LLDR - ECOLI - GREMLIN Contacts

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LLDR - Putative L-lactate dehydrogenase operon regulatory protein

UniProt:	P0ACL7	Sequences: MIVLPRRLSDEVADRVRALIDEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFIRWRHDTWSEQNIVQPLKTLMADDPDYSFDILEARYAIEASTAWHAAMRATPGDKEKIQLCFEATLSEDPDIASQADVRFHLAIAEASHNIVLLQTMRGFFDVLQSSVKHSRQRMYLVPPVFSQLTEQHQAVIDAIFAGDADGARKAMMAHLSFVHTTMKRFDEDQARHARITRLPGEHNEHSREKNA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11962
Length:	258 (202)
Sequences:	22250 (16236)
Seq/√Len:	1142.4

ECOLI - LLDR PDHR EXUR GLCC FADR UXUR NANR DGOR YIEP YDFH YJJM MCBR CSIR FRLR YEGW YIDP
BACSU - YCBG GNTR YDHC LUTR YVOA YMFC TRER YURK
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
129_Q	207_F	3.596	1.00
114_W	215_R	3.294	1.00
210_D	213_G	2.913	1.00
136_L	200_Q	2.764	1.00
19_L	24_N	2.730	1.00
26_E	29_M	2.700	1.00
19_L	40_Q	2.377	1.00
107_A	111_S	2.335	1.00
127_K	153_A	2.256	1.00
34_E	45_R	2.223	1.00
100_D	161_I	2.169	1.00
13_A	54_K	2.084	1.00
106_Y	223_S	2.077	1.00
62_L	72_R	1.996	1.00
118_M	211_A	1.992	1.00
12_V	43_V	1.976	1.00
17_R	58_E	1.955	1.00
103_E	115_H	1.940	1.00
125_K	207_F	1.847	1.00
124_D	159_H	1.829	1.00
12_V	41_L	1.787	1.00
205_A	213_G	1.779	1.00
156_E	164_L	1.773	1.00
153_A	156_E	1.753	1.00
63_S	69_T	1.741	1.00
121_T	124_D	1.713	1.00
15_R	19_L	1.685	1.00
110_A	219_M	1.684	1.00
132_F	203_I	1.661	1.00
198_Q	224_F	1.636	1.00
139_D	142_I	1.633	1.00
114_W	211_A	1.632	1.00
104_A	166_T	1.629	1.00
213_G	217_A	1.589	1.00
111_S	114_W	1.562	1.00
215_R	219_M	1.559	1.00
110_A	215_R	1.550	1.00
18_A	22_E	1.531	1.00
201_A	217_A	1.500	1.00
6_R	14_D	1.495	1.00
113_A	214_A	1.454	1.00
151_H	199_H	1.421	1.00
64_R	67_G	1.418	1.00
152_L	168_R	1.413	1.00
106_Y	219_M	1.413	1.00
155_A	167_M	1.405	1.00
165_Q	169_G	1.403	1.00
162_V	173_V	1.403	1.00
129_Q	203_I	1.401	1.00
204_D	208_A	1.391	1.00
124_D	157_A	1.385	1.00
13_A	58_E	1.383	1.00
131_C	146_A	1.367	1.00
134_A	146_A	1.352	1.00
136_L	196_T	1.348	1.00
208_A	213_G	1.337	1.00
106_Y	226_H	1.335	1.00
200_Q	204_D	1.315	1.00
120_A	125_K	1.305	1.00
211_A	215_R	1.301	1.00
35_R	39_M	1.299	1.00
100_D	162_V	1.285	1.00
129_Q	133_E	1.280	1.00
130_L	134_A	1.223	1.00
134_A	149_R	1.214	1.00
99_F	230_K	1.210	1.00
36_Q	40_Q	1.207	1.00
37_L	48_L	1.192	1.00
132_F	200_Q	1.188	1.00
216_K	220_A	1.181	1.00
30_K	70_F	1.176	1.00
11_E	15_R	1.169	1.00
131_C	153_A	1.169	1.00
64_R	70_F	1.166	1.00
106_Y	110_A	1.165	1.00
99_F	226_H	1.155	1.00
198_Q	221_H	1.154	1.00
152_L	156_E	1.148	1.00
132_F	135_T	1.134	1.00
33_A	36_Q	1.134	1.00
149_R	153_A	1.134	1.00
15_R	18_A	1.132	1.00
120_A	209_G	1.129	1.00
219_M	223_S	1.128	1.00
120_A	157_A	1.125	1.00
120_A	124_D	1.122	1.00
