DMSR - HALSA - GREMLIN Contacts

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DMSR - Dimethyl sulfoxide reductase transcriptional activator

UniProt:	Q9HR76	Sequences: MSERTASQPNTDRSRRRLRVVLDVALSDAAACPLEEIDGEVTAVRHQYTGDDCHADVTVAPACPDDDRSDVMHVATQTTDSCLCCVFSDHGCVPQITAVAADTITVETYLADRTTLTDLVADLKAVANTVSLTHLTRLAADDQSGDSHTHVTLDLFKLTDKQREAAAAAVAKGYYATPRGADLSDLATALGISKSAVSQRLSAVESKLATSAFTEAQQSAGSAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	224 (188)
Sequences:	1793 (1405)
Seq/√Len:	102.5

HALSA - DMSR Q9HSR5 O54637 Q9HR58 Q9HPS7 Q9HSM9 Q9HQD9 Q9HQU9
SULSO - Q97YT8 Q97ZB6 Q97YL7 Q97UC0 Q7LXI8 Q97WR0 Q97X87 Q97UD7 Q97Y14 Q97ZX5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
175_Y	205_E	4.787	1.00
181_A	186_L	4.079	1.00
168_A	172_K	4.075	1.00
193_S	196_A	3.797	1.00
172_K	186_L	3.697	1.00
165_A	190_L	3.641	1.00
87_F	92_C	3.204	1.00
172_K	189_A	3.162	1.00
161_K	200_R	3.110	1.00
181_A	185_D	3.096	1.00
170_V	210_T	3.012	1.00
92_C	110_L	2.950	1.00
196_A	200_R	2.864	1.00
168_A	186_L	2.863	1.00
176_A	180_G	2.843	1.00
182_D	185_D	2.585	1.00
177_T	198_S	2.442	1.00
161_K	165_A	2.405	1.00
183_L	198_S	2.188	1.00
161_K	164_E	2.140	1.00
183_L	197_V	2.078	1.00
163_R	167_A	2.030	1.00
200_R	203_A	1.980	1.00
194_K	198_S	1.978	1.00
95_Q	109_Y	1.872	1.00
165_A	200_R	1.809	1.00
186_L	197_V	1.781	1.00
179_R	202_S	1.754	1.00
192_I	197_V	1.701	1.00
166_A	209_A	1.689	1.00
165_A	192_I	1.648	1.00
200_R	207_K	1.550	1.00
177_T	199_Q	1.540	1.00
195_S	199_Q	1.534	1.00
209_A	212_A	1.534	1.00
181_A	189_A	1.517	1.00
185_D	188_T	1.478	1.00
172_K	181_A	1.455	1.00
173_G	180_G	1.455	1.00
208_L	212_A	1.449	1.00
33_P	36_E	1.436	1.00
115_T	118_D	1.425	1.00
110_L	131_S	1.419	1.00
166_A	175_Y	1.405	1.00
170_V	175_Y	1.399	1.00
167_A	171_A	1.380	1.00
158_L	204_V	1.357	0.99
56_D	59_V	1.291	0.99
196_A	204_V	1.287	0.99
112_D	115_T	1.278	0.99
177_T	202_S	1.233	0.99
196_A	201_L	1.217	0.99
76_T	84_C	1.214	0.99
188_T	191_G	1.211	0.99
165_A	197_V	1.202	0.99
109_Y	175_Y	1.200	0.99
190_L	197_V	1.164	0.98
170_V	213_F	1.155	0.98
186_L	190_L	1.149	0.98
143_Q	156_F	1.141	0.98
132_L	135_L	1.135	0.98
120_V	130_V	1.132	0.98
201_L	205_E	1.129	0.98
64_P	191_G	1.127	0.98
91_G	112_D	1.116	0.98
196_A	199_Q	1.113	0.98
35_E	102_D	1.110	0.98
104_I	107_E	1.110	0.98
96_I	175_Y	1.103	0.98
157_K	211_S	1.101	0.98
174_Y	179_R	1.092	0.97
175_Y	201_L	1.091	0.97
199_Q	203_A	1.089	0.97
209_A	213_F	1.071	0.97
58_T	197_V	1.061	0.97
165_A	204_V	1.049	0.97
123_L	128_N	1.047	0.97
183_L	200_R	1.039	0.97
193_S	202_S	1.035	0.97
94_P	108_T	1.027	0.96
