YBHD - ECOLI - GREMLIN Contacts

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YBHD - Uncharacterized HTH-type transcriptional regulator YbhD

UniProt:	P52696	Sequences: MKHELSSMKAFVILAESSSFNNAAKLLNITQPALTRRIKKMEEDLHVQLFERTTRKVTLTKAGKRLLPEARELIKKFDETLFNIRDMNAYHRGMVTLACIPTAVFYFLPLAIGKFNELYPNIKVRILEQGTNNCMESVLCNESDFGINMNNVTNSSIDFTPLVNEPFVLACRRDHPLAKKQLVEWQELVGYKMIGVRSSSGNRLLIEQQLADKPWKLDWFYEVRHLSTSLGLVEAGLGISALPGLAMPHAPYSSIIGIPLVEPVIRRTLGIIRRKDAVLSPAAERFFALLINLWTDDKDNLWTNIVERQRHALQEIG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13230
Length:	317 (288)
Sequences:	79683 (57906)
Seq/√Len:	3412.1

ECOLI - YBHD YFER LYSR CYSB OXYR CBL YAFC YNFL YEEY AAER YEIE CYNR NAC YCAN TDCA YAHB LEUO PGRR TTDR ILVY ABGR YDHB YBDO HCAR ALLS XAPR YDCI YHJC DMLR METR YFIE YBEF YIAU YNEJ NHAR YIDZ GCVA DSDC ICIA YHAJ YGFI LRHA YJIE HDFR PERR
BACSU - YWBI YCGK CYSL GLTC YTLI BSDA YYBE ALSR GLTR CITR YVBU YWQM YUST YOFA YOAU YXJO CZCR YKUM YRAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_E	76_K	3.552	1.00
17_S	26_L	3.395	1.00
160_T	291_I	2.729	1.00
98_A	143_S	2.564	1.00
69_E	83_N	2.398	1.00
233_V	240_S	2.343	1.00
166_P	244_G	2.257	1.00
114_K	293_L	2.241	1.00
175_H	191_Y	2.226	1.00
164_N	268_T	2.187	1.00
16_E	71_R	2.173	1.00
161_P	164_N	2.164	1.00
13_I	26_L	2.160	1.00
22_N	25_K	2.157	1.00
94_M	125_R	2.138	1.00
94_M	123_K	2.099	1.00
184_E	187_E	2.069	1.00
161_P	268_T	2.051	1.00
12_V	67_L	2.009	1.00
96_T	125_R	1.984	1.00
10_A	37_R	1.982	1.00
47_V	62_A	1.977	1.00
164_N	266_R	1.966	1.00
69_E	76_K	1.945	1.00
114_K	289_L	1.930	1.00
171_C	258_I	1.929	1.00
20_F	38_I	1.915	1.00
73_L	77_F	1.912	1.00
13_I	16_E	1.905	1.00
10_A	34_L	1.904	1.00
15_A	59_L	1.880	1.00
234_E	254_S	1.879	1.00
12_V	71_R	1.869	1.00
194_I	238_G	1.866	1.00
13_I	17_S	1.859	1.00
12_V	16_E	1.828	1.00
67_L	71_R	1.818	1.00
168_V	244_G	1.786	1.00
134_C	146_G	1.762	1.00
51_E	58_T	1.753	1.00
66_L	80_T	1.741	1.00
115_F	286_F	1.689	1.00
192_K	220_F	1.688	1.00
159_F	270_G	1.655	1.00
65_R	83_N	1.649	1.00
16_E	26_L	1.640	1.00
168_V	257_G	1.633	1.00
180_K	187_E	1.627	1.00
11_F	67_L	1.616	1.00
137_S	142_E	1.603	1.00
12_V	70_A	1.572	1.00
15_A	67_L	1.571	1.00
10_A	29_I	1.569	1.00
158_D	275_K	1.568	1.00
90_Y	121_N	1.553	1.00
115_F	122_I	1.553	1.00
