YTAF - BACSU - GREMLIN Contacts

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YTAF - Putative membrane protein YtaF

UniProt:	C0SP79	Sequences: MQMVSILLLALAVSLDSFSVGFTYGLRKMKIPFKAILVIACCSGAVMFISMLIGSFLTKFFPVYVTEKLGGLILVGIGAWVLYQFFKPAKDKEYLLHEKTLLNLEVRSLGIVIHILRKPMSADIDKSGVINGIEAVLLGFALSIDAFGAGIGAAILGFSPIVMSIAVAIMSSLFVSIGINAGHFLSKWKWIDKMAFLPGLLLITIGLWKL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	210 (202)
Sequences:	471 (405)
Seq/√Len:	28.5

ECOLI - MNTP
BACSU - YTAF MNTP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_P	35_A	5.957	1.00
13_V	145_D	3.176	1.00
150_G	182_G	2.807	1.00
44_G	168_A	2.501	0.99
75_V	206_G	2.493	0.99
21_G	139_G	2.489	0.99
123_D	127_S	2.440	0.99
46_V	143_S	2.344	0.99
20_V	23_T	2.318	0.99
68_K	82_L	2.294	0.99
36_I	145_D	2.269	0.98
13_V	17_S	2.251	0.98
27_R	81_V	2.212	0.98
124_I	137_L	2.205	0.98
14_S	17_S	2.203	0.98
18_F	152_G	2.182	0.98
12_A	198_P	2.138	0.98
145_D	149_A	1.982	0.96
47_M	145_D	1.941	0.96
62_P	66_T	1.914	0.96
9_L	14_S	1.844	0.95
12_A	122_A	1.838	0.94
61_F	75_V	1.823	0.94
110_G	113_I	1.817	0.94
17_S	154_A	1.785	0.93
46_V	167_V	1.775	0.93
17_S	145_D	1.767	0.93
8_L	72_L	1.759	0.93
42_C	168_A	1.725	0.92
38_V	132_G	1.714	0.92
82_L	136_V	1.689	0.91
116_L	119_P	1.656	0.91
20_V	116_L	1.617	0.90
123_D	134_E	1.609	0.89
44_G	172_S	1.608	0.89
122_A	125_D	1.564	0.88
146_A	167_V	1.561	0.88
48_F	55_S	1.559	0.88
43_S	167_V	1.556	0.88
70_G	152_G	1.552	0.87
143_S	163_M	1.473	0.85
49_I	59_K	1.467	0.84
128_G	198_P	1.465	0.84
82_L	199_G	1.437	0.83
28_K	203_I	1.431	0.83
133_I	184_F	1.425	0.82
36_I	47_M	1.422	0.82
202_L	206_G	1.407	0.82
113_I	145_D	1.406	0.82
75_V	203_I	1.371	0.80
105_E	118_K	1.349	0.79
86_F	104_L	1.345	0.79
145_D	171_S	1.340	0.78
107_R	110_G	1.339	0.78
33_F	41_C	1.331	0.78
7_L	197_L	1.330	0.78
52_L	155_I	1.327	0.78
41_C	45_A	1.321	0.77
3_M	47_M	1.310	0.77
11_L	174_F	1.303	0.76
19_S	186_S	1.293	0.76
29_M	132_G	1.292	0.76
203_I	207_L	1.282	0.75
45_A	96_L	1.280	0.75
122_A	128_G	1.279	0.75
43_S	170_M	1.279	0.75
23_T	26_L	1.250	0.73
65_V	165_I	1.235	0.72
62_P	205_I	1.229	0.72
14_S	145_D	1.225	0.72
66_T	79_A	1.220	0.71
62_P	147_F	1.217	0.71
20_V	205_I	1.206	0.71
119_P	134_E	1.206	0.71
151_I	159_S	1.181	0.69
139_G	164_S	1.166	0.68
114_H	121_S	1.165	0.68
22_F	132_G	1.163	0.68
57_L	151_I	1.137	0.66
43_S	146_A	1.122	0.65
155_I	165_I	1.120	0.65
153_A	171_S	1.111	0.64
109_L	113_I	1.107	0.64
173_L	197_L	1.107	0.64
10_A	110_G	1.097	0.63
30_K	67_E	1.096	0.63
19_S	114_H	1.093	0.63
35_A	185_L	1.078	0.62
14_S	26_L	1.078	0.62
119_P	139_G	1.075	0.61
198_P	203_I	1.073	0.61
9_L	153_A	1.069	0.61
