DUF2177 - PFAM28P - GREMLIN Contacts

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DUF2177 - Predicted membrane protein (DUF2177)

PFAM:	PF09945	Sequences: YLKLYLATLVVFLALDAVWLGLVAKGFYRPQLGDLLADKPNWAAAILFYLLYIAGLVVFAVLPALEAGSWLRALLYGALFGLVAYATYDLTNLATLKDWPLKVTVVDIAWGTVLTALVATAGYW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	124 (122)
Sequences:	8135 (5990)
Seq/√Len:	542.3
META:	0.932

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_V	76_Y	3.331	1.00
93_L	101_L	2.796	1.00
78_A	112_T	2.653	1.00
31_Q	102_K	2.630	1.00
55_G	83_V	2.578	1.00
72_R	76_Y	2.451	1.00
70_W	120_T	2.286	1.00
41_N	44_A	2.250	1.00
11_V	121_A	2.095	1.00
67_A	72_R	2.090	1.00
56_L	115_T	2.082	1.00
82_L	112_T	1.969	1.00
25_K	29_R	1.855	1.00
99_W	104_T	1.807	1.00
27_F	106_V	1.797	1.00
78_A	116_A	1.714	1.00
13_L	17_A	1.712	1.00
88_Y	95_T	1.661	1.00
92_N	95_T	1.637	1.00
8_T	122_G	1.634	1.00
93_L	104_T	1.627	1.00
8_T	57_V	1.619	1.00
74_L	116_A	1.607	1.00
51_L	86_A	1.596	1.00
44_A	93_L	1.591	1.00
105_V	109_A	1.500	1.00
86_A	108_I	1.499	1.00
26_G	30_P	1.466	1.00
89_D	104_T	1.463	1.00
74_L	120_T	1.448	1.00
90_L	108_I	1.427	1.00
34_D	98_D	1.405	1.00
62_L	66_E	1.402	1.00
41_N	93_L	1.382	1.00
73_A	77_G	1.381	1.00
37_A	41_N	1.380	1.00
31_Q	100_P	1.339	1.00
58_V	79_L	1.322	1.00
59_F	79_L	1.288	1.00
118_V	122_G	1.264	1.00
113_V	117_L	1.248	1.00
34_D	96_L	1.246	1.00
82_L	108_I	1.238	1.00
84_A	87_T	1.225	1.00
59_F	80_F	1.218	1.00
48_F	52_Y	1.218	1.00
7_A	122_G	1.208	1.00
52_Y	84_A	1.201	1.00
64_A	73_A	1.200	1.00
77_G	119_A	1.182	1.00
42_W	46_I	1.178	1.00
48_F	90_L	1.169	1.00
9_L	53_I	1.169	1.00
71_L	75_L	1.168	1.00
27_F	103_V	1.152	1.00
17_A	21_G	1.125	1.00
28_Y	89_D	1.092	1.00
23_V	26_G	1.086	1.00
54_A	58_V	1.061	1.00
109_A	113_V	1.050	1.00
40_P	44_A	1.037	1.00
48_F	87_T	1.028	1.00
55_G	80_F	1.018	1.00
82_L	86_A	1.016	1.00
80_F	83_V	1.014	1.00
102_K	106_V	0.990	1.00
59_F	83_V	0.985	1.00
79_L	83_V	0.983	1.00
11_V	118_V	0.980	1.00
51_L	82_L	0.969	1.00
38_D	97_K	0.968	1.00
2_L	6_L	0.962	1.00
77_G	116_A	0.961	1.00
51_L	90_L	0.956	1.00
57_V	62_L	0.944	1.00
37_A	40_P	0.941	1.00
5_Y	54_A	0.931	1.00
92_N	96_L	0.928	1.00
89_D	99_W	0.918	1.00
88_Y	96_L	0.916	1.00
52_Y	115_T	0.913	1.00
90_L	104_T	0.911	1.00
4_L	57_V	0.897	1.00
15_L	117_L	0.893	1.00
8_T	53_I	0.887	1.00
27_F	31_Q	0.878	1.00
80_F	84_A	0.863	1.00
117_L	120_T	0.847	1.00
68_G	123_Y	0.838	1.00
101_L	105_V	0.837	1.00
28_Y	103_V	0.824	1.00
70_W	74_L	0.822	1.00
22_L	25_K	0.819	1.00
