GLTC - BACSU - GREMLIN Contacts

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GLTC - HTH-type transcriptional regulator GltC

UniProt:	P20668	Sequences: MELRQLRYFMEVAEREHVSEAADHLHVAQSAISRQIANLEEELNVTLFEREGRNIKLTPIGKEFLIHVKTAMKAIDYAKEQIDEYLDPHRGTVKIGFPTSLASQLLPTVISAFKEEYPHVEFLLRQGSYKFLIEAVRNRDIDLALLGPVPTNFSDITGKILFTEKIYALVPLNHPLAKQKTVHLIDLRNDQFVLFPEGFVLREMAIDTCKQAGFAPLVSTEGEDLDAIKGLVSAGMGVTLLPESTFAETTPRFTVKIPIEFPQVKRTVGIIKPKNRELAPSANDFYEFVIQFFSKLEQYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	300 (286)
Sequences:	79862 (58032)
Seq/√Len:	3431.5

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

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_T	74_A	3.668	1.00
15_R	24_H	3.446	1.00
159_K	290_I	2.730	1.00
96_G	141_I	2.617	1.00
67_H	81_Q	2.493	1.00
11_E	24_H	2.356	1.00
232_V	239_T	2.313	1.00
174_H	190_D	2.248	1.00
160_I	163_T	2.243	1.00
92_T	123_L	2.241	1.00
163_T	267_T	2.235	1.00
160_I	267_T	2.155	1.00
165_K	243_E	2.143	1.00
92_T	121_E	2.114	1.00
20_E	23_D	2.113	1.00
45_V	60_I	2.112	1.00
8_Y	35_Q	2.110	1.00
163_T	265_K	2.083	1.00
14_E	69_K	2.045	1.00
67_H	74_A	2.031	1.00
112_A	288_F	2.021	1.00
10_M	69_K	2.019	1.00
229_K	249_T	2.018	1.00
183_H	186_D	2.016	1.00
94_K	123_L	1.994	1.00
10_M	65_L	1.992	1.00
10_M	14_E	1.976	1.00
167_Y	243_E	1.952	1.00
11_E	14_E	1.943	1.00
11_E	15_R	1.941	1.00
193_V	237_G	1.929	1.00
8_Y	32_I	1.923	1.00
13_A	57_L	1.912	1.00
71_A	75_I	1.897	1.00
65_L	69_K	1.852	1.00
18_V	36_I	1.777	1.00
233_S	249_T	1.754	1.00
64_F	78_A	1.751	1.00
191_Q	219_S	1.744	1.00
49_E	56_K	1.739	1.00
179_Q	186_D	1.710	1.00
63_E	81_Q	1.707	1.00
158_G	269_G	1.696	1.00
135_A	140_D	1.671	1.00
13_A	65_L	1.649	1.00
233_S	254_T	1.641	1.00
170_V	257_I	1.634	1.00
15_R	20_E	1.617	1.00
113_F	285_F	1.615	1.00
14_E	24_H	1.603	1.00
10_M	68_V	1.586	1.00
157_T	274_K	1.571	1.00
9_F	65_L	1.555	1.00
5_Q	35_Q	1.547	1.00
8_Y	27_V	1.535	1.00
134_E	138_N	1.530	1.00
159_K	272_K	1.512	1.00
67_H	70_T	1.509	1.00
113_F	120_V	1.508	1.00
17_H	20_E	1.505	1.00
5_Q	42_E	1.496	1.00
19_S	29_Q	1.495	1.00
88_P	119_H	1.491	1.00
28_A	31_A	1.488	1.00
5_Q	38_N	1.482	1.00
202_R	206_I	1.469	1.00
59_P	62_K	1.466	1.00
46_T	49_E	1.460	1.00
11_E	25_L	1.448	1.00
146_L	271_I	1.446	1.00
286_Y	290_I	1.434	1.00
278_L	282_A	1.425	1.00
157_T	272_K	1.422	1.00
103_S	226_D	1.418	1.00
10_M	72_M	1.411	1.00
67_H	77_Y	1.409	1.00
71_A	78_A	1.391	1.00
90_R	119_H	1.365	1.00
136_V	144_A	1.360	1.00
272_K	286_Y	1.358	1.00
51_E	56_K	1.354	1.00
94_K	125_R	1.353	1.00
135_A	141_I	1.345	1.00
164_E	244_S	1.331	1.00
284_D	287_E	1.329	1.00
64_F	79_K	1.325	1.00
270_I	286_Y	1.320	1.00
116_E	288_F	1.320	1.00
74_A	77_Y	1.316	1.00
137_R	155_D	1.313	1.00
112_A	116_E	1.307	1.00
