Alph_Pro_TM - PFAM28P - GREMLIN Contacts

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Alph_Pro_TM - Putative transmembrane protein (Alph_Pro_TM)

PFAM:	PF09608	Sequences: QLVADLSQHRVAITSNFTGAELLLFGAIERDAGTPYDVVVVVRGPRQPVVVRRKERVAGIWVNTDSVTFDSVPSFYAVASSRPLDEIASPETLARYQIGLDNLQLSPGGGGADPEDADEFRAALIRLKEREGLYREDPGGVTFLGGTLFRARIPLPANVPVGTYTVEVFLFRDGRVVAAATTPLEVRKVGFERFVANLAHEHPLLYGLLAVLIALLAGWLASAVFRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	227 (225)
Sequences:	4277 (2901)
Seq/√Len:	193.4
META:	0.872

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_D	82_R	4.551	1.00
55_E	64_T	4.126	1.00
21_E	154_P	3.469	1.00
88_A	171_F	3.226	1.00
57_V	64_T	3.198	1.00
171_F	176_V	3.182	1.00
39_V	171_F	2.691	1.00
128_K	131_E	2.547	1.00
88_A	93_L	2.547	1.00
196_A	200_H	2.469	1.00
41_V	169_F	2.430	1.00
43_R	167_E	2.405	1.00
198_L	209_L	2.389	1.00
77_A	135_R	2.314	1.00
208_L	212_L	2.292	1.00
220_L	223_A	2.238	1.00
21_E	152_R	2.182	1.00
191_F	195_V	2.144	1.00
39_V	80_S	2.104	1.00
48_P	70_D	2.016	1.00
79_A	151_A	1.980	1.00
81_S	143_F	1.966	1.00
5_D	9_H	1.941	1.00
10_R	187_R	1.934	1.00
197_N	201_E	1.898	1.00
54_K	63_N	1.886	1.00
43_R	46_R	1.884	1.00
165_T	181_T	1.841	1.00
4_A	168_V	1.827	1.00
159_V	186_V	1.803	1.00
163_T	185_E	1.783	1.00
83_P	86_E	1.751	1.00
26_G	149_F	1.746	1.00
116_D	119_E	1.742	1.00
31_D	34_T	1.710	1.00
88_A	92_T	1.696	1.00
96_Y	176_V	1.684	1.00
204_L	211_V	1.675	1.00
194_F	198_L	1.668	1.00
167_E	179_A	1.641	1.00
82_R	86_E	1.631	1.00
74_S	160_P	1.510	1.00
49_V	124_L	1.509	1.00
129_E	136_E	1.504	1.00
163_T	183_P	1.494	1.00
111_G	114_P	1.488	1.00
169_F	176_V	1.488	1.00
82_R	87_I	1.461	1.00
118_D	122_A	1.459	1.00
89_S	92_T	1.458	1.00
42_V	153_I	1.446	1.00
93_L	99_G	1.437	1.00
52_R	66_S	1.434	1.00
90_P	94_A	1.423	1.00
144_L	150_R	1.417	1.00
39_V	87_I	1.407	1.00
72_V	134_Y	1.399	1.00
92_T	95_R	1.398	1.00
100_L	129_E	1.392	1.00
113_D	116_D	1.392	1.00
196_A	199_A	1.385	1.00
42_V	166_V	1.364	1.00
41_V	167_E	1.363	1.00
50_V	66_S	1.340	1.00
37_D	81_S	1.320	1.00
49_V	128_K	1.313	1.00
142_T	150_R	1.304	1.00
219_W	223_A	1.304	1.00
47_Q	128_K	1.303	1.00
87_I	171_F	1.290	1.00
99_G	103_L	1.288	1.00
216_L	220_L	1.282	1.00
69_F	124_L	1.278	1.00
98_I	169_F	1.269	1.00
205_L	208_L	1.260	1.00
205_L	209_L	1.256	1.00
169_F	179_A	1.253	1.00
67_V	117_A	1.249	1.00
5_D	150_R	1.239	1.00
112_A	116_D	1.235	1.00
207_G	211_V	1.217	1.00
65_D	120_F	1.211	1.00
220_L	224_V	1.210	1.00
40_V	151_A	1.191	1.00
198_L	202_H	1.189	1.00
80_S	84_L	1.184	1.00
188_K	192_E	1.177	1.00
2_L	178_A	1.176	1.00
200_H	203_P	1.157	1.00
140_G	151_A	1.135	1.00
198_L	205_L	1.131	1.00
188_K	196_A	1.126	1.00
51_V	124_L	1.119	1.00
23_L	150_R	1.115	1.00
53_R	119_E	1.111	1.00
159_V	164_Y	1.111	1.00
57_V	62_V	1.110	1.00
7_S	23_L	1.107	1.00
36_Y	170_L	1.106	1.00
32_A	35_P	1.101	1.00
27_A	148_L	1.099	1.00
51_V	120_F	1.096	1.00
131_E	158_N	1.094	1.00
