DSDC - ECOLI - GREMLIN Contacts

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DSDC - HTH-type transcriptional regulator DsdC

UniProt:	P46068	Sequences: MEPLREIRNRLLNGWQLSKMHTFEVAARHQSFALAAEELSLSPSAVSHRINQLEEELGIQLFVRSHRKVELTHEGKRVYWALKSSLDTLNQEILDIKNQELSGTLTLYSRPSIAQCWLVPALGDFTRRYPSISLTVLTGNDNVNLQRAGIDLAIYFDDAPSAQLTHHFLMDEEILPVCSPEYAQRHALTNTVINLCHCTLLHDRQAWSNDSGTDEWHSWAQHYAVNLPTSSGIGFDRSDLAVIAAMNHIGVAMGRKRLVQKRLASGELVAPFGDMTVKCHQHYYITTLPGRQWPKIEAFIIWLREQVKTTS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13161
Length:	311 (286)
Sequences:	79490 (57660)
Seq/√Len:	3409.5

ECOLI - DSDC PGRR TTDR AAER OXYR YBEF YDCI YAFC DMLR GCVA YBDO LYSR LEUO YIDZ TDCA YHJC YCAN CYSB NAC NHAR CYNR YNEJ ABGR YFIE CBL YEIE YBHD XAPR HCAR ICIA METR YFER YIAU YAHB YDHB ILVY YEEY ALLS YHAJ PERR YNFL YGFI YJIE LRHA HDFR
BACSU - CYSL GLTC YWBI GLTR YCGK YYBE BSDA YWQM ALSR YVBU CITR YTLI YOFA YUST YKUM CZCR 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
84_S	88_T	3.731	1.00
29_H	38_E	3.412	1.00
25_V	38_E	2.685	1.00
167_H	304_R	2.613	1.00
81_A	95_D	2.607	1.00
168_F	281_Q	2.488	1.00
108_Y	150_I	2.377	1.00
59_I	74_E	2.338	1.00
24_E	83_K	2.302	1.00
175_L	256_K	2.241	1.00
171_D	281_Q	2.229	1.00
104_T	135_T	2.206	1.00
168_F	171_D	2.200	1.00
24_E	28_R	2.193	1.00
81_A	88_T	2.159	1.00
22_T	49_R	2.139	1.00
25_V	29_H	2.138	1.00
182_Y	198_C	2.043	1.00
104_T	133_S	2.041	1.00
124_D	302_W	2.016	1.00
245_A	252_A	2.010	1.00
106_T	135_T	1.995	1.00
173_E	256_K	1.995	1.00
27_A	71_L	1.962	1.00
171_D	279_C	1.961	1.00
85_S	89_L	1.934	1.00
191_T	194_N	1.908	1.00
175_L	270_A	1.899	1.00
79_Y	83_K	1.882	1.00
25_V	28_R	1.874	1.00
22_T	46_V	1.868	1.00
246_M	267_E	1.859	1.00
242_V	262_R	1.852	1.00
28_R	83_K	1.843	1.00
27_A	79_Y	1.841	1.00
34_L	37_E	1.833	1.00
24_E	79_Y	1.817	1.00
246_M	262_R	1.814	1.00
199_T	232_G	1.774	1.00
166_H	283_Y	1.749	1.00
81_A	84_S	1.748	1.00
201_L	250_G	1.733	1.00
77_R	95_D	1.725	1.00
29_H	34_L	1.685	1.00
63_V	70_E	1.657	1.00
31_S	34_L	1.633	1.00
144_N	149_G	1.618	1.00
178_C	271_P	1.614	1.00
167_H	286_T	1.572	1.00
78_V	92_E	1.565	1.00
19_K	56_E	1.551	1.00
165_T	288_L	1.534	1.00
24_E	82_L	1.529	1.00
115_Q	239_D	1.507	1.00
286_T	300_I	1.504	1.00
81_A	91_Q	1.504	1.00
65_S	70_E	1.497	1.00
