CYNR - ECOLI - GREMLIN Contacts

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CYNR - HTH-type transcriptional regulator CynR

UniProt:	P27111	Sequences: MLSRHINYFLAVAEHGSFTRAASALHVSQPALSQQIRQLEESLGVPLFDRSGRTIRLTDAGEVWRQYASRALQELGAGKRAIHDVADLTRGSLRIAVTPTFTSYFIGPLMADFYARYPSITLQLQEMSQEKIEDMLCRDELDVGIAFAPVHSPELEAIPLLTESLALVVAQHHPLAVHEQVALSRLHDEKLVLLSAEFATREQIDHYCEKAGLHPQVVIEANSISAVLELIRRTSLSTLLPAAIATQHDGLKAISLAPPLLERTAVLLRRKNSWQTAAAKAFLHMALDKCAVVGGNESR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11421
Length:	299 (284)
Sequences:	79809 (58246)
Seq/√Len:	3456.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_R	74_E	3.706	1.00
15_H	24_A	3.480	1.00
158_I	287_L	2.747	1.00
96_A	141_L	2.548	1.00
67_Y	81_A	2.514	1.00
11_A	24_A	2.390	1.00
231_I	238_T	2.308	1.00
159_P	162_T	2.274	1.00
248_H	251_L	2.270	1.00
162_T	264_T	2.257	1.00
92_S	123_Q	2.253	1.00
173_H	189_E	2.245	1.00
164_S	242_A	2.209	1.00
159_P	264_T	2.199	1.00
45_V	60_A	2.135	1.00
92_S	121_T	2.132	1.00
8_Y	35_Q	2.109	1.00
20_R	23_S	2.108	1.00
162_T	262_E	2.063	1.00
112_D	285_M	2.045	1.00
10_L	69_S	2.036	1.00
182_A	185_R	2.029	1.00
14_E	69_S	2.023	1.00
67_Y	74_E	2.015	1.00
10_L	14_E	1.996	1.00
94_R	123_Q	1.995	1.00
10_L	65_R	1.984	1.00
166_A	242_A	1.968	1.00
11_A	14_E	1.957	1.00
11_A	15_H	1.947	1.00
13_A	57_L	1.914	1.00
8_Y	32_L	1.913	1.00
71_A	75_L	1.893	1.00
192_V	236_L	1.882	1.00
65_R	69_S	1.846	1.00
18_F	36_I	1.779	1.00
49_D	56_R	1.746	1.00
190_K	218_V	1.744	1.00
64_W	78_G	1.735	1.00
135_M	140_E	1.726	1.00
63_V	81_A	1.708	1.00
157_A	266_V	1.695	1.00
13_A	65_R	1.669	1.00
132_I	144_G	1.667	1.00
169_V	254_I	1.610	1.00
15_H	20_R	1.609	1.00
113_F	282_F	1.589	1.00
14_E	24_A	1.586	1.00
156_E	271_K	1.573	1.00
10_L	68_A	1.572	1.00
134_D	138_R	1.549	1.00
9_F	65_R	1.543	1.00
5_H	35_Q	1.542	1.00
67_Y	70_R	1.512	1.00
8_Y	27_V	1.508	1.00
17_S	20_R	1.504	1.00
178_H	185_R	1.503	1.00
5_H	38_Q	1.497	1.00
158_I	269_R	1.494	1.00
5_H	42_S	1.488	1.00
113_F	120_I	1.487	1.00
88_L	119_S	1.483	1.00
28_S	31_A	1.482	1.00
19_T	29_Q	1.479	1.00
127_M	131_K	1.470	1.00
201_R	205_D	1.461	1.00
46_P	49_D	1.452	1.00
11_A	25_L	1.446	1.00
59_D	62_E	1.432	1.00
283_L	287_L	1.428	1.00
146_A	268_L	1.423	1.00
103_S	225_S	1.415	1.00
67_Y	77_A	1.412	1.00
156_E	269_R	1.409	1.00
10_L	72_L	1.402	1.00
275_Q	279_A	1.382	1.00
71_A	78_G	1.378	1.00
148_A	266_V	1.370	1.00
90_R	119_S	1.365	1.00
269_R	283_L	1.353	1.00
94_R	125_Q	1.352	1.00
51_S	56_R	1.347	1.00
281_A	284_H	1.341	1.00
163_E	243_A	1.326	1.00
135_M	141_L	1.324	1.00
116_R	285_M	1.322	1.00
64_W	79_K	1.322	1.00
74_E	77_A	1.317	1.00
267_L	283_L	1.313	1.00
112_D	116_R	1.307	1.00
137_C	154_E	1.297	1.00
232_R	250_G	1.278	1.00