44_G	74_S	1.091	1.00
6_L	184_L	1.088	1.00
217_A	221_A	1.087	1.00
17_F	159_V	1.084	1.00
30_R	35_P	1.078	1.00
28_I	38_V	1.073	1.00
167_E	181_T	1.070	1.00
132_G	135_R	1.058	1.00
166_V	184_L	1.055	1.00
151_A	154_P	1.030	1.00
80_S	138_P	1.025	1.00
79_A	153_I	1.023	1.00
46_R	71_S	1.020	1.00
127_L	130_R	1.018	1.00
155_L	159_V	1.017	1.00
37_D	171_F	1.012	1.00
22_L	184_L	1.012	1.00
53_R	64_T	0.993	1.00
204_L	208_L	0.992	1.00
14_T	189_V	0.987	0.99
93_L	102_N	0.981	0.99
7_S	25_F	0.981	0.99
15_S	18_T	0.978	0.99
93_L	98_I	0.970	0.99
223_A	226_R	0.969	0.99
8_Q	21_E	0.969	0.99
212_L	216_L	0.968	0.99
128_K	133_L	0.957	0.99
55_E	65_D	0.951	0.99
38_V	141_V	0.951	0.99
119_E	122_A	0.950	0.99
29_E	145_G	0.930	0.99
161_V	186_V	0.927	0.99
112_A	117_A	0.925	0.99
141_V	151_A	0.922	0.99
124_L	134_Y	0.914	0.99
94_A	102_N	0.913	0.99
50_V	68_T	0.912	0.99
17_F	102_N	0.891	0.99
8_Q	152_R	0.890	0.99
15_S	192_E	0.889	0.99
53_R	65_D	0.884	0.99
100_L	136_E	0.884	0.99
107_P	117_A	0.881	0.99
125_I	134_Y	0.877	0.99
110_G	114_P	0.874	0.99
97_Q	104_Q	0.865	0.99
43_R	165_T	0.860	0.99
219_W	222_S	0.856	0.99
40_V	141_V	0.855	0.99
206_Y	214_A	0.846	0.98
53_R	120_F	0.845	0.98
214_A	217_A	0.844	0.98
216_L	219_W	0.842	0.98
4_A	182_T	0.838	0.98
72_V	107_P	0.837	0.98
215_L	219_W	0.837	0.98
8_Q	20_A	0.827	0.98
161_V	189_V	0.825	0.98
193_R	197_N	0.825	0.98
202_H	205_L	0.823	0.98
91_E	94_A	0.817	0.98
110_G	113_D	0.815	0.98
91_E	95_R	0.815	0.98
11_V	155_L	0.812	0.98
137_D	153_I	0.809	0.98
72_V	105_L	0.806	0.98
69_F	134_Y	0.802	0.98
92_T	175_R	0.801	0.98
30_R	34_T	0.795	0.98
69_F	72_V	0.794	0.98
185_E	220_L	0.787	0.97
25_F	148_L	0.787	0.97
42_V	75_F	0.784	0.97
95_R	179_A	0.781	0.97
137_D	140_G	0.780	0.97
93_L	171_F	0.777	0.97
24_L	79_A	0.769	0.97
81_S	139_G	0.766	0.97
129_E	135_R	0.764	0.97
69_F	121_R	0.761	0.97
39_V	88_A	0.756	0.97
80_S	136_E	0.751	0.97
37_D	87_I	0.748	0.97
3_V	27_A	0.743	0.96
4_A	180_A	0.741	0.96
4_A	9_H	0.740	0.96
65_D	116_D	0.733	0.96
142_T	146_G	0.728	0.96
17_F	186_V	0.726	0.96
159_V	211_V	0.722	0.96
207_G	210_A	0.720	0.96
28_I	36_Y	0.715	0.96
5_D	148_L	0.713	0.95
172_R	177_V	0.712	0.95
152_R	166_V	0.711	0.95
143_F	147_T	0.705	0.95
123_A	127_L	0.704	0.95
4_A	16_N	0.702	0.95
26_G	141_V	0.697	0.95
38_V	168_V	0.694	0.95
72_V	124_L	0.694	0.95
12_A	15_S	0.693	0.95
143_F	146_G	0.692	0.95
165_T	168_V	0.691	0.95
88_A	176_V	0.690	0.95
124_L	174_G	0.685	0.94
89_S	175_R	0.684	0.94
70_D	106_S	0.675	0.94
69_F	107_P	0.672	0.94
41_V	98_I	0.666	0.94
117_A	121_R	0.664	0.93
102_N	105_L	0.662	0.93
24_L	40_V	0.660	0.93
48_P	71_S	0.659	0.93
114_P	118_D	0.656	0.93
69_F	120_F	0.656	0.93
123_A	184_L	0.655	0.93
3_V	23_L	0.654	0.93
56_R	59_G	0.654	0.93
48_P	106_S	0.650	0.93
85_D	90_P	0.649	0.93
80_S	139_G	0.648	0.93
135_R	154_P	0.647	0.93
211_V	217_A	0.646	0.92
221_A	225_F	0.645	0.92
143_F	170_L	0.643	0.92
75_F	164_Y	0.643	0.92
5_D	23_L	0.642	0.92
4_A	10_R	0.641	0.92