16_D	150_G	1.068	0.61
21_G	25_G	1.068	0.61
67_E	156_L	1.064	0.61
133_I	205_I	1.059	0.60
17_S	171_S	1.055	0.60
154_A	174_F	1.054	0.60
122_A	141_A	1.049	0.60
154_A	190_W	1.044	0.59
40_A	199_G	1.038	0.59
18_F	178_G	1.035	0.58
145_D	209_K	1.034	0.58
115_I	135_A	1.022	0.57
57_L	75_V	1.019	0.57
13_V	47_M	1.013	0.57
22_F	163_M	1.013	0.57
40_A	140_F	1.012	0.57
143_S	209_K	1.011	0.57
35_A	135_A	1.011	0.57
33_F	45_A	1.010	0.57
190_W	206_G	1.009	0.56
46_V	50_S	1.002	0.56
17_S	47_M	1.001	0.56
12_A	149_A	0.992	0.55
72_L	76_G	0.991	0.55
166_A	201_L	0.987	0.55
21_G	27_R	0.983	0.55
42_C	47_M	0.982	0.54
104_L	111_I	0.979	0.54
40_A	172_S	0.977	0.54
66_T	70_G	0.971	0.54
7_L	75_V	0.966	0.53
127_S	134_E	0.963	0.53
24_Y	127_S	0.959	0.53
46_V	146_A	0.958	0.53
71_G	120_M	0.934	0.51
125_D	134_E	0.928	0.50
79_A	200_L	0.925	0.50
125_D	131_N	0.923	0.50
64_Y	76_G	0.923	0.50
106_V	109_L	0.919	0.50
145_D	202_L	0.914	0.49
7_L	69_L	0.907	0.49
22_F	44_G	0.903	0.48
194_M	209_K	0.901	0.48
24_Y	134_E	0.900	0.48
49_I	169_I	0.895	0.48
59_K	200_L	0.886	0.47
13_V	36_I	0.885	0.47
13_V	209_K	0.880	0.47
3_M	185_L	0.873	0.46
61_F	139_G	0.869	0.46
61_F	187_K	0.868	0.46
38_V	155_I	0.861	0.45
119_P	123_D	0.856	0.45
46_V	163_M	0.855	0.45
76_G	87_K	0.853	0.44
164_S	171_S	0.852	0.44
6_I	166_A	0.850	0.44
4_V	94_Y	0.838	0.43
37_L	109_L	0.838	0.43
60_F	208_W	0.837	0.43
93_E	169_I	0.835	0.43
149_A	202_L	0.831	0.43
10_A	112_V	0.830	0.43
125_D	128_G	0.820	0.42
73_I	152_G	0.816	0.42
160_P	164_S	0.813	0.41
61_F	76_G	0.806	0.41
60_F	173_L	0.801	0.41
125_D	130_I	0.796	0.40
116_L	122_A	0.794	0.40
44_G	171_S	0.792	0.40
155_I	209_K	0.791	0.40
36_I	198_P	0.783	0.39
21_G	84_Q	0.779	0.39
14_S	74_L	0.775	0.39
135_A	142_L	0.771	0.38
60_F	197_L	0.769	0.38
42_C	175_V	0.766	0.38
145_D	198_P	0.765	0.38
155_I	197_L	0.763	0.38
115_I	118_K	0.761	0.38
78_G	199_G	0.759	0.37
97_H	177_I	0.753	0.37
45_A	62_P	0.751	0.37
137_L	140_F	0.749	0.37
191_I	205_I	0.744	0.36
77_I	163_M	0.735	0.36
35_A	73_I	0.734	0.36
21_G	36_I	0.732	0.36
123_D	135_A	0.729	0.35
53_I	95_L	0.729	0.35
156_L	159_S	0.727	0.35
33_F	165_I	0.726	0.35
27_R	70_G	0.726	0.35
119_P	122_A	0.720	0.35
66_T	73_I	0.715	0.34
7_L	112_V	0.713	0.34
32_P	131_N	0.712	0.34
148_G	202_L	0.706	0.34
69_L	184_F	0.702	0.33
15_L	36_I	0.702	0.33
65_V	185_L	0.694	0.33
119_P	125_D	0.690	0.33
134_E	138_L	0.688	0.32
183_H	201_L	0.687	0.32
16_D	182_G	0.686	0.32
112_V	115_I	0.682	0.32
67_E	175_V	0.681	0.32
43_S	186_S	0.678	0.32
90_K	103_N	0.677	0.32
57_L	96_L	0.674	0.32
20_V	146_A	0.672	0.31
44_G	164_S	0.670	0.31
143_S	150_G	0.670	0.31
128_G	167_V	0.669	0.31
145_D	194_M	0.667	0.31
