	169_G	0.914	0.92
56_L	96_F	0.908	0.92
48_G	163_S	0.904	0.92
7_G	98_D	0.895	0.91
39_A	53_A	0.892	0.91
26_T	70_L	0.886	0.91
164_S	168_D	0.882	0.91
111_E	115_E	0.881	0.91
74_Q	85_F	0.871	0.90
175_W	183_V	0.855	0.90
43_V	47_D	0.842	0.89
120_N	124_D	0.838	0.89
55_R	185_C	0.837	0.89
130_F	133_S	0.835	0.88
50_R	163_S	0.831	0.88
94_G	173_S	0.830	0.88
2_L	36_V	0.827	0.88
6_S	99_A	0.823	0.88
149_N	158_N	0.822	0.88
42_D	49_E	0.820	0.87
63_P	185_C	0.819	0.87
64_V	179_A	0.818	0.87
84_F	170_F	0.811	0.87
71_T	83_E	0.809	0.87
6_S	98_D	0.807	0.87
92_G	168_D	0.807	0.87
11_A	173_S	0.800	0.86
61_E	184_V	0.799	0.86
12_C	97_M	0.796	0.86
156_G	159_V	0.792	0.86
78_E	85_F	0.792	0.86
90_D	164_S	0.790	0.85
168_D	171_Y	0.783	0.85
54_A	94_G	0.782	0.85
120_N	123_D	0.781	0.85
20_P	23_E	0.779	0.85
5_P	31_P	0.766	0.84
73_G	79_L	0.759	0.83
96_F	162_F	0.759	0.83
25_F	173_S	0.756	0.83
65_R	181_G	0.755	0.83
63_P	176_G	0.748	0.82
12_C	24_P	0.747	0.82
130_F	161_A	0.746	0.82
14_P	98_D	0.738	0.81
90_D	167_G	0.735	0.81
131_E	135_K	0.733	0.81
9_I	29_V	0.731	0.81
14_P	32_G	0.729	0.81
43_V	49_E	0.720	0.80
3_V	158_N	0.718	0.80
11_A	96_F	0.718	0.80
133_S	148_L	0.716	0.79
89_V	164_S	0.709	0.79
177_Y	181_G	0.698	0.78
2_L	95_C	0.698	0.78
27_R	186_L	0.697	0.78
29_V	175_W	0.697	0.78
101_A	104_A	0.688	0.77
50_R	167_G	0.686	0.76
70_L	73_G	0.685	0.76
87_Y	96_F	0.684	0.76
3_V	157_A	0.678	0.76
10_V	22_A	0.678	0.76
60_D	110_E	0.677	0.75
103_R	182_E	0.675	0.75
144_G	148_L	0.674	0.75
129_L	134_Y	0.672	0.75
11_A	188_T	0.664	0.74
121_I	124_D	0.660	0.74
123_D	126_F	0.658	0.73
74_Q	86_G	0.655	0.73
26_T	72_P	0.652	0.73
29_V	53_A	0.651	0.73
105_L	160_V	0.642	0.72
122_Y	130_F	0.640	0.71
50_R	88_G	0.639	0.71
117_P	120_N	0.638	0.71
175_W	185_C	0.637	0.71
40_V	49_E	0.637	0.71
50_R	168_D	0.636	0.71
151_P	155_T	0.632	0.70
11_A	87_Y	0.632	0.70
116_N	120_N	0.628	0.70
30_P	182_E	0.626	0.70
79_L	82_G	0.624	0.69
35_P	66_W	0.616	0.68
60_D	78_E	0.615	0.68
164_S	171_Y	0.613	0.68
121_I	126_F	0.612	0.68
155_T	160_V	0.611	0.68
95_C	159_V	0.609	0.68
117_P	122_Y	0.608	0.67
122_Y	125_L	0.608	0.67
54_A	95_C	0.606	0.67
26_T	132_E	0.604	0.67
95_C	98_D	0.604	0.67
102_A	106_D	0.602	0.67
39_A	63_P	0.601	0.67
34_Y	56_L	0.597	0.66
91_A	168_D	0.596	0.66
4_L	98_D	0.594	0.66
164_S	167_G	0.592	0.65
143_D	146_D	0.592	0.65
128_D	132_E	0.589	0.65
119_G	124_D	0.587	0.65
105_L	159_V	0.586	0.65
147_W	152_L	0.584	0.64
95_C	164_S	0.583	0.64
38_L	162_F	0.582	0.64
36_V	158_N	0.582	0.64
125_L	150_W	0.582	0.64
2_L	158_N	0.580	0.64
41_A	164_S	0.580	0.64
4_L	101_A	0.577	0.63
99_A	103_R	0.577	0.63
79_L	84_F	0.575	0.63
36_V	95_C	0.575	0.63
16_V	22_A	0.574	0.63
49_E	163_S	0.573	0.63
45_D	48_G	0.572	0.63
86_G	173_S	0.571	0.63
12_C	93_T	0.568	0.62
89_V	169_G	0.568	0.62
21_D	25_F	0.568	0.62
16_V	88_G	0.566	0.62
48_G	91_A	0.564	0.62
13_D	167_G	0.557	0.61
28_T	34_Y	0.556	0.61
68_L	84_F	0.556	0.61
150_W	156_G	0.553	0.60
183_V	186_L	0.552	0.60
40_V	50_R	0.552	0.60
10_V	24_P	0.549	0.60
29_V	186_L	0.546	0.59
2_L	34_Y	0.544	0.59
101_A	159_V	0.542	0.59
75_D	85_F	0.539	0.58
132_E	135_K	0.538	0.58
123_D	128_D	0.536	0.58
88_G	170_F	0.534	0.58
56_L	156_G	0.533	0.57
97_M	101_A	0.532	0.57
82_G	85_F	0.531	0.57
51_V	145_G	0.528	0.57
34_Y	175_W	0.525	0.56
12_C	22_A	0.523	0.56
41_A	52_A	0.523	0.56
12_C	91_A	0.521	0.56
11_A	172_P	0.515	0.55
55_R	187_V	0.515	0.55
123_D	131_E	0.515	0.55
39_A	54_A	0.515	0.55
151_P	156_G	0.512	0.54
70_L	85_F	0.510	0.54
2_L	66_W	0.510	0.54
53_A	187_V	0.509	0.54
61_E	179_A	0.509	0.54
36_V	160_V	0.508	0.54
13_D	165_G	0.508	0.54
15_L	93_T	0.507	0.54
68_L	86_G	0.507	0.54
74_Q	79_L	0.506	0.54
120_N	127_A	0.506	0.54
4_L	34_Y	0.506	0.54
66_W	162_F	0.506	0.54
71_T	75_D	0.503	0.53
142_R	146_D	0.502	0.53
124_D	130_F	0.501	0.53
74_Q	170_F	0.500	0.53
43_V	50_R	0.500	0.53

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
2iu4A	2	0.3777	39	0.921	Contact Map
3ct4A	3	0.383	30.5	0.925	Contact Map
1un8A	2	0.3936	19.4	0.932	Contact Map
4pj2A	1	0.6223	18	0.933	Contact Map
1oi2A	2	0.3404	9.8	0.94	Contact Map
2ag4A	1	0.3032	5.5	0.947	Contact Map
3ottA	2	0.3723	5	0.948	Contact Map
3bwuD	1	0.5691	4.7	0.949	Contact Map
4a2lA	4	0.3298	4.3	0.949	Contact Map
3mtxA	1	0.3138	3.8	0.951	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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