YFHH - ECOLI - GREMLIN Contacts

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YFHH - Uncharacterized HTH-type transcriptional regulator YfhH

UniProt:	P37767	Sequences: MNGLLRIRQRYQGLAQSDKKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEALASQPESPSVPIHNQIRGDDPLRLVGEKLIKENTAAMYATLNVNSEEKLHECVTMLRSARRIILTGIGASGLVAQNFAWKLMKIGFNAAAVRDMHALLATVQASSPDDLLLAISYTGVRRELNLAADEMLRVGGKVLAITGFTPNALQQRASHCLYTIAEEQATNSASISACHAQGMLTDLLFIALIQQDLELAPERIRHSEALVKKLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12308
Length:	282 (259)
Sequences:	9103 (6424)
Seq/√Len:	399.2

ECOLI - YFHH MURR RPIR HEXR
BACSU - YBBH GLVR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
133_R	180_D	4.745	1.00
211_A	224_A	3.776	1.00
200_D	223_R	3.023	1.00
185_A	199_A	2.846	1.00
128_M	208_K	2.808	1.00
191_V	219_A	2.789	1.00
11_Y	23_D	2.723	1.00
137_L	147_A	2.634	1.00
125_C	210_L	2.388	1.00
38_Q	57_K	2.367	1.00
133_R	178_S	2.332	1.00
199_A	209_V	2.322	1.00
60_Y	69_A	2.317	1.00
125_C	226_H	2.293	1.00
203_L	225_S	2.288	1.00
108_A	112_A	2.241	1.00
133_R	181_D	2.209	1.00
10_R	13_G	2.186	1.00
134_R	160_N	2.175	1.00
28_Q	31_T	2.151	1.00
150_F	154_L	2.147	1.00
127_T	262_Q	2.099	1.00
177_S	207_G	2.080	1.00
241_S	244_A	2.049	1.00
178_S	181_D	2.021	1.00
107_T	111_Y	2.012	1.00
126_V	258_A	2.000	1.00
201_E	204_R	1.988	1.00
183_L	202_M	1.951	1.00
23_D	27_L	1.917	1.00
24_Y	28_Q	1.854	1.00
128_M	226_H	1.850	1.00
134_R	162_A	1.843	1.00
182_L	210_L	1.840	1.00
208_K	225_S	1.836	1.00
130_R	262_Q	1.829	1.00
199_A	220_L	1.813	1.00
137_L	150_F	1.771	1.00
185_A	195_L	1.759	1.00
186_I	252_T	1.733	1.00
132_A	182_L	1.730	1.00
186_I	212_I	1.726	1.00
147_A	186_I	1.721	1.00
9_Q	13_G	1.701	1.00
154_L	259_L	1.639	1.00
137_L	184_L	1.634	1.00
22_A	54_F	1.616	1.00
202_M	207_G	1.609	1.00
118_S	121_K	1.600	1.00
208_K	226_H	1.591	1.00
187_S	220_L	1.585	1.00
18_D	57_K	1.562	1.00
228_L	251_L	1.540	1.00
150_F	252_T	1.531	1.00
40_L	53_K	1.528	1.00
164_V	173_T	1.521	1.00
35_L	43_E	1.517	1.00
124_E	226_H	1.516	1.00
183_L	207_G	1.515	1.00
121_K	124_E	1.514	1.00
209_V	224_A	1.507	1.00
211_A	220_L	1.492	1.00
103_I	110_M	1.488	1.00
68_L	71_S	1.470	1.00
263_D	266_L	1.463	1.00
9_Q	12_Q	1.445	1.00
211_A	227_C	1.440	1.00
40_L	56_Q	1.436	1.00
35_L	39_Q	1.429	1.00
146_V	252_T	1.425	1.00
55_A	66_L	1.422	1.00
61_K	65_A	1.409	1.00
40_L	57_K	1.405	1.00
21_L	54_F	1.397	1.00
127_T	131_S	1.389	1.00
110_M	250_M	1.385	1.00
221_Q	227_C	1.383	1.00
151_A	162_A	1.378	1.00
138_T	183_L	1.367	1.00
184_L	212_I	1.362	1.00
