DCYD - ECOLI - GREMLIN Contacts

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DCYD - D-cysteine desulfhydrase

UniProt:	P76316	Sequences: MPLHNLTRFPRLEFIGAPTPLEYLPRFSDYLGREIFIKRDDVTPMAMGGNKLRKLEFLAADALREGADTLITAGAIQSNHVRQTAAVAAKLGLHCVALLENPIGTTAENYLTNGNRLLLDLFNTQIEMCDALTDPNAQLEELATRVEAQGFRPYVIPVGGSNALGALGYVESALEIAQQCEGAVNISSVVVASGSAGTHAGLAVGLEHLMPESELIGVTVSRSVADQLPKVVNLQQAIAKELELTASAEILLWDDYFAPGYGVPNDEGMEAVKLLARLEGILLDPVYTGKAMAGLIDGISQKRFKDEGPILFIHTGGAPALFAYHPHV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG14038
Length:	328 (286)
Sequences:	22354 (12670)
Seq/√Len:	749.2

ECOLI - DCYD ILVA DPAL SDHD TDCB TRPB CYSM CYSK
BACSU - ILVA SDHD MCCA CYSM TRPB THRC CYSK
HALSA - Q9HNH6 Q9HRU4 Q9HMQ7 TRPB Q9HNH0 Q9HQ70 Q9HRP3
SULSO - Q980P1 TRPB1 TRPB2 Q97ZL6 Q980F2 Q97ZT5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
88_A	95_C	4.116	1.00
34_E	309_P	3.431	1.00
142_L	145_R	3.182	1.00
23_Y	34_E	3.158	1.00
188_S	216_I	2.722	1.00
176_I	311_L	2.656	1.00
267_E	297_D	2.652	1.00
61_D	65_E	2.644	1.00
274_L	278_L	2.576	1.00
94_H	125_Q	2.501	1.00
18_P	178_Q	2.493	1.00
105_T	117_L	2.466	1.00
221_S	264_P	2.430	1.00
96_V	125_Q	2.381	1.00
101_N	130_D	2.324	1.00
214_E	259_P	2.322	1.00
63_L	93_L	2.275	1.00
69_T	72_T	2.270	1.00
166_A	170_V	2.174	1.00
69_T	96_V	2.146	1.00
36_F	309_P	2.105	1.00
96_V	127_E	2.086	1.00
222_R	265_N	2.077	1.00
264_P	267_E	2.032	1.00
18_P	179_Q	2.017	1.00
203_A	215_L	1.997	1.00
174_L	205_G	1.979	1.00
145_R	149_Q	1.978	1.00
60_A	91_L	1.972	1.00
61_D	164_L	1.948	1.00
203_A	256_Y	1.933	1.00
68_D	72_T	1.907	1.00
160_G	250_I	1.904	1.00
21_L	311_L	1.904	1.00
193_S	217_G	1.893	1.00
157_P	160_G	1.892	1.00
291_A	312_F	1.891	1.00
98_L	146_V	1.883	1.00
218_V	294_G	1.863	1.00
188_S	304_F	1.855	1.00
169_Y	208_H	1.846	1.00
230_K	233_N	1.792	1.00
169_Y	204_V	1.748	1.00
275_L	283_L	1.743	1.00
186_I	311_L	1.710	1.00
305_K	308_G	1.705	1.00
45_M	86_A	1.695	1.00
216_I	259_P	1.687	1.00
36_F	180_C	1.685	1.00
189_V	206_L	1.681	1.00
274_L	296_I	1.675	1.00
210_M	213_S	1.665	1.00
189_V	202_L	1.654	1.00
271_A	293_A	1.649	1.00
144_T	148_A	1.623	1.00
23_Y	36_F	1.610	1.00
69_T	94_H	1.609	1.00
187_S	309_P	1.601	1.00
275_L	292_M	1.596	1.00
116_R	128_M	1.590	1.00
