HYPE - ECOLI - GREMLIN Contacts

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HYPE - Hydrogenase isoenzymes formation protein HypE

UniProt:	P24193	Sequences: MNNIQLAHGSGGQAMQQLINSLFMEAFANPWLAEQEDQARLDLAQLVAEGDRLAFSTDSYVIDPLFFPGGNIGKLAICGTANDVAVSGAIPRYLSCGFILEEGLPMETLKAVVTSMAETARAAGIAIVTGDTKVVQRGAVDKLFINTAGMGAIPANIHWGAQTLTAGDVLLVSGTLGDHGATILNLREQLGLDGELVSDCAVLTPLIQTLRDIPGVKALRDATRGGVNAVVHEFAAACGCGIELSEAALPVKPAVRGVCELLGLDALNFANEGKLVIAVERNAAEQVLAALHSHPLGKDAALIGEVVERKGVRLAGLYGVKRTLDLPHAEPLPRIC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10487
Length:	336 (289)
Sequences:	14659 (9204)
Seq/√Len:	541.4

ECOLI - HYPE SELD THIL
BACSU - THIL PURL
HALSA - Q9HSM1 THIL PURL
SULSO - Q97VC5 Q7LY06 Q980P9 PURL

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
169_V	302_L	3.345	1.00
243_E	307_V	3.090	1.00
243_E	305_E	3.080	1.00
283_A	286_Q	2.739	1.00
279_V	287_V	2.726	1.00
166_A	308_E	2.602	1.00
168_D	217_K	2.563	1.00
245_S	248_A	2.531	1.00
215_G	283_A	2.462	1.00
169_V	284_A	2.411	1.00
169_V	305_E	2.344	1.00
70_G	111_A	2.338	1.00
235_A	242_I	2.323	1.00
217_K	280_E	2.323	1.00
170_L	278_A	2.310	1.00
70_G	118_E	2.308	1.00
240_C	306_V	2.299	1.00
171_L	302_L	2.288	1.00
111_A	114_T	2.252	1.00
171_L	288_L	2.233	1.00
54_A	89_A	2.208	1.00
117_A	121_R	2.128	1.00
280_E	283_A	2.099	1.00
231_V	242_I	2.082	1.00
284_A	302_L	2.071	1.00
288_L	300_A	2.059	1.00
284_A	288_L	2.005	1.00
171_L	300_A	1.972	1.00
241_G	307_V	1.968	1.00
42_D	155_A	1.960	1.00
70_G	114_T	1.907	1.00
69_G	143_L	1.879	1.00
169_V	281_R	1.863	1.00
231_V	244_L	1.859	1.00
281_R	305_E	1.837	1.00
80_T	149_G	1.836	1.00
241_G	309_R	1.824	1.00
171_L	279_V	1.799	1.00
166_A	240_C	1.795	1.00
213_I	290_A	1.764	1.00
92_R	152_A	1.745	1.00
243_E	313_R	1.739	1.00
50_G	155_A	1.730	1.00
74_K	119_T	1.724	1.00
170_L	242_I	1.722	1.00
84_V	89_A	1.694	1.00
56_S	149_G	1.688	1.00
40_R	54_A	1.669	1.00
171_L	284_A	1.669	1.00
234_F	278_A	1.664	1.00
217_K	278_A	1.662	1.00
285_E	289_A	1.633	1.00
178_D	186_L	1.601	1.00
118_E	121_R	1.575	1.00
165_T	280_E	1.574	1.00
286_Q	289_A	1.564	1.00
302_L	305_E	1.542	1.00
164_L	306_V	1.515	1.00
118_E	122_A	1.511	1.00
164_L	218_A	1.509	1.00
52_R	155_A	1.502	1.00
51_D	154_P	1.465	1.00
242_I	306_V	1.455	1.00