227_V	238_T	1.277	1.00
169_V	237_S	1.276	1.00
143_V	279_A	1.271	1.00
255_S	258_P	1.270	1.00
66_Q	70_R	1.265	1.00
171_Q	250_G	1.264	1.00
189_E	237_S	1.262	1.00
143_V	267_L	1.262	1.00
42_S	79_K	1.258	1.00
114_Y	218_V	1.256	1.00
67_Y	78_G	1.244	1.00
3_S	75_L	1.243	1.00
232_R	247_Q	1.231	1.00
114_Y	190_K	1.216	1.00
229_E	232_R	1.214	1.00
171_Q	252_K	1.212	1.00
159_P	266_V	1.211	1.00
63_V	66_Q	1.197	1.00
9_F	48_F	1.194	1.00
111_A	115_A	1.193	1.00
27_V	31_A	1.192	1.00
34_Q	38_Q	1.169	1.00
37_R	41_E	1.169	1.00
62_E	66_Q	1.168	1.00
242_A	246_T	1.161	1.00
111_A	233_R	1.157	1.00
9_F	13_A	1.154	1.00
180_Q	257_A	1.152	1.00
174_P	189_E	1.143	1.00
157_A	268_L	1.139	1.00
34_Q	37_R	1.126	1.00
123_Q	220_E	1.120	1.00
208_C	213_L	1.106	1.00
63_V	67_Y	1.103	1.00
117_Y	281_A	1.102	1.00
228_L	247_Q	1.100	1.00
9_F	47_L	1.092	1.00
70_R	77_A	1.091	1.00
6_I	68_A	1.090	1.00
33_S	37_R	1.081	1.00
112_D	115_A	1.081	1.00
284_H	287_L	1.080	1.00
102_T	126_E	1.077	1.00
136_L	144_G	1.077	1.00
18_F	55_I	1.075	1.00
190_K	216_Q	1.070	1.00
192_V	227_V	1.069	1.00
113_F	285_M	1.068	1.00
11_A	21_A	1.067	1.00
181_V	185_R	1.067	1.00
93_L	282_F	1.064	1.00
108_P	233_R	1.062	1.00
158_I	283_L	1.052	1.00
71_A	74_E	1.050	1.00
12_V	21_A	1.050	1.00
166_A	253_A	1.045	1.00
270_R	273_S	1.040	1.00
280_K	284_H	1.038	1.00
221_A	227_V	1.034	1.00
35_Q	38_Q	1.033	1.00
127_M	135_M	1.032	1.00
109_L	286_A	1.032	1.00
170_A	234_T	1.028	1.00
228_L	232_R	1.028	1.00
4_R	7_N	1.023	1.00
229_E	233_R	1.022	1.00
7_N	76_G	1.018	1.00
168_V	245_A	1.017	1.00
137_C	152_S	1.011	1.00
79_K	83_H	1.010	1.00
164_S	262_E	1.004	1.00
57_L	61_G	0.995	1.00
64_W	68_A	0.972	1.00
167_L	237_S	0.968	1.00
13_A	48_F	0.966	1.00
166_A	255_S	0.961	1.00
76_G	80_R	0.960	1.00
73_Q	77_A	0.960	1.00
27_V	32_L	0.960	1.00
125_Q	135_M	0.958	1.00
285_M	288_D	0.957	1.00
113_F	117_Y	0.956	1.00
8_Y	25_L	0.956	1.00
76_G	79_K	0.955	1.00
193_L	217_V	0.947	1.00
168_V	253_A	0.947	1.00
221_A	230_L	0.943	1.00
202_E	206_H	0.941	1.00
12_V	18_F	0.940	1.00
169_V	173_H	0.940	1.00
9_F	57_L	0.932	1.00
202_E	205_D	0.932	1.00
96_A	146_A	0.926	1.00
38_Q	41_E	0.921	1.00
21_A	32_L	0.918	1.00
135_M	138_R	0.918	1.00
276_T	279_A	0.913	1.00
116_R	288_D	0.911	1.00
164_S	255_S	0.911	1.00
109_L	285_M	0.909	1.00
9_F	39_L	0.904	1.00
20_R	24_A	0.895	1.00
45_V	82_I	0.886	1.00
48_F	55_I	0.879	1.00
121_T	216_Q	0.873	1.00
70_R	73_Q	0.868	1.00
99_P	223_S	0.866	1.00
148_A	264_T	0.864	1.00
66_Q	69_S	0.862	1.00
169_V	174_P	0.861	1.00
16_G	56_R	0.861	1.00
13_A	61_G	0.858	1.00
131_K	134_D	0.856	1.00
177_V	190_K	0.855	1.00
173_H	176_A	0.850	1.00
141_L	144_G	0.848	1.00
190_K	217_V	0.848	1.00
173_H	190_K	0.846	1.00
120_I	278_A	0.845	1.00
