SGCR - ECOLI - GREMLIN Contacts

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SGCR - Putative sgc region transcriptional regulator

UniProt:	P39361	Sequences: MSQQRPDRIKQMLHYLWQHRHLSTQQAMELFGYAEATVRRDFQYIVNQYPGMIRGHGCLDFDDSTDDKEYVFDVKRTLQSVAKREIAALARTMIKDGDCFFLDSGSTCLELAKCLADARVKVICNDIKIANELGCFPHVESYIIGGLIRPGYFSVGESLALEMINAFSVERAFISCDALSLETGITNATMFEVGVKTRIIQRSREVILMADHSKFDAVEPHAVATLSCIKTIISDSGLPETIAQRYQRAGCQLFLPHSIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12552
Length:	260 (246)
Sequences:	7677 (5623)
Seq/√Len:	358.5

ECOLI - SGCR AGAR YIHW GLPR YGBI GATR YDJF DEOR ULAR SRLR YCIT FUCR
BACSU - YULB GLCR IOLR FRUR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_D	171_R	3.324	1.00
89_L	92_T	3.042	1.00
111_L	209_M	2.934	1.00
140_E	147_L	2.719	1.00
172_A	203_S	2.615	1.00
103_D	196_K	2.436	1.00
15_Y	30_L	2.330	1.00
212_H	235_D	2.253	1.00
113_K	132_E	2.210	1.00
200_I	224_A	2.197	1.00
95_K	98_D	2.103	1.00
231_T	254_F	2.096	1.00
207_I	231_T	2.085	1.00
171_R	207_I	2.041	1.00
165_N	198_R	2.033	1.00
11_Q	14_H	2.018	1.00
101_F	169_V	2.001	1.00
15_Y	19_H	1.988	1.00
88_A	114_C	1.973	1.00
84_R	110_E	1.969	1.00
222_A	225_T	1.956	1.00
200_I	206_V	1.954	1.00
102_L	108_C	1.900	1.00
238_L	243_A	1.895	1.00
162_E	165_N	1.894	1.00
171_R	205_E	1.875	1.00
96_D	118_A	1.835	1.00
101_F	199_I	1.824	1.00
123_I	169_V	1.786	1.00
110_E	113_K	1.775	1.00
243_A	247_Q	1.761	1.00
205_E	231_T	1.757	1.00
90_A	173_F	1.714	1.00
169_V	199_I	1.692	1.00
225_T	228_C	1.679	1.00
89_L	254_F	1.657	1.00
162_E	166_A	1.640	1.00
90_A	209_M	1.616	1.00
48_Q	51_G	1.563	1.00
161_L	194_G	1.560	1.00
143_I	155_V	1.560	1.00
198_R	201_Q	1.554	1.00
79_Q	213_S	1.539	1.00
111_L	173_F	1.537	1.00
144_I	163_M	1.536	1.00
170_E	204_R	1.528	1.00
130_A	143_I	1.523	1.00
185_I	229_I	1.522	1.00
185_I	208_L	1.519	1.00
33_Y	38_V	1.504	1.00
165_N	201_Q	1.496	1.00
244_Q	248_R	1.484	1.00
91_R	114_C	1.480	1.00
27_A	38_V	1.480	1.00
21_H	60_D	1.477	1.00
9_I	48_Q	1.458	1.00
87_A	114_C	1.436	1.00
239_P	242_I	1.423	1.00
144_I	155_V	1.420	1.00
42_F	59_L	1.413	1.00
12_M	27_A	1.409	1.00
84_R	114_C	1.405	1.00
160_A	195_V	1.401	1.00
10_K	14_H	1.390	1.00
11_Q	15_Y	1.383	1.00
19_H	26_Q	1.380	1.00
15_Y	22_L	1.379	1.00
122_V	133_L	1.375	1.00
198_R	202_R	1.375	1.00
79_Q	82_A	1.367	1.00
212_H	237_G	1.364	1.00
148_I	155_V	1.356	1.00
104_S	154_S	1.355	1.00
17_W	61_F	1.354	1.00
208_L	229_I	1.352	1.00