17_S	22_N	1.546	1.00
21_N	31_Q	1.542	1.00
61_K	64_K	1.534	1.00
136_E	140_C	1.524	1.00
203_R	207_E	1.481	1.00
7_S	37_R	1.478	1.00
12_V	74_I	1.459	1.00
7_S	44_D	1.457	1.00
30_T	33_A	1.455	1.00
48_Q	51_E	1.444	1.00
160_T	273_R	1.442	1.00
279_L	283_A	1.425	1.00
19_S	22_N	1.410	1.00
13_I	27_L	1.406	1.00
287_F	291_I	1.402	1.00
4_E	7_S	1.397	1.00
7_S	40_K	1.396	1.00
173_R	254_S	1.387	1.00
158_D	273_R	1.385	1.00
73_L	80_T	1.384	1.00
148_N	272_I	1.380	1.00
69_E	72_E	1.379	1.00
69_E	79_E	1.365	1.00
5_L	77_F	1.361	1.00
150_N	270_G	1.355	1.00
92_R	121_N	1.354	1.00
139_L	156_S	1.345	1.00
114_K	118_L	1.345	1.00
145_F	283_A	1.342	1.00
271_I	287_F	1.338	1.00
273_R	287_F	1.330	1.00
105_F	227_S	1.325	1.00
285_R	288_A	1.305	1.00
96_T	127_L	1.304	1.00
44_D	81_L	1.295	1.00
171_C	239_I	1.292	1.00
191_Y	239_I	1.281	1.00
145_F	271_I	1.278	1.00
137_S	143_S	1.269	1.00
165_E	245_L	1.259	1.00
244_G	248_P	1.257	1.00
66_L	81_L	1.256	1.00
116_N	220_F	1.255	1.00
229_S	240_S	1.255	1.00
64_K	68_P	1.245	1.00
39_K	43_E	1.242	1.00
53_T	58_T	1.226	1.00
210_L	215_W	1.203	1.00
244_G	257_G	1.202	1.00
76_K	79_E	1.201	1.00
114_K	117_E	1.198	1.00
138_V	146_G	1.195	1.00
118_L	289_L	1.194	1.00
173_R	256_I	1.187	1.00
194_I	229_S	1.186	1.00
68_P	72_E	1.185	1.00
176_P	191_Y	1.182	1.00
231_G	234_E	1.177	1.00
65_R	68_P	1.176	1.00
11_F	50_F	1.175	1.00
95_V	286_F	1.167	1.00
116_N	192_K	1.166	1.00
69_E	80_T	1.165	1.00
248_P	251_P	1.156	1.00
113_G	117_E	1.156	1.00
159_F	272_I	1.152	1.00
161_P	270_G	1.152	1.00
181_Q	256_I	1.148	1.00
9_K	78_D	1.143	1.00
11_F	49_L	1.142	1.00
35_T	39_K	1.127	1.00
36_R	39_K	1.118	1.00
115_F	289_L	1.117	1.00
29_I	33_A	1.117	1.00
11_F	15_A	1.115	1.00
125_R	222_E	1.109	1.00
14_L	23_A	1.108	1.00
170_A	257_G	1.107	1.00
20_F	57_V	1.105	1.00
223_V	229_S	1.096	1.00
274_R	277_A	1.093	1.00
36_R	40_K	1.090	1.00
288_A	291_I	1.088	1.00
6_S	9_K	1.088	1.00
113_G	235_A	1.088	1.00
119_Y	285_R	1.080	1.00
72_E	79_E	1.078	1.00
192_K	218_D	1.076	1.00
284_E	288_A	1.063	1.00
73_L	76_K	1.062	1.00
289_L	293_L	1.060	1.00
104_V	128_E	1.060	1.00
13_I	23_A	1.060	1.00
8_M	70_A	1.059	1.00
59_L	63_G	1.052	1.00
172_R	236_G	1.050	1.00
37_R	40_K	1.045	1.00
111_A	290_L	1.038	1.00
182_L	261_V	1.036	1.00
250_A	253_S	1.032	1.00
257_G	260_L	1.026	1.00
