HYAF - ECOLI - GREMLIN Contacts

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HYAF - Hydrogenase-1 operon protein HyaF

UniProt:	P19932	Sequences: MSETFFHLLGPGTQPNDDSFSMNPLPITCQVNDEPSMAALEQCAHSPQVIALLNELQHQLSERQPPLGEVLAVDLLNLNADDRHFINTLLGEGEVSVRIQQADDSESEIQEAIFCGLWRVRRRRGEKLLEDKLEAGCAPLALWQAATQNLLPTDSLLPPPIDGLMNGLPLAHELLAHVRNPDAQPHSINLTQLPISEADRLFLSRLCGPGNIQIRTIGYGESYINATGLRHVWHLRCTDTLKGPLLESYEICPIPEVVLAAPEDLVDSAQRLSEVCQWLAEAAPT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10473
Length:	285 (256)
Sequences:	174 (145)
Seq/√Len:	9.1

ECOLI - HYAF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
174_L	251_I	7.855	1.00
234_H	247_E	5.212	1.00
79_N	82_D	5.188	1.00
114_F	275_V	4.410	0.99
224_I	258_V	4.265	0.99
262_P	266_V	3.373	0.95
22_M	25_L	2.876	0.89
164_L	167_G	2.431	0.78
57_Q	232_V	2.392	0.77
97_V	142_L	2.381	0.77
115_C	251_I	2.241	0.72
117_L	133_L	2.121	0.68
254_I	259_L	2.043	0.65
164_L	240_T	2.022	0.64
214_I	258_V	1.980	0.62
240_T	245_L	1.878	0.58
220_G	239_D	1.850	0.57
188_I	251_I	1.847	0.57
215_R	221_E	1.836	0.56
80_A	228_G	1.835	0.56
166_N	220_G	1.833	0.56
204_S	234_H	1.811	0.55
119_R	131_D	1.759	0.53
23_N	109_I	1.742	0.52
135_A	143_W	1.739	0.52
99_I	109_I	1.730	0.52
226_A	237_C	1.716	0.51
114_F	256_E	1.713	0.51
242_K	245_L	1.707	0.51
121_R	174_L	1.687	0.50
185_P	188_I	1.652	0.48
87_N	119_R	1.618	0.47
74_D	197_E	1.609	0.46
120_V	141_A	1.603	0.46
163_G	198_A	1.589	0.45
188_I	224_I	1.568	0.44
63_R	137_C	1.568	0.44
165_M	258_V	1.548	0.44
82_D	133_L	1.537	0.43
60_L	92_E	1.529	0.43
108_E	121_R	1.503	0.42
73_V	277_Q	1.493	0.41
260_A	264_D	1.491	0.41
79_N	196_S	1.473	0.40
82_D	213_Q	1.470	0.40
221_E	242_K	1.455	0.40
88_T	276_C	1.454	0.40
83_R	120_V	1.453	0.40
217_I	223_Y	1.446	0.39
187_S	248_S	1.444	0.39
191_T	249_Y	1.426	0.38
189_N	220_G	1.422	0.38
239_D	245_L	1.421	0.38
221_E	245_L	1.413	0.38
46_S	82_D	1.404	0.38
234_H	275_V	1.402	0.37
19_S	23_N	1.379	0.37
107_S	141_A	1.364	0.36
243_G	249_Y	1.354	0.36
136_G	185_P	1.349	0.35
193_L	220_G	1.348	0.35
90_L	133_L	1.347	0.35
31_V	251_I	1.326	0.34
221_E	257_V	1.323	0.34
24_P	152_P	1.321	0.34
138_A	142_L	1.317	0.34
25_L	92_E	1.313	0.34
138_A	258_V	1.308	0.34
44_A	51_A	1.306	0.34
29_C	240_T	1.301	0.33
216_T	222_S	1.293	0.33
240_T	244_P	1.290	0.33
110_Q	261_A	1.284	0.33
29_C	215_R	1.274	0.32
54_N	136_G	1.262	0.32
49_V	86_I	1.257	0.32
240_T	257_V	1.251	0.32
108_E	279_L	1.234	0.31
160_P	272_L	1.212	0.30
192_Q	222_S	1.205	0.30
39_A	263_E	1.204	0.30
