FRLR - ECOLI - GREMLIN Contacts

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FRLR - HTH-type transcriptional regulator FrlR

UniProt:	P45544	Sequences: MSATDRYSHQLLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFVQSQKVENALLTVSGFTDFGVSQGKATKEKVIEQERVSAAPFCEKLNIPGNSEVFHLCRVMYLDKEPLFIDSSWIPLSRYPDFDEIYVEGSSTYQLFQERFDTRVVSDKKTIDIFAATRPQAKWLKCELGEPLFRISKIAFDQNDKPVHVSELFCRANRITLTIDNKRH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12913
Length:	243 (192)
Sequences:	28604 (22493)
Seq/√Len:	1623.3

ECOLI - FRLR YIDP YIHL PHNF YEGW MNGR NANR EXUR MCBR FADR YIEP GLCC PDHR YJJM LLDR DGOR UXUR YDFH CSIR
BACSU - YURK YVOA TRER YMFC YYDK YBGA GMUR YCBG YDHC LUTR GNTR
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
23_D	28_V	4.030	1.00
30_Q	33_Q	3.975	1.00
23_D	44_Q	3.527	1.00
17_R	58_D	3.462	1.00
21_L	62_D	3.292	1.00
66_I	76_Q	2.896	1.00
38_E	49_R	2.889	1.00
187_D	190_A	2.879	1.00
16_V	47_V	2.803	1.00
19_R	23_D	2.692	1.00
67_R	73_T	2.484	1.00
16_V	45_Y	2.442	1.00
17_R	62_D	2.359	1.00
68_W	71_K	2.256	1.00
22_D	26_Q	2.201	1.00
34_Q	74_F	2.147	1.00
10_Q	18_Q	2.122	1.00
135_M	143_F	1.990	1.00
19_R	45_Y	1.931	1.00
17_R	21_L	1.905	1.00
60_V	67_R	1.855	1.00
39_N	43_T	1.848	1.00
54_K	57_S	1.813	1.00
37_T	40_E	1.773	1.00
15_T	19_R	1.741	1.00
71_K	74_F	1.707	1.00
21_L	25_A	1.667	1.00
23_D	29_Y	1.654	1.00
40_E	44_Q	1.633	1.00
19_R	22_D	1.608	1.00
192_T	196_A	1.604	1.00
182_D	190_A	1.601	1.00
12_L	15_T	1.599	1.00
41_L	52_I	1.597	1.00
192_T	195_Q	1.575	1.00
131_L	147_S	1.556	1.00
68_W	74_F	1.556	1.00
60_V	65_L	1.543	1.00
190_A	194_P	1.493	1.00
21_L	64_V	1.486	1.00
118_E	121_N	1.483	1.00
132_C	135_M	1.467	1.00
66_I	74_F	1.461	1.00
65_L	73_T	1.451	1.00
144_I	148_W	1.429	1.00
141_P	152_S	1.428	1.00
188_I	192_T	1.420	1.00
57_S	67_R	1.413	1.00
58_D	61_A	1.403	1.00
13_Y	58_D	1.401	1.00
56_I	65_L	1.391	1.00
24_I	75_V	1.390	1.00
38_E	53_R	1.365	1.00
29_Y	75_V	1.359	1.00
193_R	197_K	1.356	1.00
104_K	136_Y	1.343	1.00
10_Q	15_T	1.307	1.00
131_L	135_M	1.287	1.00
99_K	103_E	1.286	1.00
40_E	43_T	1.282	1.00
130_H	146_S	1.265	1.00
57_S	61_A	1.262	1.00
125_N	128_V	1.243	1.00
134_V	146_S	1.239	1.00
23_D	45_Y	1.233	1.00
180_V	184_K	1.227	1.00
132_C	136_Y	1.216	1.00
31_A	77_S	1.206	1.00
11_L	14_A	1.201	1.00
47_V	52_I	1.196	1.00
68_W	72_G	1.184	1.00
169_Q	173_E	1.173	1.00
57_S	60_V	1.171	1.00
56_I	73_T	1.168	1.00
34_Q	72_G	1.163	1.00
130_H	176_D	1.150	1.00
177_T	181_S	1.135	1.00
133_R	183_K	1.102	1.00
128_V	132_C	1.097	1.00
23_D	27_G	1.094	1.00
107_E	132_C	1.091	1.00
25_A	64_V	1.091	1.00
58_D	62_D	1.090	1.00
102_K	136_Y	1.081	1.00