88_T	91_Q	1.496	1.00
19_K	52_Q	1.495	1.00
32_F	50_I	1.488	1.00
128_R	302_W	1.486	1.00
28_R	38_E	1.479	1.00
42_S	45_A	1.470	1.00
300_I	304_R	1.466	1.00
165_T	286_T	1.454	1.00
25_V	39_L	1.443	1.00
19_K	49_R	1.438	1.00
144_N	150_I	1.437	1.00
155_Y	285_I	1.430	1.00
60_Q	63_V	1.387	1.00
106_T	137_L	1.380	1.00
125_F	132_I	1.377	1.00
80_W	84_S	1.377	1.00
125_F	299_F	1.375	1.00
85_S	92_E	1.374	1.00
157_D	283_Y	1.374	1.00
292_Q	296_I	1.371	1.00
284_Y	300_I	1.351	1.00
168_F	283_Y	1.349	1.00
145_L	153_A	1.345	1.00
33_A	43_P	1.342	1.00
81_A	92_E	1.337	1.00
16_Q	19_K	1.336	1.00
243_I	246_M	1.324	1.00
298_A	301_I	1.321	1.00
23_F	79_Y	1.315	1.00
213_T	217_H	1.312	1.00
24_E	86_L	1.302	1.00
17_L	89_L	1.300	1.00
41_L	45_A	1.299	1.00
102_S	131_S	1.299	1.00
241_A	252_A	1.298	1.00
172_E	257_R	1.294	1.00
78_V	93_I	1.291	1.00
73_H	76_K	1.290	1.00
152_L	284_Y	1.289	1.00
187_A	194_N	1.288	1.00
124_D	128_R	1.281	1.00
77_R	81_A	1.273	1.00
123_G	247_N	1.271	1.00
262_R	267_E	1.270	1.00
48_H	52_Q	1.262	1.00
22_T	41_L	1.260	1.00
100_E	131_S	1.247	1.00
126_T	232_G	1.246	1.00
152_L	296_I	1.234	1.00
178_C	251_V	1.232	1.00
198_C	251_V	1.231	1.00
214_D	218_S	1.220	1.00
146_Q	163_Q	1.219	1.00
77_R	80_W	1.216	1.00
126_T	199_T	1.208	1.00
84_S	91_Q	1.200	1.00
123_G	127_R	1.199	1.00
120_P	247_N	1.196	1.00
270_A	273_G	1.183	1.00
180_P	267_E	1.182	1.00
256_K	260_Q	1.180	1.00
76_K	80_W	1.165	1.00
23_F	27_A	1.164	1.00
183_A	198_C	1.162	1.00
20_M	82_L	1.161	1.00
180_P	269_V	1.157	1.00
166_H	285_I	1.149	1.00
48_H	51_N	1.139	1.00
243_I	247_N	1.137	1.00
188_L	269_V	1.136	1.00
139_G	144_N	1.130	1.00
167_H	300_I	1.129	1.00
23_F	62_F	1.127	1.00
256_K	270_A	1.122	1.00
129_Y	298_A	1.119	1.00
199_T	230_S	1.113	1.00
25_V	35_A	1.101	1.00
189_T	274_D	1.098	1.00
85_S	88_T	1.094	1.00
49_R	52_Q	1.082	1.00
137_L	144_N	1.078	1.00
242_V	246_M	1.070	1.00
51_N	55_E	1.069	1.00
214_D	217_H	1.069	1.00
173_E	279_C	1.067	1.00
302_W	305_E	1.065	1.00
32_F	69_V	1.057	1.00
56_E	93_I	1.055	1.00
105_L	299_F	1.049	1.00
135_T	234_G	1.045	1.00
89_L	93_I	1.044	1.00
93_I	97_K	1.039	1.00
190_N	194_N	1.038	1.00
179_S	248_H	1.034	1.00
297_E	301_I	1.026	1.00
201_L	241_A	1.024	1.00
261_K	265_S	1.024	1.00
202_H	231_S	1.021	1.00
87_D	91_Q	1.016	1.00
260_Q	264_A	1.012	1.00
