DUF3341 - PFAM28P - GREMLIN Contacts

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DUF3341 - Protein of unknown function (DUF3341)

PFAM:	PF11821	Sequences: YGLLAEFDDPDALLAAARKLRAAGYRRMDAYSPFPVHGLDEALGLKRSRLPLIVLIGGLTGALGGFLLQWWTSVIDYPLNIGGKPLFSWPAFIPITFELTVLFAALGAVFGMLALNGLPRPYHPVFNVPRFDRRASDDRFFLCIEADDPKFDAEETRAFLESLGAEEVEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	170 (167)
Sequences:	16028 (9191)
Seq/√Len:	711.3
META:	0.969

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_F	87_F	3.266	1.00
57_G	107_G	2.812	1.00
157_R	161_E	2.726	1.00
54_V	108_A	2.717	1.00
68_L	72_T	2.672	1.00
9_D	12_A	2.521	1.00
62_A	100_T	2.501	1.00
7_F	163_L	2.381	1.00
158_A	162_S	2.359	1.00
70_W	87_F	2.295	1.00
112_M	116_N	2.254	1.00
20_L	28_M	2.203	1.00
63_L	67_L	1.972	1.00
106_L	110_F	1.962	1.00
64_G	67_L	1.905	1.00
8_D	166_E	1.905	1.00
53_I	107_G	1.870	1.00
158_A	161_E	1.854	1.00
64_G	103_F	1.844	1.00
20_L	159_F	1.830	1.00
71_W	76_D	1.785	1.00
60_T	64_G	1.766	1.00
62_A	96_T	1.742	1.00
155_E	158_A	1.683	1.00
65_G	99_L	1.681	1.00
53_I	115_L	1.660	1.00
56_I	60_T	1.653	1.00
154_E	158_A	1.643	1.00
19_K	22_A	1.631	1.00
152_D	155_E	1.627	1.00
54_V	104_A	1.625	1.00
31_Y	143_C	1.618	1.00
8_D	12_A	1.595	1.00
109_V	113_L	1.560	1.00
4_L	125_V	1.555	1.00
19_K	23_A	1.539	1.00
69_Q	96_T	1.534	1.00
19_K	162_S	1.502	1.00
153_A	157_R	1.475	1.00
60_T	103_F	1.473	1.00
135_A	141_F	1.454	1.00
28_M	43_L	1.426	1.00
15_A	18_R	1.406	1.00
110_F	114_A	1.401	1.00
70_W	74_V	1.399	1.00
72_T	76_D	1.397	1.00
122_Y	127_N	1.378	1.00
21_R	44_G	1.370	1.00
18_R	22_A	1.344	1.00
154_E	157_R	1.332	1.00
133_R	138_D	1.329	1.00
8_D	139_R	1.319	1.00
144_I	156_T	1.314	1.00
97_F	101_V	1.313	1.00
6_E	141_F	1.307	1.00
139_R	166_E	1.301	1.00
52_L	56_I	1.301	1.00
73_S	92_F	1.293	1.00
159_F	163_L	1.286	1.00
55_L	59_L	1.259	1.00
150_K	155_E	1.238	1.00
30_A	39_L	1.237	1.00
5_A	165_A	1.236	1.00
66_F	96_T	1.218	1.00
64_G	99_L	1.207	1.00
23_A	155_E	1.197	1.00
15_A	19_K	1.195	1.00
6_E	139_R	1.162	1.00
57_G	103_F	1.154	1.00
17_A	30_A	1.152	1.00
99_L	103_F	1.143	1.00
21_R	26_R	1.142	1.00
18_R	42_A	1.109	1.00
133_R	139_R	1.103	1.00
65_G	69_Q	1.098	1.00
13_L	30_A	1.087	1.00
12_A	15_A	1.086	1.00
109_V	112_M	1.084	1.00
53_I	111_G	1.080	1.00
80_N	84_K	1.078	1.00
49_R	52_L	1.076	1.00
11_D	15_A	1.075	1.00
156_T	159_F	1.060	1.00
13_L	142_L	1.054	1.00
14_L	38_G	1.047	1.00
130_R	167_E	1.038	1.00
27_R	147_D	1.036	1.00
65_G	95_I	1.028	1.00
40_D	45_L	1.019	1.00
50_L	54_V	1.015	1.00
17_A	43_L	1.009	1.00
69_Q	92_F	0.993	1.00
57_G	111_G	0.991	1.00
21_R	42_A	0.990	1.00
62_A	66_F	0.990	1.00
34_F	140_F	0.980	1.00
2_G	143_C	0.973	1.00
20_L	142_L	0.972	1.00
125_V	128_V	0.970	1.00
58_G	104_A	0.955	1.00
107_G	111_G	0.951	1.00
59_L	63_L	0.948	1.00
19_K	163_L	0.947	1.00
123_H	126_F	0.942	1.00
20_L	144_I	0.942	1.00
66_F	70_W	0.922	1.00
117_G	120_R	0.920	1.00
66_F	89_W	0.917	1.00
53_I	57_G	0.902	1.00
17_A	42_A	0.888	1.00
74_V	87_F	0.884	1.00
87_F	92_F	0.881	1.00
68_L	71_W	0.881	1.00
133_R	137_D	0.874	1.00
17_A	39_L	0.874	1.00
57_G	61_G	0.870	1.00
70_W	75_I	0.869	1.00
64_G	68_L	0.849	1.00
156_T	160_L	0.847	1.00
103_F	107_G	0.847	1.00
11_D	14_L	0.846	1.00
17_A	21_R	0.841	1.00
80_N	86_L	0.824	1.00
49_R	115_L	0.821	1.00
32_S	36_V	0.821	1.00