93_M	207_I	1.349	1.00
93_M	233_I	1.348	1.00
98_D	170_E	1.337	1.00
147_L	191_F	1.323	1.00
53_I	62_D	1.322	1.00
25_Q	35_E	1.320	1.00
96_D	119_R	1.319	1.00
122_V	139_V	1.300	1.00
55_G	58_C	1.287	1.00
80_S	110_E	1.287	1.00
82_A	235_D	1.286	1.00
36_A	40_R	1.282	1.00
9_I	44_Y	1.281	1.00
83_K	106_S	1.268	1.00
144_I	160_A	1.261	1.00
13_L	51_G	1.259	1.00
179_L	215_F	1.244	1.00
94_I	115_L	1.243	1.00
23_S	26_Q	1.243	1.00
240_E	244_Q	1.238	1.00
97_G	119_R	1.235	1.00
224_A	228_C	1.230	1.00
89_L	93_M	1.227	1.00
205_E	230_K	1.219	1.00
84_R	113_K	1.201	1.00
11_Q	30_L	1.195	1.00
121_K	142_Y	1.190	1.00
244_Q	247_Q	1.177	1.00
201_Q	228_C	1.175	1.00
112_A	133_L	1.173	1.00
11_Q	31_F	1.167	1.00
93_M	254_F	1.167	1.00
176_C	210_A	1.154	1.00
43_Q	47_N	1.148	1.00
180_S	183_T	1.142	1.00
101_F	202_R	1.141	1.00
16_L	52_M	1.137	1.00
14_H	18_Q	1.131	1.00
81_V	84_R	1.129	1.00
173_F	207_I	1.128	1.00
82_A	212_H	1.101	1.00
161_L	195_V	1.099	1.00
80_S	84_R	1.096	1.00
215_F	238_L	1.095	1.00
121_K	140_E	1.093	1.00
178_A	186_T	1.091	1.00
95_K	171_R	1.086	1.00
206_V	229_I	1.080	1.00
19_H	30_L	1.079	1.00
13_L	16_L	1.071	1.00
16_L	61_F	1.065	1.00
159_L	163_M	1.060	1.00
52_M	59_L	1.059	1.00
53_I	60_D	1.053	1.00
207_I	233_I	1.053	1.00
231_T	252_Q	1.047	1.00
176_C	223_V	1.040	1.00
24_T	42_F	1.029	1.00
91_R	94_I	1.017	1.00
142_Y	147_L	1.010	1.00
91_R	111_L	1.008	1.00
123_I	167_F	1.001	1.00
44_Y	48_Q	1.000	1.00
102_L	111_L	0.992	1.00
94_I	173_F	0.980	1.00
90_A	111_L	0.980	1.00
7_D	11_Q	0.979	1.00
28_M	35_E	0.977	1.00
159_L	167_F	0.976	1.00
144_I	164_I	0.972	1.00
177_D	187_N	0.962	1.00
112_A	132_E	0.958	1.00
242_I	245_R	0.958	1.00
82_A	86_I	0.957	1.00
215_F	232_I	0.946	1.00
87_A	91_R	0.946	1.00
72_F	106_S	0.940	1.00
179_L	210_A	0.938	1.00
108_C	129_I	0.930	1.00
93_M	231_T	0.929	1.00
83_K	107_T	0.928	1.00
84_R	88_A	0.927	1.00
44_Y	47_N	0.926	1.00
172_A	199_I	0.922	1.00
15_Y	18_Q	0.922	1.00
194_G	197_T	0.922	1.00
161_L	198_R	0.921	1.00
227_S	249_A	0.920	1.00
105_G	108_C	0.916	1.00
111_L	114_C	0.915	1.00
83_K	214_K	0.914	1.00
107_T	211_D	0.914	1.00
176_C	208_L	0.912	1.00
43_Q	46_V	0.905	1.00
193_V	221_H	0.903	1.00
168_S	204_R	0.896	1.00
243_A	253_L	0.892	1.00
180_S	218_V	0.892	1.00
26_Q	30_L	0.890	1.00
86_I	107_T	0.889	1.00
166_A	197_T	0.889	1.00
79_Q	211_D	0.888	1.00
107_T	214_K	0.885	1.00
168_S	183_T	0.881	1.00
128_K	153_F	0.879	1.00
87_A	111_L	0.879	1.00