140_E	144_T	1.586	1.00
187_S	308_G	1.569	1.00
56_E	60_A	1.547	1.00
188_S	308_G	1.545	1.00
23_Y	28_S	1.531	1.00
63_L	91_L	1.507	1.00
173_A	202_L	1.500	1.00
165_G	168_G	1.458	1.00
271_A	296_I	1.447	1.00
117_L	120_D	1.438	1.00
190_V	298_G	1.427	1.00
228_L	232_V	1.426	1.00
141_E	144_T	1.403	1.00
173_A	206_L	1.396	1.00
207_E	258_A	1.362	1.00
30_Y	274_L	1.357	1.00
130_D	133_T	1.356	1.00
190_V	218_V	1.348	1.00
76_I	81_V	1.334	1.00
116_R	120_D	1.332	1.00
293_A	297_D	1.328	1.00
188_S	214_E	1.320	1.00
146_V	150_G	1.309	1.00
105_T	116_R	1.309	1.00
199_H	257_F	1.305	1.00
205_G	209_L	1.305	1.00
139_L	143_A	1.301	1.00
221_S	262_G	1.298	1.00
224_V	228_L	1.268	1.00
37_I	314_H	1.266	1.00
63_L	66_G	1.266	1.00
60_A	64_R	1.263	1.00
184_V	309_P	1.262	1.00
231_V	234_L	1.258	1.00
58_L	162_N	1.256	1.00
228_L	231_V	1.254	1.00
24_L	37_I	1.248	1.00
57_F	170_V	1.239	1.00
199_H	217_G	1.238	1.00
59_A	70_L	1.237	1.00
270_E	274_L	1.235	1.00
61_D	64_R	1.225	1.00
119_L	124_T	1.225	1.00
267_E	293_A	1.224	1.00
271_A	292_M	1.215	1.00
26_R	279_E	1.210	1.00
283_L	314_H	1.210	1.00
173_A	205_G	1.207	1.00
137_A	141_E	1.204	1.00
180_C	186_I	1.199	1.00
199_H	215_L	1.194	1.00
99_L	119_L	1.192	1.00
30_Y	278_L	1.190	1.00
127_E	142_L	1.182	1.00
239_A	242_L	1.177	1.00
177_A	205_G	1.170	1.00
22_E	39_R	1.165	1.00
224_V	262_G	1.161	1.00
20_P	42_V	1.160	1.00
227_Q	231_V	1.158	1.00
177_A	209_L	1.153	1.00
101_N	131_A	1.138	1.00
180_C	184_V	1.137	1.00
204_V	253_W	1.134	1.00
174_L	178_Q	1.130	1.00
276_A	282_L	1.129	1.00
81_V	119_L	1.126	1.00
61_D	163_A	1.124	1.00
267_E	270_E	1.122	1.00
150_G	153_P	1.117	1.00
185_N	309_P	1.114	1.00
206_L	213_S	1.111	1.00
266_D	270_E	1.105	1.00
21_L	180_C	1.102	1.00
21_L	176_I	1.094	1.00
242_L	290_K	1.088	1.00
102_P	131_A	1.087	1.00
188_S	310_I	1.073	1.00
259_P	303_R	1.064	1.00
138_Q	141_E	1.063	1.00
261_Y	294_G	1.063	1.00
217_G	260_G	1.062	1.00
263_V	293_A	1.060	1.00
116_R	126_I	1.052	1.00
141_E	145_R	1.048	1.00
177_A	210_M	1.045	1.00
229_P	233_N	1.045	1.00
216_I	261_Y	1.035	1.00
25_P	29_D	1.020	1.00
180_C	311_L	1.019	1.00
55_L	83_Q	1.017	1.00
138_Q	142_L	1.017	1.00
84_T	95_C	1.014	1.00
57_F	167_L	1.014	1.00
230_K	234_L	1.013	1.00
272_V	289_G	1.011	1.00
144_T	147_E	1.011	1.00
297_D	300_S	1.010	1.00