111_E	264_D	1.200	0.30
39_A	88_T	1.198	0.30
216_T	235_L	1.192	0.29
145_A	191_T	1.187	0.29
24_P	132_K	1.183	0.29
125_G	129_L	1.181	0.29
216_T	223_Y	1.181	0.29
33_D	136_G	1.177	0.29
113_I	176_A	1.176	0.29
195_I	258_V	1.176	0.29
68_G	238_T	1.175	0.29
177_H	247_E	1.172	0.29
77_N	85_F	1.171	0.29
192_Q	242_K	1.170	0.29
86_I	90_L	1.169	0.28
140_L	226_A	1.168	0.28
110_Q	221_E	1.165	0.28
234_H	278_W	1.158	0.28
29_C	32_N	1.157	0.28
82_D	252_C	1.153	0.28
178_V	231_H	1.152	0.28
72_A	132_K	1.150	0.28
23_N	32_N	1.150	0.28
196_S	229_L	1.149	0.28
267_D	274_E	1.142	0.28
171_A	226_A	1.140	0.27
234_H	256_E	1.138	0.27
56_L	90_L	1.136	0.27
240_T	250_E	1.134	0.27
39_A	221_E	1.133	0.27
256_E	259_L	1.130	0.27
57_Q	224_I	1.111	0.26
18_D	136_G	1.109	0.26
80_A	214_I	1.099	0.26
57_Q	73_V	1.096	0.26
220_G	261_A	1.091	0.26
178_V	272_L	1.081	0.25
113_I	274_E	1.079	0.25
138_A	249_Y	1.062	0.25
76_L	86_I	1.060	0.25
223_Y	235_L	1.060	0.25
61_S	154_D	1.054	0.25
86_I	204_S	1.051	0.24
123_R	237_C	1.050	0.24
78_L	191_T	1.048	0.24
139_P	218_G	1.046	0.24
128_L	135_A	1.045	0.24
23_N	113_I	1.042	0.24
186_H	244_P	1.039	0.24
225_N	236_R	1.038	0.24
111_E	260_A	1.031	0.24
40_L	88_T	1.029	0.24
192_Q	216_T	1.027	0.24
41_E	82_D	1.027	0.24
250_E	257_V	1.021	0.24
62_E	183_A	1.013	0.23
222_S	242_K	1.013	0.23
177_H	265_L	1.011	0.23
142_L	278_W	0.999	0.23
50_I	251_I	0.998	0.23
70_V	136_G	0.995	0.23
110_Q	220_G	0.994	0.23
176_A	230_R	0.992	0.23
109_I	144_Q	0.990	0.23
188_I	228_G	0.984	0.22
159_P	185_P	0.983	0.22
246_L	260_A	0.973	0.22
61_S	169_P	0.971	0.22
152_P	159_P	0.960	0.22
246_L	271_R	0.954	0.21
20_F	23_N	0.954	0.21
217_I	248_S	0.944	0.21
170_L	203_L	0.942	0.21
166_N	193_L	0.935	0.21
212_I	234_H	0.929	0.21
22_M	242_K	0.928	0.21
97_V	121_R	0.927	0.21
22_M	28_T	0.923	0.21
193_L	219_Y	0.914	0.20
18_D	86_I	0.914	0.20
87_N	196_S	0.912	0.20
129_L	188_I	0.912	0.20
221_E	240_T	0.910	0.20
56_L	275_V	0.908	0.20
99_I	234_H	0.891	0.20
98_R	278_W	0.890	0.20
236_R	249_Y	0.887	0.20
110_Q	242_K	0.887	0.20
77_N	120_V	0.881	0.19
89_L	197_E	0.881	0.19
43_C	51_A	0.874	0.19
74_D	105_S	0.869	0.19
80_A	169_P	0.867	0.19
168_L	190_L	0.865	0.19
164_L	168_L	0.860	0.19
164_L	191_T	0.856	0.19
170_L	249_Y	0.855	0.19
215_R	245_L	0.855	0.19
96_S	119_R	0.851	0.19
41_E	89_L	0.851	0.19
30_Q	279_L	0.847	0.18
52_L	170_L	0.846	0.18
170_L	195_I	0.845	0.18
32_N	213_Q	0.844	0.18
59_Q	266_V	0.844	0.18
188_I	249_Y	0.839	0.18
145_A	165_M	0.837	0.18
91_G	267_D	0.835	0.18
223_Y	242_K	0.834	0.18
