YIAJ - ECOLI - GREMLIN Contacts

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YIAJ - HTH-type transcriptional regulator YiaJ

UniProt:	P37671	Sequences: MGKEVMGKKENEMAQEKERPAGSQSLFRGLMLIEILSNYPNGCPLAHLSELAGLNKSTVHRLLQGLQSCGYVTTAPAAGSYRLTTKFIAVGQKALSSLNIIHIAAPHLEALNIATGETINFSSREDDHAILIYKLEPTTGMLRTRAYIGQHMPLYCSAMGKIYMAFGHPDYVKSYWESHQHEIQPLTRNTITELPAMFDELAHIRESGAAMDREENELGVSCIAVPVFDIHGRVPYAVSISLSTSRLKQVGEKNLLKPLRETAQAISNELGFTVRDDLGAIT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12278
Length:	282 (245)
Sequences:	12859 (9400)
Seq/√Len:	600.6

ECOLI - YIAJ ALLR KDGR ICLR MHPR RHMR YAGI YJHI
BACSU - KIPR
HALSA - Q9HHM8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_L	29_G	3.235	1.00
114_A	258_P	3.180	1.00
27_F	69_C	2.845	1.00
122_S	159_M	2.844	1.00
107_H	262_T	2.828	1.00
203_H	207_S	2.654	1.00
34_E	86_K	2.576	1.00
105_A	133_Y	2.425	1.00
173_K	198_F	2.400	1.00
161_K	200_E	2.397	1.00
30_L	71_Y	2.348	1.00
161_K	215_E	2.233	1.00
128_H	151_H	2.200	1.00
117_E	246_R	2.133	1.00
107_H	265_A	2.099	1.00
167_G	171_Y	2.074	1.00
109_E	135_L	2.069	1.00
36_L	72_V	2.053	1.00
31_M	69_C	1.996	1.00
225_V	259_L	1.934	1.00
166_F	228_F	1.895	1.00
124_R	154_L	1.886	1.00
225_V	263_A	1.854	1.00
107_H	269_E	1.832	1.00
212_D	222_C	1.832	1.00
213_R	221_S	1.817	1.00
221_S	244_T	1.794	1.00
75_A	78_A	1.774	1.00
256_L	260_R	1.767	1.00
110_A	265_A	1.760	1.00
32_L	48_L	1.730	1.00
110_A	114_A	1.730	1.00
73_T	82_R	1.722	1.00
34_E	69_C	1.716	1.00
35_I	43_C	1.693	1.00
194_L	198_F	1.690	1.00
35_I	51_L	1.679	1.00
193_E	196_A	1.675	1.00
63_L	72_V	1.661	1.00
35_I	52_A	1.658	1.00
104_A	266_I	1.655	1.00
112_N	119_I	1.651	1.00
214_E	244_T	1.636	1.00
35_I	48_L	1.630	1.00
225_V	260_R	1.627	1.00
251_G	254_N	1.627	1.00
242_L	247_L	1.612	1.00
209_A	256_L	1.567	1.00
240_I	255_L	1.563	1.00
43_C	51_L	1.554	1.00
42_G	82_R	1.545	1.00
107_H	110_A	1.510	1.00
44_P	47_H	1.507	1.00
63_L	81_Y	1.505	1.00
200_E	203_H	1.503	1.00
204_I	210_A	1.489	1.00
54_L	59_V	1.484	1.00
115_T	258_P	1.472	1.00
172_V	198_F	1.461	1.00
258_P	261_E	1.460	1.00
168_H	171_Y	1.458	1.00
42_G	80_S	1.453	1.00
86_K	89_A	1.450	1.00
214_E	219_G	1.449	1.00
129_A	163_Y	1.443	1.00
48_L	59_V	1.442	1.00
136_E	143_R	1.431	1.00
187_T	190_T	1.418	1.00
228_F	267_S	1.390	1.00
173_K	194_L	1.370	1.00
112_N	135_L	1.358	1.00
67_Q	72_V	1.355	1.00
101_I	133_Y	1.351	1.00
129_A	154_L	1.349	1.00
75_A	82_R	1.342	1.00
