DUF4281 - PFAM28P - GREMLIN Contacts

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DUF4281 - Domain of unknown function (DUF4281)

PFAM:	PF14108	Sequences: TLFSLANLLALPFWLLLIFLPRWRWTRRLVASILIPLLLALAYAYLIVLLLLGFGGAFGGFGSLAGVAALFSNPWGLLAGWIHYLAFDLFVGAWIVRDAQRRGIPHLLVIPCLLLTFMFGPVGLLLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	127 (126)
Sequences:	5170 (3514)
Seq/√Len:	313.0
META:	0.909

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_A	74_P	4.350	1.00
98_D	127_Y	4.071	1.00
95_I	116_T	3.328	1.00
68_A	77_L	3.082	1.00
6_A	82_I	2.786	1.00
60_G	66_G	2.622	1.00
44_A	122_V	2.513	1.00
62_G	66_G	2.502	1.00
114_L	118_M	2.306	1.00
90_F	124_L	2.282	1.00
18_I	110_I	2.197	1.00
98_D	102_R	2.115	1.00
42_A	82_I	2.089	1.00
80_G	84_Y	1.989	1.00
68_A	72_S	1.944	1.00
105_P	108_L	1.844	1.00
98_D	101_R	1.830	1.00
24_R	28_R	1.808	1.00
87_F	91_V	1.800	1.00
6_A	42_A	1.773	1.00
106_H	110_I	1.695	1.00
23_W	26_T	1.687	1.00
16_L	26_T	1.659	1.00
65_A	74_P	1.637	1.00
93_A	97_R	1.615	1.00
109_V	112_C	1.590	1.00
17_L	96_V	1.540	1.00
115_L	126_L	1.537	1.00
99_A	109_V	1.482	1.00
13_F	35_I	1.470	1.00
106_H	109_V	1.373	1.00
4_S	8_L	1.371	1.00
31_A	93_A	1.365	1.00
73_N	76_G	1.363	1.00
72_S	77_L	1.361	1.00
96_V	100_Q	1.350	1.00
8_L	12_P	1.342	1.00
100_Q	106_H	1.332	1.00
90_F	94_W	1.303	1.00
63_S	66_G	1.298	1.00
25_W	28_R	1.281	1.00
95_I	109_V	1.276	1.00
7_N	11_L	1.265	1.00
18_I	114_L	1.264	1.00
22_R	100_Q	1.230	1.00
112_C	126_L	1.223	1.00
15_L	19_F	1.223	1.00
20_L	23_W	1.207	1.00
69_A	72_S	1.132	1.00
71_F	80_G	1.131	1.00
39_L	82_I	1.047	1.00
96_V	109_V	1.046	1.00
71_F	77_L	1.035	1.00
5_L	9_L	1.032	1.00
47_I	119_F	1.013	1.00
46_L	75_W	1.010	1.00
53_G	56_G	1.003	1.00
111_P	114_L	0.997	1.00
95_I	112_C	0.995	1.00
36_P	40_A	0.995	1.00
97_R	101_R	0.971	1.00
57_A	60_G	0.965	1.00
43_Y	83_H	0.949	1.00
8_L	11_L	0.947	1.00
14_W	92_G	0.946	1.00
102_R	127_Y	0.923	1.00
46_L	79_A	0.915	1.00
25_W	29_L	0.914	1.00
66_G	69_A	0.914	1.00
84_Y	87_F	0.894	1.00
22_R	27_R	0.893	1.00
24_R	27_R	0.875	1.00
10_A	13_F	0.867	1.00
90_F	93_A	0.863	1.00
64_L	68_A	0.859	1.00
6_A	78_L	0.855	1.00
48_V	51_L	0.841	1.00
9_L	38_L	0.836	1.00
58_F	69_A	0.829	1.00
22_R	106_H	0.829	1.00
41_L	45_Y	0.828	1.00
27_R	97_R	0.822	1.00
55_G	59_G	0.817	1.00
59_G	70_L	0.810	1.00
9_L	13_F	0.809	1.00
16_L	23_W	0.800	1.00
26_T	29_L	0.800	1.00
6_A	85_L	0.798	1.00
78_L	82_I	0.792	1.00
47_I	50_L	0.787	1.00
50_L	53_G	0.780	1.00
3_F	67_V	0.774	0.99
51_L	54_F	0.773	0.99
16_L	20_L	0.771	0.99
70_L	80_G	0.769	0.99
30_V	35_I	0.763	0.99