146_Q	161_S	1.010	1.00
47_S	51_N	1.005	1.00
114_A	138_T	1.004	1.00
124_D	127_R	0.989	1.00
301_I	304_R	0.987	1.00
26_A	35_A	0.982	1.00
121_A	303_L	0.980	1.00
125_F	302_W	0.979	1.00
78_V	82_L	0.976	1.00
125_F	129_Y	0.972	1.00
21_H	90_N	0.969	1.00
220_A	225_V	0.961	1.00
84_S	87_D	0.959	1.00
74_E	77_R	0.954	1.00
27_A	62_F	0.948	1.00
35_A	46_V	0.948	1.00
23_F	61_L	0.945	1.00
52_Q	55_E	0.941	1.00
18_S	21_H	0.941	1.00
123_G	249_I	0.940	1.00
71_L	75_G	0.937	1.00
26_A	32_F	0.935	1.00
30_Q	70_E	0.934	1.00
165_T	168_F	0.925	1.00
182_Y	185_R	0.925	1.00
294_P	298_A	0.918	1.00
177_V	259_V	0.917	1.00
235_F	241_A	0.915	1.00
176_P	251_V	0.915	1.00
90_N	93_I	0.914	1.00
34_L	38_E	0.913	1.00
128_R	305_E	0.913	1.00
192_V	275_M	0.910	1.00
89_L	92_E	0.906	1.00
177_V	270_A	0.899	1.00
23_F	53_L	0.898	1.00
121_A	302_W	0.894	1.00
59_I	96_I	0.888	1.00
144_N	147_R	0.888	1.00
41_L	46_V	0.886	1.00
91_Q	95_D	0.885	1.00
293_W	296_I	0.884	1.00
178_C	182_Y	0.882	1.00
22_T	39_L	0.877	1.00
33_A	37_E	0.875	1.00
111_P	237_R	0.872	1.00
88_T	92_E	0.872	1.00
80_W	83_K	0.871	1.00
21_H	25_V	0.870	1.00
29_H	35_A	0.867	1.00
18_S	49_R	0.865	1.00
126_T	249_I	0.863	1.00
65_S	68_K	0.863	1.00
15_W	56_E	0.862	1.00
157_D	281_Q	0.862	1.00
23_F	71_L	0.861	1.00
28_R	79_Y	0.860	1.00
219_W	223_Y	0.851	1.00
27_A	30_Q	0.847	1.00
26_A	62_F	0.844	1.00
235_F	244_A	0.842	1.00
74_E	96_I	0.842	1.00
262_R	265_S	0.840	1.00
181_E	248_H	0.840	1.00
76_K	79_Y	0.838	1.00
184_Q	198_C	0.837	1.00
62_F	69_V	0.834	1.00
103_G	295_K	0.834	1.00
21_H	24_E	0.833	1.00
30_Q	68_K	0.833	1.00
200_L	229_T	0.830	1.00
287_T	290_G	0.828	1.00
90_N	94_L	0.827	1.00
92_E	96_I	0.819	1.00
26_A	50_I	0.815	1.00
183_A	188_L	0.815	1.00
107_L	152_L	0.814	1.00
292_Q	297_E	0.814	1.00
263_L	266_G	0.813	1.00
108_Y	153_A	0.811	1.00
199_T	231_S	0.807	1.00
244_A	249_I	0.806	1.00
237_R	240_L	0.800	1.00
193_I	196_C	0.799	1.00
267_E	270_A	0.799	1.00
218_S	222_H	0.797	1.00
215_E	218_S	0.792	1.00
43_P	47_S	0.792	1.00
298_A	302_W	0.790	1.00
26_A	46_V	0.790	1.00
137_L	150_I	0.790	1.00
215_E	219_W	0.789	1.00
83_K	87_D	0.785	1.00
39_L	46_V	0.780	1.00
132_I	295_K	0.779	1.00
182_Y	186_H	0.777	1.00
173_E	277_V	0.776	1.00
150_I	153_A	0.776	1.00
82_L	85_S	0.770	1.00
32_F	46_V	0.767	1.00
109_S	114_A	0.766	1.00