34_E	71_Y	1.339	1.00
104_A	121_F	1.332	1.00
111_L	258_P	1.329	1.00
36_L	43_C	1.324	1.00
263_A	267_S	1.316	1.00
67_Q	74_T	1.315	1.00
30_L	69_C	1.314	1.00
127_D	178_S	1.278	1.00
36_L	42_G	1.271	1.00
39_Y	51_L	1.253	1.00
108_L	121_F	1.247	1.00
201_L	204_I	1.246	1.00
261_E	265_A	1.241	1.00
39_Y	43_C	1.241	1.00
169_P	198_F	1.232	1.00
60_H	64_Q	1.225	1.00
49_S	59_V	1.216	1.00
111_L	262_T	1.215	1.00
177_E	194_L	1.208	1.00
55_N	58_T	1.206	1.00
48_L	63_L	1.206	1.00
105_A	109_E	1.206	1.00
191_I	200_E	1.189	1.00
166_F	226_P	1.180	1.00
189_N	214_E	1.162	1.00
228_F	234_V	1.158	1.00
165_A	204_I	1.148	1.00
260_R	264_Q	1.137	1.00
122_S	129_A	1.135	1.00
156_C	190_T	1.132	1.00
124_R	167_G	1.130	1.00
156_C	186_L	1.125	1.00
169_P	173_K	1.125	1.00
115_T	255_L	1.107	1.00
45_L	60_H	1.106	1.00
229_D	233_R	1.103	1.00
124_R	127_D	1.098	1.00
46_A	50_E	1.097	1.00
166_F	234_V	1.092	1.00
123_S	236_Y	1.091	1.00
109_E	113_I	1.091	1.00
27_F	68_S	1.089	1.00
265_A	269_E	1.082	1.00
176_W	194_L	1.081	1.00
44_P	80_S	1.078	1.00
225_V	256_L	1.074	1.00
169_P	172_V	1.073	1.00
121_F	236_Y	1.067	1.00
172_V	205_R	1.058	1.00
27_F	65_G	1.053	1.00
37_S	40_P	1.045	1.00
115_T	240_I	1.045	1.00
159_M	237_A	1.038	1.00
121_F	227_V	1.034	1.00
108_L	119_I	1.025	1.00
169_P	202_A	1.023	1.00
238_V	266_I	1.020	1.00
155_Y	190_T	1.018	1.00
125_E	151_H	1.016	1.00
45_L	49_S	1.015	1.00
23_S	65_G	1.014	1.00
87_F	94_A	1.010	1.00
105_A	135_L	1.006	1.00
173_K	177_E	1.002	1.00
157_S	160_G	0.998	1.00
71_Y	90_V	0.996	1.00
47_H	50_E	0.990	1.00
110_A	262_T	0.985	1.00
257_K	261_E	0.980	1.00
188_R	218_L	0.975	1.00
264_Q	268_N	0.968	1.00
158_A	222_C	0.962	1.00
114_A	261_E	0.958	1.00
226_P	234_V	0.948	1.00
171_Y	174_S	0.948	1.00
185_P	192_T	0.947	1.00
42_G	75_A	0.945	1.00
122_S	131_L	0.944	1.00
186_L	190_T	0.939	1.00
100_I	236_Y	0.935	1.00
22_G	68_S	0.927	1.00
24_Q	28_R	0.925	1.00
248_K	251_G	0.924	1.00
204_I	207_S	0.919	1.00
130_I	151_H	0.918	1.00
162_I	166_F	0.916	1.00
46_A	56_K	0.916	1.00
199_D	202_A	0.905	1.00
223_I	256_L	0.899	1.00
196_A	200_E	0.895	1.00
253_K	257_K	0.895	1.00
103_I	269_E	0.895	1.00
199_D	203_H	0.886	1.00
172_V	201_L	0.885	1.00
108_L	133_Y	0.884	1.00
174_S	178_S	0.883	1.00
119_I	240_I	0.879	1.00
38_N	51_L	0.879	1.00
33_I	87_F	0.878	1.00
207_S	256_L	0.874	1.00
202_A	206_E	0.869	1.00
47_H	51_L	0.862	1.00
164_M	197_M	0.860	1.00
120_N	241_S	0.857	1.00
198_F	202_A	0.855	1.00