143_L	282_A	1.303	1.00
3_L	75_I	1.301	1.00
143_L	270_I	1.286	1.00
170_V	238_V	1.285	1.00
228_I	239_T	1.285	1.00
42_E	79_K	1.277	1.00
114_K	219_S	1.276	1.00
66_I	70_T	1.274	1.00
190_D	238_V	1.272	1.00
230_G	233_S	1.256	1.00
67_H	78_A	1.250	1.00
63_E	66_I	1.229	1.00
160_I	269_G	1.217	1.00
114_K	191_Q	1.212	1.00
9_F	48_F	1.210	1.00
111_S	115_E	1.205	1.00
243_E	247_A	1.194	1.00
62_K	66_I	1.183	1.00
37_A	41_E	1.183	1.00
27_V	31_A	1.178	1.00
158_G	271_I	1.176	1.00
34_R	38_N	1.173	1.00
175_P	190_D	1.171	1.00
9_F	13_A	1.165	1.00
249_T	254_T	1.165	1.00
111_S	234_A	1.148	1.00
123_L	221_E	1.140	1.00
127_G	135_A	1.140	1.00
34_R	37_A	1.134	1.00
209_C	214_F	1.126	1.00
193_V	228_I	1.118	1.00
9_F	47_L	1.114	1.00
112_A	115_E	1.113	1.00
191_Q	217_L	1.112	1.00
181_T	260_E	1.106	1.00
70_T	77_Y	1.104	1.00
102_A	126_Q	1.103	1.00
33_S	37_A	1.102	1.00
287_E	290_I	1.100	1.00
6_L	68_V	1.099	1.00
117_Y	284_D	1.098	1.00
18_V	55_I	1.097	1.00
63_E	67_H	1.093	1.00
113_F	288_F	1.086	1.00
222_G	228_I	1.084	1.00
93_V	285_F	1.081	1.00
11_E	21_A	1.079	1.00
108_T	234_A	1.077	1.00
12_V	21_A	1.076	1.00
159_K	286_Y	1.069	1.00
71_A	74_A	1.065	1.00
182_V	186_D	1.060	1.00
283_N	287_E	1.058	1.00
229_K	233_S	1.054	1.00
137_R	153_F	1.049	1.00
109_V	289_V	1.043	1.00
35_Q	38_N	1.042	1.00
171_P	235_G	1.041	1.00
7_R	76_D	1.040	1.00
230_G	234_A	1.038	1.00
4_R	7_R	1.036	1.00
203_E	206_I	1.034	1.00
57_L	61_G	1.033	1.00
79_K	83_D	1.030	1.00
165_K	265_K	1.020	1.00
247_A	251_P	1.015	1.00
180_K	256_K	1.009	1.00
248_E	252_R	1.001	1.00
169_L	246_F	0.998	1.00
64_F	68_V	0.993	1.00
8_Y	25_L	0.992	1.00
27_V	32_I	0.986	1.00
12_V	18_V	0.984	1.00
13_A	48_F	0.983	1.00
73_K	77_Y	0.981	1.00
76_D	80_E	0.980	1.00
168_A	238_V	0.980	1.00
194_L	218_V	0.979	1.00
76_D	79_K	0.967	1.00
288_F	291_Q	0.965	1.00
113_F	117_Y	0.964	1.00
9_F	57_L	0.962	1.00
172_L	253_F	0.955	1.00
125_R	135_A	0.954	1.00
135_A	138_N	0.946	1.00
38_N	41_E	0.944	1.00
222_G	231_L	0.941	1.00
170_V	174_H	0.939	1.00
21_A	32_I	0.938	1.00
116_E	291_Q	0.938	1.00
174_H	177_A	0.937	1.00
109_V	288_F	0.930	1.00
279_A	282_A	0.927	1.00
96_G	144_A	0.926	1.00
9_F	39_L	0.922	1.00
48_F	55_I	0.915	1.00
20_E	24_H	0.910	1.00
45_V	82_I	0.896	1.00
203_E	207_D	0.895	1.00
141_I	144_A	0.894	1.00
13_A	61_G	0.890	1.00
121_E	217_L	0.887	1.00
70_T	73_K	0.882	1.00
99_T	224_D	0.881	1.00
66_I	69_K	0.878	1.00
16_E	56_K	0.877	1.00
174_H	178_K	0.876	1.00
170_V	175_P	0.865	1.00
191_Q	218_V	0.865	1.00
273_P	276_R	0.864	1.00
19_S	23_D	0.864	1.00
178_K	191_Q	0.862	1.00
25_L	32_I	0.860	1.00
174_H	191_Q	0.858	1.00
95_I	143_L	0.855	1.00
120_V	281_S	0.851	1.00
156_I	271_I	0.851	1.00
175_P	180_K	0.850	1.00
96_G	146_L	0.849	1.00
186_D	189_N	0.849	1.00