194_N	197_H	0.758	1.00
178_C	183_A	0.756	1.00
108_Y	155_Y	0.754	1.00
17_L	86_L	0.750	1.00
125_F	298_A	0.750	1.00
133_S	230_S	0.750	1.00
148_A	287_T	0.747	1.00
115_Q	243_I	0.743	1.00
51_N	60_Q	0.742	1.00
71_L	76_K	0.740	1.00
179_S	249_I	0.737	1.00
73_H	77_R	0.737	1.00
21_H	86_L	0.737	1.00
23_F	78_V	0.734	1.00
81_A	85_S	0.733	1.00
164_L	285_I	0.729	1.00
186_H	199_T	0.727	1.00
204_R	234_G	0.727	1.00
177_V	254_G	0.726	1.00
23_F	75_G	0.725	1.00
19_K	22_T	0.724	1.00
63_V	72_T	0.723	1.00
120_P	123_G	0.723	1.00
179_S	182_Y	0.721	1.00
219_W	222_H	0.721	1.00
259_V	262_R	0.717	1.00
151_D	296_I	0.717	1.00
27_A	75_G	0.713	1.00
101_L	129_Y	0.710	1.00
30_Q	76_K	0.708	1.00
146_Q	164_L	0.707	1.00
185_R	269_V	0.707	1.00
216_W	219_W	0.707	1.00
152_L	299_F	0.702	1.00
27_A	76_K	0.701	1.00
191_T	274_D	0.700	1.00
176_P	253_M	0.700	1.00
128_R	298_A	0.696	1.00
106_T	151_D	0.695	1.00
178_C	269_V	0.691	1.00
163_Q	288_L	0.687	1.00
301_I	305_E	0.685	1.00
266_G	270_A	0.684	1.00
177_V	252_A	0.683	1.00
37_E	40_S	0.675	1.00
139_G	143_V	0.673	1.00
255_R	258_L	0.669	1.00
203_D	241_A	0.668	1.00
220_A	223_Y	0.665	1.00
45_A	49_R	0.665	1.00
246_M	265_S	0.664	1.00
74_E	78_V	0.661	1.00
63_V	68_K	0.659	1.00
181_E	185_R	0.659	1.00
78_V	96_I	0.658	1.00
18_S	52_Q	0.658	1.00
216_W	220_A	0.658	1.00
133_S	234_G	0.656	1.00
86_L	90_N	0.655	1.00
103_G	132_I	0.653	1.00
200_L	251_V	0.646	1.00
177_V	263_L	0.641	1.00
156_F	280_H	0.641	1.00
118_L	121_A	0.641	1.00
70_E	76_K	0.640	1.00
294_P	297_E	0.637	1.00
290_G	293_W	0.635	1.00
233_I	244_A	0.634	1.00
106_T	150_I	0.633	1.00
178_C	184_Q	0.632	1.00
91_Q	94_L	0.632	1.00
57_L	78_V	0.629	1.00
204_R	236_D	0.625	1.00
263_L	270_A	0.619	1.00
218_S	221_Q	0.615	1.00
212_G	216_W	0.613	1.00
191_T	275_M	0.612	1.00
213_T	234_G	0.611	1.00
235_F	240_L	0.609	1.00
213_T	219_W	0.607	1.00
217_H	221_Q	0.602	1.00
299_F	303_L	0.600	1.00
196_C	225_V	0.600	1.00
189_T	272_F	0.599	1.00
145_L	164_L	0.599	1.00
181_E	184_Q	0.598	1.00
152_L	300_I	0.597	1.00
119_V	123_G	0.595	1.00
15_W	93_I	0.593	1.00
105_L	152_L	0.593	1.00
259_V	263_L	0.592	1.00
54_E	64_R	0.591	1.00
77_R	96_I	0.591	1.00
173_E	272_F	0.589	1.00
180_P	266_G	0.588	1.00
26_A	31_S	0.585	1.00
261_K	264_A	0.583	1.00
138_T	236_D	0.583	1.00
57_L	60_Q	0.582	1.00
