GldM_N - PFAM28P - GREMLIN Contacts

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GldM_N - GldM N-terminal domain

PFAM:	PF12081	Sequences: EVLNAFKLVNESLEKSNENVDEKNEAIYASFEAKAKENPEKVKPWYEKAQEVKKLSDELYNYIEDLKDELIKEAGGKDGDLGDIKKKDNLDAPTRLMIGEGGKGKGKELKKKINEYREKLLALLDDIPKDRKSIEKNLSTDDPKKVKDKDGKKKDWEEYNFEGMPLVAALTILSKLQNDVKNAESEVLNYLLSN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	194 (193)
Sequences:	6450 (5030)
Seq/√Len:	362.1
META:	0.924

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_K	108_E	3.883	1.00
46_Y	50_Q	3.582	1.00
115_E	119_K	3.379	1.00
55_L	119_K	3.210	1.00
57_D	61_N	2.726	1.00
69_E	105_K	2.663	1.00
43_K	47_E	2.618	1.00
111_K	115_E	2.559	1.00
175_K	179_D	2.547	1.00
62_Y	112_K	2.477	1.00
107_K	111_K	2.366	1.00
110_K	114_N	2.353	1.00
54_K	58_E	2.279	1.00
158_E	162_E	2.183	1.00
55_L	58_E	2.167	1.00
58_E	112_K	2.163	1.00
10_N	14_E	2.092	1.00
108_E	112_K	2.057	1.00
64_E	68_D	2.053	1.00
118_E	122_A	2.004	1.00
65_D	69_E	1.934	1.00
51_E	54_K	1.917	1.00
110_K	157_E	1.892	1.00
112_K	115_E	1.881	1.00
63_I	173_L	1.861	1.00
56_S	116_Y	1.812	1.00
107_K	157_E	1.801	1.00
61_N	65_D	1.797	1.00
25_E	29_A	1.790	1.00
86_K	89_N	1.754	1.00
32_E	50_Q	1.728	1.00
119_K	122_A	1.708	1.00
67_K	177_Q	1.703	1.00
68_D	72_K	1.674	1.00
29_A	32_E	1.621	1.00
60_Y	177_Q	1.611	1.00
52_V	123_L	1.605	1.00
52_V	120_L	1.602	1.00
32_E	36_K	1.550	1.00
32_E	46_Y	1.547	1.00
73_E	95_R	1.538	1.00
28_Y	53_K	1.537	1.00
127_I	130_D	1.515	1.00
51_E	55_L	1.512	1.00
53_K	184_E	1.482	1.00
53_K	57_D	1.469	1.00
89_N	92_A	1.443	1.00
114_N	118_E	1.435	1.00
106_G	157_E	1.414	1.00
47_E	51_E	1.407	1.00
96_L	105_K	1.396	1.00
174_S	177_Q	1.388	1.00
21_D	25_E	1.357	1.00
56_S	180_V	1.351	1.00
29_A	33_A	1.340	1.00
155_D	158_E	1.330	1.00
111_K	114_N	1.311	1.00
62_Y	66_L	1.307	1.00
64_E	177_Q	1.299	1.00
35_A	43_K	1.254	1.00
91_D	95_R	1.254	1.00
117_R	121_L	1.253	1.00
44_P	48_K	1.248	1.00
69_E	72_K	1.242	1.00
69_E	73_E	1.239	1.00
51_E	119_K	1.229	1.00
93_P	169_A	1.228	1.00
128_P	131_R	1.210	1.00
59_L	180_V	1.201	1.00
136_K	139_S	1.198	1.00
116_Y	120_L	1.193	1.00
33_A	36_K	1.187	1.00
50_Q	53_K	1.185	1.00
57_D	181_K	1.184	1.00
59_L	113_I	1.166	1.00
74_A	166_L	1.154	1.00
108_E	111_K	1.152	1.00
35_A	42_V	1.127	1.00
21_D	181_K	1.126	1.00
90_L	163_G	1.117	1.00
121_L	135_E	1.113	1.00
22_E	25_E	1.081	1.00
67_K	174_S	1.061	1.00
52_V	187_V	1.058	1.00
128_P	132_K	1.054	1.00
18_E	22_E	1.049	1.00
99_G	103_K	1.048	1.00
66_L	109_L	1.047	1.00
70_L	166_L	1.047	1.00