183_V	187_E	1.019	1.00
169_L	239_I	1.015	1.00
139_L	154_N	1.010	1.00
185_W	262_E	1.009	1.00
65_R	69_E	1.004	1.00
231_G	235_A	1.000	1.00
78_D	82_F	0.996	1.00
170_A	247_M	0.995	1.00
110_L	235_A	0.994	1.00
118_L	292_N	0.994	1.00
10_A	27_L	0.993	1.00
160_T	287_F	0.987	1.00
81_L	85_R	0.984	1.00
15_A	50_F	0.982	1.00
29_I	34_L	0.979	1.00
166_P	266_R	0.975	1.00
204_L	207_E	0.972	1.00
78_D	81_L	0.971	1.00
115_F	119_Y	0.967	1.00
230_L	234_E	0.966	1.00
137_S	140_C	0.956	1.00
249_H	252_Y	0.956	1.00
11_F	59_L	0.952	1.00
175_H	192_K	0.946	1.00
156_S	275_K	0.943	1.00
171_C	175_H	0.943	1.00
14_L	20_F	0.938	1.00
66_L	70_A	0.935	1.00
280_S	283_A	0.935	1.00
195_G	219_W	0.931	1.00
204_L	208_Q	0.930	1.00
50_F	57_V	0.929	1.00
15_A	63_G	0.928	1.00
75_K	79_E	0.926	1.00
289_L	292_N	0.924	1.00
223_V	232_L	0.923	1.00
111_A	289_L	0.922	1.00
47_V	84_I	0.921	1.00
11_F	41_M	0.918	1.00
123_K	218_D	0.910	1.00
23_A	34_L	0.900	1.00
98_A	148_N	0.895	1.00
143_S	146_G	0.894	1.00
127_L	137_S	0.893	1.00
133_N	136_E	0.893	1.00
40_K	43_E	0.888	1.00
171_C	176_P	0.882	1.00
175_H	178_A	0.880	1.00
68_P	71_R	0.878	1.00
157_I	272_I	0.873	1.00
101_P	225_H	0.869	1.00
122_I	282_A	0.866	1.00
187_E	190_G	0.866	1.00
179_K	192_K	0.865	1.00
21_N	25_K	0.864	1.00
22_N	26_L	0.855	1.00
192_K	219_W	0.854	1.00
170_A	240_S	0.853	1.00
18_S	58_T	0.852	1.00
150_N	268_T	0.852	1.00
97_L	145_F	0.851	1.00
288_A	292_N	0.850	1.00
98_A	134_C	0.849	1.00
14_L	38_I	0.838	1.00
176_P	181_Q	0.831	1.00
175_H	179_K	0.826	1.00
65_R	87_M	0.824	1.00
53_T	56_K	0.824	1.00
27_L	34_L	0.821	1.00
98_A	146_G	0.819	1.00
193_M	217_L	0.813	1.00
72_E	75_K	0.811	1.00
6_S	37_R	0.810	1.00
91_H	119_Y	0.809	1.00
62_A	84_I	0.807	1.00
174_D	178_A	0.806	1.00
5_L	74_I	0.804	1.00
158_D	161_P	0.803	1.00
127_L	143_S	0.803	1.00
39_K	48_Q	0.802	1.00
11_F	66_L	0.799	1.00
186_Q	189_V	0.792	1.00
209_Q	213_K	0.788	1.00
14_L	50_F	0.787	1.00
18_S	64_K	0.787	1.00
279_L	284_E	0.786	1.00
15_A	18_S	0.781	1.00
177_L	191_Y	0.780	1.00
16_E	67_L	0.778	1.00
93_G	282_A	0.776	1.00
203_R	222_E	0.772	1.00
113_G	237_L	0.770	1.00
172_R	237_L	0.768	1.00
31_Q	35_T	0.768	1.00
76_K	80_T	0.762	1.00
59_L	64_K	0.761	1.00
147_I	290_L	0.761	1.00
145_F	286_F	0.760	1.00
232_L	237_L	0.756	1.00
166_P	259_P	0.755	1.00
77_F	80_T	0.755	1.00