59_I	63_V	0.579	1.00
18_S	22_T	0.575	1.00
35_A	39_L	0.574	1.00
146_Q	149_G	0.572	1.00
123_G	126_T	0.569	1.00
211_S	214_D	0.569	1.00
145_L	285_I	0.568	1.00
174_I	253_M	0.568	1.00
87_D	90_N	0.568	1.00
295_K	298_A	0.567	1.00
176_P	195_L	0.566	1.00
129_Y	132_I	0.565	1.00
220_A	229_T	0.564	1.00
32_F	43_P	0.562	1.00
286_T	297_E	0.562	1.00
94_L	98_N	0.562	1.00
182_Y	199_T	0.561	1.00
95_D	98_N	0.560	1.00
120_P	124_D	0.560	1.00
286_T	292_Q	0.560	1.00
102_S	133_S	0.559	1.00
117_W	121_A	0.557	1.00
183_A	186_H	0.555	1.00
62_F	71_L	0.551	1.00
169_L	284_Y	0.547	1.00
30_Q	69_V	0.546	1.00
176_P	200_L	0.546	1.00
182_Y	251_V	0.545	1.00
183_A	187_A	0.545	1.00
57_L	96_I	0.545	1.00
60_Q	74_E	0.544	1.00
197_H	230_S	0.543	1.00
109_S	118_L	0.543	1.00
16_Q	56_E	0.543	1.00
45_A	48_H	0.538	1.00
297_E	300_I	0.536	1.00
239_D	243_I	0.535	1.00
20_M	78_V	0.534	1.00
157_D	166_H	0.534	1.00
92_E	95_D	0.534	1.00
111_P	140_N	0.534	1.00
108_Y	137_L	0.534	1.00
133_S	232_G	0.531	1.00
254_G	259_V	0.531	1.00
124_D	305_E	0.531	1.00
296_I	300_I	0.526	1.00
217_H	220_A	0.526	1.00
184_Q	190_N	0.524	1.00
44_S	48_H	0.524	1.00
193_I	225_V	0.524	1.00
103_G	131_S	0.522	1.00
16_Q	52_Q	0.521	1.00
241_A	245_A	0.520	1.00
172_E	280_H	0.519	1.00
154_I	303_L	0.518	1.00
109_S	136_V	0.517	1.00
101_L	131_S	0.516	1.00
120_P	243_I	0.516	1.00
44_S	47_S	0.514	1.00
82_L	86_L	0.514	1.00
41_L	49_R	0.513	1.00
24_E	90_N	0.511	1.00
110_R	113_I	0.510	1.00
115_Q	237_R	0.508	1.00
213_T	216_W	0.508	1.00
50_I	54_E	0.507	1.00
203_D	238_S	0.507	1.00
98_N	101_L	0.506	1.00
71_L	79_Y	0.505	1.00
94_L	97_K	0.505	1.00
218_S	223_Y	0.500	1.00
212_G	215_E	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
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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
1uthA	2	0.7074	100	0.12	Contact Map
2esnA	3	0.9453	100	0.129	Contact Map
3szpA	3	0.926	100	0.138	Contact Map
3fzvA	4	0.9132	100	0.139	Contact Map
1ixcA	4	0.9293	100	0.14	Contact Map
4x6gA	4	0.9518	100	0.141	Contact Map
3fxqA	3	0.9293	100	0.141	Contact Map
1al3A	1	0.6624	100	0.146	Contact Map
2h98A	2	0.6559	100	0.151	Contact Map
2h9bA	2	0.6559	100	0.155	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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