19_T	23_S	0.835	1.00
182_A	257_A	0.833	1.00
251_L	257_A	0.826	1.00
185_R	188_D	0.825	1.00
174_P	179_E	0.825	1.00
25_L	32_L	0.822	1.00
242_A	255_S	0.817	1.00
155_L	268_L	0.815	1.00
95_I	143_V	0.814	1.00
96_A	144_G	0.814	1.00
175_L	189_E	0.814	1.00
51_S	54_T	0.814	1.00
156_E	159_P	0.812	1.00
91_G	278_A	0.812	1.00
75_L	79_K	0.808	1.00
111_A	235_S	0.807	1.00
125_Q	141_L	0.805	1.00
60_A	82_I	0.800	1.00
154_E	271_K	0.799	1.00
284_H	288_D	0.799	1.00
74_E	78_G	0.792	1.00
29_Q	33_S	0.789	1.00
133_E	137_C	0.788	1.00
63_V	85_V	0.788	1.00
13_A	16_G	0.788	1.00
246_T	249_D	0.787	1.00
207_Y	211_A	0.786	1.00
9_F	64_W	0.785	1.00
168_V	238_T	0.784	1.00
4_R	35_Q	0.784	1.00
275_Q	280_K	0.783	1.00
60_A	63_V	0.782	1.00
3_S	72_L	0.780	1.00
77_A	81_A	0.778	1.00
75_L	78_G	0.776	1.00
16_G	62_E	0.775	1.00
14_E	65_R	0.775	1.00
184_S	187_H	0.774	1.00
37_R	46_P	0.774	1.00
191_L	215_P	0.772	1.00
16_G	54_T	0.769	1.00
114_Y	235_S	0.769	1.00
12_V	48_F	0.767	1.00
204_I	208_C	0.764	1.00
91_G	120_I	0.762	1.00
164_S	260_L	0.760	1.00
170_A	235_S	0.759	1.00
277_A	281_A	0.759	1.00
12_V	36_I	0.758	1.00
247_Q	251_L	0.755	1.00
15_H	21_A	0.754	1.00
96_A	132_I	0.749	1.00
247_Q	250_G	0.747	1.00
7_N	11_A	0.743	1.00
143_V	282_F	0.740	1.00
5_H	8_Y	0.738	1.00
172_H	176_A	0.738	1.00
230_L	235_S	0.737	1.00
83_H	86_A	0.729	1.00
78_G	82_I	0.728	1.00
60_A	85_V	0.726	1.00
18_F	32_L	0.725	1.00
168_V	240_L	0.725	1.00
89_T	117_Y	0.724	1.00
68_A	71_A	0.723	1.00
116_R	281_A	0.720	1.00
97_V	102_T	0.719	1.00
12_V	32_L	0.716	1.00
251_L	255_S	0.714	1.00
49_D	58_T	0.713	1.00
242_A	253_A	0.711	1.00
113_F	281_A	0.711	1.00
137_C	155_L	0.709	1.00
69_S	73_Q	0.703	1.00
170_A	173_H	0.703	1.00
223_S	226_A	0.700	1.00
206_H	210_K	0.695	1.00
187_H	213_L	0.693	1.00
201_R	220_E	0.690	1.00
31_A	35_Q	0.690	1.00
273_S	276_T	0.687	1.00
62_E	65_R	0.687	1.00
131_K	135_M	0.686	1.00
56_R	62_E	0.686	1.00
206_H	209_E	0.685	1.00
207_Y	210_K	0.684	1.00
173_H	177_V	0.683	1.00
241_P	244_I	0.682	1.00
57_L	62_E	0.681	1.00
60_A	64_W	0.680	1.00
139_D	270_R	0.679	1.00
94_R	141_L	0.679	1.00
195_S	220_E	0.679	1.00
169_V	175_L	0.677	1.00
247_Q	252_K	0.669	1.00
281_A	285_M	0.668	1.00
142_D	279_A	0.668	1.00
49_D	54_T	0.666	1.00
94_R	142_D	0.664	1.00
59_D	63_V	0.661	1.00
252_K	255_S	0.657	1.00
184_S	211_A	0.653	1.00
205_D	209_E	0.650	1.00
194_L	227_V	0.650	1.00
7_N	10_L	0.650	1.00
103_S	229_E	0.649	1.00
40_E	45_V	0.649	1.00
172_H	234_T	0.649	1.00
127_M	132_I	0.648	1.00
112_D	288_D	0.647	1.00
172_H	175_L	0.642	1.00
203_Q	207_Y	0.640	1.00
219_I	230_L	0.640	1.00
64_W	82_I	0.640	1.00
188_D	216_Q	0.637	1.00
73_Q	76_G	0.628	1.00
77_A	80_R	0.627	1.00
232_R	252_K	0.626	1.00
137_C	140_E	0.625	1.00