177_T	195_S	1.016	0.96
121_A	125_A	1.014	0.96
88_S	186_L	1.009	0.96
155_L	212_A	0.997	0.96
30_A	33_P	0.994	0.96
69_S	73_H	0.981	0.95
47_Q	196_A	0.979	0.95
98_A	105_T	0.979	0.95
170_V	209_A	0.976	0.95
165_A	186_L	0.974	0.95
164_E	167_A	0.957	0.95
187_A	197_V	0.957	0.95
203_A	208_L	0.954	0.95
184_S	194_K	0.954	0.95
69_S	74_V	0.952	0.94
85_C	89_D	0.951	0.94
45_R	72_M	0.950	0.94
118_D	121_A	0.946	0.94
94_P	118_D	0.945	0.94
196_A	203_A	0.943	0.94
57_V	76_T	0.935	0.94
168_A	189_A	0.923	0.93
92_C	96_I	0.905	0.93
19_R	190_L	0.898	0.93
41_V	44_V	0.893	0.92
70_D	74_V	0.884	0.92
77_Q	155_L	0.878	0.92
206_S	210_T	0.875	0.92
204_V	209_A	0.858	0.91
107_E	116_L	0.856	0.91
183_L	194_K	0.834	0.89
43_A	46_H	0.833	0.89
177_T	184_S	0.830	0.89
184_S	202_S	0.827	0.89
172_K	197_V	0.820	0.89
16_R	21_V	0.818	0.89
24_V	130_V	0.815	0.88
161_K	199_Q	0.813	0.88
105_T	133_T	0.812	0.88
154_D	203_A	0.803	0.88
135_L	174_Y	0.797	0.87
23_D	131_S	0.796	0.87
143_Q	160_D	0.794	0.87
30_A	134_H	0.794	0.87
82_C	85_C	0.793	0.87
43_A	166_A	0.784	0.86
177_T	206_S	0.782	0.86
67_D	70_D	0.780	0.86
99_V	104_I	0.777	0.86
91_G	122_D	0.772	0.86
74_V	193_S	0.771	0.85
176_A	206_S	0.771	0.85
203_A	206_S	0.758	0.84
192_I	195_S	0.758	0.84
164_E	168_A	0.757	0.84
16_R	116_L	0.757	0.84
65_D	102_D	0.756	0.84
24_V	33_P	0.756	0.84
34_L	80_D	0.755	0.84
31_A	50_G	0.754	0.84
102_D	125_A	0.753	0.84
116_L	134_H	0.753	0.84
139_A	153_L	0.752	0.84
93_V	109_Y	0.751	0.84
174_Y	183_L	0.751	0.84
48_Y	70_D	0.739	0.83
87_F	108_T	0.734	0.83
194_K	209_A	0.733	0.82
75_A	81_S	0.729	0.82
90_H	122_D	0.729	0.82
183_L	196_A	0.725	0.82
86_V	182_D	0.724	0.82
117_T	120_V	0.720	0.81
97_T	106_V	0.718	0.81
51_D	54_H	0.714	0.81
33_P	106_V	0.714	0.81
119_L	194_K	0.714	0.81
208_L	211_S	0.713	0.81
38_D	42_T	0.711	0.81
166_A	204_V	0.704	0.80
34_L	87_F	0.695	0.79
25_A	32_C	0.693	0.79
46_H	78_T	0.693	0.79
157_K	210_T	0.691	0.79
34_L	97_T	0.690	0.78
183_L	204_V	0.690	0.78
92_C	95_Q	0.688	0.78
96_I	205_E	0.686	0.78
108_T	119_L	0.685	0.78
168_A	190_L	0.679	0.77
132_L	159_T	0.679	0.77
194_K	203_A	0.678	0.77
41_V	59_V	0.675	0.77
52_D	55_A	0.674	0.77
55_A	77_Q	0.674	0.77
69_S	184_S	0.672	0.77
132_L	192_I	0.672	0.77
153_L	191_G	0.670	0.76
111_A	124_K	0.670	0.76
32_C	36_E	0.668	0.76
31_A	35_E	0.666	0.76
177_T	200_R	0.659	0.75
32_C	38_D	0.658	0.75
54_H	60_A	0.657	0.75
33_P	37_I	0.655	0.75
155_L	163_R	0.636	0.73
173_G	198_S	0.631	0.72
51_D	111_A	0.628	0.72
119_L	199_Q	0.625	0.71
131_S	139_A	0.625	0.71
135_L	195_S	0.624	0.71
96_I	111_A	0.622	0.71
107_E	194_K	0.621	0.71