93_G	122_I	0.754	1.00
118_L	285_R	0.754	1.00
62_A	87_M	0.753	1.00
281_P	285_R	0.751	1.00
17_S	23_A	0.747	1.00
139_L	157_I	0.744	1.00
206_I	210_L	0.744	1.00
58_T	64_K	0.744	1.00
114_K	292_N	0.738	1.00
79_E	83_N	0.736	1.00
18_S	56_K	0.732	1.00
170_A	242_L	0.730	1.00
85_R	88_N	0.727	1.00
184_E	261_V	0.726	1.00
96_T	143_S	0.725	1.00
33_A	37_R	0.723	1.00
171_C	256_I	0.722	1.00
7_S	10_A	0.716	1.00
116_N	237_L	0.716	1.00
208_Q	212_D	0.715	1.00
208_Q	211_A	0.714	1.00
135_M	139_L	0.712	1.00
250_A	257_G	0.712	1.00
111_A	293_L	0.710	1.00
80_T	84_I	0.709	1.00
20_F	56_K	0.705	1.00
77_F	81_L	0.703	1.00
62_A	65_R	0.703	1.00
247_M	250_A	0.702	1.00
178_A	256_I	0.702	1.00
209_Q	212_D	0.701	1.00
115_F	285_R	0.700	1.00
70_A	73_L	0.699	1.00
20_F	34_L	0.699	1.00
243_P	246_A	0.696	1.00
99_C	108_L	0.694	1.00
51_E	60_T	0.692	1.00
14_L	34_L	0.690	1.00
9_K	13_I	0.689	1.00
166_P	264_V	0.688	1.00
190_G	218_D	0.687	1.00
225_H	228_T	0.685	1.00
189_V	215_W	0.685	1.00
99_C	104_V	0.684	1.00
221_Y	232_L	0.683	1.00
182_L	259_P	0.680	1.00
51_E	56_K	0.679	1.00
171_C	177_L	0.679	1.00
75_K	78_D	0.678	1.00
172_R	175_H	0.677	1.00
70_A	74_I	0.677	1.00
177_L	180_K	0.677	1.00
234_E	252_Y	0.677	1.00
96_T	144_D	0.676	1.00
174_D	256_I	0.676	1.00
95_V	282_A	0.675	1.00
62_A	66_L	0.675	1.00
210_L	217_L	0.672	1.00
277_A	280_S	0.671	1.00
170_A	250_A	0.670	1.00
186_Q	213_K	0.670	1.00
173_R	253_S	0.662	1.00
42_E	47_V	0.662	1.00
196_V	229_S	0.660	1.00
144_D	283_A	0.658	1.00
71_R	75_K	0.656	1.00
206_I	209_Q	0.650	1.00
79_E	82_F	0.650	1.00
138_V	272_I	0.647	1.00
197_R	222_E	0.646	1.00
23_A	27_L	0.645	1.00
61_K	65_R	0.644	1.00
205_L	209_Q	0.642	1.00
285_R	289_L	0.640	1.00
42_E	52_R	0.639	1.00
174_D	177_L	0.638	1.00
92_R	123_K	0.637	1.00
163_V	269_L	0.636	1.00
169_L	188_L	0.636	1.00
66_L	84_I	0.635	1.00
64_K	67_L	0.634	1.00
6_S	40_K	0.632	1.00
141_N	274_R	0.631	1.00
25_K	28_N	0.631	1.00
14_L	19_S	0.627	1.00
123_K	222_E	0.626	1.00
204_L	209_Q	0.626	1.00
207_E	211_A	0.625	1.00
38_I	42_E	0.619	1.00
193_M	239_I	0.618	1.00
128_E	224_R	0.618	1.00
65_R	84_I	0.617	1.00
69_E	73_L	0.615	1.00
184_E	262_E	0.613	1.00
174_D	236_G	0.612	1.00
169_L	193_M	0.605	1.00
286_F	290_L	0.604	1.00
145_F	287_F	0.604	1.00
232_L	238_G	0.602	1.00
59_L	67_L	0.601	1.00
108_L	111_A	0.600	1.00
