DUF4197 - PFAM28P - GREMLIN Contacts

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DUF4197 - Protein of unknown function (DUF4197)

PFAM:	PF13852	Sequences: NLSNAEIAAGLKEALEVGTENAVAKLGKTDGFLGNPAVKIPLPEELQKVEKTLRKIGMGKLVDELVLSMNRAAEDAAPEAKPIFVDAIKQMTIQDAKGILKGGDDAATQYFKRKTSAQLTAAFKPIVKKSLDKVGATKYYNDLAGKYNKAIPLVKKVNPDLDDYVTEKALDGLFLMIAEEEKKIRKNPAARTTDLLKKVFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	201 (200)
Sequences:	8903 (5526)
Seq/√Len:	390.7
META:	0.913

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_D	109_Q	3.819	1.00
79_E	122_A	3.046	1.00
33_L	67_L	3.031	1.00
30_D	34_G	3.004	1.00
112_K	116_S	2.474	1.00
7_I	97_K	2.361	1.00
26_L	38_V	2.246	1.00
6_E	198_K	2.240	1.00
168_K	171_D	2.157	1.00
109_Q	112_K	2.137	1.00
67_L	71_R	2.130	1.00
35_N	176_M	2.127	1.00
78_P	82_P	2.066	1.00
180_E	183_K	2.009	1.00
90_Q	114_K	1.950	1.00
128_K	162_D	1.920	1.00
104_D	182_K	1.912	1.00
86_D	118_Q	1.909	1.00
97_K	101_K	1.897	1.00
75_D	133_K	1.883	1.00
50_E	54_R	1.877	1.00
128_K	132_D	1.875	1.00
86_D	90_Q	1.848	1.00
81_K	85_V	1.833	1.00
26_L	176_M	1.822	1.00
13_E	16_E	1.798	1.00
75_D	130_S	1.785	1.00
183_K	187_N	1.717	1.00
117_A	121_A	1.715	1.00
124_K	163_D	1.712	1.00
120_T	167_E	1.704	1.00
61_L	64_E	1.674	1.00
120_T	163_D	1.645	1.00
104_D	186_K	1.615	1.00
44_E	47_Q	1.614	1.00
37_A	179_E	1.609	1.00
30_D	71_R	1.583	1.00
20_E	81_K	1.581	1.00
105_D	182_K	1.557	1.00
58_M	61_L	1.538	1.00
105_D	178_A	1.531	1.00
60_K	64_E	1.520	1.00
52_T	55_K	1.514	1.00
194_D	197_K	1.501	1.00
17_V	21_N	1.479	1.00
79_E	126_I	1.473	1.00
85_V	89_K	1.451	1.00
32_F	77_A	1.431	1.00
37_A	41_P	1.422	1.00
109_Q	113_R	1.401	1.00
175_L	179_E	1.395	1.00
124_K	128_K	1.388	1.00
183_K	190_A	1.370	1.00
167_E	171_D	1.363	1.00
94_Q	98_G	1.357	1.00
80_A	123_F	1.356	1.00
47_Q	50_E	1.351	1.00
191_R	196_L	1.346	1.00
179_E	182_K	1.339	1.00
135_G	138_K	1.329	1.00
79_E	82_P	1.324	1.00
131_L	136_A	1.296	1.00
50_E	66_V	1.288	1.00
20_E	24_A	1.282	1.00
160_D	163_D	1.279	1.00
116_S	120_T	1.267	1.00
124_K	162_D	1.266	1.00
13_E	193_T	1.254	1.00
182_K	186_K	1.254	1.00
37_A	175_L	1.253	1.00
82_P	86_D	1.249	1.00
93_I	96_A	1.247	1.00
3_S	6_E	1.246	1.00
16_E	85_V	1.245	1.00
163_D	167_E	1.236	1.00
138_K	142_D	1.235	1.00
97_K	100_L	1.225	1.00
38_V	172_G	1.202	1.00
54_R	59_G	1.199	1.00
9_A	195_L	1.198	1.00
39_K	66_V	1.183	1.00
7_I	100_L	1.158	1.00
71_R	74_E	1.154	1.00
176_M	179_E	1.152	1.00
103_G	106_A	1.138	1.00
16_E	89_K	1.137	1.00
118_Q	121_A	1.137	1.00
96_A	100_L	1.135	1.00
32_F	169_A	1.123	1.00
52_T	56_I	1.116	1.00
49_V	52_T	1.111	1.00
54_R	63_D	1.089	1.00