23_W	27_R	0.763	0.99
40_A	124_L	0.761	0.99
119_F	122_V	0.761	0.99
40_A	86_A	0.754	0.99
22_R	25_W	0.744	0.99
21_P	26_T	0.737	0.99
27_R	31_A	0.735	0.99
13_F	17_L	0.734	0.99
52_L	57_A	0.729	0.99
96_V	106_H	0.724	0.99
54_F	57_A	0.720	0.99
83_H	121_P	0.717	0.99
72_S	76_G	0.714	0.99
93_A	96_V	0.713	0.99
107_L	111_P	0.711	0.99
48_V	52_L	0.711	0.99
65_A	68_A	0.709	0.99
37_L	125_L	0.707	0.99
51_L	55_G	0.702	0.99
83_H	88_D	0.702	0.99
4_S	7_N	0.692	0.99
95_I	98_D	0.687	0.99
74_P	77_L	0.684	0.99
32_S	97_R	0.681	0.99
2_L	46_L	0.681	0.99
27_R	100_Q	0.681	0.99
109_V	113_L	0.670	0.99
94_W	124_L	0.665	0.98
112_C	127_Y	0.659	0.98
10_A	117_F	0.654	0.98
64_L	78_L	0.653	0.98
59_G	62_G	0.652	0.98
109_V	127_Y	0.651	0.98
22_R	26_T	0.647	0.98
39_L	42_A	0.647	0.98
55_G	58_F	0.644	0.98
35_I	38_L	0.643	0.98
37_L	41_L	0.640	0.98
60_G	63_S	0.640	0.98
15_L	20_L	0.640	0.98
31_A	36_P	0.635	0.98
91_V	124_L	0.633	0.98
7_N	62_G	0.625	0.98
52_L	55_G	0.622	0.98
99_A	104_I	0.615	0.97
97_R	100_Q	0.614	0.97
92_G	113_L	0.613	0.97
53_G	57_A	0.610	0.97
56_G	59_G	0.606	0.97
87_F	120_G	0.605	0.97
99_A	127_Y	0.602	0.97
70_L	76_G	0.593	0.97
40_A	125_L	0.592	0.97
14_W	113_L	0.589	0.97
64_L	77_L	0.585	0.97
96_V	113_L	0.580	0.96
47_I	51_L	0.574	0.96
81_W	88_D	0.574	0.96
60_G	69_A	0.573	0.96
38_L	42_A	0.571	0.96
49_L	52_L	0.568	0.96
5_L	8_L	0.565	0.96
7_N	10_A	0.565	0.96
117_F	120_G	0.564	0.96
84_Y	92_G	0.562	0.96
52_L	56_G	0.560	0.96
108_L	111_P	0.559	0.96
43_Y	87_F	0.559	0.96
67_V	70_L	0.558	0.96
7_N	84_Y	0.556	0.95
104_I	108_L	0.552	0.95
8_L	15_L	0.551	0.95
49_L	53_G	0.547	0.95
16_L	30_V	0.539	0.95
100_Q	109_V	0.538	0.95
21_P	106_H	0.538	0.95
12_P	16_L	0.531	0.94
33_I	97_R	0.528	0.94
31_A	97_R	0.528	0.94
2_L	78_L	0.527	0.94
10_A	85_L	0.526	0.94
83_H	87_F	0.524	0.94
43_Y	80_G	0.521	0.94
9_L	12_P	0.519	0.93
80_G	88_D	0.518	0.93
26_T	31_A	0.515	0.93
116_T	123_G	0.514	0.93
93_A	101_R	0.504	0.92
16_L	29_L	0.504	0.92
31_A	96_V	0.502	0.92
59_G	63_S	0.502	0.92
96_V	99_A	0.500	0.92
9_L	35_I	0.500	0.92

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
3v42A	2	0.4724	2.5	0.938	Contact Map
4l6vF	1	0.4409	2.2	0.94	Contact Map
2mwrA	1	0.2126	1.2	0.949	Contact Map
3wu2J	1	0.2283	1	0.951	Contact Map
4xk8J	1	0.3071	0.9	0.953	Contact Map
4kt0J	1	0.315	0.8	0.954	Contact Map
1jb0J	1	0.3228	0.8	0.954	Contact Map
3mk7C	2	0.5433	0.6	0.957	Contact Map
5a63B	1	0.4803	0.6	0.958	Contact Map
1rh5B	1	0.3386	0.6	0.958	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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