Na_trans_assoc - PFAM28P - GREMLIN Contacts

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Na_trans_assoc - Sodium ion transport-associated

PFAM:	PF06512	Sequences: DGEMNNLQIAIARIQRGIDFVKRTILDFCCKLLKKKKLKEKKPLDELKDLDSKKENCISNHTGAEIKDLDDESDHMSFITNPSLTVTVPIAVGESDLENLEDEDESSESSDEEKSKQSSSSEGSTVDLKPPEEELEEIEEEAEESKEPEDCFTEGCVRRFPCCQVDITKGPGKIWWNLRKTCYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	184 (184)
Sequences:	785 (498)
Seq/√Len:	36.7
META:	0.004

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_E	115_S	3.397	1.00
112_E	116_K	3.211	1.00
121_S	125_T	2.946	1.00
40_E	45_D	2.934	1.00
78_F	81_N	2.724	1.00
148_P	151_C	2.641	1.00
106_S	109_S	2.613	1.00
67_K	70_D	2.577	1.00
119_S	122_E	2.355	1.00
121_S	127_D	2.352	1.00
111_D	115_S	2.164	0.99
110_S	115_S	2.154	0.99
121_S	124_S	2.121	0.99
40_E	47_L	2.099	0.99
104_D	107_S	2.090	0.99
43_P	46_E	2.053	0.99
111_D	116_K	2.051	0.99
58_I	61_H	1.941	0.98
89_P	94_E	1.934	0.98
63_G	66_I	1.926	0.98
38_L	41_K	1.921	0.98
110_S	116_K	1.883	0.98
78_F	82_P	1.839	0.97
41_K	44_L	1.828	0.97
77_S	81_N	1.816	0.97
113_E	116_K	1.795	0.97
156_C	162_C	1.763	0.97
91_A	94_E	1.753	0.96
74_D	77_S	1.747	0.96
157_V	176_W	1.686	0.96
102_D	105_E	1.679	0.96
64_A	68_D	1.663	0.95
39_K	42_K	1.656	0.95
111_D	114_K	1.636	0.95
38_L	43_P	1.620	0.95
103_E	106_S	1.615	0.94
57_C	61_H	1.614	0.94
176_W	180_K	1.581	0.94
28_F	33_L	1.558	0.93
104_D	109_S	1.555	0.93
40_E	44_L	1.528	0.93
1_D	5_N	1.485	0.91
73_S	76_M	1.475	0.91
91_A	96_D	1.433	0.90
124_S	127_D	1.419	0.89
40_E	43_P	1.408	0.89
41_K	45_D	1.399	0.89
110_S	117_Q	1.398	0.89
47_L	51_D	1.395	0.89
54_K	61_H	1.359	0.87
13_R	148_P	1.356	0.87
72_E	76_M	1.351	0.87
77_S	80_T	1.342	0.87
40_E	46_E	1.307	0.85
34_K	37_K	1.285	0.84
76_M	79_I	1.262	0.83
119_S	123_G	1.257	0.83
123_G	143_E	1.255	0.83
54_K	60_N	1.231	0.81
7_L	156_C	1.228	0.81
104_D	108_E	1.224	0.81
62_T	65_E	1.205	0.80
41_K	48_K	1.196	0.80
89_P	182_C	1.195	0.79
102_D	106_S	1.191	0.79
111_D	117_Q	1.183	0.79
39_K	46_E	1.175	0.78
137_E	140_E	1.153	0.77
54_K	57_C	1.149	0.77
16_R	166_D	1.147	0.77
176_W	182_C	1.145	0.76
101_E	106_S	1.126	0.75
6_N	91_A	1.119	0.75
82_P	85_T	1.110	0.74
37_K	41_K	1.104	0.74
39_K	45_D	1.095	0.73
39_K	43_P	1.086	0.73
66_I	69_L	1.085	0.72
12_A	183_Y	1.083	0.72
6_N	12_A	1.082	0.72
75_H	78_F	1.065	0.71
103_E	108_E	1.054	0.70
8_Q	94_E	1.050	0.70
35_K	38_L	1.044	0.70