114_W	212_D	1.119	1.00
15_R	41_L	1.118	1.00
110_A	114_W	1.115	1.00
154_I	206_I	1.115	1.00
56_V	63_S	1.110	1.00
105_R	109_E	1.109	1.00
19_L	41_L	1.108	1.00
213_G	216_K	1.103	1.00
112_T	155_A	1.098	1.00
113_A	218_M	1.096	1.00
113_A	117_A	1.086	1.00
100_D	160_N	1.084	1.00
125_K	209_G	1.081	1.00
226_H	230_K	1.075	1.00
125_K	203_I	1.065	1.00
131_C	149_R	1.063	1.00
204_D	207_F	1.062	1.00
142_I	145_Q	1.061	1.00
132_F	136_L	1.050	1.00
153_A	157_A	1.046	1.00
203_I	207_F	1.041	1.00
146_A	149_R	1.024	1.00
103_E	160_N	1.023	1.00
25_L	71_I	1.019	1.00
147_D	151_H	1.018	1.00
166_T	169_G	1.018	1.00
127_K	156_E	1.018	1.00
56_V	61_L	1.011	1.00
151_H	221_H	0.991	1.00
129_Q	200_Q	0.989	1.00
6_R	11_E	0.985	1.00
115_H	119_R	0.977	1.00
50_E	53_A	0.977	1.00
117_A	211_A	0.977	1.00
127_K	130_L	0.973	1.00
133_E	136_L	0.973	1.00
62_L	70_F	0.969	1.00
111_S	215_R	0.968	1.00
150_F	203_I	0.967	1.00
19_L	25_L	0.965	1.00
205_A	210_D	0.961	1.00
94_D	97_Y	0.960	1.00
201_A	220_A	0.942	1.00
127_K	131_C	0.931	1.00
109_E	151_H	0.928	1.00
126_E	130_L	0.927	1.00
201_A	213_G	0.919	1.00
199_H	221_H	0.919	1.00
52_L	69_T	0.917	1.00
34_E	49_R	0.915	1.00
9_S	54_K	0.911	1.00
20_I	71_I	0.902	1.00
202_V	218_M	0.902	1.00
145_Q	149_R	0.901	1.00
197_E	201_A	0.899	1.00
61_L	69_T	0.895	1.00
158_S	164_L	0.894	1.00
117_A	206_I	0.893	1.00
30_K	68_G	0.890	1.00
164_L	168_R	0.889	1.00
54_K	57_S	0.884	1.00
64_R	68_G	0.883	1.00
119_R	159_H	0.878	1.00
131_C	134_A	0.875	1.00
111_S	115_H	0.871	1.00
13_A	17_R	0.863	1.00
201_A	204_D	0.859	1.00
212_D	216_K	0.852	1.00
134_A	137_S	0.849	1.00
104_A	162_V	0.848	1.00
17_R	60_V	0.847	1.00
120_A	206_I	0.846	1.00
116_A	157_A	0.845	1.00
38_A	48_L	0.845	1.00
17_R	21_D	0.845	1.00
105_R	222_L	0.834	1.00
96_D	100_D	0.831	1.00
196_T	200_Q	0.831	1.00
122_P	126_E	0.828	1.00
97_Y	162_V	0.819	1.00
67_G	70_F	0.819	1.00
212_D	215_R	0.817	1.00
133_E	137_S	0.815	1.00
129_Q	204_D	0.812	1.00
53_A	56_V	0.803	1.00
96_D	159_H	0.803	1.00
125_K	129_Q	0.802	1.00
147_D	199_H	0.801	1.00
117_A	209_G	0.801	1.00
201_A	205_A	0.800	1.00
44_S	47_S	0.797	1.00
115_H	118_M	0.797	1.00
116_A	120_A	0.795	1.00
36_Q	39_M	0.794	1.00
122_P	209_G	0.793	1.00
52_L	61_L	0.790	1.00
202_V	217_A	0.777	1.00
53_A	63_S	0.773	1.00
7_R	10_D	0.773	1.00
133_E	200_Q	0.771	1.00
128_I	153_A	0.770	1.00
117_A	214_A	0.769	1.00
124_D	127_K	0.766	1.00
126_E	207_F	0.763	1.00
8_L	47_S	0.760	1.00
205_A	217_A	0.755	1.00
8_L	11_E	0.754	1.00
10_D	54_K	0.753	1.00
114_W	118_M	0.750	1.00
162_V	165_Q	0.749	1.00
223_S	227_T	0.744	1.00
217_A	220_A	0.742	1.00
135_T	143_A	0.740	1.00
103_E	226_H	0.736	1.00
162_V	166_T	0.735	1.00
193_S	197_E	0.732	1.00
152_L	171_F	0.727	1.00
102_L	225_V	0.725	1.00
37_L	52_L	0.724	1.00
128_I	203_I	0.721	1.00