258_A	262_Q	1.359	1.00
11_Y	19_K	1.348	1.00
130_R	259_L	1.327	1.00
185_A	209_V	1.321	1.00
113_T	231_I	1.313	1.00
128_M	182_L	1.299	1.00
193_R	197_L	1.277	1.00
134_R	181_D	1.274	1.00
130_R	263_D	1.269	1.00
19_K	23_D	1.246	1.00
203_L	223_R	1.230	1.00
148_Q	165_R	1.225	1.00
62_G	65_A	1.223	1.00
67_K	71_S	1.194	1.00
197_L	200_D	1.182	1.00
17_S	20_K	1.174	1.00
55_A	73_A	1.173	1.00
230_T	248_Q	1.170	1.00
63_F	67_K	1.163	1.00
94_P	97_L	1.153	1.00
17_S	50_S	1.153	1.00
129_L	182_L	1.149	1.00
66_L	70_L	1.147	1.00
153_K	253_D	1.128	1.00
185_A	202_M	1.115	1.00
65_A	68_L	1.111	1.00
144_G	148_Q	1.105	1.00
151_A	161_A	1.103	1.00
37_S	52_V	1.102	1.00
31_T	43_E	1.102	1.00
124_E	128_M	1.080	1.00
60_Y	66_L	1.064	1.00
113_T	230_T	1.064	1.00
177_S	181_D	1.064	1.00
181_D	207_G	1.061	1.00
93_D	101_K	1.060	1.00
258_A	261_Q	1.060	1.00
154_L	161_A	1.057	1.00
69_A	72_E	1.052	1.00
24_Y	44_A	1.042	1.00
109_A	247_A	1.027	1.00
129_L	259_L	1.026	1.00
142_A	241_S	1.025	1.00
11_Y	22_A	1.015	1.00
31_T	35_L	1.013	1.00
121_K	226_H	1.012	1.00
131_S	208_K	1.010	1.00
136_I	181_D	1.009	1.00
111_Y	115_N	1.008	1.00
36_S	39_Q	1.007	1.00
150_F	184_L	1.002	1.00
177_S	183_L	0.998	1.00
137_L	154_L	0.997	1.00
160_N	164_V	0.995	1.00
136_I	177_S	0.993	1.00
100_E	104_K	0.991	1.00
52_V	62_G	0.986	1.00
20_K	52_V	0.983	1.00
21_L	44_A	0.977	1.00
135_I	182_L	0.976	1.00
145_L	148_Q	0.973	1.00
100_E	114_L	0.969	1.00
125_C	128_M	0.969	1.00
25_L	66_L	0.968	1.00
126_V	262_Q	0.963	1.00
201_E	205_V	0.962	1.00
154_L	256_F	0.956	1.00
37_S	41_A	0.948	1.00
200_D	204_R	0.946	1.00
149_N	153_K	0.945	1.00
24_Y	35_L	0.942	1.00
171_L	197_L	0.935	1.00
128_M	131_S	0.929	1.00
221_Q	229_Y	0.928	1.00
29_P	33_R	0.923	1.00
151_A	155_M	0.917	1.00
136_I	162_A	0.907	1.00
120_E	123_H	0.903	1.00
129_L	184_L	0.900	1.00
112_A	115_N	0.898	1.00
137_L	161_A	0.891	1.00
14_L	40_L	0.891	1.00
72_E	75_A	0.890	1.00
24_Y	43_E	0.882	1.00
15_A	18_D	0.876	1.00
137_L	151_A	0.875	1.00
125_C	228_L	0.874	1.00
202_M	209_V	0.872	1.00
24_Y	31_T	0.870	1.00
108_A	111_Y	0.866	1.00
64_P	67_K	0.862	1.00
134_R	178_S	0.856	1.00
196_N	219_A	0.854	1.00
123_H	262_Q	0.853	1.00
149_N	245_C	0.852	1.00
212_I	252_T	0.850	1.00
40_L	63_F	0.849	1.00
146_V	186_I	0.841	1.00
40_L	51_V	0.840	1.00
242_I	245_C	0.834	1.00
32_A	70_L	0.831	1.00
132_A	181_D	0.831	1.00
107_T	110_M	0.830	1.00
58_L	72_E	0.830	1.00
38_Q	48_Q	0.826	1.00
116_V	119_E	0.823	1.00
65_A	69_A	0.822	1.00
129_L	135_I	0.818	1.00
156_K	174_V	0.812	1.00
126_V	130_R	0.809	1.00
