DUF4293 - PFAM28P - GREMLIN Contacts

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DUF4293 - Domain of unknown function (DUF4293)

PFAM:	PF14126	Sequences: IQRIQTLYLLLAAILAGLLFFFPLASFTGGDGTYTFYALGLSDAGGGVVLATSTWPLLILTILSALLSLITIFLYKNRKLQIRLCRLNILLNLGLLGLFFYYLLFLSLNLSGETFVVGEYGIGAFLPLIAIILLFLANRGIKKDEKLVKSADRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	154 (151)
Sequences:	5918 (4809)
Seq/√Len:	391.3
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_Y	140_G	3.133	1.00
82_I	138_N	2.743	1.00
85_C	138_N	2.541	1.00
78_R	148_V	2.535	1.00
74_L	80_L	2.346	1.00
142_K	146_K	2.276	1.00
88_N	134_L	2.264	1.00
16_A	130_A	2.251	1.00
97_G	101_Y	2.180	1.00
9_L	85_C	2.164	1.00
85_C	141_I	2.104	1.00
80_L	83_R	2.094	1.00
145_E	149_K	2.067	1.00
9_L	141_I	2.059	1.00
14_I	18_L	2.031	1.00
77_N	80_L	2.008	1.00
145_E	148_V	2.001	1.00
12_A	68_S	1.955	1.00
85_C	134_L	1.925	1.00
12_A	134_L	1.894	1.00
68_S	134_L	1.885	1.00
149_K	152_D	1.870	1.00
78_R	145_E	1.828	1.00
70_I	74_L	1.819	1.00
79_K	83_R	1.779	1.00
71_T	84_L	1.772	1.00
26_S	121_G	1.760	1.00
13_A	68_S	1.619	1.00
71_T	85_C	1.606	1.00
68_S	88_N	1.604	1.00
6_T	72_I	1.529	1.00
13_A	17_G	1.523	1.00
136_L	140_G	1.478	1.00
147_L	150_S	1.473	1.00
13_A	69_L	1.468	1.00
15_L	126_L	1.466	1.00
92_N	134_L	1.433	1.00
92_N	130_A	1.431	1.00
8_Y	136_L	1.423	1.00
17_G	65_A	1.419	1.00
82_I	142_K	1.403	1.00
12_A	130_A	1.402	1.00
71_T	88_N	1.378	1.00
89_I	134_L	1.363	1.00
55_W	59_I	1.357	1.00
138_N	142_K	1.355	1.00
13_A	65_A	1.354	1.00
4_I	7_L	1.339	1.00
18_L	22_F	1.339	1.00
89_I	131_I	1.315	1.00
86_R	138_N	1.301	1.00
58_L	62_I	1.294	1.00
7_L	11_L	1.292	1.00
83_R	86_R	1.279	1.00
16_A	64_S	1.278	1.00
93_L	131_I	1.256	1.00
140_G	143_K	1.244	1.00
79_K	145_E	1.241	1.00
38_A	41_L	1.230	1.00
112_G	115_F	1.185	1.00
61_T	95_L	1.168	1.00
12_A	88_N	1.164	1.00
9_L	137_A	1.144	1.00
106_L	109_N	1.143	1.00
74_L	84_L	1.140	1.00
139_R	142_K	1.087	1.00
94_G	98_L	1.085	1.00
1_I	6_T	1.070	1.00
92_N	131_I	1.056	1.00
146_K	150_S	1.052	1.00
66_L	70_I	1.044	1.00
1_I	73_F	1.044	1.00
96_L	128_L	1.044	1.00
4_I	143_K	1.033	1.00
83_R	87_L	1.029	1.00
4_I	8_Y	1.021	1.00
82_I	86_R	1.012	1.00
125_F	129_I	1.002	1.00
80_L	84_L	0.989	1.00
106_L	110_L	0.986	1.00
64_S	92_N	0.981	1.00
34_Y	38_A	0.979	1.00
104_L	108_L	0.973	1.00
67_L	84_L	0.971	1.00
10_L	72_I	0.967	1.00
82_I	140_G	0.966	1.00
9_L	68_S	0.947	1.00
115_F	118_G	0.942	1.00
16_A	65_A	0.942	1.00
39_L	42_S	0.932	1.00
11_L	133_L	0.925	1.00
13_A	72_I	0.919	1.00
16_A	92_N	0.911	1.00
64_S	88_N	0.910	1.00
122_I	126_L	0.906	1.00
64_S	95_L	0.904	1.00
85_C	88_N	0.903	1.00
17_G	21_F	0.901	1.00
151_A	154_L	0.901	1.00
104_L	107_S	0.889	1.00
22_F	123_G	0.883	1.00
107_S	110_L	0.882	1.00
25_A	118_G	0.881	1.00
11_L	15_L	0.877	1.00
29_G	32_G	0.876	1.00
37_Y	40_G	0.872	1.00
37_Y	42_S	0.870	1.00
34_Y	37_Y	0.865	1.00
65_A	69_L	0.845	1.00
64_S	68_S	0.836	1.00
4_I	140_G	0.835	1.00
9_L	71_T	0.820	1.00
137_A	141_I	0.808	1.00
89_I	135_F	0.805	1.00
