TRER - BACSU - GREMLIN Contacts

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TRER - Trehalose operon transcriptional repressor

UniProt:	P39796	Sequences: MKVNKFITIYKDIAQQIEGGRWKAEEILPSEHELTAQYGTSRETVRKALHMLAQNGYIQKIRGKGSVVLNREKMQFPVSGLVSFKELAQTLGKETKTTVHKFGLEPPSELIQKQLRANLDDDIWEVIRSRKIDGEHVILDKDYFFRKHVPHLTKEICENSIYEYIEGELGLSISYAQKEIVAEPCTDEDRELLDLRGYDHMVVVRNYVFLEDTSLFQYTESRHRLDKFRFVDFARRGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	238 (192)
Sequences:	25286 (20268)
Seq/√Len:	1462.7

ECOLI - MNGR YIDP YIHL PHNF FRLR YEGW LLDR DGOR FADR NANR PDHR YIEP EXUR GLCC
BACSU - TRER YYDK YURK YBGA YVOA GMUR YMFC YCBG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_K	26_E	4.070	1.00
16_Q	21_R	3.961	1.00
14_A	55_N	3.441	1.00
16_Q	37_Q	3.327	1.00
10_Y	51_M	3.314	1.00
59_Q	69_L	2.905	1.00
181_V	184_P	2.703	1.00
12_D	16_Q	2.601	1.00
9_I	40_T	2.582	1.00
31_E	42_R	2.561	1.00
60_K	66_S	2.497	1.00
61_I	64_K	2.459	1.00
10_Y	55_N	2.370	1.00
9_I	38_Y	2.246	1.00
27_I	67_V	2.213	1.00
15_Q	19_G	2.183	1.00
12_D	38_Y	2.015	1.00
10_Y	14_A	1.976	1.00
64_K	67_V	1.926	1.00
53_A	60_K	1.853	1.00
130_R	138_I	1.847	1.00
47_K	50_H	1.823	1.00
14_A	18_E	1.774	1.00
33_E	37_Q	1.711	1.00
32_H	36_A	1.683	1.00
186_T	189_D	1.648	1.00
12_D	15_Q	1.636	1.00
16_Q	22_W	1.617	1.00
108_S	111_I	1.588	1.00
53_A	58_I	1.580	1.00
14_A	57_Y	1.578	1.00
31_E	46_R	1.571	1.00
186_T	190_R	1.568	1.00
8_T	12_D	1.565	1.00
30_S	33_E	1.549	1.00
34_L	45_V	1.546	1.00
58_I	66_S	1.542	1.00
49_L	58_I	1.541	1.00
184_P	188_E	1.521	1.00
126_V	142_D	1.489	1.00
61_I	67_V	1.445	1.00
17_I	68_V	1.421	1.00
96_K	131_K	1.420	1.00
5_K	8_T	1.420	1.00
50_H	60_K	1.405	1.00
127_I	130_R	1.395	1.00
176_A	184_P	1.367	1.00
126_V	130_R	1.354	1.00
51_M	54_Q	1.332	1.00
24_A	70_N	1.328	1.00
40_T	45_V	1.309	1.00
50_H	54_Q	1.304	1.00
33_E	36_A	1.297	1.00
22_W	68_V	1.296	1.00
174_S	178_K	1.276	1.00
98_T	131_K	1.272	1.00
59_Q	67_V	1.265	1.00
187_D	191_E	1.261	1.00
6_F	51_M	1.253	1.00
125_E	141_K	1.253	1.00
182_A	186_T	1.231	1.00
50_H	53_A	1.213	1.00
92_G	96_K	1.212	1.00
16_Q	20_G	1.180	1.00
120_D	123_I	1.179	1.00
105_E	125_E	1.166	1.00
113_K	116_R	1.163	1.00
136_H	147_K	1.149	1.00
27_I	65_G	1.146	1.00
139_L	143_Y	1.143	1.00
102_F	105_E	1.137	1.00
51_M	55_N	1.136	1.00
18_E	57_Y	1.134	1.00
89_Q	92_G	1.132	1.00
61_I	65_G	1.120	1.00
101_K	104_L	1.119	1.00
89_Q	96_K	1.111	1.00
118_N	121_D	1.109	1.00
171_L	175_Y	1.104	1.00
111_I	143_Y	1.099	1.00
162_Y	166_E	1.094	1.00
89_Q	93_K	1.091	1.00
22_W	26_E	1.091	1.00
101_K	105_E	1.085	1.00
16_Q	38_Y	1.082	1.00
