YHJC - ECOLI - GREMLIN Contacts

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YHJC - Uncharacterized HTH-type transcriptional regulator YhjC

UniProt:	P37641	Sequences: MDKIHAMQLFIKVAELESFSRAADFFALPKGSVSRQIQALEHQLGTQLLQRTTRRVKLTPEGMTYYQRAKDVLSNLSELDGLFQQDATSISGKLRIDIPPGIAKSLLLPRLSEFLYLHPGIELELSSHDRPVDILHDGFDCVIRTGALPEDGVIARPLGKLTMVNCASPHYLTRFGYPQSPDDLTSHAIVRYTPHLGVHPLGFEVASVNGVQWFKSGGMLTVNSSENYLTAGLAGLGIIQIPRIAVREALRAGRLIEVLPGYRAEPLSLSLVYPQRRELSRRVNLFMQWLAGVMKEYLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12247
Length:	299 (284)
Sequences:	79702 (57799)
Seq/√Len:	3429.7

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_D	75_N	3.527	1.00
16_L	25_F	3.330	1.00
156_R	291_A	2.656	1.00
97_D	139_F	2.496	1.00
68_R	82_L	2.390	1.00
232_G	239_I	2.275	1.00
12_K	25_F	2.235	1.00
160_K	268_S	2.187	1.00
171_Y	187_H	2.178	1.00
157_P	160_K	2.176	1.00
162_T	243_R	2.156	1.00
93_K	124_E	2.123	1.00
157_P	268_S	2.094	1.00
21_R	24_D	2.069	1.00
93_K	122_E	2.037	1.00
15_E	70_K	2.032	1.00
46_T	61_E	2.030	1.00
9_L	36_Q	2.024	1.00
180_S	183_D	2.020	1.00
160_K	266_P	1.979	1.00
113_E	289_W	1.961	1.00
68_R	75_N	1.954	1.00
229_L	249_A	1.947	1.00
11_I	66_Y	1.937	1.00
11_I	70_K	1.937	1.00
233_L	254_R	1.934	1.00
95_R	124_E	1.925	1.00
12_K	15_E	1.889	1.00
11_I	15_E	1.882	1.00
190_V	237_G	1.881	1.00
167_A	258_V	1.867	1.00
12_K	16_L	1.867	1.00
164_V	243_R	1.863	1.00
9_L	33_V	1.858	1.00
72_V	76_L	1.846	1.00
14_A	58_L	1.841	1.00
233_L	249_A	1.818	1.00
66_Y	70_K	1.795	1.00
19_F	37_I	1.761	1.00
50_Q	57_K	1.712	1.00
65_Y	79_L	1.688	1.00
188_A	219_M	1.684	1.00
164_V	257_E	1.667	1.00
155_A	270_S	1.658	1.00
64_T	82_L	1.658	1.00
133_D	138_G	1.597	1.00
14_A	66_Y	1.590	1.00
114_F	286_F	1.589	1.00
176_G	183_D	1.586	1.00
15_E	25_F	1.572	1.00
16_L	21_R	1.560	1.00
154_I	275_Q	1.558	1.00
11_I	69_A	1.553	1.00
130_R	142_V	1.548	1.00
10_F	66_Y	1.540	1.00
9_L	28_L	1.516	1.00
6_A	36_Q	1.516	1.00
6_A	43_Q	1.489	1.00
89_S	120_G	1.488	1.00
20_S	30_K	1.479	1.00
132_V	136_H	1.477	1.00
60_P	63_M	1.452	1.00
68_R	71_D	1.451	1.00
156_R	273_Y	1.450	1.00
29_P	32_S	1.440	1.00
6_A	39_A	1.439	1.00
114_F	121_I	1.434	1.00
18_S	21_R	1.433	1.00
47_Q	50_Q	1.429	1.00
12_K	26_F	1.406	1.00
287_M	291_A	1.402	1.00
279_L	283_V	1.399	1.00
11_I	73_L	1.392	1.00
154_I	273_Y	1.385	1.00
144_R	272_V	1.382	1.00
146_G	270_S	1.381	1.00
68_R	78_E	1.374	1.00
72_V	79_L	1.369	1.00
91_S	120_G	1.353	1.00
169_P	254_R	1.343	1.00
104_K	226_E	1.340	1.00
273_Y	287_M	1.339	1.00
135_L	152_G	1.338	1.00
271_L	287_M	1.317	1.00
3_K	6_A	1.316	1.00
4_I	76_L	1.314	1.00
285_L	288_Q	1.303	1.00
95_R	126_S	1.299	1.00
133_D	139_F	1.297	1.00
113_E	117_L	1.294	1.00
141_C	283_V	1.289	1.00