99_L	128_M	1.000	1.00
26_R	29_D	0.996	1.00
298_G	303_R	0.995	1.00
57_F	60_A	0.993	1.00
59_A	91_L	0.991	1.00
288_T	314_H	0.980	1.00
57_F	61_D	0.980	1.00
59_A	87_V	0.976	1.00
26_R	278_L	0.975	1.00
202_L	313_I	0.969	1.00
89_A	95_C	0.960	1.00
261_Y	297_D	0.957	1.00
304_F	308_G	0.954	1.00
35_I	295_L	0.951	1.00
273_K	277_R	0.951	1.00
193_S	199_H	0.949	1.00
86_A	122_F	0.945	1.00
237_A	243_E	0.944	1.00
240_K	243_E	0.939	1.00
227_Q	230_K	0.937	1.00
295_L	312_F	0.936	1.00
170_V	174_L	0.936	1.00
117_L	121_L	0.934	1.00
176_I	186_I	0.933	1.00
142_L	146_V	0.927	1.00
120_D	125_Q	0.923	1.00
147_E	155_V	0.918	1.00
33_R	308_G	0.907	1.00
83_Q	87_V	0.901	1.00
85_A	124_T	0.898	1.00
214_E	258_A	0.897	1.00
236_Q	239_A	0.894	1.00
271_A	274_L	0.887	1.00
190_V	216_I	0.882	1.00
172_S	313_I	0.881	1.00
139_L	142_L	0.880	1.00
205_G	208_H	0.865	1.00
28_S	31_L	0.859	1.00
238_I	269_M	0.857	1.00
283_L	288_T	0.855	1.00
174_L	209_L	0.850	1.00
242_L	245_T	0.847	1.00
191_V	202_L	0.843	1.00
190_V	295_L	0.842	1.00
168_G	172_S	0.842	1.00
169_Y	205_G	0.839	1.00
38_K	175_E	0.835	1.00
251_L	255_D	0.832	1.00
288_T	315_T	0.830	1.00
89_A	122_F	0.826	1.00
68_D	152_R	0.825	1.00
246_A	249_E	0.820	1.00
248_A	251_L	0.818	1.00
98_L	142_L	0.806	1.00
120_D	128_M	0.801	1.00
39_R	314_H	0.800	1.00
204_V	208_H	0.799	1.00
39_R	42_V	0.795	1.00
200_A	251_L	0.792	1.00
86_A	90_K	0.791	1.00
15_I	56_E	0.788	1.00
19_T	43_T	0.785	1.00
188_S	298_G	0.783	1.00
31_L	274_L	0.774	1.00
227_Q	262_G	0.772	1.00
65_E	163_A	0.770	1.00
145_R	148_A	0.768	1.00
223_S	229_P	0.768	1.00
24_L	292_M	0.758	1.00
190_V	294_G	0.755	1.00
27_F	296_I	0.751	1.00
82_R	118_L	0.750	1.00
214_E	308_G	0.748	1.00
140_E	143_A	0.739	1.00
98_L	127_E	0.738	1.00
242_L	286_V	0.737	1.00
137_A	140_E	0.733	1.00
32_G	306_D	0.732	1.00
237_A	240_K	0.731	1.00
167_L	170_V	0.728	1.00
37_I	312_F	0.728	1.00
199_H	253_W	0.725	1.00
254_D	257_F	0.725	1.00
58_L	156_I	0.723	1.00
298_G	304_F	0.720	1.00
172_S	202_L	0.719	1.00
61_D	166_A	0.717	1.00
230_K	260_G	0.714	1.00
185_N	210_M	0.714	1.00
292_M	312_F	0.714	1.00
177_A	206_L	0.713	1.00
55_L	87_V	0.709	1.00
82_R	119_L	0.709	1.00
98_L	129_C	0.708	1.00
97_A	119_L	0.708	1.00
162_N	165_G	0.707	1.00
25_P	28_S	0.706	1.00
186_I	213_S	0.705	1.00
