DUF2127 - PFAM28P - GREMLIN Contacts

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DUF2127 - Predicted membrane protein (DUF2127)

PFAM:	PF09900	Sequences: GLRLIALFKLLKGLLLLALGIGLLLLLHSRDLADLAERLARELHLDPDDRFARHLLDKASHLTPSTLRFLAAGALAYAALKLVEGVGLWLRKRWAEWLTIIATALFIPLEIYELVRRPSWLKVALLVVNLAIVVYLLREY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (136)
Sequences:	11744 (7873)
Seq/√Len:	675.1
META:	0.96

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
86_V	90_L	3.905	1.00
13_G	82_L	2.697	1.00
6_A	89_W	2.521	1.00
114_L	123_V	2.452	1.00
118_P	123_V	2.389	1.00
50_R	54_H	2.355	1.00
102_A	105_L	2.314	1.00
114_L	118_P	2.168	1.00
119_S	122_K	2.148	1.00
20_G	75_L	2.058	1.00
10_L	85_G	2.004	1.00
99_T	136_L	1.972	1.00
33_A	37_E	1.962	1.00
134_V	138_R	1.947	1.00
104_A	133_V	1.929	1.00
17_L	78_A	1.868	1.00
100_I	137_L	1.852	1.00
63_T	66_T	1.818	1.00
120_W	124_A	1.768	1.00
113_E	122_K	1.751	1.00
8_F	12_K	1.736	1.00
54_H	58_K	1.725	1.00
24_L	71_A	1.687	1.00
65_S	69_F	1.681	1.00
21_I	25_L	1.672	1.00
88_L	99_T	1.669	1.00
107_I	130_L	1.634	1.00
114_L	126_L	1.610	1.00
68_R	72_A	1.524	1.00
112_Y	116_R	1.515	1.00
34_D	38_R	1.501	1.00
58_K	61_H	1.474	1.00
117_R	122_K	1.407	1.00
100_I	136_L	1.404	1.00
79_A	83_V	1.348	1.00
20_G	24_L	1.342	1.00
23_L	74_A	1.333	1.00
121_L	124_A	1.316	1.00
34_D	37_E	1.279	1.00
57_D	60_S	1.267	1.00
42_E	45_L	1.263	1.00
38_R	42_E	1.259	1.00
113_E	117_R	1.248	1.00
69_F	73_G	1.217	1.00
35_L	38_R	1.203	1.00
54_H	57_D	1.198	1.00
120_W	123_V	1.188	1.00
57_D	61_H	1.175	1.00
4_L	7_L	1.175	1.00
107_I	133_V	1.161	1.00
100_I	133_V	1.158	1.00
37_E	41_R	1.153	1.00
80_L	102_A	1.148	1.00
64_P	68_R	1.137	1.00
87_G	92_K	1.106	1.00
51_F	55_L	1.100	1.00
53_R	57_D	1.099	1.00
52_A	55_L	1.088	1.00
66_T	69_F	1.087	1.00
7_L	11_L	1.084	1.00
18_A	22_G	1.083	1.00
123_V	127_V	1.080	1.00
114_L	117_R	1.061	1.00
111_I	115_V	1.050	1.00
6_A	85_G	1.048	1.00
110_E	126_L	1.032	1.00
51_F	54_H	1.014	1.00
78_A	82_L	1.012	1.00
14_L	82_L	1.010	1.00
93_R	96_E	1.007	1.00
115_V	118_P	0.999	1.00
100_I	104_A	0.998	1.00
65_S	68_R	0.995	1.00
13_G	17_L	0.983	1.00
6_A	10_L	0.981	1.00
2_L	91_R	0.972	1.00
103_T	133_V	0.966	1.00
83_V	98_L	0.965	1.00
19_L	74_A	0.958	1.00
98_L	102_A	0.934	1.00
27_L	68_R	0.932	1.00
3_R	89_W	0.932	1.00
112_Y	115_V	0.925	1.00
9_K	16_L	0.919	1.00
81_K	105_L	0.918	1.00
130_L	134_V	0.916	1.00
111_I	126_L	0.912	1.00
99_T	103_T	0.911	1.00
47_P	51_F	0.908	1.00
30_R	34_D	0.905	1.00
105_L	109_L	0.903	1.00
4_L	8_F	0.902	1.00
79_A	82_L	0.901	1.00
98_L	101_I	0.898	1.00
23_L	26_L	0.898	1.00
49_D	52_A	0.898	1.00
83_V	87_G	0.882	1.00
118_P	122_K	0.880	1.00
56_L	59_A	0.874	1.00
19_L	22_G	0.858	1.00
23_L	70_L	0.855	1.00
55_L	58_K	0.855	1.00