134_I	142_V	1.289	1.00
52_T	57_K	1.287	1.00
187_H	238_I	1.277	1.00
141_C	271_L	1.276	1.00
65_Y	80_D	1.272	1.00
75_N	78_E	1.271	1.00
161_L	244_I	1.271	1.00
228_Y	239_I	1.264	1.00
115_L	219_M	1.259	1.00
167_A	238_I	1.256	1.00
249_A	254_R	1.253	1.00
43_Q	80_D	1.247	1.00
117_L	289_W	1.246	1.00
67_Q	71_D	1.221	1.00
230_T	233_L	1.221	1.00
199_H	203_F	1.213	1.00
243_R	247_R	1.209	1.00
243_R	257_E	1.206	1.00
68_R	79_L	1.201	1.00
247_R	251_R	1.195	1.00
64_T	67_Q	1.194	1.00
115_L	188_A	1.192	1.00
157_P	270_S	1.188	1.00
169_P	256_I	1.185	1.00
209_N	214_F	1.183	1.00
38_Q	42_H	1.183	1.00
63_M	67_Q	1.178	1.00
10_F	49_L	1.176	1.00
112_S	116_Y	1.172	1.00
155_A	272_V	1.163	1.00
172_L	187_H	1.150	1.00
177_Y	256_I	1.150	1.00
28_L	32_S	1.141	1.00
10_F	14_A	1.139	1.00
35_R	39_A	1.128	1.00
112_S	234_A	1.126	1.00
113_E	116_Y	1.119	1.00
10_F	48_L	1.117	1.00
188_A	217_G	1.106	1.00
178_P	261_G	1.106	1.00
35_R	38_Q	1.104	1.00
190_V	228_Y	1.100	1.00
124_E	221_T	1.099	1.00
94_L	286_F	1.093	1.00
288_Q	291_A	1.092	1.00
5_H	8_Q	1.091	1.00
71_D	78_E	1.090	1.00
34_S	38_Q	1.090	1.00
19_F	56_V	1.088	1.00
114_F	289_W	1.086	1.00
13_V	22_A	1.085	1.00
118_H	285_L	1.079	1.00
7_M	69_A	1.078	1.00
166_C	257_E	1.068	1.00
229_L	233_L	1.064	1.00
222_V	228_Y	1.063	1.00
64_T	68_R	1.061	1.00
12_K	22_A	1.059	1.00
72_V	75_N	1.059	1.00
109_P	234_A	1.058	1.00
284_N	288_Q	1.053	1.00
257_E	260_P	1.050	1.00
8_Q	77_S	1.046	1.00
36_Q	39_A	1.042	1.00
135_L	150_E	1.041	1.00
156_R	287_M	1.037	1.00
110_R	290_L	1.027	1.00
168_S	235_G	1.017	1.00
181_P	262_Y	1.015	1.00
230_T	234_A	1.015	1.00
58_L	62_G	1.011	1.00
162_T	266_P	1.007	1.00
80_D	84_Q	1.001	1.00
166_C	246_V	0.999	1.00
179_Q	183_D	0.995	1.00
248_E	252_A	0.992	1.00
77_S	80_D	0.987	1.00
28_L	33_V	0.980	1.00
165_N	238_I	0.976	1.00
114_F	118_H	0.971	1.00
77_S	81_G	0.969	1.00
9_L	26_F	0.967	1.00
14_A	49_L	0.965	1.00
133_D	136_H	0.963	1.00
13_V	19_F	0.961	1.00
10_F	58_L	0.958	1.00
74_S	78_E	0.952	1.00
167_A	171_Y	0.951	1.00
65_Y	69_A	0.950	1.00
171_Y	174_R	0.946	1.00
222_V	231_A	0.943	1.00
191_R	218_G	0.942	1.00
280_S	283_V	0.938	1.00
117_L	292_G	0.932	1.00
289_W	292_G	0.926	1.00
39_A	42_H	0.924	1.00
10_F	40_L	0.918	1.00
110_R	289_W	0.918	1.00
22_A	33_V	0.913	1.00
49_L	56_V	0.907	1.00
46_T	83_F	0.907	1.00
21_R	25_F	0.903	1.00
64_T	86_D	0.900	1.00
14_A	62_G	0.895	1.00
122_E	217_G	0.891	1.00
171_Y	188_A	0.890	1.00
139_F	142_V	0.888	1.00
126_S	133_D	0.888	1.00
67_Q	70_K	0.885	1.00
274_P	277_R	0.878	1.00
171_Y	175_F	0.871	1.00
5_H	36_Q	0.871	1.00
97_D	144_R	0.866	1.00
152_G	275_Q	0.866	1.00
100_P	224_S	0.863	1.00
189_I	216_S	0.860	1.00
20_S	24_D	0.860	1.00
71_D	74_S	0.860	1.00
146_G	268_S	0.859	1.00