139_Y	142_D	1.080	1.00
4_N	8_A	1.078	1.00
59_G	63_D	1.077	1.00
2_L	10_G	1.066	1.00
144_A	159_P	1.060	1.00
164_Y	168_K	1.060	1.00
13_E	195_L	1.059	1.00
6_E	9_A	1.056	1.00
19_T	22_A	1.053	1.00
191_R	194_D	1.052	1.00
5_A	9_A	1.043	1.00
50_E	62_V	1.039	1.00
130_S	134_V	1.036	1.00
30_D	33_L	1.027	1.00
62_V	143_L	1.022	1.00
16_E	20_E	1.020	1.00
94_Q	97_K	1.017	1.00
19_T	84_F	1.014	1.00
65_L	143_L	1.007	1.00
26_L	77_A	1.006	1.00
132_D	137_T	0.994	1.00
187_N	190_A	0.992	1.00
47_Q	51_K	0.988	1.00
75_D	78_P	0.986	1.00
33_L	66_V	0.985	1.00
68_S	139_Y	0.979	1.00
78_P	81_K	0.978	1.00
8_A	96_A	0.976	1.00
42_L	65_L	0.975	1.00
129_K	133_K	0.974	1.00
51_K	55_K	0.973	1.00
189_A	192_T	0.962	1.00
7_I	11_L	0.955	1.00
103_G	109_Q	0.952	1.00
130_S	133_K	0.933	1.00
2_L	7_I	0.932	1.00
18_G	177_I	0.931	1.00
25_K	176_M	0.930	1.00
25_K	28_K	0.926	1.00
17_V	192_T	0.922	1.00
117_A	120_T	0.916	1.00
45_E	48_K	0.911	1.00
119_L	170_L	0.906	1.00
141_N	145_G	0.905	1.00
147_Y	154_V	0.902	1.00
99_I	107_A	0.902	1.00
158_N	163_D	0.902	1.00
33_L	39_K	0.901	1.00
116_S	171_D	0.892	1.00
112_K	171_D	0.891	1.00
35_N	38_V	0.887	1.00
120_T	170_L	0.885	1.00
4_N	97_K	0.883	1.00
87_A	114_K	0.883	1.00
49_V	144_A	0.878	1.00
68_S	134_V	0.878	1.00
64_E	68_S	0.868	1.00
21_N	24_A	0.864	1.00
27_G	78_P	0.854	1.00
116_S	170_L	0.847	1.00
146_K	149_K	0.843	1.00
17_V	193_T	0.843	1.00
44_E	48_K	0.828	1.00
194_D	198_K	0.828	1.00
129_K	132_D	0.826	1.00
122_A	126_I	0.825	1.00
69_M	165_V	0.825	1.00
17_V	20_E	0.821	1.00
83_I	122_A	0.821	1.00
126_I	129_K	0.816	1.00
25_K	35_N	0.815	1.00
127_V	166_T	0.812	1.00
193_T	196_L	0.811	1.00
38_V	176_M	0.803	1.00
53_L	58_M	0.791	1.00
21_N	180_E	0.786	1.00
34_G	39_K	0.785	1.00
87_A	115_T	0.785	1.00
98_G	113_R	0.782	1.00
127_V	165_V	0.778	1.00
131_L	162_D	0.777	1.00
34_G	71_R	0.768	1.00
120_T	166_T	0.759	1.00
38_V	175_L	0.752	1.00
65_L	69_M	0.749	1.00
168_K	175_L	0.745	1.00
141_N	162_D	0.740	1.00
69_M	131_L	0.739	1.00
192_T	196_L	0.737	1.00
116_S	167_E	0.737	1.00
36_P	41_P	0.735	1.00
151_I	154_V	0.734	1.00
180_E	190_A	0.731	1.00
48_K	52_T	0.731	1.00
32_F	123_F	0.729	1.00
9_A	13_E	0.728	1.00
11_L	93_I	0.727	1.00
5_A	8_A	0.721	1.00
32_F	173_L	0.714	1.00
46_L	140_Y	0.713	1.00
19_T	23_V	0.711	1.00
142_D	145_G	0.709	1.00
21_N	25_K	0.708	1.00
21_N	183_K	0.703	1.00
19_T	88_I	0.700	1.00
63_D	66_V	0.698	1.00
24_A	81_K	0.696	1.00
75_D	129_K	0.694	1.00
118_Q	122_A	0.693	1.00
13_E	196_L	0.692	0.99
61_L	143_L	0.690	0.99
21_N	192_T	0.686	0.99
53_L	62_V	0.683	0.99
17_V	196_L	0.673	0.99
65_L	68_S	0.673	0.99
13_E	17_V	0.673	0.99