20_G	71_A	0.848	1.00
12_K	15_L	0.845	1.00
36_A	59_A	0.839	1.00
16_L	74_A	0.831	1.00
97_W	101_I	0.830	1.00
6_A	9_K	0.823	1.00
83_V	95_A	0.819	1.00
39_L	43_L	0.818	1.00
37_E	40_A	0.813	1.00
72_A	76_A	0.808	1.00
82_L	86_V	0.806	1.00
31_D	34_D	0.806	1.00
37_E	60_S	0.802	1.00
39_L	42_E	0.800	1.00
113_E	116_R	0.796	1.00
9_K	12_K	0.794	1.00
5_I	132_I	0.782	1.00
124_A	128_V	0.761	1.00
16_L	81_K	0.759	1.00
38_R	41_R	0.758	1.00
107_I	126_L	0.757	1.00
112_Y	122_K	0.755	1.00
13_G	85_G	0.754	1.00
49_D	53_R	0.750	1.00
30_R	35_L	0.746	1.00
12_K	81_K	0.743	1.00
22_G	25_L	0.739	1.00
74_A	81_K	0.738	1.00
92_K	95_A	0.737	1.00
56_L	60_S	0.736	1.00
116_R	122_K	0.735	1.00
2_L	96_E	0.725	1.00
10_L	82_L	0.722	1.00
6_A	88_L	0.710	1.00
3_R	7_L	0.704	1.00
13_G	78_A	0.702	1.00
121_L	125_L	0.698	1.00
24_L	28_H	0.698	1.00
86_V	92_K	0.693	1.00
102_A	106_F	0.687	1.00
40_A	44_H	0.683	1.00
55_L	59_A	0.675	1.00
33_A	60_S	0.674	1.00
10_L	95_A	0.670	1.00
11_L	15_L	0.663	1.00
32_L	35_L	0.662	1.00
71_A	75_L	0.656	1.00
3_R	6_A	0.656	1.00
80_L	98_L	0.647	1.00
75_L	79_A	0.639	1.00
17_L	75_L	0.638	1.00
20_G	74_A	0.636	1.00
101_I	105_L	0.633	1.00
36_A	40_A	0.632	1.00
8_F	81_K	0.629	1.00
24_L	75_L	0.626	1.00
41_R	45_L	0.618	1.00
76_A	81_K	0.616	1.00
122_K	135_Y	0.608	1.00
69_F	72_A	0.604	1.00
35_L	39_L	0.604	1.00
107_I	111_I	0.600	1.00
25_L	28_H	0.599	1.00
15_L	19_L	0.598	1.00
62_L	67_L	0.595	1.00
127_V	131_A	0.594	1.00
11_L	14_L	0.590	1.00
21_I	24_L	0.587	1.00
110_E	125_L	0.583	1.00
91_R	96_E	0.580	1.00
45_L	48_D	0.579	1.00
7_L	10_L	0.575	1.00
58_K	62_L	0.575	1.00
32_L	36_A	0.575	1.00
46_D	49_D	0.575	1.00
39_L	44_H	0.568	1.00
16_L	106_F	0.567	1.00
14_L	18_A	0.566	1.00
64_P	67_L	0.564	1.00
27_L	30_R	0.562	1.00
78_A	81_K	0.561	1.00
44_H	47_P	0.560	1.00
126_L	130_L	0.559	1.00
129_N	135_Y	0.554	1.00
33_A	36_A	0.554	1.00
84_E	99_T	0.552	1.00
31_D	35_L	0.550	1.00
68_R	71_A	0.541	1.00
47_P	55_L	0.539	1.00
5_I	12_K	0.528	1.00
132_I	135_Y	0.526	1.00
125_L	128_V	0.524	0.99
10_L	89_W	0.523	0.99
3_R	91_R	0.521	0.99
83_V	90_L	0.519	0.99
108_P	129_N	0.518	0.99
27_L	31_D	0.513	0.99
20_G	78_A	0.511	0.99
76_A	102_A	0.504	0.99
25_L	30_R	0.502	0.99
10_L	14_L	0.500	0.99
43_L	47_P	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
3w5aC	1	0.2071	3.9	0.93	Contact Map
3rlfF	1	0.3357	3.8	0.93	Contact Map
1b9uA	1	0.1714	2.1	0.939	Contact Map
3wu2A	1	0.6643	1.3	0.945	Contact Map
4mo1A	1	0.4	1.3	0.946	Contact Map
1fftB	1	0.3071	1.2	0.947	Contact Map
1x9gA	3	0.4786	1.2	0.947	Contact Map
3j08A	2	0.4786	1.2	0.947	Contact Map
1iijA	1	0.25	1.1	0.949	Contact Map
1orqC	4	0.3857	1	0.95	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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