47_E	50_Q	1.042	1.00
16_S	20_V	1.036	1.00
120_L	183_A	1.034	1.00
48_K	51_E	1.023	1.00
28_Y	49_A	1.021	1.00
69_E	96_L	1.020	1.00
50_Q	54_K	1.019	1.00
40_E	44_P	1.015	1.00
35_A	46_Y	1.012	1.00
39_P	43_K	1.005	1.00
60_Y	64_E	0.973	1.00
9_V	171_T	0.971	1.00
34_K	37_E	0.966	1.00
63_I	180_V	0.961	1.00
24_N	188_L	0.957	1.00
62_Y	65_D	0.954	1.00
65_D	68_D	0.953	1.00
1_E	4_N	0.950	1.00
107_K	110_K	0.941	1.00
148_D	154_K	0.933	1.00
71_I	76_G	0.927	1.00
114_N	140_T	0.924	1.00
33_A	37_E	0.921	1.00
12_S	175_K	0.920	1.00
133_S	137_N	0.917	1.00
129_K	132_K	0.917	1.00
115_E	118_E	0.915	1.00
35_A	39_P	0.912	1.00
99_G	104_G	0.906	1.00
58_E	62_Y	0.906	1.00
186_E	189_N	0.905	1.00
119_K	123_L	0.903	1.00
104_G	107_K	0.901	1.00
73_E	96_L	0.888	1.00
59_L	112_K	0.877	1.00
44_P	47_E	0.863	1.00
45_W	48_K	0.858	1.00
7_K	87_K	0.856	1.00
135_E	139_S	0.856	1.00
70_L	96_L	0.853	1.00
59_L	63_I	0.849	1.00
139_S	143_P	0.843	1.00
81_L	84_I	0.842	1.00
17_N	178_N	0.836	1.00
63_I	109_L	0.834	1.00
139_S	142_D	0.831	1.00
10_N	174_S	0.828	1.00
38_N	41_K	0.819	1.00
90_L	93_P	0.816	1.00
62_Y	105_K	0.813	1.00
60_Y	181_K	0.812	1.00
31_F	49_A	0.809	1.00
84_I	166_L	0.799	1.00
66_L	97_M	0.799	1.00
94_T	162_E	0.789	1.00
172_I	175_K	0.783	1.00
20_V	23_K	0.780	1.00
26_A	29_A	0.774	1.00
10_N	67_K	0.773	1.00
55_L	115_E	0.770	1.00
73_E	92_A	0.764	1.00
74_A	86_K	0.762	1.00
185_S	189_N	0.760	1.00
92_A	95_R	0.755	1.00
164_M	169_A	0.753	1.00
132_K	135_E	0.753	1.00
140_T	143_P	0.752	1.00
90_L	94_T	0.752	1.00
126_D	131_R	0.746	1.00
13_L	174_S	0.743	1.00
84_I	87_K	0.742	1.00
66_L	96_L	0.740	1.00
14_E	18_E	0.740	1.00
31_F	45_W	0.733	1.00
127_I	131_R	0.732	1.00
121_L	131_R	0.731	1.00
55_L	116_Y	0.731	1.00
34_K	192_L	0.729	1.00
28_Y	188_L	0.722	1.00
107_K	155_D	0.721	1.00
136_K	142_D	0.720	0.99
23_K	27_I	0.715	0.99
147_K	153_K	0.713	0.99
182_N	185_S	0.712	0.99
137_N	140_T	0.711	0.99
72_K	77_K	0.710	0.99
132_K	136_K	0.709	0.99
80_D	83_D	0.709	0.99
154_K	158_E	0.706	0.99
52_V	188_L	0.705	0.99
32_E	35_A	0.703	0.99
164_M	172_I	0.700	0.99
12_S	179_D	0.700	0.99
51_E	123_L	0.699	0.99
151_G	154_K	0.697	0.99
52_V	55_L	0.696	0.99
181_K	184_E	0.696	0.99
71_I	170_L	0.695	0.99
30_S	33_A	0.690	0.99
9_V	13_L	0.688	0.99
4_N	7_K	0.685	0.99
187_V	191_L	0.682	0.99
165_P	168_A	0.682	0.99
135_E	140_T	0.678	0.99
66_L	105_K	0.677	0.99
138_L	141_D	0.676	0.99
22_E	26_A	0.675	0.99
61_N	64_E	0.675	0.99
138_L	142_D	0.674	0.99
90_L	162_E	0.673	0.99
118_E	121_L	0.670	0.99
55_L	59_L	0.667	0.99