42_L	66_V	0.671	0.99
90_Q	118_Q	0.670	0.99
77_A	173_L	0.658	0.99
79_E	129_K	0.649	0.99
88_I	111_F	0.649	0.99
135_G	139_Y	0.647	0.99
86_D	89_K	0.646	0.99
23_V	81_K	0.641	0.99
116_S	174_F	0.641	0.99
64_E	67_L	0.635	0.99
139_Y	143_L	0.633	0.99
23_V	77_A	0.631	0.99
8_A	93_I	0.631	0.99
183_K	186_K	0.631	0.99
16_E	19_T	0.630	0.99
23_V	26_L	0.627	0.99
120_T	124_K	0.625	0.99
30_D	67_L	0.623	0.99
68_S	137_T	0.609	0.99
140_Y	144_A	0.607	0.99
172_G	176_M	0.606	0.99
105_D	112_K	0.606	0.99
111_F	116_S	0.603	0.99
188_P	194_D	0.602	0.99
50_E	53_L	0.602	0.99
146_K	150_A	0.601	0.99
8_A	12_K	0.598	0.99
162_D	165_V	0.594	0.98
142_D	146_K	0.592	0.98
189_A	193_T	0.591	0.98
104_D	109_Q	0.589	0.98
149_K	152_P	0.589	0.98
50_E	59_G	0.589	0.98
42_L	69_M	0.589	0.98
53_L	143_L	0.588	0.98
189_A	194_D	0.588	0.98
93_I	97_K	0.587	0.98
20_E	85_V	0.584	0.98
4_N	7_I	0.582	0.98
132_D	141_N	0.582	0.98
136_A	165_V	0.582	0.98
99_I	110_Y	0.575	0.98
181_E	185_R	0.573	0.98
131_L	165_V	0.570	0.98
156_K	159_P	0.570	0.98
7_I	101_K	0.570	0.98
178_A	182_K	0.567	0.98
8_A	19_T	0.567	0.98
131_L	137_T	0.566	0.98
136_A	142_D	0.564	0.98
17_V	177_I	0.563	0.98
80_A	169_A	0.560	0.98
27_G	77_A	0.559	0.98
121_A	124_K	0.558	0.98
172_G	175_L	0.557	0.98
131_L	161_L	0.555	0.98
90_Q	94_Q	0.551	0.98
84_F	119_L	0.551	0.98
144_A	157_V	0.550	0.97
10_G	13_E	0.549	0.97
61_L	139_Y	0.548	0.97
82_P	85_V	0.546	0.97
33_L	71_R	0.545	0.97
68_S	136_A	0.544	0.97
29_T	71_R	0.543	0.97
184_I	191_R	0.541	0.97
62_V	65_L	0.541	0.97
22_A	177_I	0.540	0.97
83_I	115_T	0.539	0.97
19_T	111_F	0.538	0.97
4_N	96_A	0.537	0.97
166_T	169_A	0.535	0.97
124_K	166_T	0.532	0.97
170_L	175_L	0.531	0.97
94_Q	114_K	0.531	0.97
62_V	66_V	0.526	0.97
173_L	176_M	0.524	0.97
175_L	178_A	0.524	0.97
65_L	137_T	0.521	0.97
41_P	47_Q	0.521	0.97
19_T	81_K	0.518	0.96
144_A	147_Y	0.515	0.96
83_I	118_Q	0.509	0.96
145_G	159_P	0.508	0.96
90_Q	110_Y	0.505	0.96
191_R	197_K	0.504	0.96
54_R	62_V	0.503	0.96
19_T	177_I	0.502	0.96
145_G	149_K	0.502	0.96
24_A	28_K	0.501	0.96
180_E	184_I	0.500	0.96
192_T	197_K	0.500	0.96

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
3lapA	6	0.5672	54.2	0.926	Contact Map
1b4aA	5	0.5771	31.8	0.935	Contact Map
3v4gA	5	0.607	19.8	0.941	Contact Map
1b4bA	4	0.3532	18.7	0.942	Contact Map
1xxaA	4	0.3582	16.5	0.943	Contact Map
4u6uB	1	0.7512	14.4	0.945	Contact Map
2zfzA	4	0.393	13	0.946	Contact Map
2w72B	1	0.6965	9.1	0.95	Contact Map
2p5mA	4	0.408	8.8	0.95	Contact Map
4o8aA	2	0.2189	8.8	0.95	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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