202_V	214_A	0.720	1.00
104_A	163_L	0.719	1.00
30_K	33_A	0.717	1.00
115_H	160_N	0.711	1.00
216_K	219_M	0.709	1.00
103_E	119_R	0.708	1.00
9_S	13_A	0.706	1.00
126_E	129_Q	0.700	1.00
148_V	175_Q	0.694	1.00
54_K	58_E	0.685	1.00
142_I	146_A	0.682	1.00
223_S	226_H	0.682	1.00
43_V	48_L	0.681	1.00
104_A	112_T	0.678	1.00
127_K	149_R	0.675	1.00
148_V	171_F	0.669	1.00
149_R	152_L	0.666	1.00
220_A	224_F	0.665	1.00
134_A	142_I	0.660	1.00
224_F	228_T	0.660	1.00
124_D	153_A	0.659	1.00
152_L	164_L	0.656	1.00
24_N	40_Q	0.654	1.00
47_S	51_A	0.649	1.00
202_V	221_H	0.639	1.00
132_F	196_T	0.634	1.00
103_E	111_S	0.634	1.00
198_Q	201_A	0.630	1.00
19_L	23_K	0.623	1.00
113_A	211_A	0.621	1.00
130_L	133_E	0.619	1.00
107_A	163_L	0.619	1.00
125_K	206_I	0.619	1.00
25_L	29_M	0.619	1.00
27_A	73_W	0.613	1.00
104_A	108_I	0.610	1.00
116_A	154_I	0.607	1.00
112_T	158_S	0.604	1.00
227_T	230_K	0.602	1.00
97_Y	161_I	0.601	1.00
143_A	195_L	0.601	1.00
116_A	158_S	0.599	1.00
112_T	163_L	0.599	1.00
9_S	50_E	0.599	1.00
106_Y	222_L	0.598	1.00
124_D	156_E	0.595	1.00
31_L	61_L	0.580	1.00
97_Y	100_D	0.576	1.00
165_Q	173_V	0.576	1.00
128_I	157_A	0.572	1.00
41_L	48_L	0.570	1.00
66_G	69_T	0.570	1.00
6_R	10_D	0.567	1.00
109_E	199_H	0.563	1.00
114_W	219_M	0.560	1.00
113_A	154_I	0.557	1.00
107_A	110_A	0.557	1.00
110_A	211_A	0.553	1.00
110_A	218_M	0.551	1.00
108_I	167_M	0.550	1.00
35_R	38_A	0.549	1.00
135_T	196_T	0.549	1.00
122_P	207_F	0.546	1.00
70_F	73_W	0.542	1.00
227_T	231_R	0.537	1.00
111_S	163_L	0.537	1.00
197_E	200_Q	0.535	1.00
28_G	73_W	0.534	1.00
21_D	60_V	0.533	1.00
202_V	205_A	0.532	1.00
109_E	222_L	0.532	1.00
103_E	106_Y	0.531	1.00
128_I	132_F	0.528	1.00
72_R	176_S	0.527	1.00
129_Q	132_F	0.526	1.00
19_L	22_E	0.525	1.00
115_H	158_S	0.520	1.00
123_G	127_K	0.519	1.00
148_V	152_L	0.518	1.00
96_D	99_F	0.517	1.00
191_V	194_Q	0.517	1.00
220_A	223_S	0.513	1.00
65_R	68_G	0.513	1.00
95_P	99_F	0.511	1.00
198_Q	220_A	0.511	1.00
39_M	42_G	0.510	1.00
95_P	230_K	0.510	1.00
96_D	161_I	0.509	1.00
117_A	218_M	0.509	1.00
155_A	171_F	0.508	1.00
16_V	37_L	0.508	1.00
165_Q	168_R	0.507	1.00
53_A	57_S	0.507	1.00
110_A	113_A	0.503	1.00
191_V	228_T	0.503	1.00
25_L	31_L	0.501	1.00
10_D	14_D	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
4p96A	2	0.9302	100	0.218	Contact Map
3sxyA	2	0.7674	100	0.241	Contact Map
3c7jA	4	0.8411	100	0.243	Contact Map
2di3A	2	0.8721	100	0.243	Contact Map
2hs5A	1	0.7868	100	0.245	Contact Map
3ihuA	1	0.7752	100	0.254	Contact Map
1hw1A	2	0.876	100	0.254	Contact Map
4p9fA	1	0.8023	100	0.256	Contact Map
3ic7A	2	0.4302	99.9	0.572	Contact Map
3by6A	2	0.469	99.8	0.573	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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