YIEP - ECOLI - GREMLIN Contacts

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YIEP - Uncharacterized HTH-type transcriptional regulator YieP

UniProt:	P31475	Sequences: MPLSAQQLAAQKNLSYVLAEKLAQRILKGEYEPGTILPGEIELGEQFGVSRTAVREAVKTLTAKGMVLPRPRIGTRVMPQSNWNFLDQELLTWWMTEENFHQVIDHFLVMRICLEPQACLLAATVGTAEQKAHLNTLMAEMAALKENFRRERWIEVDMAWHEHIYEMSANPFLTSFASLFHSVYHTYFTSITSDTVIKLDLHQAIVDAIIQSDGDAAFKACQALLRSPDK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11733
Length:	230 (196)
Sequences:	23496 (17191)
Seq/√Len:	1227.9

ECOLI - YIEP GLCC PDHR DGOR YJJM NANR LLDR MCBR UXUR EXUR YDFH CSIR FADR FRLR YEGW YIDP MNGR YIHL PHNF
BACSU - GNTR YDHC LUTR YCBG YVOA YMFC YURK TRER YYDK YBGA
SULSO - Q97YR4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
135_N	210_I	3.744	1.00
120_L	218_F	3.256	1.00
213_D	216_A	2.911	1.00
142_A	203_Q	2.764	1.00
32_E	35_T	2.706	1.00
25_R	30_E	2.664	1.00
25_R	46_Q	2.355	1.00
113_C	117_Q	2.301	1.00
40_E	51_R	2.242	1.00
106_H	171_P	2.206	1.00
133_H	163_H	2.181	1.00
19_A	60_T	2.059	1.00
68_L	78_M	2.021	1.00
23_A	64_K	1.974	1.00
124_T	214_G	1.944	1.00
109_V	121_L	1.926	1.00
18_L	49_V	1.924	1.00
112_I	226_R	1.881	1.00
208_A	216_A	1.786	1.00
131_K	210_I	1.776	1.00
166_E	174_T	1.768	1.00
18_L	47_F	1.764	1.00
130_Q	169_A	1.742	1.00
69_P	75_T	1.737	1.00
127_T	130_Q	1.719	1.00
163_H	166_E	1.682	1.00
138_M	206_V	1.669	1.00
21_K	25_R	1.663	1.00
149_R	152_R	1.653	1.00
116_P	222_Q	1.652	1.00
120_L	214_G	1.610	1.00
110_M	176_F	1.588	1.00
12_K	20_E	1.585	1.00
24_Q	28_K	1.577	1.00
216_A	220_A	1.556	1.00
116_P	218_F	1.548	1.00
218_F	222_Q	1.541	1.00
161_H	202_H	1.531	1.00
117_Q	120_L	1.490	1.00
204_A	220_A	1.434	1.00
175_S	179_L	1.420	1.00
162_E	178_S	1.414	1.00
172_F	183_V	1.409	1.00
207_D	211_Q	1.406	1.00
19_A	64_K	1.400	1.00
112_I	222_Q	1.399	1.00
201_L	227_S	1.395	1.00
140_E	156_V	1.387	1.00
130_Q	167_M	1.380	1.00
137_L	156_V	1.378	1.00
211_Q	216_A	1.376	1.00
70_R	73_I	1.368	1.00
119_C	217_A	1.356	1.00
165_Y	177_A	1.352	1.00
135_N	206_V	1.341	1.00
142_A	199_L	1.340	1.00
41_I	45_E	1.311	1.00
106_H	172_F	1.308	1.00
126_G	131_K	1.292	1.00
203_Q	207_D	1.291	1.00
214_G	218_F	1.255	1.00
136_T	140_E	1.255	1.00
135_N	139_A	1.252	1.00
140_E	159_A	1.245	1.00
112_I	116_P	1.214	1.00
36_I	76_R	1.205	1.00
137_L	163_H	1.203	1.00
42_E	46_Q	1.198	1.00
43_L	54_V	1.186	1.00
17_V	21_K	1.185	1.00
219_K	223_A	1.174	1.00
138_M	203_Q	1.171	1.00
21_K	24_Q	1.170	1.00
38_P	42_E	1.165	1.00
111_R	115_E	1.149	1.00
21_K	47_F	1.146	1.00
216_A	219_K	1.145	1.00
70_R	76_R	1.145	1.00
126_G	212_S	1.141	1.00
162_E	166_E	1.132	1.00
159_A	163_H	1.123	1.00
116_P	120_L	1.117	1.00
25_R	47_F	1.115	1.00