174_L	188_I	0.834	0.18
97_V	214_I	0.834	0.18
115_C	236_R	0.831	0.18
195_I	200_R	0.823	0.18
203_L	277_Q	0.821	0.18
109_I	274_E	0.819	0.18
245_L	261_A	0.817	0.18
216_T	258_V	0.813	0.18
112_A	196_S	0.804	0.17
20_F	221_E	0.797	0.17
57_Q	247_E	0.797	0.17
86_I	231_H	0.795	0.17
55_E	59_Q	0.793	0.17
32_N	157_L	0.792	0.17
200_R	234_H	0.792	0.17
33_D	112_A	0.791	0.17
222_S	237_C	0.789	0.17
55_E	129_L	0.786	0.17
136_G	269_A	0.785	0.17
222_S	235_L	0.780	0.17
114_F	234_H	0.777	0.17
23_N	61_S	0.776	0.17
120_V	176_A	0.775	0.17
56_L	88_T	0.773	0.17
33_D	269_A	0.772	0.17
189_N	192_Q	0.770	0.17
142_L	269_A	0.767	0.16
51_A	84_H	0.766	0.16
146_A	268_S	0.764	0.16
110_Q	245_L	0.761	0.16
83_R	87_N	0.760	0.16
71_L	188_I	0.759	0.16
115_C	217_I	0.759	0.16
147_T	195_I	0.759	0.16
130_E	196_S	0.757	0.16
74_D	109_I	0.755	0.16
51_A	71_L	0.755	0.16
56_L	204_S	0.755	0.16
237_C	257_V	0.754	0.16
166_N	239_D	0.754	0.16
63_R	265_L	0.751	0.16
17_D	33_D	0.748	0.16
92_E	272_L	0.742	0.16
23_N	265_L	0.742	0.16
55_E	159_P	0.740	0.16
223_Y	260_A	0.737	0.16
163_G	174_L	0.728	0.16
17_D	47_P	0.727	0.16
241_L	247_E	0.724	0.15
89_L	113_I	0.722	0.15
164_L	249_Y	0.721	0.15
20_F	115_C	0.716	0.15
46_S	170_L	0.715	0.15
56_L	133_L	0.712	0.15
43_C	143_W	0.709	0.15
55_E	81_D	0.707	0.15
192_Q	235_L	0.706	0.15
59_Q	73_V	0.704	0.15
250_E	271_R	0.704	0.15
105_S	279_L	0.703	0.15
46_S	79_N	0.702	0.15
155_S	201_L	0.701	0.15
166_N	264_D	0.700	0.15
87_N	96_S	0.691	0.15
27_I	143_W	0.690	0.15
170_L	278_W	0.688	0.15
68_G	165_M	0.676	0.14
112_A	275_V	0.675	0.14
80_A	211_N	0.674	0.14
93_G	139_P	0.673	0.14
65_P	262_P	0.671	0.14
52_L	259_L	0.670	0.14
190_L	203_L	0.669	0.14
156_L	253_P	0.656	0.14
222_S	245_L	0.656	0.14
265_L	273_S	0.653	0.14
164_L	242_K	0.652	0.14
94_E	111_E	0.651	0.14
92_E	270_Q	0.651	0.14
35_P	87_N	0.649	0.14
215_R	222_S	0.647	0.14
58_H	120_V	0.643	0.14
56_L	123_R	0.643	0.14
117_L	198_A	0.641	0.14
190_L	247_E	0.640	0.14
83_R	259_L	0.640	0.14
50_I	253_P	0.636	0.14
225_N	232_V	0.635	0.14
86_I	237_C	0.633	0.14
166_N	257_V	0.631	0.13
89_L	129_L	0.631	0.13
60_L	270_Q	0.631	0.13
188_I	209_P	0.630	0.13
144_Q	179_R	0.629	0.13
217_I	251_I	0.625	0.13
219_Y	250_E	0.625	0.13
178_V	229_L	0.625	0.13
49_V	231_H	0.624	0.13
22_M	29_C	0.623	0.13
77_N	231_H	0.622	0.13
86_I	185_P	0.622	0.13
94_E	239_D	0.622	0.13
69_E	183_A	0.620	0.13
166_N	237_C	0.619	0.13
114_F	254_I	0.615	0.13
171_A	195_I	0.612	0.13
192_Q	220_G	0.608	0.13
139_P	210_G	0.608	0.13
17_D	254_I	0.606	0.13