38_G	41_E	0.820	1.00
131_F	141_F	0.812	1.00
13_L	140_F	0.811	1.00
23_A	159_F	0.806	1.00
111_G	115_L	0.804	1.00
27_R	145_E	0.802	1.00
148_D	151_F	0.799	1.00
71_W	75_I	0.795	1.00
85_P	88_S	0.794	1.00
48_S	51_P	0.790	1.00
69_Q	95_I	0.786	1.00
106_L	109_V	0.786	1.00
130_R	133_R	0.785	1.00
71_W	74_V	0.767	1.00
37_H	40_D	0.766	1.00
67_L	70_W	0.758	1.00
3_L	157_R	0.752	1.00
58_G	100_T	0.749	1.00
88_S	92_F	0.747	1.00
113_L	119_P	0.745	1.00
4_L	128_V	0.742	1.00
129_P	132_D	0.738	1.00
6_E	135_A	0.738	1.00
14_L	18_R	0.731	1.00
57_G	106_L	0.730	1.00
78_P	86_L	0.726	1.00
10_P	36_V	0.717	1.00
41_E	44_G	0.713	1.00
42_A	45_L	0.713	1.00
16_A	163_L	0.708	1.00
105_A	109_V	0.701	1.00
3_L	156_T	0.698	1.00
28_M	142_L	0.695	1.00
93_I	97_F	0.693	1.00
6_E	130_R	0.689	1.00
59_L	62_A	0.687	1.00
25_Y	156_T	0.683	1.00
36_V	39_L	0.676	1.00
13_L	16_A	0.671	1.00
94_P	100_T	0.669	1.00
23_A	162_S	0.666	1.00
73_S	79_L	0.659	1.00
46_K	49_R	0.658	1.00
54_V	107_G	0.658	1.00
10_P	14_L	0.657	1.00
6_E	167_E	0.656	1.00
30_A	142_L	0.654	1.00
40_D	43_L	0.650	1.00
14_L	42_A	0.649	1.00
108_A	112_M	0.648	1.00
4_L	143_C	0.644	1.00
159_F	162_S	0.643	1.00
89_W	93_I	0.642	1.00
10_P	34_F	0.642	1.00
47_R	52_L	0.637	1.00
81_I	86_L	0.637	1.00
29_D	45_L	0.636	1.00
73_S	86_L	0.635	1.00
95_I	99_L	0.633	1.00
17_A	142_L	0.629	1.00
13_L	39_L	0.623	1.00
132_D	169_E	0.622	1.00
160_L	165_A	0.621	1.00
32_S	35_P	0.621	1.00
25_Y	159_F	0.617	1.00
161_E	165_A	0.616	1.00
36_V	140_F	0.614	1.00
10_P	38_G	0.614	1.00
60_T	63_L	0.611	1.00
20_L	23_A	0.611	1.00
103_F	106_L	0.610	1.00
67_L	71_W	0.610	1.00
33_P	39_L	0.603	1.00
90_P	95_I	0.601	1.00
47_R	51_P	0.597	1.00
98_E	102_L	0.595	1.00
85_P	90_P	0.593	1.00
93_I	96_T	0.584	1.00
98_E	101_V	0.581	1.00
62_A	104_A	0.580	1.00
50_L	108_A	0.579	1.00
128_V	169_E	0.579	1.00
32_S	39_L	0.579	1.00
13_L	32_S	0.578	1.00
61_G	65_G	0.576	1.00
165_A	168_V	0.576	1.00
65_G	96_T	0.574	1.00
18_R	21_R	0.573	1.00
68_L	99_L	0.573	1.00
88_S	91_A	0.571	1.00
61_G	103_F	0.566	1.00
149_P	152_D	0.565	1.00
21_R	28_M	0.564	1.00
94_P	98_E	0.563	1.00
90_P	93_I	0.563	1.00
72_T	95_I	0.558	1.00
65_G	97_F	0.557	1.00
56_I	63_L	0.557	1.00
13_L	17_A	0.555	1.00
72_T	79_L	0.552	1.00
60_T	107_G	0.552	1.00
60_T	67_L	0.549	1.00
56_I	107_G	0.549	1.00
4_L	141_F	0.548	1.00
57_G	60_T	0.545	1.00
66_F	93_I	0.545	1.00
33_P	36_V	0.544	1.00
30_A	43_L	0.543	1.00
91_A	94_P	0.542	1.00
91_A	95_I	0.541	1.00
73_S	88_S	0.536	1.00
114_A	117_G	0.536	1.00
70_W	73_S	0.534	1.00
49_R	53_I	0.531	1.00
50_L	111_G	0.530	1.00
6_E	166_E	0.529	1.00
17_A	28_M	0.529	1.00
31_Y	131_F	0.528	1.00
129_P	169_E	0.524	1.00
132_D	139_R	0.519	1.00
38_G	44_G	0.518	1.00
150_K	156_T	0.514	1.00
65_G	68_L	0.504	0.99
13_L	139_R	0.502	0.99
151_F	156_T	0.500	0.99

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
1x60A	1	0.1941	28.5	0.929	Contact Map
1utaA	1	0.3588	28.5	0.929	Contact Map
4i0uA	4	0.5941	11.3	0.941	Contact Map
4ev6A	3	0.6059	10.6	0.942	Contact Map
3a9sA	5	0.9529	10.1	0.942	Contact Map
2lfvA	1	0.2353	9.3	0.943	Contact Map
4fp1A	5	0.6353	8.9	0.943	Contact Map
2qrrA	2	0.2	7.2	0.946	Contact Map
3ju3A	4	0.5588	7	0.946	Contact Map
1gccA	1	0.2176	6.9	0.946	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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