101_I	105_A	0.850	1.00
67_Q	81_Y	0.844	1.00
171_Y	175_Y	0.842	1.00
57_S	60_H	0.840	1.00
32_L	52_A	0.840	1.00
162_I	234_V	0.837	1.00
229_D	235_P	0.831	1.00
159_M	239_S	0.829	1.00
224_A	239_S	0.823	1.00
214_E	218_L	0.822	1.00
162_I	204_I	0.816	1.00
186_L	216_N	0.816	1.00
125_E	130_I	0.816	1.00
108_L	238_V	0.815	1.00
32_L	62_L	0.814	1.00
259_L	263_A	0.814	1.00
28_R	58_T	0.808	1.00
196_A	199_D	0.797	1.00
213_R	252_E	0.794	1.00
213_R	244_T	0.793	1.00
203_H	206_E	0.792	1.00
158_A	224_A	0.786	1.00
107_H	266_I	0.782	1.00
22_G	27_F	0.780	1.00
124_R	171_Y	0.776	1.00
36_L	39_Y	0.771	1.00
45_L	63_L	0.770	1.00
262_T	265_A	0.769	1.00
165_A	201_L	0.768	1.00
243_S	246_R	0.764	1.00
36_L	41_N	0.761	1.00
200_E	207_S	0.756	1.00
100_I	104_A	0.756	1.00
52_A	59_V	0.750	1.00
200_E	204_I	0.748	1.00
222_C	241_S	0.748	1.00
54_L	58_T	0.747	1.00
163_Y	237_A	0.745	1.00
73_T	84_T	0.744	1.00
83_L	87_F	0.744	1.00
191_I	196_A	0.741	1.00
25_S	29_G	0.740	1.00
120_N	134_K	0.726	1.00
254_N	257_K	0.723	1.00
33_I	71_Y	0.722	1.00
223_I	252_E	0.719	1.00
252_E	256_L	0.718	1.00
87_F	90_V	0.716	1.00
156_C	216_N	0.713	1.00
254_N	258_P	0.713	1.00
211_M	252_E	0.712	1.00
257_K	260_R	0.710	1.00
43_C	48_L	0.707	1.00
64_Q	68_S	0.707	1.00
228_F	235_P	0.707	1.00
64_Q	67_Q	0.704	1.00
74_T	78_A	0.703	1.00
222_C	239_S	0.700	1.00
74_T	79_G	0.698	1.00
87_F	91_G	0.697	1.00
108_L	135_L	0.691	1.00
161_K	204_I	0.689	1.00
127_D	175_Y	0.688	1.00
191_I	197_M	0.687	1.00
120_N	146_A	0.687	1.00
172_V	175_Y	0.686	1.00
252_E	257_K	0.683	1.00
124_R	163_Y	0.680	1.00
45_L	59_V	0.680	1.00
26_L	62_L	0.675	1.00
32_L	59_V	0.674	1.00
213_R	249_Q	0.671	1.00
251_G	255_L	0.668	1.00
45_L	81_Y	0.668	1.00
261_E	264_Q	0.667	1.00
49_S	52_A	0.663	1.00
112_N	137_P	0.660	1.00
262_T	266_I	0.660	1.00
172_V	202_A	0.660	1.00
264_Q	267_S	0.657	1.00
176_W	182_E	0.657	1.00
26_L	30_L	0.656	1.00
123_S	132_I	0.652	1.00
192_T	196_A	0.649	1.00
260_R	263_A	0.648	1.00
167_G	172_V	0.647	1.00
238_V	263_A	0.647	1.00
172_V	176_W	0.646	1.00
202_A	205_R	0.643	1.00
110_A	113_I	0.641	1.00
111_L	115_T	0.637	1.00
34_E	89_A	0.637	1.00
45_L	56_K	0.633	1.00
111_L	240_I	0.630	1.00
99_N	102_H	0.627	1.00
163_Y	167_G	0.627	1.00
28_R	54_L	0.625	1.00
73_T	85_T	0.622	1.00
225_V	267_S	0.622	1.00
187_T	191_I	0.620	1.00
103_I	106_P	0.620	1.00
25_S	62_L	0.615	1.00
117_E	242_L	0.614	1.00
157_S	222_C	0.613	1.00
113_I	138_T	0.612	1.00