51_D	152_A	1.452	1.00
168_D	280_E	1.450	1.00
219_L	277_I	1.448	1.00
291_L	300_A	1.444	1.00
114_T	118_E	1.439	1.00
55_F	95_S	1.403	1.00
38_Q	87_S	1.399	1.00
98_F	109_L	1.389	1.00
218_A	234_F	1.381	1.00
178_D	252_K	1.366	1.00
285_E	288_L	1.365	1.00
59_S	146_N	1.364	1.00
84_V	149_G	1.360	1.00
96_C	116_M	1.354	1.00
90_I	208_Q	1.353	1.00
164_L	278_A	1.350	1.00
159_W	219_L	1.346	1.00
31_W	52_R	1.343	1.00
279_V	284_A	1.340	1.00
71_N	74_K	1.337	1.00
165_T	217_K	1.334	1.00
231_V	276_V	1.334	1.00
95_S	129_T	1.333	1.00
210_L	287_V	1.316	1.00
278_A	306_V	1.306	1.00
288_L	302_L	1.295	1.00
71_N	115_S	1.292	1.00
241_G	310_K	1.292	1.00
99_I	135_V	1.276	1.00
168_D	306_V	1.260	1.00
55_F	150_M	1.254	1.00
50_G	156_N	1.247	1.00
119_T	122_A	1.247	1.00
219_L	275_L	1.247	1.00
180_G	183_I	1.246	1.00
153_I	158_H	1.240	1.00
252_K	255_V	1.228	1.00
76_A	145_I	1.225	1.00
222_A	230_V	1.224	1.00
209_T	212_D	1.219	1.00
213_I	286_Q	1.216	1.00
288_L	292_H	1.214	1.00
196_L	200_C	1.204	1.00
39_A	128_V	1.202	1.00
197_V	200_C	1.200	1.00
245_S	305_E	1.198	1.00
171_L	287_V	1.193	1.00
57_T	97_G	1.189	1.00
190_L	193_D	1.188	1.00
206_L	291_L	1.186	1.00
86_V	219_L	1.185	1.00
289_A	293_S	1.176	1.00
93_Y	128_V	1.167	1.00
222_A	276_V	1.160	1.00
57_T	148_A	1.159	1.00
38_Q	54_A	1.155	1.00
286_Q	290_A	1.154	1.00
77_I	116_M	1.153	1.00
208_Q	212_D	1.146	1.00
169_V	279_V	1.137	1.00
206_L	209_T	1.125	1.00
120_A	127_I	1.122	1.00
175_T	178_D	1.118	1.00
160_G	163_T	1.113	1.00
69_G	108_T	1.110	1.00
77_I	94_L	1.102	1.00
170_L	276_V	1.101	1.00
74_K	122_A	1.095	1.00
81_A	149_G	1.089	1.00
154_P	157_I	1.087	1.00
48_A	51_D	1.083	1.00
100_L	109_L	1.080	1.00
157_I	212_D	1.079	1.00
19_I	25_E	1.079	1.00
218_A	278_A	1.077	1.00
290_A	293_S	1.069	1.00
94_L	149_G	1.068	1.00
19_I	22_L	1.067	1.00
52_R	153_I	1.060	1.00
95_S	148_A	1.055	1.00
78_C	119_T	1.052	1.00
209_T	213_I	1.046	1.00
135_V	144_F	1.045	1.00
107_E	111_A	1.044	1.00
52_R	158_H	1.038	1.00
164_L	234_F	1.033	1.00
68_P	71_N	1.033	1.00
178_D	183_I	1.032	1.00
290_A	296_L	1.031	1.00
105_P	108_T	1.028	1.00
214_P	287_V	1.021	1.00
287_V	290_A	1.020	1.00
54_A	84_V	1.012	1.00
168_D	278_A	1.010	1.00
293_S	296_L	1.007	1.00
43_L	152_A	1.003	1.00
251_V	256_R	0.999	1.00
188_E	192_L	0.997	1.00
55_F	148_A	0.989	1.00