172_Q	178_R	1.075	1.00
98_G	102_K	1.070	1.00
181_S	185_T	1.070	1.00
109_E	112_S	1.066	1.00
14_A	58_D	1.065	1.00
14_A	18_Q	1.050	1.00
190_A	193_R	1.042	1.00
116_F	148_W	1.041	1.00
196_A	200_K	1.039	1.00
168_Y	172_Q	1.034	1.00
29_Y	33_Q	1.033	1.00
173_E	201_C	1.020	1.00
48_S	51_T	0.997	1.00
111_V	130_H	0.995	1.00
123_P	126_S	0.987	1.00
96_S	99_K	0.986	1.00
105_V	192_T	0.969	1.00
178_R	194_P	0.967	1.00
143_F	147_S	0.958	1.00
185_T	190_A	0.949	1.00
20_L	41_L	0.936	1.00
132_C	146_S	0.914	1.00
144_I	195_Q	0.912	1.00
107_E	130_H	0.910	1.00
99_K	102_K	0.907	1.00
97_Q	101_T	0.895	1.00
12_L	51_T	0.893	1.00
105_V	108_Q	0.891	1.00
145_D	148_W	0.890	1.00
34_Q	37_T	0.889	1.00
141_P	144_I	0.886	1.00
166_S	169_Q	0.876	1.00
32_G	66_I	0.870	1.00
129_F	180_V	0.869	1.00
41_L	56_I	0.864	1.00
107_E	110_R	0.863	1.00
137_L	143_F	0.861	1.00
70_G	73_T	0.859	1.00
105_V	112_S	0.855	1.00
13_Y	17_R	0.843	1.00
120_L	123_P	0.835	1.00
32_G	77_S	0.834	1.00
86_T	140_E	0.830	1.00
10_Q	14_A	0.824	1.00
54_K	58_D	0.822	1.00
181_S	184_K	0.822	1.00
98_G	101_T	0.818	1.00
105_V	109_E	0.817	1.00
42_C	52_I	0.817	1.00
102_K	105_V	0.816	1.00
88_S	91_T	0.812	1.00
104_K	112_S	0.811	1.00
89_G	92_D	0.810	1.00
182_D	187_D	0.806	1.00
127_E	151_L	0.804	1.00
18_Q	21_L	0.803	1.00
92_D	200_K	0.802	1.00
179_V	195_Q	0.799	1.00
95_V	98_G	0.796	1.00
38_E	67_R	0.790	1.00
28_V	44_Q	0.786	1.00
92_D	96_S	0.782	1.00
35_I	65_L	0.781	1.00
97_Q	100_A	0.780	1.00
13_Y	54_K	0.770	1.00
166_S	170_L	0.770	1.00
93_F	97_Q	0.765	1.00
110_R	114_A	0.763	1.00
115_P	119_K	0.761	1.00
106_I	110_R	0.761	1.00
178_R	181_S	0.759	1.00
191_A	201_C	0.754	1.00
95_V	99_K	0.753	1.00
16_V	19_R	0.753	1.00
102_K	106_I	0.753	1.00
94_G	99_K	0.749	1.00
100_A	103_E	0.745	1.00
189_F	192_T	0.745	1.00
23_D	26_Q	0.745	1.00
96_S	100_A	0.743	1.00
179_V	194_P	0.734	1.00
111_V	114_A	0.726	1.00
107_E	114_A	0.726	1.00
79_K	83_A	0.724	1.00
19_R	44_Q	0.723	1.00
101_T	105_V	0.718	1.00
18_Q	22_D	0.717	1.00
109_E	130_H	0.713	1.00
193_R	196_A	0.707	1.00
131_L	150_P	0.706	1.00
189_F	195_Q	0.705	1.00
31_A	76_Q	0.705	1.00
189_F	193_R	0.704	1.00
89_G	139_K	0.702	1.00
167_T	171_F	0.700	1.00
39_N	42_C	0.698	1.00
104_K	108_Q	0.697	1.00
178_R	190_A	0.695	1.00
38_E	73_T	0.687	1.00
43_T	46_N	0.687	1.00
121_N	124_G	0.685	1.00
194_P	197_K	0.685	1.00
108_Q	112_S	0.685	1.00
116_F	119_K	0.678	1.00
110_R	151_L	0.678	1.00
56_I	60_V	0.674	1.00
97_Q	102_K	0.673	1.00
29_Y	35_I	0.673	1.00
197_K	201_C	0.669	1.00
132_C	194_P	0.666	1.00
86_T	139_K	0.665	1.00
195_Q	198_W	0.665	1.00
119_K	122_I	0.664	1.00
152_S	155_P	0.662	1.00