108_C	111_L	0.874	1.00
28_M	38_V	0.863	1.00
87_A	110_E	0.862	1.00
116_A	136_F	0.861	1.00
22_L	59_L	0.859	1.00
22_L	27_A	0.849	1.00
134_G	153_F	0.848	1.00
141_S	148_I	0.842	1.00
126_D	129_I	0.836	1.00
112_A	129_I	0.835	1.00
116_A	132_E	0.827	1.00
204_R	218_V	0.826	1.00
167_F	190_M	0.823	1.00
45_I	51_G	0.820	1.00
152_Y	177_D	0.818	1.00
164_I	199_I	0.817	1.00
173_F	209_M	0.810	1.00
7_D	10_K	0.810	1.00
245_R	248_R	0.805	1.00
159_L	166_A	0.805	1.00
168_S	222_A	0.803	1.00
90_A	233_I	0.802	1.00
187_N	193_V	0.801	1.00
14_H	17_W	0.799	1.00
119_R	138_H	0.796	1.00
206_V	230_K	0.796	1.00
13_L	17_W	0.795	1.00
168_S	218_V	0.793	1.00
26_Q	29_E	0.784	1.00
85_E	88_A	0.784	1.00
79_Q	212_H	0.781	1.00
179_L	185_I	0.781	1.00
75_K	177_D	0.780	1.00
43_Q	54_R	0.778	1.00
132_E	135_C	0.775	1.00
101_F	164_I	0.769	1.00
7_D	21_H	0.766	1.00
164_I	198_R	0.766	1.00
190_M	221_H	0.765	1.00
108_C	209_M	0.762	1.00
238_L	242_I	0.761	1.00
183_T	218_V	0.757	1.00
176_C	185_I	0.751	1.00
168_S	202_R	0.740	1.00
149_R	192_E	0.736	1.00
102_L	122_V	0.733	1.00
186_T	218_V	0.733	1.00
130_A	155_V	0.732	1.00
106_S	214_K	0.731	1.00
238_L	253_L	0.731	1.00
71_V	74_V	0.730	1.00
102_L	112_A	0.727	1.00
109_L	132_E	0.727	1.00
166_A	222_A	0.726	1.00
131_N	153_F	0.723	0.99
81_V	85_E	0.716	0.99
145_G	160_A	0.709	0.99
20_R	61_F	0.705	0.99
9_I	13_L	0.705	0.99
200_I	223_V	0.695	0.99
33_Y	36_A	0.692	0.99
104_S	152_Y	0.690	0.99
130_A	148_I	0.689	0.99
169_V	203_S	0.689	0.99
187_N	223_V	0.689	0.99
179_L	226_L	0.687	0.99
210_A	232_I	0.687	0.99
172_A	206_V	0.686	0.99
69_E	75_K	0.684	0.99
117_D	136_F	0.682	0.99
25_Q	29_E	0.680	0.99
185_I	223_V	0.678	0.99
187_N	192_E	0.678	0.99
125_N	199_I	0.677	0.99
110_E	114_C	0.677	0.99
88_A	92_T	0.676	0.99
42_F	54_R	0.675	0.99
99_C	123_I	0.674	0.99
145_G	163_M	0.673	0.99
211_D	214_K	0.669	0.99
149_R	156_G	0.668	0.99
136_F	139_V	0.668	0.99
157_E	160_A	0.665	0.99
55_G	60_D	0.661	0.99
127_I	155_V	0.660	0.99
13_L	45_I	0.655	0.99
76_R	109_L	0.652	0.99
27_A	42_F	0.652	0.99
6_P	9_I	0.652	0.99
174_I	203_S	0.649	0.99
165_N	202_R	0.643	0.99
212_H	238_L	0.641	0.99
24_T	38_V	0.641	0.99
240_E	243_A	0.641	0.99
100_F	171_R	0.641	0.99
100_F	122_V	0.640	0.99
207_I	230_K	0.639	0.99
197_T	201_Q	0.637	0.99
245_R	249_A	0.637	0.99
46_V	54_R	0.637	0.99
135_C	153_F	0.636	0.99
85_E	89_L	0.635	0.99
205_E	252_Q	0.634	0.99
109_L	128_K	0.634	0.99
16_L	22_L	0.632	0.99
162_E	194_G	0.632	0.99
