GMUR - BACSU - GREMLIN Contacts

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GMUR - HTH-type transcriptional regulator GmuR

UniProt:	O05509	Sequences: MNKYEIIANEMRNRIKNNVYPIDQPIPDEVSLAKEFNSSRMTMKRALDNLVAEGLLFRKRGHGTFIIQSAIQDDHVHVVSNEILGLTNLLKDKKIKSKVIQFEVQFPTEEVAAHLSIDQKTPVYYVVRLRIVEGEPYVLEKTYMPTHLIPGINDDVLHDSIYNHITNVLQLKIAGTHRKIRACKSDHIDQQHLGCKQDDPILEVEHVGFLDTGIPFEYSFSRHRHDKFVVTSVNIRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	237 (187)
Sequences:	21460 (16075)
Seq/√Len:	1175.5

ECOLI - MNGR YIHL YIDP PHNF YEGW FRLR
BACSU - GMUR YYDK YBGA TRER YURK YVOA YMFC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_P	24_Q	3.805	1.00
14_R	19_V	3.752	1.00
12_R	53_E	3.137	1.00
8_A	49_N	3.046	1.00
14_R	35_E	2.966	1.00
57_F	67_I	2.877	1.00
101_Q	189_D	2.658	1.00
116_S	181_R	2.619	1.00
7_I	38_S	2.471	1.00
10_E	14_R	2.468	1.00
59_K	62_H	2.404	1.00
184_K	187_H	2.400	1.00
29_E	40_R	2.392	1.00
58_R	64_T	2.295	1.00
108_T	111_V	2.171	1.00
8_A	53_E	2.168	1.00
7_I	36_F	2.057	1.00
25_P	65_F	2.057	1.00
13_N	17_N	2.052	1.00
10_E	36_F	1.948	1.00
111_V	153_N	1.931	1.00
62_H	65_F	1.897	1.00
128_R	174_A	1.882	1.00
8_A	12_R	1.852	1.00
51_V	58_R	1.767	1.00
187_H	191_Q	1.753	1.00
107_P	112_A	1.729	1.00
105_Q	185_S	1.722	1.00
12_R	16_K	1.703	1.00
45_R	48_D	1.684	1.00
94_K	98_K	1.678	1.00
12_R	55_L	1.592	1.00
96_K	131_I	1.552	1.00
186_D	189_D	1.544	1.00
32_L	43_M	1.539	1.00
31_S	35_E	1.529	1.00
125_Y	141_K	1.521	1.00
14_R	20_Y	1.510	1.00
6_I	10_E	1.507	1.00
189_D	193_L	1.507	1.00
51_V	56_L	1.486	1.00
48_D	58_R	1.467	1.00
30_V	34_K	1.465	1.00
47_L	56_L	1.455	1.00
28_D	31_S	1.445	1.00
111_V	143_Y	1.415	1.00
22_I	68_Q	1.397	1.00
127_V	141_K	1.377	1.00
56_L	64_T	1.371	1.00
10_E	13_N	1.365	1.00
15_I	66_I	1.361	1.00
107_P	111_V	1.347	1.00
38_S	43_M	1.347	1.00
112_A	181_R	1.341	1.00
14_R	18_N	1.317	1.00
48_D	52_A	1.317	1.00
179_K	187_H	1.305	1.00
184_K	200_P	1.289	1.00
20_Y	66_I	1.277	1.00
31_S	34_K	1.269	1.00
147_H	150_P	1.268	1.00
114_H	147_H	1.266	1.00
57_F	65_F	1.256	1.00
178_R	182_A	1.255	1.00
104_V	122_P	1.227	1.00
29_E	44_K	1.219	1.00
98_K	131_I	1.186	1.00
116_S	177_H	1.184	1.00
101_Q	185_S	1.183	1.00
100_I	192_H	1.174	1.00
107_P	183_C	1.154	1.00
49_N	52_A	1.146	1.00
25_P	63_G	1.144	1.00
16_K	55_L	1.144	1.00
59_K	65_F	1.140	1.00
97_S	189_D	1.138	1.00
48_D	51_V	1.138	1.00
133_E	136_P	1.130	1.00
3_K	6_I	1.125	1.00
139_L	189_D	1.091	1.00
104_V	146_T	1.088	1.00
185_S	195_C	1.081	1.00
146_T	150_P	1.079	1.00