91_A	98_E	1.035	0.69
175_W	179_R	1.027	0.68
55_E	60_N	1.027	0.68
167_I	170_G	1.025	0.68
94_E	182_C	1.017	0.67
110_S	114_K	1.017	0.67
157_V	164_Q	1.015	0.67
120_S	184_R	1.008	0.67
12_A	126_V	1.005	0.67
21_V	25_I	1.004	0.66
56_N	61_H	0.991	0.65
81_N	86_V	0.988	0.65
85_T	97_L	0.987	0.65
42_K	45_D	0.986	0.65
41_K	47_L	0.984	0.65
78_F	86_V	0.983	0.65
61_H	66_I	0.982	0.65
163_C	176_W	0.978	0.64
41_K	46_E	0.968	0.64
149_E	166_D	0.968	0.64
62_T	67_K	0.959	0.63
20_F	24_T	0.956	0.63
61_H	64_A	0.952	0.62
64_A	67_K	0.950	0.62
4_M	183_Y	0.945	0.62
95_S	98_E	0.943	0.62
35_K	183_Y	0.937	0.61
6_N	17_G	0.933	0.61
15_Q	19_D	0.932	0.61
100_L	103_E	0.927	0.60
161_P	166_D	0.922	0.60
7_L	13_R	0.917	0.59
122_E	133_E	0.917	0.59
36_K	41_K	0.916	0.59
107_S	116_K	0.904	0.58
135_L	138_I	0.904	0.58
39_K	44_L	0.897	0.58
93_G	103_E	0.894	0.57
89_P	125_T	0.888	0.57
82_P	152_F	0.886	0.57
17_G	175_W	0.880	0.56
91_A	124_S	0.871	0.55
173_K	184_R	0.863	0.55
42_K	47_L	0.862	0.55
165_V	168_T	0.854	0.54
135_L	139_E	0.848	0.53
94_E	124_S	0.847	0.53
81_N	84_L	0.842	0.53
157_V	165_V	0.837	0.52
26_L	30_C	0.836	0.52
82_P	86_V	0.835	0.52
79_I	82_P	0.830	0.52
171_P	177_N	0.829	0.52
155_G	163_C	0.826	0.51
175_W	182_C	0.825	0.51
151_C	179_R	0.820	0.51
44_L	47_L	0.819	0.51
38_L	48_K	0.816	0.51
24_T	159_R	0.815	0.51
101_E	109_S	0.814	0.50
155_G	158_R	0.812	0.50
133_E	136_E	0.809	0.50
57_C	60_N	0.802	0.49
8_Q	182_C	0.796	0.49
56_N	59_S	0.794	0.49
163_C	183_Y	0.790	0.48
27_D	33_L	0.790	0.48
78_F	85_T	0.785	0.48
153_T	184_R	0.782	0.48
157_V	160_F	0.782	0.48
110_S	113_E	0.780	0.47
170_G	173_K	0.773	0.47
34_K	41_K	0.767	0.46
25_I	33_L	0.767	0.46
45_D	48_K	0.765	0.46
49_D	53_K	0.762	0.46
9_I	181_T	0.761	0.46
120_S	153_T	0.759	0.46
51_D	62_T	0.756	0.45
35_K	41_K	0.750	0.45
62_T	66_I	0.749	0.45
53_K	61_H	0.747	0.45
103_E	109_S	0.740	0.44
163_C	166_D	0.735	0.44
14_I	17_G	0.723	0.42
91_A	182_C	0.722	0.42
132_E	135_L	0.721	0.42
102_D	108_E	0.720	0.42
12_A	16_R	0.720	0.42
21_V	24_T	0.718	0.42
164_Q	170_G	0.716	0.42
125_T	182_C	0.711	0.41
43_P	47_L	0.710	0.41
124_S	182_C	0.710	0.41
113_E	117_Q	0.710	0.41
89_P	124_S	0.707	0.41
88_V	95_S	0.705	0.41
15_Q	163_C	0.703	0.41
29_C	146_K	0.701	0.41
53_K	59_S	0.696	0.40
125_T	149_E	0.696	0.40
2_G	144_E	0.692	0.40
43_P	48_K	0.692	0.40
2_G	75_H	0.691	0.40
24_T	27_D	0.691	0.40
12_A	17_G	0.682	0.39
8_Q	11_I	0.681	0.39