10_R	185_E	0.640	0.92
101_D	129_E	0.638	0.92
28_I	147_T	0.636	0.92
213_I	216_L	0.636	0.92
129_E	213_I	0.634	0.92
93_L	101_D	0.634	0.92
80_S	140_G	0.633	0.92
74_S	128_K	0.626	0.91
12_A	187_R	0.625	0.91
133_L	159_V	0.624	0.91
153_I	156_P	0.624	0.91
52_R	63_N	0.623	0.91
52_R	120_F	0.622	0.91
191_F	222_S	0.619	0.91
9_H	15_S	0.619	0.91
170_L	178_A	0.618	0.91
81_S	87_I	0.618	0.91
161_V	164_Y	0.618	0.91
193_R	203_P	0.610	0.90
111_G	116_D	0.606	0.90
126_R	129_E	0.604	0.90
75_F	153_I	0.602	0.90
84_L	93_L	0.602	0.90
9_H	142_T	0.601	0.90
6_L	24_L	0.598	0.89
114_P	117_A	0.598	0.89
160_P	184_L	0.597	0.89
81_S	141_V	0.595	0.89
202_H	210_A	0.590	0.89
23_L	184_L	0.590	0.89
194_F	209_L	0.589	0.89
66_S	105_L	0.589	0.89
195_V	199_A	0.585	0.88
5_D	25_F	0.585	0.88
70_D	91_E	0.583	0.88
5_D	16_N	0.582	0.88
90_P	102_N	0.580	0.88
123_A	143_F	0.578	0.88
31_D	36_Y	0.577	0.88
35_P	177_V	0.576	0.87
215_L	222_S	0.573	0.87
30_R	36_Y	0.572	0.87
166_V	169_F	0.571	0.87
48_P	68_T	0.571	0.87
47_Q	74_S	0.569	0.87
82_R	171_F	0.563	0.86
92_T	96_Y	0.563	0.86
209_L	212_L	0.562	0.86
9_H	183_P	0.562	0.86
191_F	194_F	0.561	0.86
166_V	180_A	0.561	0.86
40_V	166_V	0.559	0.86
20_A	30_R	0.558	0.86
115_E	118_D	0.555	0.85
179_A	183_P	0.555	0.85
126_R	130_R	0.554	0.85
13_I	188_K	0.553	0.85
13_I	186_V	0.553	0.85
90_P	93_L	0.549	0.85
8_Q	22_L	0.548	0.85
158_N	180_A	0.548	0.85
187_R	193_R	0.547	0.85
194_F	202_H	0.546	0.85
57_V	60_I	0.545	0.84
96_Y	171_F	0.545	0.84
80_S	87_I	0.543	0.84
122_A	129_E	0.542	0.84
213_I	217_A	0.542	0.84
94_A	107_P	0.542	0.84
70_D	94_A	0.541	0.84
123_A	126_R	0.539	0.84
101_D	122_A	0.538	0.84
185_E	213_I	0.534	0.83
96_Y	179_A	0.533	0.83
84_L	88_A	0.532	0.83
132_G	197_N	0.532	0.83
3_V	9_H	0.530	0.83
104_Q	122_A	0.528	0.83
118_D	121_R	0.527	0.82
59_G	66_S	0.526	0.82
58_A	66_S	0.525	0.82
97_Q	100_L	0.525	0.82
161_V	193_R	0.523	0.82
106_S	114_P	0.523	0.82
104_Q	113_D	0.521	0.82
89_S	93_L	0.520	0.82
207_G	218_G	0.518	0.81
112_A	115_E	0.515	0.81
109_G	114_P	0.512	0.81
168_V	185_E	0.512	0.81
42_V	151_A	0.511	0.80
76_Y	103_L	0.510	0.80
210_A	216_L	0.510	0.80
101_D	109_G	0.506	0.80
167_E	222_S	0.505	0.80
45_P	219_W	0.505	0.80
216_L	222_S	0.505	0.80
213_I	222_S	0.503	0.79
106_S	130_R	0.503	0.79
197_N	205_L	0.502	0.79
11_V	14_T	0.502	0.79
62_V	112_A	0.501	0.79
180_A	183_P	0.501	0.79
100_L	103_L	0.500	0.79
67_V	76_Y	0.500	0.79

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
2ag4A	1	0.5991	74.7	0.933	Contact Map
2p9rA	1	0.4493	28.4	0.95	Contact Map
2pn5A	1	0.859	21	0.953	Contact Map
4p02B	1	0.8238	17	0.955	Contact Map
4acqA	4	0.8811	16.8	0.955	Contact Map
1xwvA	1	0.5507	12.6	0.957	Contact Map
4f92B	1	0.5859	10.6	0.959	Contact Map
2b39A	1	0.8767	10.4	0.959	Contact Map
3cu7A	2	0.8899	9.7	0.959	Contact Map
3isyA	1	0.4978	9.4	0.96	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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