82_I	148_V	0.801	1.00
103_L	106_L	0.798	1.00
86_R	90_L	0.794	1.00
6_T	10_L	0.791	1.00
120_Y	125_F	0.791	1.00
68_S	71_T	0.786	1.00
1_I	10_L	0.774	1.00
78_R	82_I	0.765	1.00
111_S	114_T	0.762	1.00
36_F	40_G	0.758	1.00
78_R	141_I	0.756	1.00
53_S	56_P	0.751	1.00
10_L	14_I	0.751	1.00
97_G	100_F	0.741	1.00
9_L	72_I	0.740	1.00
37_Y	41_L	0.736	1.00
82_I	145_E	0.735	1.00
86_R	142_K	0.728	1.00
67_L	88_N	0.722	1.00
133_L	136_L	0.717	1.00
100_F	104_L	0.716	1.00
69_L	73_F	0.710	1.00
95_L	99_F	0.707	1.00
19_L	61_T	0.704	1.00
10_L	13_A	0.704	1.00
12_A	133_L	0.701	1.00
35_T	38_A	0.698	1.00
87_L	90_L	0.696	1.00
62_I	66_L	0.695	1.00
55_W	58_L	0.692	0.99
105_F	108_L	0.689	0.99
36_F	39_L	0.688	0.99
51_A	54_T	0.685	0.99
127_P	130_A	0.683	0.99
15_L	129_I	0.680	0.99
2_Q	5_Q	0.673	0.99
18_L	126_L	0.671	0.99
79_K	82_I	0.669	0.99
108_L	112_G	0.667	0.99
103_L	110_L	0.666	0.99
107_S	111_S	0.664	0.99
15_L	133_L	0.663	0.99
34_Y	40_G	0.661	0.99
64_S	91_L	0.660	0.99
134_L	138_N	0.658	0.99
10_L	69_L	0.657	0.99
104_L	110_L	0.657	0.99
19_L	99_F	0.655	0.99
109_N	112_G	0.648	0.99
60_L	98_L	0.644	0.99
135_F	139_R	0.642	0.99
142_K	145_E	0.636	0.99
18_L	21_F	0.635	0.99
71_T	74_L	0.634	0.99
65_A	68_S	0.630	0.99
13_A	73_F	0.628	0.99
39_L	58_L	0.628	0.99
132_I	136_L	0.626	0.99
53_S	58_L	0.623	0.99
79_K	142_K	0.619	0.99
129_I	133_L	0.619	0.99
82_I	85_C	0.618	0.99
36_F	41_L	0.617	0.99
34_Y	41_L	0.615	0.99
54_T	58_L	0.614	0.99
88_N	92_N	0.613	0.99
12_A	89_I	0.610	0.99
28_T	31_D	0.610	0.99
49_V	53_S	0.610	0.99
89_I	138_N	0.608	0.99
20_F	58_L	0.606	0.99
7_L	14_I	0.602	0.99
74_L	77_N	0.602	0.99
139_R	143_K	0.601	0.99
104_L	109_N	0.598	0.99
23_P	26_S	0.597	0.99
111_S	115_F	0.594	0.98
19_L	127_P	0.594	0.98
23_P	123_G	0.591	0.98
82_I	146_K	0.589	0.98
92_N	96_L	0.578	0.98
147_L	151_A	0.576	0.98
19_L	123_G	0.573	0.98
107_S	112_G	0.571	0.98
16_A	68_S	0.566	0.98
29_G	33_T	0.565	0.98
15_L	130_A	0.563	0.98
89_I	92_N	0.552	0.98
77_N	153_R	0.548	0.97
44_A	48_V	0.544	0.97
27_F	30_G	0.544	0.97
35_T	40_G	0.540	0.97
139_R	146_K	0.536	0.97
92_N	95_L	0.534	0.97
88_N	91_L	0.534	0.97
120_Y	124_A	0.532	0.97
148_V	151_A	0.529	0.97
16_A	61_T	0.528	0.97
98_L	101_Y	0.528	0.97
121_G	125_F	0.528	0.97
71_T	75_Y	0.526	0.97
130_A	134_L	0.524	0.97
20_F	62_I	0.523	0.97
104_L	113_E	0.523	0.97
33_T	41_L	0.521	0.97
136_L	139_R	0.511	0.96
54_T	57_L	0.511	0.96
122_I	125_F	0.510	0.96
119_E	122_I	0.506	0.96
86_R	96_L	0.506	0.96
67_L	71_T	0.501	0.96
30_G	33_T	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
4ev6A	3	0.461	6.5	0.936	Contact Map
4i0uA	4	0.4481	6.1	0.936	Contact Map
1iijA	1	0.2273	4	0.942	Contact Map
2l2tA	2	0.2727	3.8	0.942	Contact Map
2jwaA	2	0.2857	3.8	0.942	Contact Map
3rkoN	1	0.6688	3.7	0.943	Contact Map
1jb0I	1	0.2208	3.4	0.943	Contact Map
4tllB	2	0.3636	2.9	0.946	Contact Map
2k9pA	1	0.5195	2.9	0.946	Contact Map
2hjdA	2	0.2532	2.7	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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