DUF4126 - PFAM28P - GREMLIN Contacts

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DUF4126 - Domain of unknown function (DUF4126)

PFAM:	PF13548	Sequences: IALALGLAAAAGLRLYAPLLVLGLAARFGWLDLPPGLAWLGSPWVLGAAGVLALVEFVADKIPWVDSLWDAVHTFIRPPAGALLAAAAAGDLDMDPPAAWVLAALLGGGVALAVHGAKAGTRAAVNASPEPFSNPVVSLAEDVLAVGLSWLALLHPVLALVLVALLLVLAVWLLRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (169)
Sequences:	13208 (7893)
Seq/√Len:	607.2
META:	0.92

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_A	41_G	4.051	1.00
125_V	137_V	3.916	1.00
20_L	50_G	3.210	1.00
61_K	139_L	2.907	1.00
27_R	43_P	2.890	1.00
43_P	47_G	2.772	1.00
168_V	172_W	2.693	1.00
21_V	149_S	2.560	1.00
42_S	45_V	2.381	1.00
35_P	38_A	2.317	1.00
157_V	161_V	2.236	1.00
59_A	65_V	2.220	1.00
23_G	46_L	2.168	1.00
44_W	47_G	2.044	1.00
10_A	148_L	2.036	1.00
24_L	28_F	1.903	1.00
129_P	133_S	1.903	1.00
81_G	107_G	1.865	1.00
74_T	115_H	1.841	1.00
120_G	124_A	1.762	1.00
24_L	46_L	1.739	1.00
159_A	163_V	1.635	1.00
25_A	30_W	1.576	1.00
148_L	159_A	1.538	1.00
112_L	116_G	1.532	1.00
150_W	154_L	1.505	1.00
169_L	173_L	1.499	1.00
70_D	73_H	1.499	1.00
27_R	46_L	1.498	1.00
78_P	112_L	1.468	1.00
139_L	143_V	1.463	1.00
4_A	8_A	1.454	1.00
132_F	135_P	1.439	1.00
61_K	142_D	1.428	1.00
46_L	50_G	1.421	1.00
109_G	113_A	1.408	1.00
47_G	51_V	1.403	1.00
120_G	123_A	1.385	1.00
26_A	33_L	1.378	1.00
136_V	140_A	1.373	1.00
38_A	41_G	1.354	1.00
115_H	118_K	1.325	1.00
14_R	53_A	1.308	1.00
43_P	46_L	1.294	1.00
126_N	134_N	1.286	1.00
85_A	89_A	1.263	1.00
101_V	105_L	1.258	1.00
132_F	136_V	1.254	1.00
75_F	78_P	1.232	1.00
20_L	46_L	1.227	1.00
73_H	76_I	1.224	1.00
24_L	50_G	1.224	1.00
136_V	139_L	1.223	1.00
22_L	84_L	1.209	1.00
169_L	172_W	1.196	1.00
117_A	120_G	1.194	1.00
11_A	18_P	1.194	1.00
116_G	120_G	1.193	1.00
115_H	119_A	1.189	1.00
145_A	149_S	1.187	1.00
130_E	133_S	1.186	1.00
2_A	160_L	1.183	1.00
119_A	123_A	1.181	1.00
15_L	59_A	1.172	1.00
100_W	104_A	1.169	1.00
124_A	127_A	1.167	1.00
133_S	136_V	1.163	1.00
96_P	99_A	1.156	1.00
135_P	139_L	1.154	1.00
19_L	49_A	1.151	1.00
21_V	25_A	1.133	1.00
54_L	58_V	1.127	1.00
123_A	127_A	1.105	1.00
140_A	144_L	1.101	1.00
71_A	75_F	1.095	1.00
144_L	148_L	1.094	1.00
89_A	92_L	1.090	1.00
155_H	158_L	1.089	1.00
164_A	168_V	1.076	1.00
160_L	164_A	1.076	1.00
150_W	155_H	1.065	1.00
125_V	133_S	1.062	1.00
27_R	41_G	1.058	1.00
62_I	65_V	1.054	1.00
121_T	124_A	1.050	1.00
110_V	113_A	1.048	1.00
96_P	100_W	1.048	1.00
68_L	71_A	1.041	1.00
86_A	104_A	1.039	1.00
74_T	119_A	1.036	1.00
47_G	50_G	1.016	1.00
81_G	111_A	1.013	1.00
53_A	57_F	1.012	1.00
45_V	48_A	0.997	1.00
72_V	75_F	0.983	1.00
117_A	121_T	0.973	1.00
44_W	48_A	0.970	1.00
22_L	31_L	0.963	1.00
140_A	143_V	0.963	1.00
98_A	101_V	0.955	1.00
77_R	118_K	0.955	1.00
99_A	102_L	0.953	1.00
80_A	84_L	0.945	1.00
67_S	71_A	0.945	1.00
15_L	80_A	0.944	1.00
113_A	116_G	0.943	1.00
91_D	96_P	0.941	1.00
152_A	159_A	0.937	1.00
11_A	80_A	0.933	1.00
20_L	53_A	0.932	1.00
57_F	139_L	0.931	1.00
32_D	35_P	0.930	1.00
160_L	163_V	0.928	1.00
130_E	134_N	0.914	1.00
40_L	87_A	0.905	1.00
138_S	142_D	0.903	1.00
165_L	169_L	0.902	1.00
51_V	55_V	0.901	1.00
10_A	149_S	0.898	1.00
121_T	125_V	0.894	1.00
85_A	88_A	0.887	1.00
101_V	104_A	0.883	1.00
168_V	171_V	0.883	1.00
167_L	171_V	0.880	1.00
7_L	22_L	0.879	1.00
143_V	146_V	0.869	1.00
124_A	128_S	0.868	1.00