36_A	126_D	0.630	0.99
167_F	221_H	0.629	0.99
86_I	209_M	0.627	0.99
241_T	245_R	0.627	0.99
177_D	219_E	0.625	0.99
158_S	162_E	0.624	0.99
124_C	130_A	0.621	0.98
8_R	41_D	0.620	0.98
31_F	38_V	0.619	0.98
242_I	246_Y	0.616	0.98
224_A	229_I	0.616	0.98
158_S	194_G	0.612	0.98
46_V	52_M	0.610	0.98
215_F	242_I	0.602	0.98
188_A	219_E	0.601	0.98
123_I	220_P	0.599	0.98
105_G	175_S	0.596	0.98
69_E	149_R	0.595	0.98
203_S	206_V	0.594	0.98
103_D	108_C	0.591	0.98
126_D	192_E	0.591	0.98
177_D	192_E	0.588	0.98
193_V	223_V	0.587	0.98
127_I	143_I	0.582	0.98
82_A	237_G	0.580	0.98
158_S	161_L	0.578	0.98
94_I	111_L	0.577	0.98
75_K	192_E	0.577	0.98
160_A	163_M	0.576	0.98
149_R	189_T	0.572	0.97
174_I	223_V	0.572	0.97
175_S	187_N	0.569	0.97
161_L	165_N	0.569	0.97
36_A	177_D	0.567	0.97
191_F	194_G	0.567	0.97
105_G	177_D	0.566	0.97
100_F	173_F	0.562	0.97
181_L	242_I	0.562	0.97
76_R	110_E	0.562	0.97
119_R	140_E	0.561	0.97
83_K	211_D	0.558	0.97
128_K	131_N	0.556	0.97
127_I	131_N	0.555	0.97
180_S	186_T	0.555	0.97
196_K	223_V	0.554	0.97
215_F	234_S	0.553	0.97
99_C	220_P	0.553	0.97
100_F	111_L	0.551	0.97
195_V	198_R	0.551	0.97
177_D	188_A	0.550	0.97
12_M	31_F	0.548	0.97
177_D	196_K	0.546	0.97
154_S	192_E	0.544	0.97
123_I	142_Y	0.543	0.96
206_V	228_C	0.541	0.96
29_E	32_G	0.541	0.96
187_N	196_K	0.538	0.96
85_E	236_S	0.538	0.96
40_R	179_L	0.537	0.96
174_I	200_I	0.536	0.96
185_I	224_A	0.533	0.96
181_L	245_R	0.532	0.96
158_S	191_F	0.532	0.96
75_K	106_S	0.532	0.96
174_I	206_V	0.526	0.96
237_G	243_A	0.519	0.95
162_E	197_T	0.519	0.95
240_E	247_Q	0.517	0.95
101_F	172_A	0.515	0.95
102_L	129_I	0.513	0.95
22_L	55_G	0.513	0.95
24_T	28_M	0.512	0.95
178_A	219_E	0.511	0.95
178_A	217_A	0.509	0.95
120_V	139_V	0.509	0.95
101_F	123_I	0.507	0.95
216_D	242_I	0.505	0.95
105_G	126_D	0.502	0.95
73_D	76_R	0.502	0.95
24_T	56_H	0.502	0.95
140_E	150_P	0.501	0.95
117_D	138_H	0.500	0.94

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
1stzA	3	0.9385	100	0.517	Contact Map
3rrlB	1	0.6654	100	0.533	Contact Map
2w48A	3	0.9	100	0.587	Contact Map
3l7oA	2	0.5885	100	0.617	Contact Map
1o8bA	2	0.5808	100	0.621	Contact Map
2o0mA	1	0.6769	100	0.628	Contact Map
1m0sA	2	0.6038	100	0.63	Contact Map
1uj6A	2	0.5962	100	0.63	Contact Map
1lk5A	4	0.6	100	0.631	Contact Map
4io1A	2	0.6038	100	0.635	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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