74_K	118_E	0.982	1.00
289_A	292_H	0.974	1.00
27_F	90_I	0.971	1.00
163_T	217_K	0.970	1.00
190_L	198_S	0.969	1.00
227_V	276_V	0.961	1.00
220_R	233_E	0.959	1.00
180_G	269_F	0.952	1.00
214_P	290_A	0.948	1.00
81_A	125_I	0.943	1.00
77_I	120_A	0.938	1.00
277_I	287_V	0.937	1.00
204_T	208_Q	0.930	1.00
196_L	199_D	0.928	1.00
36_E	87_S	0.927	1.00
220_R	276_V	0.926	1.00
182_T	185_N	0.922	1.00
48_A	152_A	0.919	1.00
231_V	235_A	0.915	1.00
287_V	291_L	0.914	1.00
42_D	50_G	0.913	1.00
157_I	214_P	0.912	1.00
17_Q	21_S	0.911	1.00
199_D	202_V	0.903	1.00
123_A	202_V	0.902	1.00
19_I	23_F	0.901	1.00
71_N	201_A	0.899	1.00
188_E	193_D	0.898	1.00
178_D	181_A	0.896	1.00
42_D	48_A	0.894	1.00
73_G	112_V	0.892	1.00
90_I	212_D	0.886	1.00
207_I	275_L	0.885	1.00
56_S	84_V	0.881	1.00
75_L	272_E	0.880	1.00
73_G	115_S	0.879	1.00
116_M	147_T	0.876	1.00
207_I	211_R	0.875	1.00
40_R	158_H	0.875	1.00
93_Y	150_M	0.872	1.00
167_G	305_E	0.870	1.00
243_E	246_E	0.865	1.00
189_Q	192_L	0.862	1.00
267_L	272_E	0.854	1.00
106_M	110_K	0.849	1.00
173_S	277_I	0.848	1.00
93_Y	126_A	0.847	1.00
22_L	25_E	0.846	1.00
77_I	81_A	0.846	1.00
74_K	78_C	0.845	1.00
271_N	274_K	0.844	1.00
173_S	291_L	0.842	1.00
68_P	194_G	0.840	1.00
20_N	24_M	0.837	1.00
164_L	238_C	0.829	1.00
100_L	112_V	0.829	1.00
202_V	206_L	0.825	1.00
160_G	164_L	0.825	1.00
256_R	260_E	0.824	1.00
59_S	97_G	0.822	1.00
109_L	134_V	0.820	1.00
183_I	187_R	0.818	1.00
255_V	259_C	0.818	1.00
42_D	52_R	0.811	1.00
209_T	296_L	0.808	1.00
97_G	146_N	0.807	1.00
21_S	110_K	0.805	1.00
37_D	220_R	0.804	1.00
241_G	311_G	0.802	1.00
101_E	104_L	0.801	1.00
120_A	125_I	0.801	1.00
31_W	42_D	0.801	1.00
32_L	160_G	0.801	1.00
94_L	120_A	0.790	1.00
235_A	306_V	0.788	1.00
29_N	41_L	0.784	1.00
81_A	119_T	0.782	1.00
94_L	147_T	0.781	1.00
166_A	307_V	0.780	1.00
76_A	147_T	0.779	1.00
135_V	138_G	0.778	1.00
215_G	286_Q	0.777	1.00
40_R	87_S	0.775	1.00
63_D	142_K	0.772	1.00
214_P	283_A	0.772	1.00
222_A	274_K	0.771	1.00
102_E	105_P	0.770	1.00
80_T	147_T	0.769	1.00
227_V	231_V	0.767	1.00
30_P	33_A	0.767	1.00
166_A	169_V	0.766	1.00
170_L	306_V	0.765	1.00
77_I	119_T	0.765	1.00
90_I	124_G	0.764	1.00
94_L	116_M	0.756	1.00
230_V	276_V	0.754	1.00
188_E	191_G	0.754	1.00
161_A	164_L	0.754	1.00