229_S	233_V	0.599	1.00
158_D	276_D	0.599	1.00
128_E	225_H	0.599	1.00
95_V	145_F	0.594	1.00
9_K	12_V	0.591	1.00
281_P	284_E	0.590	1.00
203_R	209_Q	0.587	1.00
32_P	36_R	0.587	1.00
197_R	224_R	0.586	1.00
133_N	137_S	0.585	1.00
177_L	183_V	0.583	1.00
82_F	86_D	0.582	1.00
105_F	231_G	0.582	1.00
182_L	187_E	0.582	1.00
169_L	241_A	0.580	1.00
112_I	124_V	0.580	1.00
205_L	208_Q	0.579	1.00
180_K	183_V	0.574	1.00
176_P	179_K	0.574	1.00
165_E	267_R	0.574	1.00
176_P	180_K	0.572	1.00
138_V	157_I	0.570	1.00
45_L	66_L	0.570	1.00
167_F	241_A	0.569	1.00
33_A	36_R	0.568	1.00
45_L	84_I	0.567	1.00
110_L	114_K	0.563	1.00
6_S	10_A	0.562	1.00
223_V	228_T	0.562	1.00
38_I	50_F	0.561	1.00
47_V	51_E	0.560	1.00
149_M	267_R	0.560	1.00
103_A	107_F	0.555	1.00
50_F	59_L	0.554	1.00
207_E	210_L	0.554	1.00
198_S	222_E	0.553	1.00
105_F	225_H	0.550	1.00
68_P	83_N	0.550	1.00
30_T	36_R	0.549	1.00
74_I	77_F	0.548	1.00
70_A	77_F	0.547	1.00
93_G	119_Y	0.543	1.00
10_A	38_I	0.542	1.00
45_L	48_Q	0.537	1.00
147_I	271_I	0.537	1.00
273_R	284_E	0.535	1.00
98_A	127_L	0.534	1.00
110_L	113_G	0.534	1.00
230_L	247_M	0.533	1.00
242_L	247_M	0.531	1.00
171_C	178_A	0.530	1.00
226_L	243_P	0.528	1.00
9_K	74_I	0.527	1.00
186_Q	215_W	0.526	1.00
175_H	239_I	0.525	1.00
8_M	66_L	0.521	1.00
74_I	78_D	0.520	1.00
93_G	121_N	0.519	1.00
162_L	271_I	0.514	1.00
283_A	287_F	0.512	1.00
20_F	52_R	0.511	1.00
48_Q	62_A	0.511	1.00
136_E	142_E	0.510	1.00
117_E	178_A	0.508	1.00
10_A	23_A	0.508	1.00
119_Y	122_I	0.507	1.00
260_L	263_P	0.507	1.00
69_E	84_I	0.507	1.00
131_T	148_N	0.506	1.00
18_S	59_L	0.506	1.00
20_F	31_Q	0.504	1.00
73_L	81_L	0.502	1.00
18_S	57_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
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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
2esnA	3	0.9274	100	0.14	Contact Map
3fzvA	4	0.9085	100	0.141	Contact Map
1uthA	2	0.7129	100	0.146	Contact Map
1ixcA	4	0.9211	100	0.148	Contact Map
3fxqA	3	0.9211	100	0.149	Contact Map
1al3A	1	0.7256	100	0.15	Contact Map
4x6gA	4	0.9527	100	0.153	Contact Map
2h98A	2	0.6688	100	0.155	Contact Map
2h9bA	2	0.6688	100	0.16	Contact Map
3hhgA	3	0.9243	100	0.171	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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