127_I	131_K	1.075	1.00
86_E	90_T	1.056	1.00
49_L	66_S	1.050	1.00
25_E	59_Q	1.030	1.00
161_I	164_Y	1.024	1.00
7_I	51_M	1.022	1.00
127_I	141_K	1.019	1.00
93_K	97_T	1.019	1.00
128_R	177_Q	1.005	1.00
138_I	142_D	0.996	1.00
87_L	91_L	0.978	1.00
129_S	141_K	0.974	1.00
139_L	189_D	0.971	1.00
172_S	188_E	0.960	1.00
161_I	165_I	0.955	1.00
163_E	167_G	0.955	1.00
190_R	194_D	0.953	1.00
103_G	125_E	0.951	1.00
63_G	66_S	0.950	1.00
27_I	30_S	0.948	1.00
7_I	11_K	0.947	1.00
97_T	100_H	0.947	1.00
11_K	14_A	0.933	1.00
93_K	96_K	0.931	1.00
107_P	112_Q	0.929	1.00
175_Y	179_E	0.926	1.00
107_P	111_I	0.926	1.00
109_E	113_K	0.925	1.00
196_R	199_D	0.924	1.00
47_K	51_M	0.909	1.00
13_I	34_L	0.898	1.00
41_S	44_T	0.898	1.00
153_T	156_I	0.897	1.00
80_G	135_E	0.896	1.00
6_F	10_Y	0.889	1.00
110_L	113_K	0.889	1.00
101_K	125_E	0.882	1.00
125_E	170_G	0.878	1.00
89_Q	95_T	0.874	1.00
160_S	163_E	0.869	1.00
103_G	106_P	0.865	1.00
91_L	95_T	0.865	1.00
90_T	93_K	0.864	1.00
152_L	155_E	0.863	1.00
110_L	114_Q	0.861	1.00
152_L	156_I	0.858	1.00
179_E	184_P	0.857	1.00
85_K	88_A	0.853	1.00
184_P	187_D	0.845	1.00
5_K	44_T	0.842	1.00
127_I	188_E	0.842	1.00
96_K	100_H	0.838	1.00
124_W	174_S	0.830	1.00
100_H	104_L	0.830	1.00
132_I	138_I	0.826	1.00
175_Y	178_K	0.823	1.00
145_F	148_H	0.823	1.00
49_L	53_A	0.822	1.00
104_L	108_S	0.819	1.00
117_A	121_D	0.818	1.00
34_L	49_L	0.817	1.00
85_K	89_Q	0.816	1.00
74_M	77_P	0.815	1.00
111_I	114_Q	0.814	1.00
28_L	58_I	0.812	1.00
89_Q	94_E	0.812	1.00
105_E	108_S	0.804	1.00
76_F	80_G	0.800	1.00
35_T	45_V	0.797	1.00
183_E	189_D	0.791	1.00
88_A	132_I	0.791	1.00
108_S	112_Q	0.781	1.00
119_L	123_I	0.781	1.00
124_W	128_R	0.781	1.00
9_I	12_D	0.780	1.00
189_D	192_L	0.777	1.00
25_E	70_N	0.776	1.00
24_A	69_L	0.772	1.00
104_L	107_P	0.771	1.00
92_G	97_T	0.759	1.00
160_S	165_I	0.758	1.00
31_E	60_K	0.754	1.00
112_Q	117_A	0.754	1.00
183_E	187_D	0.750	1.00
185_C	195_L	0.748	1.00
140_D	143_Y	0.747	1.00
11_K	15_Q	0.741	1.00
6_F	47_K	0.734	1.00
102_F	108_S	0.734	1.00
173_I	189_D	0.721	1.00
109_E	112_Q	0.719	1.00
16_Q	19_G	0.718	1.00
112_Q	115_L	0.717	1.00
96_K	134_G	0.717	1.00
108_S	114_Q	0.716	1.00
136_H	139_L	0.710	1.00
84_F	88_A	0.709	1.00
101_K	108_S	0.708	1.00
188_E	191_E	0.707	1.00
21_R	37_Q	0.703	1.00
104_L	146_R	0.701	1.00
107_P	110_L	0.700	1.00
75_Q	79_S	0.693	1.00
166_E	172_S	0.691	1.00
13_I	22_W	0.690	1.00
9_I	45_V	0.687	1.00
195_L	199_D	0.685	1.00
86_E	194_D	0.684	1.00
98_T	103_G	0.683	1.00
36_A	39_G	0.680	1.00
94_E	97_T	0.679	1.00
32_H	35_T	0.678	1.00
12_D	37_Q	0.674	1.00