97_D	130_R	0.856	1.00
17_E	57_K	0.856	1.00
183_D	186_S	0.854	1.00
153_V	272_V	0.852	1.00
175_F	188_A	0.850	1.00
188_A	218_G	0.848	1.00
166_C	239_I	0.848	1.00
121_I	282_R	0.847	1.00
167_A	172_L	0.846	1.00
26_F	33_V	0.843	1.00
96_I	141_C	0.838	1.00
173_T	187_H	0.838	1.00
246_V	249_A	0.833	1.00
52_T	55_R	0.829	1.00
97_D	142_V	0.826	1.00
172_L	177_Y	0.824	1.00
61_E	86_D	0.822	1.00
92_G	282_R	0.818	1.00
288_Q	292_G	0.818	1.00
249_A	252_A	0.817	1.00
154_I	157_P	0.817	1.00
279_L	284_N	0.813	1.00
4_I	73_L	0.811	1.00
14_A	17_E	0.811	1.00
17_E	63_M	0.806	1.00
30_K	34_S	0.802	1.00
10_F	65_Y	0.801	1.00
112_S	236_L	0.800	1.00
131_P	135_L	0.799	1.00
38_Q	47_Q	0.798	1.00
61_E	83_F	0.796	1.00
168_S	236_L	0.794	1.00
15_E	66_Y	0.794	1.00
180_S	261_G	0.790	1.00
75_N	79_L	0.787	1.00
182_D	185_T	0.787	1.00
126_S	139_F	0.783	1.00
76_L	79_L	0.783	1.00
76_L	80_D	0.782	1.00
13_V	37_I	0.779	1.00
61_E	64_T	0.778	1.00
162_T	264_A	0.775	1.00
13_V	49_L	0.774	1.00
16_L	22_A	0.771	1.00
162_T	259_L	0.768	1.00
117_L	285_L	0.767	1.00
185_T	214_F	0.764	1.00
17_E	55_R	0.763	1.00
281_R	285_L	0.763	1.00
78_E	82_L	0.761	1.00
6_A	9_L	0.760	1.00
141_C	286_F	0.760	1.00
115_L	236_L	0.760	1.00
231_A	236_L	0.754	1.00
170_H	174_R	0.750	1.00
182_D	212_Q	0.749	1.00
90_I	118_H	0.749	1.00
166_C	241_I	0.748	1.00
8_Q	12_K	0.746	1.00
79_L	83_F	0.742	1.00
135_L	153_V	0.741	1.00
129_D	132_V	0.741	1.00
98_I	103_A	0.740	1.00
84_Q	87_A	0.737	1.00
13_V	33_V	0.735	1.00
19_F	33_V	0.727	1.00
199_H	221_T	0.726	1.00
168_S	171_Y	0.723	1.00
114_F	285_L	0.723	1.00
69_A	72_V	0.722	1.00
57_K	63_M	0.720	1.00
50_Q	59_T	0.719	1.00
58_L	63_M	0.717	1.00
70_K	74_S	0.715	1.00
180_S	262_Y	0.714	1.00
95_R	139_F	0.713	1.00
174_R	256_I	0.711	1.00
61_E	65_Y	0.703	1.00
242_P	245_A	0.700	1.00
167_A	173_T	0.697	1.00
167_A	256_I	0.696	1.00
50_Q	55_R	0.696	1.00
140_D	283_V	0.693	1.00
32_S	36_Q	0.693	1.00
122_E	221_T	0.691	1.00
186_S	217_G	0.689	1.00
41_E	46_T	0.686	1.00
63_M	66_Y	0.685	1.00
137_D	274_P	0.684	1.00
95_R	140_D	0.684	1.00
143_I	290_L	0.683	1.00
113_E	292_G	0.683	1.00
60_P	64_T	0.682	1.00
224_S	227_N	0.679	1.00
92_G	121_I	0.678	1.00
285_L	289_W	0.677	1.00
192_Y	228_Y	0.677	1.00
5_H	39_A	0.673	1.00
74_S	77_S	0.670	1.00
189_I	238_I	0.663	1.00
178_P	259_L	0.661	1.00
98_I	107_L	0.661	1.00
220_L	231_A	0.660	1.00
41_E	51_R	0.658	1.00
78_E	81_G	0.657	1.00
8_Q	11_I	0.657	1.00
37_I	41_E	0.657	1.00
248_E	251_R	0.656	1.00
170_H	235_G	0.656	1.00
19_F	55_R	0.656	1.00
24_D	27_A	0.655	1.00
69_A	73_L	0.655	1.00
65_Y	83_F	0.652	1.00
170_H	173_T	0.650	1.00
172_L	175_F	0.649	1.00
169_P	253_G	0.646	1.00
94_L	282_R	0.645	1.00
170_H	256_I	0.639	1.00
104_K	230_T	0.638	1.00
193_T	221_T	0.635	1.00