183_A	187_S	0.604	0.13
21_S	24_P	0.603	0.13
165_M	231_H	0.602	0.13
170_L	236_R	0.602	0.13
211_N	265_L	0.601	0.13
33_D	163_G	0.597	0.13
61_S	273_S	0.596	0.13
90_L	98_R	0.593	0.13
118_W	233_W	0.592	0.13
233_W	255_P	0.592	0.13
194_P	233_W	0.592	0.13
118_W	194_P	0.592	0.13
118_W	255_P	0.592	0.13
194_P	255_P	0.592	0.13
128_L	179_R	0.592	0.13
58_H	154_D	0.591	0.13
220_G	245_L	0.591	0.13
169_P	277_Q	0.590	0.13
213_Q	269_A	0.589	0.13
215_R	242_K	0.583	0.13
89_L	152_P	0.582	0.12
124_R	128_L	0.581	0.12
78_L	193_L	0.581	0.12
142_L	211_N	0.580	0.12
237_C	241_L	0.579	0.12
48_Q	170_L	0.579	0.12
166_N	242_K	0.577	0.12
19_S	44_A	0.576	0.12
40_L	46_S	0.576	0.12
120_V	152_P	0.573	0.12
52_L	107_S	0.573	0.12
52_L	69_E	0.570	0.12
142_L	275_V	0.570	0.12
77_N	84_H	0.563	0.12
84_H	88_T	0.562	0.12
82_D	88_T	0.561	0.12
146_A	210_G	0.559	0.12
52_L	143_W	0.558	0.12
79_N	277_Q	0.556	0.12
140_L	144_Q	0.554	0.12
131_D	172_H	0.552	0.12
166_N	219_Y	0.550	0.12
70_V	128_L	0.550	0.12
140_L	181_P	0.550	0.12
27_I	213_Q	0.549	0.12
200_R	244_P	0.549	0.12
112_A	243_G	0.547	0.12
19_S	184_Q	0.546	0.12
67_L	71_L	0.546	0.12
92_E	133_L	0.545	0.12
148_Q	188_I	0.543	0.12
44_A	181_P	0.542	0.12
49_V	257_V	0.538	0.12
24_P	90_L	0.534	0.12
86_I	138_A	0.534	0.12
166_N	260_A	0.533	0.12
215_R	240_T	0.533	0.12
216_T	237_C	0.531	0.12
115_C	198_A	0.530	0.12
246_L	267_D	0.529	0.12
170_L	197_E	0.527	0.11
60_L	185_P	0.526	0.11
95_V	267_D	0.526	0.11
43_C	114_F	0.523	0.11
222_S	260_A	0.521	0.11
79_N	112_A	0.519	0.11
180_N	183_A	0.518	0.11
82_D	117_L	0.518	0.11
223_Y	245_L	0.518	0.11
220_G	260_A	0.517	0.11
192_Q	219_Y	0.514	0.11
166_N	245_L	0.513	0.11
200_R	278_W	0.513	0.11
220_G	264_D	0.512	0.11
219_Y	264_D	0.510	0.11
199_D	263_E	0.510	0.11
236_R	247_E	0.507	0.11
114_F	137_C	0.504	0.11
196_S	276_C	0.504	0.11
49_V	191_T	0.503	0.11
147_T	244_P	0.502	0.11
198_A	229_L	0.502	0.11
152_P	185_P	0.501	0.11
44_A	148_Q	0.500	0.11
235_L	248_S	0.500	0.11

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
3sb1A	2	0.414	100	0.632	Contact Map
2ka6B	1	0.1439	49.5	0.967	Contact Map
2wulA	3	0.2982	16.2	0.974	Contact Map
3gx8A	1	0.3088	15.4	0.975	Contact Map
4wxtA	1	0.3298	10.8	0.976	Contact Map
3zywA	1	0.3088	10.1	0.977	Contact Map
2i0kA	1	0.4175	8.7	0.977	Contact Map
1q7lB	2	0.193	8.7	0.977	Contact Map
3js8A	1	0.414	8.5	0.977	Contact Map
1iloA	1	0.2491	8.3	0.977	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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