112_V	116_M	0.752	1.00
257_G	261_L	0.751	1.00
285_E	302_L	0.750	1.00
189_Q	193_D	0.749	1.00
36_E	161_A	0.742	1.00
173_S	275_L	0.741	1.00
179_H	271_N	0.740	1.00
30_P	126_A	0.738	1.00
65_L	142_K	0.736	1.00
85_A	208_Q	0.736	1.00
170_L	174_G	0.728	1.00
209_T	290_A	0.721	1.00
98_F	145_I	0.720	1.00
59_S	99_I	0.720	1.00
202_V	205_P	0.719	1.00
235_A	312_V	0.718	1.00
281_R	284_A	0.716	1.00
86_V	275_L	0.712	1.00
180_G	184_L	0.707	1.00
171_L	277_I	0.701	1.00
70_G	115_S	0.701	1.00
101_E	105_P	0.700	1.00
179_H	182_T	0.693	1.00
292_H	299_D	0.691	1.00
210_L	291_L	0.691	1.00
254_A	257_G	0.690	1.00
60_Y	76_A	0.688	1.00
266_A	270_A	0.688	1.00
90_I	205_P	0.684	1.00
206_L	296_L	0.682	1.00
56_S	80_T	0.681	1.00
108_T	112_V	0.681	1.00
259_C	263_G	0.681	1.00
64_P	75_L	0.680	1.00
52_R	156_N	0.680	1.00
89_A	153_I	0.675	1.00
112_V	145_I	0.675	1.00
250_P	301_A	0.670	1.00
21_S	106_M	0.670	1.00
41_L	93_Y	0.668	1.00
204_T	207_I	0.667	1.00
25_E	121_R	0.667	1.00
73_G	116_M	0.667	1.00
60_Y	79_G	0.666	1.00
159_W	211_R	0.665	1.00
228_N	268_N	0.665	1.00
307_V	313_R	0.659	1.00
207_I	219_L	0.658	1.00
235_A	238_C	0.658	1.00
90_I	152_A	0.657	1.00
239_G	309_R	0.657	1.00
205_P	274_K	0.655	1.00
29_N	42_D	0.654	1.00
40_R	52_R	0.652	1.00
165_T	168_D	0.652	1.00
159_W	216_V	0.652	1.00
201_A	298_K	0.650	1.00
181_A	255_V	0.649	1.00
195_E	199_D	0.649	1.00
21_S	25_E	0.644	1.00
222_A	227_V	0.643	1.00
207_I	277_I	0.641	1.00
110_K	114_T	0.638	1.00
182_T	187_R	0.637	1.00
257_G	260_E	0.637	1.00
108_T	111_A	0.635	1.00
54_A	153_I	0.633	1.00
229_A	268_N	0.631	1.00
199_D	203_L	0.629	1.00
229_A	233_E	0.629	1.00
252_K	259_C	0.628	1.00
116_M	145_I	0.625	1.00
74_K	200_C	0.625	1.00
183_I	186_L	0.625	1.00
25_E	110_K	0.623	1.00
99_I	133_K	0.620	1.00
181_A	185_N	0.620	1.00
27_F	126_A	0.616	1.00
209_T	293_S	0.614	1.00
94_L	127_I	0.610	1.00
253_P	256_R	0.603	1.00
180_G	265_D	0.602	1.00
221_D	233_E	0.601	1.00
205_P	208_Q	0.601	1.00
228_N	267_L	0.600	1.00
182_T	186_L	0.600	1.00
57_T	95_S	0.600	1.00
309_R	313_R	0.600	1.00
172_V	176_L	0.598	1.00
177_G	181_A	0.597	1.00
184_L	187_R	0.597	1.00
27_F	30_P	0.597	1.00
37_D	221_D	0.597	1.00
68_P	111_A	0.597	1.00
83_D	221_D	0.595	1.00
190_L	195_E	0.595	1.00
252_K	257_G	0.595	1.00
58_D	83_D	0.594	1.00
253_P	257_G	0.594	1.00