157_T	160_I	0.848	1.00
155_D	274_K	0.844	1.00
249_T	252_R	0.836	1.00
51_E	54_N	0.836	1.00
125_R	141_I	0.827	1.00
60_I	82_I	0.826	1.00
169_L	239_T	0.826	1.00
176_L	190_D	0.822	1.00
75_I	79_K	0.821	1.00
278_L	283_N	0.819	1.00
287_E	291_Q	0.817	1.00
172_L	255_V	0.815	1.00
246_F	249_T	0.814	1.00
111_S	236_M	0.813	1.00
16_E	62_K	0.812	1.00
29_Q	33_S	0.809	1.00
9_F	64_F	0.807	1.00
91_G	281_S	0.806	1.00
4_R	35_Q	0.803	1.00
205_A	209_C	0.802	1.00
165_K	258_P	0.802	1.00
74_A	78_A	0.799	1.00
63_E	85_Y	0.799	1.00
12_V	48_F	0.798	1.00
13_A	16_E	0.798	1.00
114_K	236_M	0.794	1.00
37_A	46_T	0.794	1.00
75_I	78_A	0.792	1.00
3_L	72_M	0.792	1.00
185_I	188_R	0.792	1.00
149_V	269_G	0.791	1.00
12_V	36_I	0.789	1.00
15_R	21_A	0.787	1.00
14_E	65_L	0.787	1.00
171_P	236_M	0.787	1.00
60_I	63_E	0.786	1.00
165_K	263_Q	0.784	1.00
208_T	212_A	0.783	1.00
77_Y	81_Q	0.781	1.00
16_E	54_N	0.780	1.00
91_G	120_V	0.778	1.00
133_I	137_R	0.777	1.00
280_P	284_D	0.774	1.00
5_Q	8_Y	0.767	1.00
192_F	216_P	0.766	1.00
173_N	177_A	0.763	1.00
7_R	11_E	0.762	1.00
231_L	236_M	0.760	1.00
143_L	285_F	0.758	1.00
83_D	86_L	0.753	1.00
183_H	260_E	0.752	1.00
169_L	241_L	0.749	1.00
89_H	117_Y	0.747	1.00
184_L	261_F	0.746	1.00
68_V	71_A	0.746	1.00
97_F	102_A	0.744	1.00
78_A	82_I	0.742	1.00
60_I	85_Y	0.739	1.00
257_I	260_E	0.738	1.00
113_F	284_D	0.738	1.00
137_R	156_I	0.738	1.00
18_V	32_I	0.738	1.00
49_E	58_T	0.736	1.00
116_E	284_D	0.735	1.00
233_S	253_F	0.735	1.00
12_V	32_I	0.730	1.00
69_K	73_K	0.724	1.00
188_R	214_F	0.721	1.00
56_K	62_K	0.717	1.00
57_L	62_K	0.714	1.00
60_I	64_F	0.712	1.00
224_D	227_A	0.712	1.00
208_T	211_Q	0.710	1.00
31_A	35_Q	0.710	1.00
242_P	245_T	0.705	1.00
62_K	65_L	0.702	1.00
171_P	174_H	0.701	1.00
94_K	141_I	0.701	1.00
185_I	212_A	0.697	1.00
94_K	142_D	0.695	1.00
204_M	208_T	0.691	1.00
196_P	221_E	0.689	1.00
169_L	250_T	0.688	1.00
170_V	176_L	0.687	1.00
142_D	282_A	0.686	1.00
202_R	221_E	0.685	1.00
59_P	63_E	0.682	1.00
7_R	10_M	0.681	1.00
139_R	273_P	0.680	1.00
207_D	211_Q	0.679	1.00
246_F	250_T	0.678	1.00
40_E	45_V	0.678	1.00
284_D	288_F	0.676	1.00
64_F	82_I	0.674	1.00
49_E	54_N	0.673	1.00
103_S	230_G	0.668	1.00
97_F	106_L	0.666	1.00
195_F	228_I	0.665	1.00
173_N	235_G	0.663	1.00
176_L	179_Q	0.661	1.00
189_N	217_L	0.659	1.00
112_A	291_Q	0.658	1.00
73_K	76_D	0.656	1.00
220_T	231_L	0.655	1.00
173_N	176_L	0.655	1.00
192_F	238_V	0.652	1.00
40_E	50_R	0.651	1.00
205_A	208_T	0.650	1.00
77_Y	80_E	0.648	1.00
23_D	26_H	0.646	1.00
67_H	71_A	0.644	1.00
68_V	72_M	0.639	1.00
206_I	210_K	0.638	1.00
36_I	40_E	0.637	1.00
248_E	251_P	0.636	1.00
168_A	187_L	0.632	1.00
93_V	281_S	0.630	1.00
126_Q	223_E	0.629	1.00
121_E	221_E	0.628	1.00
12_V	17_H	0.628	1.00
207_D	210_K	0.626	1.00