40_E	50_R	0.624	1.00
97_V	106_I	0.624	1.00
191_L	237_S	0.623	1.00
67_Y	71_A	0.620	1.00
121_T	220_E	0.620	1.00
23_S	26_H	0.619	1.00
179_E	254_I	0.617	1.00
202_E	207_Y	0.616	1.00
248_H	253_A	0.616	1.00
36_I	40_E	0.612	1.00
68_A	72_L	0.611	1.00
203_Q	206_H	0.610	1.00
167_L	239_L	0.609	1.00
251_L	256_L	0.607	1.00
204_I	207_Y	0.604	1.00
4_R	38_Q	0.602	1.00
126_E	222_N	0.602	1.00
12_V	17_S	0.601	1.00
93_L	278_A	0.599	1.00
195_S	222_N	0.599	1.00
143_V	283_L	0.595	1.00
208_C	215_P	0.595	1.00
201_R	207_Y	0.594	1.00
108_P	111_A	0.594	1.00
167_L	186_L	0.594	1.00
176_A	252_K	0.592	1.00
21_A	25_L	0.591	1.00
232_R	248_H	0.586	1.00
145_I	286_A	0.584	1.00
277_A	280_K	0.584	1.00
99_P	128_S	0.584	1.00
90_R	121_T	0.584	1.00
80_R	84_D	0.581	1.00
63_V	82_I	0.577	1.00
106_I	109_L	0.576	1.00
93_L	143_V	0.571	1.00
31_A	34_Q	0.569	1.00
282_F	286_A	0.564	1.00
126_E	223_S	0.564	1.00
7_N	72_L	0.564	1.00
43_L	64_W	0.563	1.00
18_F	54_T	0.563	1.00
147_F	263_R	0.562	1.00
30_P	34_Q	0.562	1.00
175_L	178_H	0.558	1.00
221_A	226_A	0.555	1.00
251_L	254_I	0.554	1.00
9_F	61_G	0.554	1.00
134_D	137_C	0.552	1.00
43_L	82_I	0.552	1.00
4_R	8_Y	0.552	1.00
134_D	140_E	0.550	1.00
45_V	49_D	0.548	1.00
227_V	231_I	0.547	1.00
161_L	265_A	0.546	1.00
175_L	181_V	0.544	1.00
57_L	65_R	0.543	1.00
72_L	76_G	0.543	1.00
108_P	112_D	0.542	1.00
48_F	57_L	0.541	1.00
167_L	191_L	0.541	1.00
28_S	34_Q	0.541	1.00
165_L	239_L	0.536	1.00
230_L	236_L	0.536	1.00
269_R	280_K	0.535	1.00
173_H	237_S	0.532	1.00
117_Y	120_I	0.530	1.00
201_R	204_I	0.529	1.00
163_E	263_R	0.529	1.00
156_E	272_N	0.524	1.00
169_V	252_K	0.524	1.00
101_F	105_F	0.522	1.00
96_A	125_Q	0.520	1.00
171_Q	249_D	0.519	1.00
18_F	29_Q	0.518	1.00
148_A	157_A	0.518	1.00
196_A	220_E	0.518	1.00
205_D	208_C	0.517	1.00
136_L	155_L	0.517	1.00
174_P	178_H	0.517	1.00
8_Y	36_I	0.515	1.00
43_L	46_P	0.513	1.00
66_Q	81_A	0.510	1.00
91_G	119_S	0.509	1.00
110_M	122_L	0.508	1.00
13_A	62_E	0.508	1.00
96_A	127_M	0.505	1.00
180_Q	185_R	0.503	1.00
115_A	176_A	0.502	1.00
240_L	245_A	0.502	1.00
72_L	75_L	0.501	1.00
103_S	223_S	0.501	1.00
182_A	258_P	0.501	1.00
80_R	83_H	0.501	1.00
224_I	241_P	0.500	1.00
8_Y	21_A	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
1ixcA	4	0.9732	100	0.081	Contact Map
1al3A	1	0.7157	100	0.086	Contact Map
1uthA	2	0.7492	100	0.088	Contact Map
2h98A	2	0.699	100	0.09	Contact Map
4x6gA	4	1	100	0.09	Contact Map
2esnA	3	0.9699	100	0.091	Contact Map
2h9bA	2	0.699	100	0.094	Contact Map
3fzvA	4	0.9498	100	0.095	Contact Map
3fxqA	3	0.9666	100	0.099	Contact Map
3szpA	3	0.9599	100	0.119	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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