169_P	205_R	0.609	1.00
106_P	269_E	0.606	1.00
164_M	201_L	0.604	1.00
155_Y	183_I	0.603	1.00
75_A	80_S	0.602	1.00
265_A	268_N	0.601	1.00
153_P	156_C	0.600	1.00
74_T	81_Y	0.599	1.00
47_H	80_S	0.597	1.00
91_G	94_A	0.597	1.00
31_M	34_E	0.596	1.00
120_N	222_C	0.595	1.00
109_E	133_Y	0.591	1.00
64_Q	74_T	0.591	1.00
31_M	35_I	0.590	1.00
37_S	90_V	0.588	1.00
238_V	259_L	0.587	1.00
111_L	119_I	0.585	1.00
238_V	262_T	0.585	1.00
164_M	172_V	0.584	1.00
190_T	193_E	0.582	1.00
40_P	51_L	0.582	1.00
117_E	240_I	0.578	1.00
162_I	224_A	0.578	1.00
214_E	221_S	0.578	1.00
134_K	146_A	0.575	1.00
147_Y	150_Q	0.570	1.00
189_N	218_L	0.569	1.00
37_S	83_L	0.569	1.00
71_Y	86_K	0.569	1.00
195_P	198_F	0.567	1.00
36_L	40_P	0.565	1.00
49_S	56_K	0.564	1.00
129_A	152_M	0.562	1.00
209_A	260_R	0.561	1.00
258_P	262_T	0.559	1.00
70_G	86_K	0.557	1.00
131_L	146_A	0.557	1.00
26_L	65_G	0.557	1.00
162_I	226_P	0.557	1.00
208_G	228_F	0.554	0.99
133_Y	148_I	0.553	0.99
104_A	108_L	0.552	0.99
42_G	78_A	0.550	0.99
119_I	135_L	0.549	0.99
33_I	90_V	0.549	0.99
116_G	138_T	0.549	0.99
34_E	90_V	0.549	0.99
134_K	148_I	0.549	0.99
29_G	62_L	0.548	0.99
255_L	258_P	0.548	0.99
161_K	212_D	0.547	0.99
225_V	238_V	0.546	0.99
227_V	267_S	0.544	0.99
162_I	210_A	0.543	0.99
23_S	62_L	0.542	0.99
185_P	188_R	0.541	0.99
227_V	236_Y	0.541	0.99
129_A	159_M	0.540	0.99
195_P	199_D	0.539	0.99
136_E	147_Y	0.535	0.99
88_I	95_L	0.535	0.99
131_L	159_M	0.533	0.99
120_N	239_S	0.532	0.99
166_F	205_R	0.523	0.99
163_Y	236_Y	0.522	0.99
197_M	201_L	0.521	0.99
92_Q	95_L	0.520	0.99
35_I	39_Y	0.518	0.99
146_A	150_Q	0.517	0.99
29_G	66_L	0.515	0.99
28_R	62_L	0.514	0.99
129_A	157_S	0.511	0.99
44_P	56_K	0.511	0.99
142_L	245_S	0.510	0.99
122_S	157_S	0.509	0.99
155_Y	175_Y	0.508	0.99
183_I	187_T	0.507	0.99
118_T	134_K	0.504	0.99
35_I	38_N	0.504	0.99
227_V	266_I	0.503	0.99
24_Q	65_G	0.501	0.99
27_F	31_M	0.500	0.99

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
3mq0A	2	0.8901	100	0.15	Contact Map
2ia2A	4	0.883	100	0.159	Contact Map
2g7uA	6	0.8901	100	0.164	Contact Map
3r4kA	2	0.9043	100	0.171	Contact Map
1mkmA	4	0.8759	100	0.174	Contact Map
2xrnA	3	0.8546	100	0.186	Contact Map
2o0yA	4	0.9043	100	0.21	Contact Map
1ysqA	1	0.6277	100	0.435	Contact Map
1tf1A	1	0.6525	100	0.454	Contact Map
1yspA	1	0.5816	100	0.457	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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