149_K	152_K	0.666	0.99
172_I	176_L	0.665	0.99
12_S	20_V	0.663	0.99
71_I	74_A	0.662	0.99
136_K	141_D	0.662	0.99
125_D	128_P	0.662	0.99
58_E	61_N	0.658	0.99
70_L	93_P	0.654	0.99
15_K	18_E	0.649	0.99
42_V	45_W	0.646	0.99
148_D	152_K	0.642	0.99
144_K	147_K	0.642	0.99
94_T	98_I	0.640	0.99
167_V	171_T	0.640	0.99
160_N	172_I	0.638	0.99
142_D	153_K	0.638	0.99
7_K	167_V	0.635	0.99
131_R	135_E	0.635	0.99
63_I	176_L	0.628	0.99
4_N	87_K	0.627	0.99
137_N	142_D	0.620	0.99
60_Y	180_V	0.616	0.98
59_L	62_Y	0.614	0.98
137_N	141_D	0.610	0.98
14_E	67_K	0.607	0.98
135_E	141_D	0.605	0.98
190_Y	193_S	0.604	0.98
68_D	71_I	0.601	0.98
28_Y	184_E	0.599	0.98
28_Y	31_F	0.595	0.98
27_I	30_S	0.595	0.98
48_K	125_D	0.594	0.98
114_N	117_R	0.594	0.98
58_E	119_K	0.592	0.98
36_K	39_P	0.589	0.98
77_K	84_I	0.587	0.98
101_G	104_G	0.582	0.98
178_N	182_N	0.581	0.98
70_L	169_A	0.580	0.98
116_Y	119_K	0.577	0.98
30_S	34_K	0.575	0.98
113_I	180_V	0.573	0.98
39_P	42_V	0.567	0.97
7_K	11_E	0.567	0.97
147_K	150_D	0.567	0.97
92_A	96_L	0.566	0.97
65_D	105_K	0.566	0.97
143_P	146_V	0.565	0.97
31_F	188_L	0.564	0.97
95_R	100_E	0.562	0.97
12_S	16_S	0.562	0.97
55_L	123_L	0.561	0.97
34_K	42_V	0.561	0.97
52_V	119_K	0.559	0.97
24_N	185_S	0.556	0.97
41_K	44_P	0.555	0.97
59_L	116_Y	0.549	0.97
9_V	172_I	0.547	0.97
64_E	67_K	0.546	0.97
62_Y	108_E	0.544	0.97
89_N	93_P	0.543	0.97
94_T	163_G	0.542	0.97
74_A	92_A	0.539	0.96
189_N	193_S	0.539	0.96
98_I	162_E	0.537	0.96
134_I	137_N	0.537	0.96
187_V	190_Y	0.537	0.96
23_K	189_N	0.535	0.96
48_K	123_L	0.535	0.96
2_V	7_K	0.533	0.96
124_L	131_R	0.529	0.96
165_P	174_S	0.529	0.96
26_A	30_S	0.528	0.96
56_S	60_Y	0.528	0.96
23_K	185_S	0.528	0.96
24_N	27_I	0.527	0.96
27_I	189_N	0.526	0.96
113_I	176_L	0.526	0.96
137_N	143_P	0.524	0.96
116_Y	180_V	0.523	0.96
138_L	143_P	0.521	0.96
28_Y	46_Y	0.518	0.96
32_E	53_K	0.514	0.95
55_L	122_A	0.513	0.95
11_E	14_E	0.513	0.95
38_N	43_K	0.511	0.95
118_E	135_E	0.509	0.95
112_K	116_Y	0.504	0.95
9_V	12_S	0.500	0.95

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
1t3jA	2	0.3196	9.1	0.925	Contact Map
2ieqA	3	0.3557	7.2	0.928	Contact Map
1i4dA	2	0.5052	6.4	0.93	Contact Map
4k1pA	1	0.3196	4.9	0.934	Contact Map
2marA	1	0.3763	3	0.94	Contact Map
4gipD	3	0.1546	2.8	0.941	Contact Map
2ch7A	2	0.3454	2.7	0.942	Contact Map
1k04A	2	0.3505	2.5	0.943	Contact Map
1pehA	1	0.1701	2.1	0.945	Contact Map
4e9mA	2	0.2732	2	0.945	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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