63_F	66_L	0.808	1.00
129_L	132_A	0.805	1.00
68_L	72_E	0.805	1.00
59_G	62_G	0.804	1.00
124_E	127_T	0.803	1.00
60_Y	63_F	0.798	1.00
144_G	163_A	0.795	1.00
196_N	200_D	0.795	1.00
151_A	163_A	0.790	1.00
187_S	190_G	0.789	1.00
14_L	19_K	0.788	1.00
168_H	194_E	0.787	1.00
136_I	183_L	0.787	1.00
33_R	36_S	0.782	1.00
127_T	130_R	0.781	1.00
17_S	56_Q	0.781	1.00
55_A	62_G	0.781	1.00
213_T	221_Q	0.780	1.00
14_L	56_Q	0.779	1.00
85_I	88_Q	0.778	1.00
125_C	255_L	0.773	1.00
99_G	119_E	0.773	1.00
157_I	256_F	0.769	1.00
131_S	180_D	0.769	1.00
216_T	229_Y	0.765	1.00
49_S	52_V	0.765	1.00
245_C	248_Q	0.764	1.00
226_H	229_Y	0.763	1.00
103_I	250_M	0.758	1.00
50_S	53_K	0.756	1.00
86_H	89_I	0.754	1.00
123_H	258_A	0.752	1.00
120_E	124_E	0.752	1.00
33_R	71_S	0.751	1.00
97_L	100_E	0.751	1.00
96_R	100_E	0.747	1.00
113_T	247_A	0.746	1.00
182_L	208_K	0.745	1.00
154_L	255_L	0.743	1.00
55_A	70_L	0.739	1.00
18_D	59_G	0.738	1.00
20_K	45_G	0.738	1.00
85_I	90_R	0.734	1.00
185_A	198_A	0.734	1.00
144_G	165_R	0.733	1.00
133_R	160_N	0.732	1.00
14_L	57_K	0.732	1.00
184_L	210_L	0.730	1.00
95_L	104_K	0.725	1.00
135_I	184_L	0.725	1.00
238_N	241_S	0.724	1.00
89_I	93_D	0.711	1.00
60_Y	65_A	0.711	1.00
21_L	50_S	0.711	1.00
102_L	106_N	0.710	1.00
247_A	250_M	0.697	1.00
256_F	260_I	0.695	1.00
53_K	57_K	0.694	1.00
15_A	57_K	0.684	0.99
32_A	35_L	0.682	0.99
155_M	173_T	0.679	0.99
69_A	73_A	0.678	0.99
53_K	56_Q	0.677	0.99
25_L	54_F	0.677	0.99
153_K	256_F	0.673	0.99
180_D	208_K	0.672	0.99
196_N	220_L	0.671	0.99
148_Q	151_A	0.668	0.99
174_V	205_V	0.668	0.99
36_S	41_A	0.667	0.99
159_F	263_D	0.667	0.99
139_G	143_S	0.664	0.99
128_M	132_A	0.662	0.99
54_F	58_L	0.662	0.99
39_Q	42_N	0.660	0.99
10_R	14_L	0.659	0.99
261_Q	268_P	0.657	0.99
21_L	46_V	0.655	0.99
121_K	125_C	0.651	0.99
29_P	32_A	0.650	0.99
21_L	51_V	0.649	0.99
106_N	250_M	0.646	0.99
244_A	247_A	0.643	0.99
140_I	192_R	0.643	0.99
15_A	40_L	0.643	0.99
66_L	73_A	0.641	0.99
179_P	206_G	0.637	0.99
196_N	223_R	0.635	0.99
199_A	223_R	0.635	0.99
106_N	246_H	0.634	0.99
8_R	45_G	0.633	0.99
191_V	214_G	0.633	0.99
20_K	51_V	0.633	0.99
18_D	66_L	0.632	0.99
211_A	218_N	0.630	0.99
219_A	223_R	0.629	0.99
96_R	119_E	0.629	0.99
150_F	153_K	0.628	0.99
213_T	227_C	0.624	0.99
126_V	259_L	0.622	0.99
175_Q	201_E	0.622	0.99
197_L	201_E	0.620	0.99
161_A	164_V	0.619	0.99
103_I	113_T	0.619	0.99
71_S	75_A	0.618	0.99
95_L	123_H	0.615	0.99
48_Q	52_V	0.613	0.99
213_T	218_N	0.609	0.99
250_M	253_D	0.609	0.99
119_E	123_H	0.609	0.99
84_P	87_N	0.607	0.99