201_L	224_L	1.115	1.00
157_D	161_H	1.114	1.00
106_H	170_N	1.105	1.00
120_L	215_D	1.095	1.00
131_K	206_V	1.087	1.00
126_G	167_M	1.086	1.00
164_I	209_I	1.084	1.00
119_C	221_C	1.083	1.00
119_C	123_A	1.081	1.00
126_G	130_Q	1.075	1.00
163_H	167_M	1.073	1.00
152_R	155_E	1.057	1.00
62_T	69_P	1.056	1.00
137_L	159_A	1.056	1.00
206_V	210_I	1.054	1.00
109_V	170_N	1.050	1.00
207_D	210_I	1.049	1.00
135_N	203_Q	1.042	1.00
138_M	142_A	1.041	1.00
138_M	141_M	1.040	1.00
31_Y	77_V	1.040	1.00
118_A	165_Y	1.033	1.00
133_H	166_E	1.024	1.00
222_Q	226_R	1.023	1.00
133_H	136_T	1.010	1.00
131_K	212_S	1.010	1.00
56_E	59_K	1.005	1.00
202_H	224_L	0.996	1.00
139_A	142_A	0.996	1.00
176_F	179_L	0.983	1.00
68_L	76_R	0.982	1.00
62_T	67_V	0.968	1.00
168_S	174_T	0.967	1.00
12_K	17_V	0.966	1.00
160_W	206_V	0.958	1.00
123_A	214_G	0.956	1.00
156_V	159_A	0.953	1.00
208_A	213_D	0.942	1.00
204_A	223_A	0.942	1.00
200_D	204_A	0.935	1.00
121_L	125_V	0.935	1.00
204_A	216_A	0.924	1.00
161_H	224_L	0.923	1.00
123_A	209_I	0.921	1.00
25_R	31_Y	0.919	1.00
117_Q	218_F	0.918	1.00
58_V	75_T	0.916	1.00
155_E	159_A	0.916	1.00
215_D	219_K	0.908	1.00
15_S	60_T	0.905	1.00
132_A	136_T	0.902	1.00
131_K	135_N	0.900	1.00
133_H	137_L	0.898	1.00
204_A	207_D	0.892	1.00
205_I	221_C	0.887	1.00
19_A	23_A	0.877	1.00
174_T	178_S	0.875	1.00
115_E	161_H	0.872	1.00
36_I	74_G	0.872	1.00
67_V	75_T	0.870	1.00
103_V	172_F	0.870	1.00
60_T	63_A	0.870	1.00
110_M	172_F	0.867	1.00
125_V	169_A	0.864	1.00
70_R	74_G	0.863	1.00
26_I	77_V	0.862	1.00
73_I	76_R	0.861	1.00
117_Q	121_L	0.860	1.00
137_L	140_E	0.859	1.00
215_D	218_F	0.858	1.00
102_Q	106_H	0.857	1.00
40_E	55_R	0.848	1.00
102_Q	169_A	0.847	1.00
140_E	143_A	0.841	1.00
59_K	62_T	0.839	1.00
14_L	17_V	0.837	1.00
44_G	54_V	0.836	1.00
144_L	152_R	0.830	1.00
126_G	209_I	0.830	1.00
23_A	66_M	0.824	1.00
135_N	207_D	0.823	1.00
199_L	203_Q	0.823	1.00
49_V	54_V	0.812	1.00
130_Q	133_H	0.810	1.00
128_A	132_A	0.808	1.00
139_A	143_A	0.806	1.00
123_A	217_A	0.806	1.00
13_N	16_Y	0.805	1.00
42_E	45_E	0.804	1.00
157_D	202_H	0.801	1.00
205_I	220_A	0.798	1.00
23_A	27_L	0.798	1.00
123_A	212_S	0.794	1.00
58_V	67_V	0.785	1.00
50_S	53_A	0.783	1.00
38_P	41_I	0.780	1.00
134_L	163_H	0.777	1.00
139_A	203_Q	0.773	1.00
204_A	208_A	0.771	1.00
172_F	176_F	0.771	1.00
141_M	153_W	0.771	1.00
122_A	167_M	0.770	1.00
43_L	58_V	0.767	1.00
196_V	200_D	0.762	1.00
15_S	19_A	0.760	1.00
14_L	53_A	0.759	1.00
134_L	206_V	0.759	1.00
208_A	220_A	0.759	1.00
16_Y	60_T	0.754	1.00
162_E	181_H	0.753	1.00
128_A	212_S	0.752	1.00
121_L	170_N	0.733	1.00
121_L	124_T	0.729	1.00
172_F	175_S	0.725	1.00
120_L	124_T	0.716	1.00
110_M	173_L	0.714	1.00
152_R	156_V	0.708	1.00