65_V	75_V	0.667	0.31
55_S	76_G	0.657	0.30
44_G	83_Y	0.654	0.30
119_P	153_A	0.642	0.29
174_F	178_G	0.641	0.29
47_M	209_K	0.638	0.29
80_W	147_F	0.638	0.29
26_L	71_G	0.638	0.29
146_A	209_K	0.637	0.29
37_L	185_L	0.635	0.29
13_V	149_A	0.635	0.29
43_S	182_G	0.633	0.29
33_F	72_L	0.630	0.29
147_F	191_I	0.623	0.28
145_D	193_K	0.623	0.28
70_G	138_L	0.623	0.28
139_G	143_S	0.623	0.28
7_L	160_P	0.621	0.28
82_L	122_A	0.621	0.28
95_L	181_A	0.620	0.28
24_Y	125_D	0.616	0.28
7_L	49_I	0.616	0.28
204_T	207_L	0.613	0.28
149_A	174_F	0.613	0.28
39_I	142_L	0.612	0.28
96_L	161_I	0.611	0.27
71_G	128_G	0.609	0.27
14_S	209_K	0.609	0.27
110_G	114_H	0.608	0.27
202_L	205_I	0.607	0.27
71_G	206_G	0.606	0.27
17_S	36_I	0.606	0.27
31_I	46_V	0.606	0.27
19_S	205_I	0.606	0.27
47_M	171_S	0.605	0.27
10_A	118_K	0.603	0.27
143_S	152_G	0.602	0.27
53_I	60_F	0.599	0.27
156_L	204_T	0.597	0.27
138_L	142_L	0.597	0.27
21_G	128_G	0.596	0.27
47_M	163_M	0.595	0.26
73_I	202_L	0.594	0.26
43_S	142_L	0.594	0.26
21_G	70_G	0.593	0.26
159_S	201_L	0.592	0.26
7_L	61_F	0.591	0.26
165_I	197_L	0.589	0.26
155_I	190_W	0.589	0.26
47_M	81_V	0.574	0.25
31_I	85_F	0.573	0.25
69_L	183_H	0.571	0.25
40_A	171_S	0.570	0.25
175_V	200_L	0.567	0.25
134_E	142_L	0.564	0.25
155_I	201_L	0.562	0.25
30_K	126_K	0.559	0.24
122_A	138_L	0.559	0.24
17_S	67_E	0.550	0.24
37_L	169_I	0.550	0.24
115_I	177_I	0.550	0.24
41_C	86_F	0.550	0.24
21_G	147_F	0.546	0.24
29_M	156_L	0.544	0.24
22_F	66_T	0.544	0.24
69_L	105_E	0.542	0.23
104_L	197_L	0.542	0.23
32_P	138_L	0.542	0.23
14_S	175_V	0.540	0.23
95_L	185_L	0.540	0.23
29_M	122_A	0.540	0.23
164_S	195_A	0.537	0.23
130_I	178_G	0.535	0.23
30_K	59_K	0.533	0.23
51_M	163_M	0.532	0.23
41_C	173_L	0.531	0.23
165_I	192_D	0.531	0.23
70_G	128_G	0.529	0.23
36_I	171_S	0.529	0.23
31_I	138_L	0.528	0.23
11_L	133_I	0.523	0.22
22_F	53_I	0.517	0.22
24_Y	27_R	0.515	0.22
30_K	49_I	0.515	0.22
75_V	162_V	0.507	0.22
14_S	18_F	0.506	0.21
32_P	39_I	0.506	0.21
14_S	146_A	0.506	0.21
3_M	194_M	0.505	0.21
79_A	207_L	0.505	0.21
152_G	208_W	0.505	0.21
77_I	188_W	0.503	0.21
61_F	169_I	0.503	0.21
81_V	84_Q	0.500	0.21

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
2cfqA	1	0.9095	37	0.941	Contact Map
4xnjA	1	0.9714	34.1	0.942	Contact Map
3o7qA	1	0.8905	20.4	0.948	Contact Map
4fc4A	3	0.4	12.9	0.952	Contact Map
4zw9A	1	0.3952	9.3	0.955	Contact Map
3w4tA	1	0.4238	9	0.956	Contact Map
3tdsE	3	0.3524	8.9	0.956	Contact Map
4ldsA	2	0.9619	8.5	0.956	Contact Map
3j1zP	8	0.4238	8.3	0.956	Contact Map
4dveA	3	0.3524	7.4	0.957	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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