72_I	112_V	0.594	1.00
248_A	301_A	0.593	1.00
198_S	202_V	0.592	1.00
207_I	210_L	0.590	1.00
81_A	123_A	0.588	1.00
18_L	22_L	0.587	1.00
255_V	258_V	0.587	1.00
57_T	146_N	0.585	0.99
200_C	204_T	0.582	0.99
211_R	219_L	0.580	0.99
250_P	253_P	0.578	0.99
48_A	154_P	0.577	0.99
24_M	35_Q	0.576	0.99
200_C	203_L	0.576	0.99
246_E	314_L	0.576	0.99
55_F	93_Y	0.575	0.99
100_L	108_T	0.572	0.99
99_I	144_F	0.570	0.99
123_A	204_T	0.568	0.99
122_A	205_P	0.567	0.99
214_P	286_Q	0.566	0.99
96_C	113_V	0.566	0.99
154_P	212_D	0.566	0.99
164_L	217_K	0.562	0.99
170_L	244_L	0.561	0.99
115_S	119_T	0.559	0.99
30_P	128_V	0.559	0.99
62_I	66_F	0.557	0.99
136_Q	142_K	0.556	0.99
195_E	198_S	0.555	0.99
28_A	33_A	0.554	0.99
215_G	290_A	0.552	0.99
215_G	280_E	0.552	0.99
41_L	128_V	0.550	0.99
285_E	292_H	0.548	0.99
256_R	259_C	0.548	0.99
174_G	301_A	0.548	0.99
159_W	163_T	0.548	0.99
229_A	232_H	0.546	0.99
232_H	236_A	0.543	0.99
205_P	209_T	0.540	0.99
203_L	275_L	0.538	0.99
108_T	141_D	0.535	0.99
180_G	185_N	0.535	0.99
95_S	128_V	0.533	0.99
43_L	48_A	0.531	0.99
119_T	202_V	0.529	0.99
104_L	108_T	0.528	0.99
201_A	205_P	0.527	0.99
206_L	298_K	0.525	0.99
174_G	299_D	0.522	0.99
307_V	310_K	0.522	0.99
251_V	266_A	0.519	0.99
164_L	240_C	0.519	0.99
62_I	67_F	0.518	0.99
210_L	216_V	0.517	0.99
85_A	204_T	0.516	0.99
49_E	154_P	0.514	0.99
18_L	23_F	0.514	0.99
287_V	300_A	0.514	0.99
251_V	259_C	0.513	0.99
308_E	311_G	0.512	0.99
246_E	267_L	0.512	0.99
296_L	299_D	0.510	0.99
19_I	24_M	0.507	0.99
20_N	25_E	0.507	0.99
232_H	312_V	0.506	0.99
59_S	62_I	0.505	0.99
168_D	281_R	0.505	0.99
102_E	134_V	0.503	0.98
208_Q	211_R	0.502	0.98
78_C	200_C	0.502	0.98
27_F	41_L	0.502	0.98
203_L	207_I	0.501	0.98
21_S	24_M	0.500	0.98

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
2z1uA	2	0.9643	100	0.176	Contact Map
3wjpA	2	0.9673	100	0.195	Contact Map
3vtiC	2	0.9048	100	0.207	Contact Map
2rb9A	2	0.9524	100	0.213	Contact Map
2zodA	2	0.8631	100	0.28	Contact Map
3fd5A	2	0.9286	100	0.28	Contact Map
3viuA	1	0.8958	100	0.287	Contact Map
1vk3A	1	0.875	100	0.294	Contact Map
3u0oA	2	0.878	100	0.303	Contact Map
3mcqA	2	0.869	100	0.313	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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