57_C	68_D	0.675	0.38
44_L	86_V	0.674	0.38
62_T	68_D	0.673	0.38
78_F	97_L	0.672	0.38
150_D	154_E	0.672	0.38
128_L	131_P	0.664	0.38
167_I	172_G	0.662	0.37
81_N	85_T	0.658	0.37
45_D	51_D	0.657	0.37
138_I	141_E	0.645	0.36
57_C	92_V	0.644	0.36
30_C	144_E	0.641	0.36
73_S	77_S	0.640	0.36
94_E	180_K	0.640	0.36
126_V	181_T	0.640	0.36
166_D	169_K	0.639	0.35
39_K	51_D	0.638	0.35
89_P	96_D	0.636	0.35
56_N	60_N	0.635	0.35
51_D	54_K	0.630	0.35
22_K	151_C	0.630	0.35
38_L	46_E	0.629	0.35
53_K	57_C	0.625	0.34
78_F	84_L	0.624	0.34
52_S	55_E	0.623	0.34
38_L	45_D	0.619	0.34
91_A	181_T	0.612	0.33
104_D	112_E	0.611	0.33
33_L	172_G	0.610	0.33
125_T	181_T	0.608	0.33
6_N	181_T	0.605	0.33
119_S	163_C	0.604	0.33
5_N	176_W	0.604	0.33
5_N	86_V	0.601	0.32
48_K	59_S	0.594	0.32
26_L	33_L	0.592	0.32
74_D	86_V	0.591	0.32
38_L	44_L	0.590	0.32
177_N	180_K	0.588	0.31
151_C	156_C	0.579	0.31
36_K	39_K	0.573	0.30
91_A	125_T	0.571	0.30
39_K	47_L	0.569	0.30
171_P	174_I	0.564	0.30
16_R	136_E	0.564	0.30
122_E	131_P	0.563	0.30
36_K	53_K	0.559	0.29
152_F	158_R	0.559	0.29
140_E	183_Y	0.558	0.29
100_L	104_D	0.557	0.29
81_N	101_E	0.557	0.29
10_A	16_R	0.552	0.29
8_Q	96_D	0.552	0.29
172_G	175_W	0.552	0.29
165_V	182_C	0.549	0.29
119_S	128_L	0.544	0.28
169_K	184_R	0.543	0.28
99_N	128_L	0.542	0.28
46_E	58_I	0.541	0.28
53_K	60_N	0.538	0.28
42_K	58_I	0.536	0.28
26_L	172_G	0.536	0.28
8_Q	89_P	0.534	0.28
44_L	51_D	0.533	0.27
152_F	165_V	0.532	0.27
6_N	95_S	0.531	0.27
88_V	101_E	0.531	0.27
129_K	144_E	0.530	0.27
122_E	127_D	0.529	0.27
131_P	147_E	0.526	0.27
3_E	7_L	0.526	0.27
22_K	156_C	0.524	0.27
99_N	102_D	0.522	0.27
105_E	109_S	0.515	0.26
130_P	145_S	0.514	0.26
7_L	10_A	0.511	0.26
6_N	10_A	0.510	0.26
128_L	153_T	0.509	0.26
27_D	30_C	0.508	0.26
9_I	17_G	0.507	0.26
2_G	15_Q	0.506	0.26
11_I	48_K	0.505	0.26
53_K	56_N	0.505	0.26
20_F	155_G	0.502	0.25
4_M	17_G	0.500	0.25

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
3lhrA	2	0.1957	11.2	0.95	Contact Map
2fi2A	2	0.2011	9.9	0.951	Contact Map
4bhxA	2	0.1957	9.3	0.952	Contact Map
4e6sA	2	0.1957	6.8	0.955	Contact Map
1y7qA	2	0.212	5.7	0.957	Contact Map
2msqA	1	0.125	5.6	0.957	Contact Map
2bezF	1	0.1196	3.8	0.96	Contact Map
3mwbA	3	0.3207	3.7	0.96	Contact Map
2k13X	1	0.2011	3.4	0.961	Contact Map
3j39U	1	0.3804	3	0.962	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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