59_V	65_D	0.620	0.71
154_D	157_K	0.616	0.70
94_P	155_L	0.614	0.70
30_A	34_L	0.614	0.70
163_R	212_A	0.611	0.70
112_D	163_R	0.610	0.70
113_R	135_L	0.610	0.70
143_Q	153_L	0.609	0.69
81_S	182_D	0.607	0.69
190_L	198_S	0.604	0.69
166_A	213_F	0.602	0.69
53_C	60_A	0.597	0.68
117_T	196_A	0.596	0.68
120_V	196_A	0.595	0.68
173_G	176_A	0.593	0.67
133_T	141_D	0.592	0.67
48_Y	141_D	0.590	0.67
192_I	200_R	0.588	0.67
116_L	188_T	0.587	0.67
39_G	42_T	0.586	0.66
69_S	72_M	0.585	0.66
127_A	160_D	0.585	0.66
15_R	212_A	0.584	0.66
92_C	97_T	0.583	0.66
90_H	159_T	0.583	0.66
87_F	94_P	0.582	0.66
20_V	23_D	0.582	0.66
137_R	157_K	0.581	0.66
129_T	156_F	0.580	0.66
164_E	192_I	0.580	0.66
55_A	58_T	0.577	0.65
60_A	64_P	0.576	0.65
46_H	137_R	0.574	0.65
83_L	106_V	0.574	0.65
167_A	213_F	0.573	0.65
118_D	180_G	0.572	0.65
44_V	47_Q	0.572	0.65
50_G	142_D	0.569	0.64
60_A	189_A	0.568	0.64
142_D	196_A	0.566	0.64
41_V	70_D	0.559	0.63
175_Y	209_A	0.557	0.63
86_V	126_V	0.557	0.63
22_L	32_C	0.557	0.63
116_L	164_E	0.556	0.62
70_D	167_A	0.555	0.62
72_M	96_I	0.555	0.62
160_D	170_V	0.554	0.62
168_A	181_A	0.551	0.62
33_P	104_I	0.548	0.61
119_L	195_S	0.544	0.61
196_A	208_L	0.544	0.61
65_D	69_S	0.544	0.61
182_D	212_A	0.542	0.60
100_A	141_D	0.539	0.60
123_L	127_A	0.538	0.60
37_I	41_V	0.537	0.60
95_Q	182_D	0.537	0.60
175_Y	204_V	0.533	0.59
39_G	172_K	0.531	0.59
22_L	26_L	0.529	0.59
139_A	142_D	0.528	0.59
102_D	114_T	0.525	0.58
130_V	198_S	0.524	0.58
70_D	73_H	0.523	0.58
37_I	191_G	0.521	0.58
44_V	48_Y	0.518	0.57
124_K	192_I	0.515	0.57
108_T	115_T	0.515	0.57
108_T	112_D	0.515	0.57
185_D	190_L	0.515	0.57
124_K	188_T	0.514	0.56
163_R	215_E	0.512	0.56
76_T	88_S	0.511	0.56
86_V	89_D	0.510	0.56
166_A	205_E	0.509	0.56
51_D	65_D	0.509	0.56
105_T	211_S	0.508	0.56
25_A	94_P	0.507	0.55
71_V	87_F	0.506	0.55
15_R	175_Y	0.506	0.55
19_R	22_L	0.505	0.55
73_H	170_V	0.504	0.55
44_V	67_D	0.504	0.55
116_L	135_L	0.504	0.55
30_A	190_L	0.503	0.55
96_I	171_A	0.503	0.55
108_T	207_K	0.502	0.55
110_L	175_Y	0.500	0.54

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
1je8A	2	0.2902	97.3	0.85	Contact Map
1s7oA	3	0.3438	97.3	0.851	Contact Map
1ku3A	1	0.2723	97.2	0.852	Contact Map
1xsvA	2	0.3438	97.1	0.854	Contact Map
3hugA	3	0.3571	97.1	0.854	Contact Map
4wszA	2	0.2545	97.1	0.855	Contact Map
2o8xA	7	0.2723	97	0.856	Contact Map
1ttyA	1	0.3527	96.8	0.861	Contact Map
3c57A	2	0.2143	96.7	0.862	Contact Map
2rnjA	1	0.2545	96.7	0.863	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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