95_T	98_T	0.671	1.00
172_S	184_P	0.669	1.00
173_I	188_E	0.669	1.00
115_L	118_N	0.669	1.00
99_V	103_G	0.668	1.00
103_G	107_P	0.667	1.00
22_W	28_L	0.663	1.00
91_L	94_E	0.659	1.00
86_E	89_Q	0.657	1.00
189_D	193_L	0.654	1.00
171_L	174_S	0.652	1.00
164_Y	167_G	0.651	1.00
49_L	60_K	0.649	1.00
102_F	106_P	0.649	1.00
172_S	175_Y	0.647	1.00
84_F	87_L	0.644	1.00
187_D	190_R	0.643	1.00
129_S	145_F	0.641	1.00
160_S	164_Y	0.638	1.00
191_E	195_L	0.638	1.00
93_K	133_D	0.637	1.00
35_T	38_Y	0.634	1.00
113_K	117_A	0.632	1.00
96_K	99_V	0.629	1.00
163_E	166_E	0.626	1.00
121_D	147_K	0.621	1.00
107_P	117_A	0.621	1.00
146_R	150_P	0.620	1.00
183_E	186_T	0.619	1.00
101_K	127_I	0.615	1.00
10_Y	48_A	0.615	1.00
131_K	134_G	0.614	1.00
185_C	193_L	0.611	1.00
132_I	137_V	0.611	1.00
185_C	190_R	0.610	1.00
76_F	79_S	0.609	1.00
90_T	96_K	0.609	1.00
38_Y	45_V	0.608	1.00
92_G	95_T	0.608	1.00
119_L	122_D	0.608	1.00
95_T	99_V	0.608	1.00
29_P	37_Q	0.607	1.00
94_E	186_T	0.606	1.00
162_Y	165_I	0.604	1.00
154_K	157_C	0.603	1.00
176_A	181_V	0.598	1.00
101_K	106_P	0.597	1.00
44_T	48_A	0.595	1.00
34_L	38_Y	0.595	1.00
53_A	66_S	0.592	1.00
185_C	189_D	0.592	1.00
95_T	100_H	0.590	1.00
45_V	58_I	0.586	1.00
9_I	48_A	0.585	1.00
147_K	150_P	0.583	1.00
126_V	145_F	0.578	1.00
177_Q	180_I	0.573	1.00
142_D	145_F	0.568	1.00
141_K	189_D	0.568	1.00
27_I	64_K	0.565	1.00
112_Q	116_R	0.565	1.00
126_V	138_I	0.564	1.00
94_E	98_T	0.562	1.00
30_S	63_G	0.557	1.00
106_P	122_D	0.552	1.00
43_E	47_K	0.551	1.00
104_L	122_D	0.548	1.00
29_P	44_T	0.547	1.00
172_S	191_E	0.542	1.00
97_T	101_K	0.541	1.00
107_P	121_D	0.541	1.00
100_H	103_G	0.536	1.00
117_A	120_D	0.532	1.00
35_T	43_E	0.532	1.00
185_C	199_D	0.528	1.00
107_P	114_Q	0.520	1.00
107_P	113_K	0.517	1.00
9_I	13_I	0.517	1.00
44_T	47_K	0.517	1.00
111_I	115_L	0.514	1.00
184_P	199_D	0.511	1.00
97_T	130_R	0.510	1.00
62_R	65_G	0.509	1.00
111_I	117_A	0.506	1.00
122_D	146_R	0.504	1.00
82_V	85_K	0.503	1.00
81_L	85_K	0.502	1.00
22_W	29_P	0.501	1.00
7_I	10_Y	0.501	1.00
145_F	149_V	0.500	1.00

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
4u0wA	2	0.9916	100	0.123	Contact Map
3f8mA	2	0.9622	100	0.149	Contact Map
2ra5A	2	0.6218	100	0.162	Contact Map
3edpA	2	0.9202	100	0.169	Contact Map
3eetA	2	0.9664	100	0.181	Contact Map
3bwgA	2	0.9622	100	0.188	Contact Map
3f8lA	2	0.6807	100	0.439	Contact Map
2di3A	2	0.8529	99.9	0.454	Contact Map
1hw1A	2	0.8529	99.9	0.455	Contact Map
4p96A	2	0.8992	99.9	0.469	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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