126_S	152_S	0.660	1.00
120_L	184_K	0.657	1.00
131_L	143_F	0.656	1.00
141_P	145_D	0.655	1.00
167_T	170_L	0.654	1.00
92_D	196_A	0.652	1.00
102_K	139_K	0.652	1.00
157_F	160_I	0.650	1.00
94_G	98_G	0.642	1.00
195_Q	199_L	0.638	1.00
127_E	150_P	0.637	1.00
159_E	162_V	0.634	1.00
45_Y	52_I	0.632	1.00
109_E	113_A	0.630	1.00
158_D	161_Y	0.630	1.00
157_F	161_Y	0.629	1.00
110_R	113_A	0.626	1.00
107_E	111_V	0.624	1.00
86_T	91_T	0.619	1.00
177_T	180_V	0.617	1.00
83_A	141_P	0.617	1.00
170_L	173_E	0.616	1.00
134_V	150_P	0.616	1.00
127_E	154_Y	0.616	1.00
90_F	145_D	0.611	1.00
51_T	55_A	0.607	1.00
16_V	52_I	0.602	1.00
98_G	103_E	0.596	1.00
17_R	55_A	0.596	1.00
150_P	153_R	0.594	1.00
37_T	70_G	0.593	1.00
20_L	29_Y	0.592	1.00
126_S	130_H	0.590	1.00
126_S	176_D	0.590	1.00
106_I	109_E	0.586	1.00
81_E	85_L	0.583	1.00
130_H	198_W	0.583	1.00
91_T	95_V	0.582	1.00
137_L	142_L	0.582	1.00
9_H	15_T	0.581	1.00
42_C	49_R	0.581	1.00
87_V	91_T	0.578	1.00
127_E	131_L	0.577	1.00
42_C	45_Y	0.574	1.00
39_N	49_R	0.574	1.00
16_V	55_A	0.573	1.00
111_V	116_F	0.572	1.00
94_G	97_Q	0.569	1.00
171_F	177_T	0.567	1.00
119_K	123_P	0.567	1.00
88_S	92_D	0.565	1.00
182_D	194_P	0.564	1.00
57_S	73_T	0.564	1.00
154_Y	158_D	0.561	1.00
108_Q	111_V	0.561	1.00
93_F	101_T	0.560	1.00
99_K	138_D	0.559	1.00
104_K	111_V	0.557	1.00
191_A	195_Q	0.554	1.00
74_F	77_S	0.553	1.00
69_Q	72_G	0.553	1.00
42_C	50_I	0.548	1.00
93_F	98_G	0.547	1.00
104_K	109_E	0.545	1.00
109_E	184_K	0.543	1.00
179_V	191_A	0.543	1.00
101_T	104_K	0.542	1.00
176_D	198_W	0.542	1.00
86_T	89_G	0.539	1.00
178_R	197_K	0.533	1.00
146_S	195_Q	0.532	1.00
108_Q	129_F	0.530	1.00
95_V	102_K	0.530	1.00
178_R	182_D	0.530	1.00
22_D	28_V	0.527	1.00
51_T	54_K	0.526	1.00
112_S	127_E	0.522	1.00
60_V	73_T	0.519	1.00
100_A	104_K	0.518	1.00
128_V	131_L	0.518	1.00
169_Q	172_Q	0.517	1.00
93_F	96_S	0.517	1.00
50_I	54_K	0.516	1.00
41_L	45_Y	0.512	1.00
34_Q	71_K	0.508	1.00
95_V	101_T	0.507	1.00
136_Y	139_K	0.506	1.00
147_S	150_P	0.506	1.00
160_I	163_E	0.500	1.00
124_G	128_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
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
4u0wA	2	0.9918	100	0.165	Contact Map
2ra5A	2	0.6049	100	0.184	Contact Map
3f8mA	2	0.9342	100	0.198	Contact Map
3eetA	2	0.9547	100	0.221	Contact Map
3edpA	2	0.9053	100	0.227	Contact Map
3bwgA	2	0.9342	100	0.227	Contact Map
1hw1A	2	0.8313	100	0.399	Contact Map
2di3A	2	0.8313	100	0.411	Contact Map
3sxyA	2	0.786	100	0.413	Contact Map
2hs5A	1	0.8148	100	0.413	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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