3_K	7_A	0.808	1.00
17_A	22_L	0.793	1.00
31_Q	34_D	0.788	1.00
12_F	114_L	0.776	1.00
9_L	13_L	0.771	1.00
44_A	90_L	0.764	1.00
66_E	72_R	0.756	1.00
60_A	77_G	0.749	1.00
46_I	50_L	0.741	1.00
71_L	74_L	0.740	1.00
22_L	26_G	0.739	1.00
47_L	90_L	0.735	1.00
32_L	36_L	0.731	1.00
56_L	119_A	0.731	1.00
117_L	121_A	0.723	1.00
6_L	10_V	0.723	1.00
20_L	89_D	0.722	1.00
7_A	11_V	0.717	1.00
27_F	102_K	0.716	1.00
14_A	18_V	0.707	1.00
70_W	123_Y	0.705	1.00
32_L	96_L	0.700	1.00
113_V	116_A	0.699	1.00
14_A	17_A	0.695	1.00
45_A	49_Y	0.690	1.00
102_K	105_V	0.690	1.00
54_A	79_L	0.688	1.00
72_R	75_L	0.686	1.00
18_V	22_L	0.685	1.00
53_I	57_V	0.685	1.00
32_L	95_T	0.680	1.00
58_V	75_L	0.674	1.00
68_G	72_R	0.673	1.00
114_L	118_V	0.664	1.00
12_F	52_Y	0.658	1.00
31_Q	103_V	0.657	1.00
52_Y	87_T	0.655	1.00
109_A	112_T	0.652	1.00
18_V	21_G	0.651	1.00
60_A	73_A	0.645	1.00
56_L	61_V	0.644	1.00
5_Y	9_L	0.641	1.00
43_A	46_I	0.637	1.00
48_F	94_A	0.633	1.00
75_L	78_A	0.629	1.00
33_G	36_L	0.627	1.00
86_A	90_L	0.626	1.00
12_F	53_I	0.626	1.00
11_V	15_L	0.625	1.00
110_W	114_L	0.617	1.00
69_S	72_R	0.615	1.00
114_L	117_L	0.613	1.00
4_L	7_A	0.603	1.00
51_L	83_V	0.598	1.00
35_L	96_L	0.594	1.00
4_L	8_T	0.585	0.99
29_R	36_L	0.585	0.99
58_V	83_V	0.583	0.99
35_L	98_D	0.580	0.99
60_A	80_F	0.575	0.99
23_V	30_P	0.572	0.99
8_T	61_V	0.572	0.99
11_V	14_A	0.562	0.99
21_G	42_W	0.559	0.99
112_T	116_A	0.559	0.99
32_L	99_W	0.558	0.99
19_W	28_Y	0.558	0.99
40_P	45_A	0.554	0.99
60_A	64_A	0.552	0.99
104_T	108_I	0.550	0.99
8_T	118_V	0.548	0.99
89_D	108_I	0.545	0.99
44_A	94_A	0.544	0.99
45_A	94_A	0.542	0.99
26_G	29_R	0.542	0.99
32_L	35_L	0.541	0.99
100_P	103_V	0.538	0.99
116_A	120_T	0.532	0.99
25_K	30_P	0.530	0.99
34_D	37_A	0.529	0.99
21_G	25_K	0.528	0.99
108_I	112_T	0.528	0.99
84_A	115_T	0.524	0.99
34_D	100_P	0.521	0.99
13_L	46_I	0.518	0.99
34_D	38_D	0.518	0.99
24_A	30_P	0.517	0.99
80_F	115_T	0.510	0.99
98_D	102_K	0.505	0.99
43_A	47_L	0.500	0.98

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
2rddB	1	0.2984	7.3	0.908	Contact Map
3qnqA	2	0.3468	2.3	0.928	Contact Map
2ru8A	1	0.2661	2.2	0.929	Contact Map
2l8sA	1	0.25	0.8	0.945	Contact Map
4he8J	1	0.5	0.8	0.946	Contact Map
4hygA	3	0.8952	0.7	0.948	Contact Map
2m3eA	1	0.2823	0.7	0.949	Contact Map
1ijdA	3	0.2339	0.6	0.949	Contact Map
2m20A	2	0.2016	0.6	0.95	Contact Map
4gx0A	3	0.6855	0.6	0.951	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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