29_D	32_G	0.704	1.00
192_A	315_T	0.701	1.00
172_S	198_T	0.694	1.00
40_D	53_R	0.690	1.00
229_P	234_L	0.690	1.00
269_M	285_P	0.689	1.00
161_S	247_S	0.688	1.00
138_Q	143_A	0.686	1.00
202_L	206_L	0.685	1.00
147_E	153_P	0.685	1.00
24_L	279_E	0.683	1.00
96_V	152_R	0.681	1.00
50_N	198_T	0.681	1.00
95_C	124_T	0.679	1.00
143_A	147_E	0.677	1.00
160_G	200_A	0.676	1.00
268_G	290_K	0.675	1.00
229_P	232_V	0.675	1.00
180_C	309_P	0.671	1.00
37_I	292_M	0.671	1.00
189_V	313_I	0.670	1.00
220_V	242_L	0.666	1.00
101_N	134_D	0.665	1.00
70_L	88_A	0.665	1.00
133_T	138_Q	0.663	1.00
68_D	94_H	0.663	1.00
172_S	176_I	0.662	1.00
227_Q	260_G	0.662	1.00
239_A	268_G	0.661	1.00
166_A	169_Y	0.660	1.00
225_A	230_K	0.659	1.00
31_L	296_I	0.659	1.00
101_N	128_M	0.657	1.00
235_Q	238_I	0.657	1.00
214_E	303_R	0.656	1.00
292_M	314_H	0.655	1.00
72_T	84_T	0.653	1.00
300_S	304_F	0.653	1.00
193_S	260_G	0.651	1.00
28_S	35_I	0.649	1.00
253_W	257_F	0.648	1.00
33_R	307_E	0.647	1.00
162_N	168_G	0.646	1.00
216_I	298_G	0.644	1.00
166_A	204_V	0.642	1.00
162_N	166_A	0.636	1.00
300_S	303_R	0.635	1.00
118_L	121_L	0.635	1.00
54_K	58_L	0.635	1.00
228_L	233_N	0.634	1.00
176_I	202_L	0.633	1.00
78_S	81_V	0.633	1.00
34_E	307_E	0.632	1.00
17_A	44_P	0.631	1.00
283_L	289_G	0.628	1.00
177_A	180_C	0.626	1.00
58_L	164_L	0.626	1.00
81_V	97_A	0.626	1.00
239_A	245_T	0.625	1.00
45_M	122_F	0.623	1.00
238_I	241_E	0.623	1.00
275_L	314_H	0.622	1.00
247_S	251_L	0.615	1.00
251_L	254_D	0.615	1.00
296_I	300_S	0.613	1.00
99_L	116_R	0.612	1.00
24_L	27_F	0.612	1.00
253_W	256_Y	0.610	1.00
225_A	229_P	0.608	1.00
33_R	310_I	0.607	1.00
186_I	309_P	0.604	1.00
39_R	281_I	0.602	1.00
16_G	52_L	0.602	1.00
294_G	298_G	0.601	1.00
27_F	271_A	0.600	1.00
96_V	150_G	0.600	1.00
224_V	229_P	0.598	1.00
241_E	244_L	0.597	1.00
96_V	146_V	0.596	1.00
27_F	292_M	0.594	1.00
53_R	175_E	0.593	1.00
103_I	116_R	0.592	1.00
200_A	249_E	0.592	1.00
240_K	245_T	0.592	1.00
21_L	36_F	0.591	1.00
62_A	66_G	0.591	1.00
269_M	273_K	0.589	1.00
164_L	168_G	0.587	1.00
236_Q	240_K	0.583	1.00
275_L	281_I	0.582	1.00
250_I	254_D	0.582	1.00
94_H	152_R	0.582	1.00
99_L	103_I	0.581	1.00
30_Y	296_I	0.581	1.00
275_L	279_E	0.579	1.00
71_I	146_V	0.578	1.00
28_S	34_E	0.577	1.00