59_A	69_W	0.863	1.00
67_S	126_N	0.860	1.00
116_G	119_A	0.858	1.00
10_A	18_P	0.846	1.00
82_A	104_A	0.845	1.00
8_A	85_A	0.829	1.00
2_A	6_G	0.826	1.00
114_V	117_A	0.820	1.00
125_V	128_S	0.814	1.00
110_V	114_V	0.814	1.00
161_V	165_L	0.813	1.00
149_S	153_L	0.807	1.00
20_L	24_L	0.806	1.00
89_A	103_A	0.806	1.00
4_A	7_L	0.806	1.00
5_L	14_R	0.790	1.00
166_L	170_A	0.787	1.00
158_L	161_V	0.787	1.00
60_D	138_S	0.781	1.00
126_N	130_E	0.766	1.00
98_A	102_L	0.761	1.00
100_W	103_A	0.760	1.00
151_L	155_H	0.754	1.00
165_L	168_V	0.753	1.00
58_V	62_I	0.753	1.00
75_F	79_P	0.751	1.00
40_L	49_A	0.743	1.00
166_L	173_L	0.742	1.00
67_S	70_D	0.737	1.00
74_T	78_P	0.732	1.00
66_D	134_N	0.730	1.00
25_A	29_G	0.725	1.00
83_L	87_A	0.721	1.00
137_V	140_A	0.717	1.00
82_A	108_G	0.714	1.00
159_A	166_L	0.714	1.00
42_S	46_L	0.708	1.00
29_G	32_D	0.707	1.00
45_V	105_L	0.707	1.00
117_A	170_A	0.706	1.00
34_P	37_L	0.704	1.00
45_V	49_A	0.701	1.00
6_G	152_A	0.699	1.00
85_A	107_G	0.698	1.00
81_G	85_A	0.679	1.00
20_L	49_A	0.678	1.00
22_L	26_A	0.678	1.00
19_L	80_A	0.666	1.00
151_L	154_L	0.662	1.00
134_N	137_V	0.659	1.00
55_V	59_A	0.656	1.00
48_A	52_L	0.656	1.00
57_F	142_D	0.652	1.00
131_P	134_N	0.650	1.00
143_V	147_G	0.648	1.00
60_D	142_D	0.644	1.00
22_L	40_L	0.644	1.00
128_S	133_S	0.642	1.00
148_L	152_A	0.640	1.00
17_A	146_V	0.638	1.00
166_L	172_W	0.636	1.00
23_G	27_R	0.633	1.00
9_A	13_L	0.633	1.00
91_D	99_A	0.625	1.00
92_L	97_P	0.620	1.00
8_A	110_V	0.620	1.00
129_P	132_F	0.619	1.00
110_V	163_V	0.617	1.00
62_I	66_D	0.616	1.00
158_L	162_L	0.612	1.00
51_V	54_L	0.610	1.00
49_A	53_A	0.610	1.00
86_A	103_A	0.607	1.00
7_L	84_L	0.606	1.00
97_P	100_W	0.599	1.00
121_T	137_V	0.595	1.00
89_A	96_P	0.586	1.00
113_A	117_A	0.586	1.00
114_V	118_K	0.585	1.00
58_V	65_V	0.585	1.00
29_G	41_G	0.582	1.00
10_A	145_A	0.582	1.00
122_R	134_N	0.582	1.00
129_P	135_P	0.581	1.00
48_A	97_P	0.581	1.00
170_A	173_L	0.580	1.00
131_P	135_P	0.580	1.00
17_A	53_A	0.579	1.00
70_D	119_A	0.579	1.00
39_W	45_V	0.577	1.00
67_S	119_A	0.573	1.00
56_E	141_E	0.572	1.00
10_A	152_A	0.571	1.00
82_A	85_A	0.571	1.00
21_V	146_V	0.570	1.00
91_D	100_W	0.568	1.00
70_D	118_K	0.564	1.00
97_P	101_V	0.563	1.00
25_A	153_L	0.562	1.00
103_A	110_V	0.559	1.00
124_A	129_P	0.559	1.00
74_T	77_R	0.557	1.00
114_V	119_A	0.548	0.99
126_N	129_P	0.548	0.99
73_H	78_P	0.546	0.99
15_L	73_H	0.545	0.99
15_L	76_I	0.545	0.99
101_V	106_L	0.543	0.99
23_G	49_A	0.535	0.99
78_P	115_H	0.532	0.99
23_G	45_V	0.531	0.99
16_Y	52_L	0.527	0.99
55_V	65_V	0.527	0.99
14_R	56_E	0.524	0.99
25_A	28_F	0.524	0.99
148_L	162_L	0.522	0.99
125_V	134_N	0.515	0.99
26_A	32_D	0.515	0.99
3_L	97_P	0.514	0.99
129_P	134_N	0.513	0.99
60_D	122_R	0.513	0.99
69_W	118_K	0.512	0.99
106_L	109_G	0.511	0.99
5_L	110_V	0.508	0.99
110_V	117_A	0.506	0.99
125_V	129_P	0.502	0.99
23_G	50_G	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
2l2tA	2	0.2102	5	0.932	Contact Map
2ks1B	1	0.2102	2.7	0.941	Contact Map
2m20A	2	0.1591	2.1	0.943	Contact Map
1iflA	10	0.267	2	0.944	Contact Map
1ifkA	9	0.2557	2	0.944	Contact Map
4p6vD	1	0.8011	1.6	0.947	Contact Map
2l9uA	2	0.1761	1.5	0.948	Contact Map
1zcdA	1	0.9659	1.5	0.948	Contact Map
4czbA	2	0.9602	1.4	0.949	Contact Map
4xk8I	1	0.1648	1.4	0.949	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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