4_Y	49_N	1.067	1.00
93_K	193_L	1.067	1.00
156_V	160_S	1.062	1.00
93_K	197_Q	1.058	1.00
49_N	53_E	1.057	1.00
20_Y	24_Q	1.040	1.00
182_A	187_H	1.033	1.00
47_L	64_T	1.020	1.00
14_R	36_F	1.018	1.00
93_K	97_S	1.015	1.00
174_A	178_R	1.013	1.00
59_K	63_G	1.010	1.00
127_V	188_I	1.009	1.00
112_A	177_H	1.004	1.00
177_H	181_R	0.997	1.00
145_P	148_L	0.982	1.00
190_Q	194_G	0.974	1.00
106_F	122_P	0.957	1.00
103_E	125_Y	0.953	1.00
23_D	57_F	0.953	1.00
97_S	193_L	0.939	1.00
11_M	32_L	0.938	1.00
91_K	102_F	0.936	1.00
45_R	49_N	0.932	1.00
109_E	113_A	0.928	1.00
163_N	167_N	0.920	1.00
196_K	199_D	0.919	1.00
100_I	104_V	0.916	1.00
160_S	163_N	0.905	1.00
9_N	12_R	0.905	1.00
101_Q	186_D	0.903	1.00
5_E	9_N	0.896	1.00
187_H	190_Q	0.896	1.00
186_D	190_Q	0.893	1.00
143_Y	147_H	0.889	1.00
126_V	143_Y	0.881	1.00
172_K	198_D	0.877	1.00
123_V	143_Y	0.876	1.00
99_V	149_I	0.868	1.00
123_V	140_E	0.858	1.00
33_A	43_M	0.858	1.00
110_E	114_H	0.857	1.00
112_A	183_C	0.840	1.00
111_V	151_G	0.837	1.00
136_P	139_L	0.828	1.00
159_D	163_N	0.824	1.00
107_P	151_G	0.824	1.00
105_Q	125_Y	0.821	1.00
122_P	126_V	0.817	1.00
85_G	88_N	0.814	1.00
130_R	140_E	0.808	1.00
25_P	28_D	0.805	1.00
162_Y	165_I	0.800	1.00
27_P	35_E	0.799	1.00
112_A	116_S	0.798	1.00
107_P	115_L	0.798	1.00
141_K	145_P	0.794	1.00
185_S	189_D	0.793	1.00
39_S	42_T	0.790	1.00
98_K	101_Q	0.789	1.00
10_E	35_E	0.787	1.00
7_I	43_M	0.786	1.00
5_E	49_N	0.785	1.00
102_F	153_N	0.780	1.00
101_Q	105_Q	0.768	1.00
29_E	58_R	0.764	1.00
26_I	56_L	0.756	1.00
47_L	51_V	0.755	1.00
111_V	114_H	0.755	1.00
125_Y	128_R	0.755	1.00
22_I	67_I	0.753	1.00
147_H	151_G	0.749	1.00
160_S	165_I	0.748	1.00
104_V	180_I	0.748	1.00
144_M	177_H	0.747	1.00
88_N	91_K	0.745	1.00
36_F	43_M	0.743	1.00
125_Y	129_L	0.741	1.00
114_H	150_P	0.740	1.00
11_M	20_Y	0.736	1.00
156_V	164_H	0.736	1.00
23_D	68_Q	0.735	1.00
171_L	175_G	0.733	1.00
155_D	158_H	0.731	1.00
160_S	164_H	0.729	1.00
34_K	37_N	0.727	1.00
88_N	155_D	0.727	1.00
86_L	90_L	0.722	1.00
125_Y	143_Y	0.721	1.00
98_K	102_F	0.721	1.00
139_L	143_Y	0.715	1.00
195_C	199_D	0.709	1.00
126_V	130_R	0.708	1.00
9_N	13_N	0.706	1.00
61_G	64_T	0.705	1.00
184_K	199_D	0.702	1.00
32_L	47_L	0.701	1.00
115_L	123_V	0.697	1.00
124_Y	127_V	0.695	1.00
8_A	46_A	0.694	1.00
156_V	159_D	0.692	1.00
91_K	106_F	0.692	1.00
158_H	162_Y	0.690	1.00
96_K	134_G	0.690	1.00
7_I	10_E	0.688	1.00
145_P	173_I	0.686	1.00
193_L	197_Q	0.676	1.00
92_D	96_K	0.675	1.00
115_L	147_H	0.665	1.00
124_Y	128_R	0.664	1.00