59_K	69_P	0.705	1.00
140_E	152_R	0.704	1.00
205_I	217_A	0.700	1.00
109_V	125_V	0.695	1.00
132_A	210_I	0.694	1.00
219_K	222_Q	0.693	1.00
81_S	103_V	0.692	1.00
220_A	223_A	0.692	1.00
30_E	46_Q	0.690	1.00
132_A	135_N	0.687	1.00
142_A	146_E	0.684	1.00
110_M	118_A	0.684	1.00
158_M	185_H	0.681	1.00
133_H	159_A	0.677	1.00
138_M	199_L	0.676	1.00
103_V	171_P	0.666	1.00
140_E	144_L	0.665	1.00
136_T	139_A	0.658	1.00
162_E	174_T	0.653	1.00
60_T	64_K	0.651	1.00
122_A	126_G	0.649	1.00
131_K	209_I	0.646	1.00
119_C	214_G	0.642	1.00
144_L	156_V	0.642	1.00
12_K	16_Y	0.636	1.00
159_A	162_E	0.630	1.00
201_L	204_A	0.629	1.00
113_C	173_L	0.628	1.00
158_M	181_H	0.628	1.00
109_V	117_Q	0.626	1.00
130_Q	166_E	0.623	1.00
112_I	225_L	0.620	1.00
122_A	168_S	0.620	1.00
53_A	57_A	0.620	1.00
15_S	56_E	0.619	1.00
153_W	198_K	0.616	1.00
130_Q	163_H	0.614	1.00
110_M	114_L	0.611	1.00
31_Y	35_T	0.608	1.00
223_A	227_S	0.603	1.00
118_A	168_S	0.602	1.00
72_R	75_T	0.600	1.00
129_E	133_H	0.595	1.00
116_P	214_G	0.595	1.00
25_R	29_G	0.593	1.00
205_I	224_L	0.591	1.00
111_R	225_L	0.589	1.00
175_S	183_V	0.588	1.00
144_L	149_R	0.586	1.00
78_M	186_T	0.579	1.00
141_M	199_L	0.579	1.00
33_P	79_P	0.578	1.00
118_A	173_L	0.577	1.00
47_F	54_V	0.576	1.00
41_I	44_G	0.575	1.00
134_L	167_M	0.574	1.00
115_E	202_H	0.568	1.00
102_Q	171_P	0.566	1.00
120_L	222_Q	0.562	1.00
122_A	164_I	0.560	1.00
113_C	116_P	0.559	1.00
37_L	67_V	0.559	1.00
193_S	196_V	0.559	1.00
34_G	79_P	0.558	1.00
11_Q	17_V	0.556	1.00
116_P	221_C	0.554	1.00
22_L	43_L	0.547	1.00
114_L	177_A	0.540	1.00
45_E	48_G	0.540	1.00
128_A	210_I	0.538	1.00
59_K	63_A	0.536	1.00
71_P	74_G	0.531	1.00
217_A	221_C	0.529	1.00
194_D	197_I	0.525	1.00
76_R	79_P	0.525	1.00
200_D	203_Q	0.522	1.00
117_Q	173_L	0.522	1.00
165_Y	181_H	0.520	1.00
25_R	28_K	0.519	1.00
102_Q	105_D	0.518	1.00
134_L	138_M	0.518	1.00
142_A	200_D	0.517	1.00
134_L	137_L	0.516	1.00
157_D	198_K	0.514	1.00
27_L	66_M	0.513	1.00
110_M	113_C	0.510	1.00
205_I	208_A	0.509	1.00
144_L	148_F	0.504	1.00
16_Y	20_E	0.503	1.00
116_P	119_C	0.502	1.00
31_Y	46_Q	0.500	1.00
121_L	168_S	0.500	1.00
175_S	178_S	0.500	1.00
119_C	164_I	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
3ihuA	1	0.8609	100	0.15	Contact Map
4p96A	2	0.9696	100	0.162	Contact Map
3sxyA	2	0.8348	100	0.163	Contact Map
3c7jA	4	0.9	100	0.172	Contact Map
2hs5A	1	0.8565	100	0.172	Contact Map
2di3A	2	0.9217	100	0.173	Contact Map
4p9fA	1	0.8652	100	0.185	Contact Map
1hw1A	2	0.9304	100	0.208	Contact Map
3by6A	2	0.5391	99.9	0.533	Contact Map
3ic7A	2	0.4826	99.9	0.536	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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