239_S	242_I	0.607	0.99
224_A	227_C	0.602	0.99
63_F	73_A	0.601	0.99
221_Q	224_A	0.601	0.99
22_A	26_L	0.601	0.99
257_I	260_I	0.599	0.99
234_E	237_T	0.594	0.99
150_F	256_F	0.592	0.99
102_L	250_M	0.589	0.98
14_L	53_K	0.587	0.98
218_N	221_Q	0.586	0.98
146_V	248_Q	0.586	0.98
159_F	163_A	0.583	0.98
245_C	249_G	0.581	0.98
39_Q	43_E	0.581	0.98
171_L	201_E	0.581	0.98
15_A	56_Q	0.581	0.98
35_L	40_L	0.579	0.98
81_P	84_P	0.578	0.98
58_L	73_A	0.578	0.98
112_A	231_I	0.578	0.98
20_K	48_Q	0.578	0.98
122_L	254_L	0.577	0.98
97_L	119_E	0.575	0.98
113_T	251_L	0.573	0.98
104_K	111_Y	0.572	0.98
103_I	106_N	0.567	0.98
189_T	192_R	0.566	0.98
264_L	267_A	0.559	0.98
138_T	185_A	0.557	0.98
107_T	114_L	0.557	0.98
84_P	88_Q	0.557	0.98
62_G	66_L	0.556	0.98
146_V	249_G	0.554	0.98
135_I	159_F	0.551	0.98
136_I	164_V	0.550	0.98
98_V	101_K	0.549	0.98
140_I	194_E	0.548	0.98
257_I	261_Q	0.546	0.98
136_I	169_A	0.545	0.98
104_K	107_T	0.544	0.97
25_L	32_A	0.544	0.97
165_R	168_H	0.544	0.97
210_L	226_H	0.541	0.97
174_V	207_G	0.541	0.97
123_H	126_V	0.539	0.97
263_D	267_A	0.538	0.97
139_G	144_G	0.538	0.97
230_T	251_L	0.538	0.97
114_L	250_M	0.538	0.97
203_L	209_V	0.537	0.97
261_Q	265_E	0.536	0.97
133_R	179_P	0.535	0.97
238_N	244_A	0.533	0.97
260_I	267_A	0.532	0.97
231_I	234_E	0.530	0.97
236_A	239_S	0.528	0.97
103_I	254_L	0.528	0.97
135_I	154_L	0.527	0.97
254_L	257_I	0.526	0.97
238_N	245_C	0.523	0.97
212_I	230_T	0.521	0.97
80_S	84_P	0.520	0.97
146_V	230_T	0.519	0.97
185_A	211_A	0.518	0.97
241_S	246_H	0.517	0.97
43_E	53_K	0.515	0.97
153_K	158_G	0.514	0.96
199_A	224_A	0.514	0.96
187_S	211_A	0.514	0.96
153_K	156_K	0.512	0.96
137_L	252_T	0.508	0.96
249_G	253_D	0.507	0.96
230_T	247_A	0.505	0.96
174_V	201_E	0.505	0.96
248_Q	252_T	0.505	0.96
138_T	177_S	0.505	0.96
41_A	51_V	0.504	0.96
195_L	199_A	0.504	0.96
8_R	26_L	0.504	0.96
44_A	51_V	0.504	0.96
97_L	101_K	0.503	0.96
8_R	13_G	0.502	0.96
106_N	253_D	0.501	0.96
14_L	22_A	0.501	0.96
38_Q	42_N	0.501	0.96
148_Q	163_A	0.500	0.96

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
4ivnA	2	0.9326	100	0.18	Contact Map
3shoA	4	0.656	100	0.531	Contact Map
2xhzA	4	0.6064	100	0.551	Contact Map
3fxaA	4	0.6738	100	0.557	Contact Map
3etnA	4	0.6525	100	0.564	Contact Map
1m3sA	4	0.6312	100	0.575	Contact Map
1jeoA	4	0.6099	99.9	0.583	Contact Map
2pocA	4	0.6631	99.9	0.583	Contact Map
1vimA	4	0.6489	99.9	0.585	Contact Map
3tbfA	2	0.6809	99.9	0.587	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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