14_R	17_N	0.664	1.00
19_V	35_E	0.659	1.00
129_L	136_P	0.659	1.00
20_Y	26_I	0.656	1.00
107_P	180_I	0.656	1.00
146_T	162_Y	0.654	1.00
188_I	192_H	0.650	1.00
131_I	134_G	0.648	1.00
176_T	191_Q	0.642	1.00
190_Q	193_L	0.640	1.00
92_D	95_I	0.639	1.00
126_V	129_L	0.636	1.00
136_P	140_E	0.635	1.00
4_Y	8_A	0.634	1.00
47_L	58_R	0.627	1.00
33_A	36_F	0.619	1.00
116_S	125_Y	0.617	1.00
97_S	100_I	0.617	1.00
123_V	126_V	0.616	1.00
102_F	106_F	0.616	1.00
164_H	167_N	0.615	1.00
87_T	91_K	0.611	1.00
166_T	170_Q	0.607	1.00
178_R	181_R	0.600	1.00
164_H	169_L	0.591	1.00
97_S	101_Q	0.591	1.00
175_G	191_Q	0.586	1.00
4_Y	45_R	0.583	1.00
183_C	189_D	0.581	1.00
101_Q	125_Y	0.579	1.00
116_S	174_A	0.578	1.00
167_N	170_Q	0.578	1.00
100_I	129_L	0.577	1.00
42_T	46_A	0.577	1.00
51_V	64_T	0.577	1.00
126_V	140_E	0.577	1.00
25_P	62_H	0.574	1.00
172_K	195_C	0.570	1.00
93_K	200_P	0.570	1.00
111_V	150_P	0.568	1.00
42_T	45_R	0.567	1.00
113_A	116_S	0.567	1.00
101_Q	127_V	0.567	1.00
84_L	88_N	0.566	1.00
20_Y	27_P	0.565	1.00
104_V	185_S	0.562	1.00
91_K	95_I	0.560	1.00
140_E	143_Y	0.559	1.00
124_Y	174_A	0.558	1.00
191_Q	194_G	0.556	1.00
108_T	143_Y	0.555	1.00
32_L	36_F	0.550	1.00
127_V	139_L	0.548	1.00
105_Q	143_Y	0.548	1.00
41_M	45_R	0.547	1.00
149_I	165_I	0.547	1.00
175_G	187_H	0.546	1.00
107_P	123_V	0.545	1.00
99_V	152_I	0.545	1.00
33_A	40_R	0.540	1.00
7_I	11_M	0.540	1.00
30_V	40_R	0.539	1.00
30_V	33_A	0.539	1.00
13_N	16_K	0.538	1.00
114_H	143_Y	0.537	1.00
179_K	184_K	0.535	1.00
143_Y	146_T	0.534	1.00
112_A	115_L	0.534	1.00
28_D	43_M	0.532	1.00
91_K	154_D	0.529	1.00
123_V	147_H	0.526	1.00
175_G	178_R	0.525	1.00
157_L	160_S	0.525	1.00
98_K	189_D	0.524	1.00
122_P	146_T	0.523	1.00
176_T	192_H	0.522	1.00
131_I	136_P	0.521	1.00
111_V	115_L	0.521	1.00
5_E	8_A	0.520	1.00
43_M	56_L	0.519	1.00
158_H	165_I	0.514	1.00
115_L	151_G	0.511	1.00
115_L	177_H	0.508	1.00
124_Y	177_H	0.506	1.00
155_D	159_D	0.504	1.00
166_T	172_K	0.503	1.00
3_K	42_T	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	0.9789	100	0.13	Contact Map
3bwgA	2	0.9705	100	0.153	Contact Map
3f8mA	2	0.9536	100	0.156	Contact Map
2ra5A	2	0.6203	100	0.16	Contact Map
3edpA	2	0.9241	100	0.163	Contact Map
3eetA	2	0.9747	100	0.185	Contact Map
3f8lA	2	0.6751	100	0.443	Contact Map
2di3A	2	0.8523	99.9	0.534	Contact Map
3c7jA	4	0.8312	99.9	0.543	Contact Map
1hw1A	2	0.8228	99.9	0.544	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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