177_A	184_V	0.576	1.00
218_V	290_K	0.575	1.00
189_V	213_S	0.575	1.00
133_T	141_E	0.575	1.00
44_P	52_L	0.574	1.00
272_V	285_P	0.574	1.00
259_P	298_G	0.573	1.00
299_I	304_F	0.572	1.00
33_R	299_I	0.571	1.00
61_D	67_A	0.570	1.00
62_A	154_Y	0.570	1.00
147_E	150_G	0.569	1.00
238_I	242_L	0.566	1.00
71_I	153_P	0.565	1.00
191_V	199_H	0.564	1.00
226_D	229_P	0.564	1.00
71_I	147_E	0.562	1.00
27_F	31_L	0.562	1.00
192_A	291_A	0.561	1.00
165_G	251_L	0.554	1.00
98_L	145_R	0.552	1.00
45_M	49_G	0.549	1.00
218_V	261_Y	0.548	1.00
54_K	80_H	0.548	1.00
241_E	245_T	0.547	1.00
146_V	149_Q	0.547	1.00
21_L	179_Q	0.545	1.00
68_D	151_F	0.545	1.00
235_Q	240_K	0.545	1.00
69_T	152_R	0.545	1.00
222_R	235_Q	0.544	1.00
12_L	15_I	0.544	1.00
227_Q	233_N	0.544	1.00
27_F	274_L	0.541	1.00
265_N	269_M	0.541	1.00
288_T	291_A	0.541	1.00
58_L	165_G	0.540	1.00
16_G	56_E	0.539	1.00
178_Q	209_L	0.538	1.00
57_F	163_A	0.537	1.00
58_L	155_V	0.537	1.00
238_I	245_T	0.536	1.00
189_V	215_L	0.534	1.00
154_Y	157_P	0.532	1.00
131_A	138_Q	0.532	1.00
252_L	257_F	0.532	1.00
217_G	257_F	0.532	1.00
85_A	119_L	0.531	1.00
72_T	97_A	0.530	1.00
228_L	234_L	0.530	1.00
157_P	161_S	0.529	1.00
156_I	162_N	0.528	1.00
52_L	86_A	0.527	1.00
17_A	43_T	0.526	1.00
176_I	313_I	0.525	1.00
153_P	156_I	0.524	1.00
69_T	145_R	0.521	1.00
207_E	256_Y	0.521	1.00
190_V	310_I	0.520	1.00
54_K	165_G	0.520	1.00
226_D	230_K	0.520	1.00
133_T	140_E	0.519	1.00
134_D	137_A	0.518	1.00
118_L	122_F	0.517	1.00
304_F	310_I	0.517	1.00
292_M	296_I	0.512	1.00
97_A	124_T	0.512	1.00
225_A	246_A	0.510	1.00
63_L	67_A	0.506	1.00
75_A	156_I	0.504	1.00
85_A	95_C	0.504	1.00
32_G	305_K	0.504	1.00
295_L	299_I	0.502	1.00
207_E	255_D	0.502	1.00
270_E	273_K	0.500	1.00
28_S	32_G	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
4d9bA	2	0.997	100	0.156	Contact Map
1j0aA	5	0.9634	100	0.174	Contact Map
1f2dA	2	0.9787	100	0.182	Contact Map
1tzjA	4	0.9848	100	0.192	Contact Map
2gn0A	2	0.9329	100	0.197	Contact Map
1v71A	2	0.9268	100	0.198	Contact Map
3l6bA	2	0.9299	100	0.202	Contact Map
1tdjA	2	0.9268	100	0.207	Contact Map
4h27A	1	0.9055	100	0.215	Contact Map
2d1fA	2	0.9329	100	0.215	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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