68_R	72_V	0.634	1.00
165_N	184_L	0.633	1.00
281_R	284_N	0.628	1.00
22_A	26_F	0.627	1.00
13_V	18_S	0.626	1.00
277_R	280_S	0.622	1.00
107_L	110_R	0.619	1.00
141_C	287_M	0.616	1.00
134_I	272_V	0.614	1.00
129_D	133_D	0.612	1.00
103_A	127_S	0.612	1.00
165_N	240_Q	0.609	1.00
286_F	290_L	0.609	1.00
159_G	269_L	0.606	1.00
64_T	83_F	0.605	1.00
94_L	141_C	0.601	1.00
193_T	223_N	0.601	1.00
81_G	85_Q	0.599	1.00
109_P	112_S	0.598	1.00
5_H	9_L	0.598	1.00
176_G	179_Q	0.596	1.00
44_L	65_Y	0.593	1.00
228_Y	232_G	0.593	1.00
145_T	267_L	0.593	1.00
165_N	189_I	0.590	1.00
231_A	237_G	0.588	1.00
44_L	83_F	0.587	1.00
58_L	66_Y	0.586	1.00
222_V	227_N	0.586	1.00
31_G	35_R	0.586	1.00
49_L	58_L	0.582	1.00
8_Q	73_L	0.579	1.00
273_Y	284_N	0.578	1.00
154_I	276_R	0.577	1.00
32_S	35_R	0.577	1.00
161_L	267_L	0.576	1.00
46_T	50_Q	0.574	1.00
91_S	122_E	0.574	1.00
134_I	153_V	0.574	1.00
29_P	35_R	0.574	1.00
173_T	176_G	0.570	1.00
173_T	179_Q	0.570	1.00
130_R	137_D	0.570	1.00
163_M	240_Q	0.567	1.00
92_G	118_H	0.565	1.00
209_N	216_S	0.563	1.00
109_P	113_E	0.563	1.00
158_L	271_L	0.561	1.00
225_S	242_P	0.560	1.00
73_L	77_S	0.560	1.00
102_I	106_L	0.559	1.00
3_K	39_A	0.559	1.00
171_Y	238_I	0.557	1.00
172_L	176_G	0.553	1.00
194_P	221_T	0.551	1.00
10_F	62_G	0.551	1.00
9_L	37_I	0.549	1.00
146_G	155_A	0.549	1.00
44_L	47_Q	0.548	1.00
241_I	246_V	0.545	1.00
143_I	271_L	0.544	1.00
132_V	138_G	0.542	1.00
67_Q	82_L	0.541	1.00
73_L	76_L	0.540	1.00
19_F	30_K	0.537	1.00
9_L	22_A	0.536	1.00
37_I	49_L	0.532	1.00
167_A	174_R	0.531	1.00
111_L	123_L	0.531	1.00
185_T	215_K	0.528	1.00
233_L	252_A	0.528	1.00
28_L	36_Q	0.528	1.00
85_Q	90_I	0.526	1.00
92_G	120_G	0.526	1.00
249_A	253_G	0.526	1.00
283_V	287_M	0.523	1.00
47_Q	61_E	0.522	1.00
68_R	83_F	0.520	1.00
19_F	51_R	0.520	1.00
81_G	84_Q	0.519	1.00
14_A	63_M	0.519	1.00
175_F	178_P	0.518	1.00
118_H	121_I	0.516	1.00
210_G	213_W	0.516	1.00
99_P	102_I	0.514	1.00
109_P	230_T	0.513	1.00
17_E	56_V	0.512	1.00
178_P	183_D	0.512	1.00
273_Y	279_L	0.511	1.00
116_Y	174_R	0.510	1.00
97_D	126_S	0.508	1.00
199_H	202_G	0.508	1.00
209_N	212_Q	0.506	1.00
104_K	224_S	0.504	1.00
96_I	286_F	0.500	1.00
192_Y	225_S	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
3fxqA	3	0.9699	100	0.084	Contact Map
2esnA	3	0.9732	100	0.087	Contact Map
1ixcA	4	0.9666	100	0.094	Contact Map
3fzvA	4	0.9532	100	0.097	Contact Map
3szpA	3	0.9699	100	0.097	Contact Map
3hhgA	3	0.9799	100	0.099	Contact Map
1uthA	2	0.7458	100	0.102	Contact Map
4x6gA	4	0.9967	100	0.103	Contact Map
1al3A	1	0.699	100	0.103	Contact Map
2h98A	2	0.6789	100	0.106	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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