276_R	279_A	0.626	1.00
18_V	54_N	0.625	1.00
172_L	254_T	0.625	1.00
145_L	289_V	0.624	1.00
280_P	283_N	0.619	1.00
21_A	25_L	0.618	1.00
99_T	128_S	0.617	1.00
201_L	205_A	0.616	1.00
168_A	240_L	0.611	1.00
196_P	223_E	0.610	1.00
108_T	111_S	0.610	1.00
4_R	38_N	0.609	1.00
106_L	109_V	0.604	1.00
63_E	82_I	0.603	1.00
136_V	271_I	0.602	1.00
147_G	266_R	0.602	1.00
203_E	208_T	0.599	1.00
175_P	179_Q	0.598	1.00
143_L	286_Y	0.596	1.00
80_E	84_E	0.595	1.00
93_V	143_L	0.595	1.00
31_A	34_R	0.595	1.00
7_R	72_M	0.594	1.00
168_A	192_F	0.593	1.00
90_R	121_E	0.593	1.00
285_F	289_V	0.592	1.00
162_F	268_V	0.592	1.00
228_I	232_V	0.591	1.00
209_C	216_P	0.591	1.00
204_M	207_D	0.590	1.00
4_R	8_Y	0.587	1.00
136_V	156_I	0.586	1.00
30_S	34_R	0.583	1.00
43_L	64_F	0.582	1.00
96_G	127_G	0.581	1.00
206_I	209_C	0.581	1.00
48_F	57_L	0.578	1.00
164_E	266_R	0.577	1.00
149_V	267_T	0.576	1.00
43_L	82_I	0.576	1.00
45_V	49_E	0.575	1.00
126_Q	224_D	0.574	1.00
108_T	112_A	0.571	1.00
222_G	227_A	0.571	1.00
28_A	34_R	0.569	1.00
9_F	61_G	0.567	1.00
166_I	240_L	0.567	1.00
57_L	65_L	0.564	1.00
72_M	76_D	0.564	1.00
176_L	182_V	0.562	1.00
231_L	237_G	0.562	1.00
157_T	275_N	0.561	1.00
172_L	256_K	0.559	1.00
202_R	205_A	0.558	1.00
272_K	283_N	0.556	1.00
8_Y	36_I	0.556	1.00
149_V	153_F	0.555	1.00
96_G	125_R	0.555	1.00
201_L	204_M	0.554	1.00
117_Y	120_V	0.551	1.00
241_L	246_F	0.549	1.00
110_I	122_F	0.547	1.00
91_G	119_H	0.545	1.00
43_L	46_T	0.545	1.00
197_E	221_E	0.545	1.00
183_H	261_F	0.544	1.00
101_L	105_L	0.544	1.00
18_V	29_Q	0.542	1.00
169_L	256_K	0.542	1.00
174_H	238_V	0.539	1.00
46_T	60_I	0.535	1.00
66_I	81_Q	0.535	1.00
225_L	242_P	0.534	1.00
233_S	251_P	0.533	1.00
170_V	177_A	0.533	1.00
161_L	270_I	0.530	1.00
115_E	177_A	0.529	1.00
103_S	224_D	0.528	1.00
105_L	109_V	0.528	1.00
13_A	62_K	0.528	1.00
72_M	75_I	0.527	1.00
27_V	35_Q	0.522	1.00
8_Y	21_A	0.521	1.00
181_T	258_P	0.520	1.00
175_P	178_K	0.520	1.00
181_T	186_D	0.519	1.00
80_E	83_D	0.517	1.00
97_F	124_L	0.516	1.00
108_T	230_G	0.515	1.00
134_E	140_D	0.512	1.00
16_E	55_I	0.512	1.00
84_E	89_H	0.509	1.00
36_I	48_F	0.508	1.00
282_A	286_Y	0.506	1.00
67_H	82_I	0.506	1.00
18_V	50_R	0.506	1.00
145_L	270_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
1ixcA	4	0.9733	100	0.081	Contact Map
1al3A	1	0.7133	100	0.086	Contact Map
3fzvA	4	0.9533	100	0.087	Contact Map
2esnA	3	0.9733	100	0.09	Contact Map
4x6gA	4	0.9967	100	0.09	Contact Map
1uthA	2	0.7533	100	0.091	Contact Map
2h98A	2	0.69	100	0.095	Contact Map
3fxqA	3	0.97	100	0.098	Contact Map
2h9bA	2	0.6933	100	0.1	Contact Map
3szpA	3	0.9633	100	0.112	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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