HYBA - ECOLI - GREMLIN Contacts

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HYBA - Hydrogenase-2 operon protein HybA

UniProt:	P0AAJ8	Sequences: MNRRNFIKAASCGALLTGALPSVSHAAAENRPPIPGSLGMLYDSTLCVGCQACVTKCQDINFPERNPQGEQTWSNNDKLSPYTNNIIQVWTSGTGVNKDQEENGYAYIKKQCMHCVDPNCVSVCPVSALKKDPKTGIVHYDKDVCTGCRYCMVACPYNVPKYDYNNPFGALHKCELCNQKGVERLDKGGLPGCVEVCPAGAVIFGTREELMAEAKKRLALKPGSEYHYPRQTLKSGDTYLHTVPKYYPHLYGEKEGGGTQVLVLTGVPYENLDLPKLDDLSTGARSENIQHTLYKGMMLPLAVLAGLTVLVRRNTKNDHHDGGDDHES	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11799
Length:	328 (263)
Sequences:	569 (346)
Seq/√Len:	21.3

ECOLI - HYBA FDNH FDOH NRFC YDHX
HALSA - DMSB
SULSO - Q97V38 Q97XX9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
132_D	135_T	5.480	1.00
194_V	202_V	4.647	1.00
215_K	250_L	3.951	1.00
162_Y	171_L	3.609	1.00
215_K	253_E	3.078	1.00
265_T	269_Y	3.006	0.99
213_E	216_K	2.984	0.99
65_R	83_T	2.963	0.99
121_V	129_L	2.949	0.99
60_I	192_G	2.861	0.99
211_M	250_L	2.801	0.99
203_I	213_E	2.707	0.99
54_V	76_N	2.704	0.99
60_I	183_E	2.574	0.98
45_T	266_G	2.502	0.98
85_N	109_K	2.460	0.98
40_M	261_V	2.401	0.97
39_G	210_L	2.339	0.97
118_P	131_K	2.334	0.97
132_D	139_H	2.301	0.96
42_Y	261_V	2.300	0.96
116_V	260_Q	2.223	0.96
207_R	211_M	2.221	0.96
178_N	186_D	2.181	0.95
125_P	146_T	2.180	0.95
211_M	253_E	2.179	0.95
78_K	161_K	2.173	0.95
183_E	192_G	2.139	0.94
252_G	255_E	2.115	0.94
61_N	175_E	2.099	0.94
30_N	33_P	2.087	0.94
184_R	195_E	1.946	0.91
149_R	152_M	1.914	0.90
41_L	262_L	1.850	0.89
212_A	216_K	1.833	0.88
48_V	199_A	1.825	0.88
319_H	322_G	1.800	0.87
29_E	32_P	1.784	0.87
117_D	122_S	1.720	0.85
298_M	302_A	1.719	0.85
152_M	171_L	1.702	0.84
36_G	208_E	1.692	0.84
38_L	137_I	1.691	0.84
31_R	34_I	1.669	0.83
317_N	322_G	1.653	0.82
78_K	88_Q	1.616	0.81
212_A	215_K	1.596	0.80
40_M	202_V	1.574	0.79
296_G	300_P	1.573	0.79
211_M	215_K	1.569	0.79
295_K	299_L	1.556	0.78
41_L	210_L	1.555	0.78
58_Q	83_T	1.531	0.77
43_D	258_G	1.524	0.77
206_T	209_E	1.505	0.76
152_M	162_Y	1.495	0.75
149_R	162_Y	1.479	0.74
290_Q	293_L	1.448	0.73
272_L	279_D	1.434	0.72
32_P	35_P	1.406	0.71
42_Y	176_L	1.406	0.71
142_K	153_V	1.398	0.70
65_R	68_Q	1.397	0.70
108_I	287_E	1.387	0.70
61_N	176_L	1.379	0.69
157_Y	191_P	1.369	0.68
87_I	107_Y	1.362	0.68
160_P	257_G	1.336	0.67
126_V	149_R	1.327	0.66
42_Y	111_Q	1.326	0.66
46_L	203_I	1.312	0.65
315_T	319_H	1.311	0.65
37_S	116_V	1.295	0.64
31_R	35_P	1.292	0.64
33_P	36_G	1.291	0.64
302_A	311_V	1.289	0.64
309_V	314_N	1.288	0.64
316_K	319_H	1.288	0.64
318_D	322_G	1.287	0.64
163_D	171_L	1.285	0.63
211_M	252_G	1.245	0.61
48_V	52_A	1.239	0.61
137_I	185_L	1.233	0.60
210_L	262_L	1.223	0.60
99_D	102_E	1.222	0.59
210_L	264_L	1.222	0.59
38_L	206_T	1.211	0.59
308_T	314_N	1.210	0.59
274_L	277_L	1.204	0.58
308_T	313_R	1.201	0.58
157_Y	259_T	1.189	0.57
159_V	316_K	1.173	0.56
118_P	135_T	1.167	0.56
313_R	317_N	1.163	0.56
250_L	262_L	1.162	0.56
130_K	141_D	1.155	0.55
81_P	163_D	1.145	0.54
205_G	210_L	1.142	0.54
184_R	189_G	1.140	0.54
54_V	75_N	1.139	0.54
163_D	166_N	1.138	0.54
196_V	313_R	1.138	0.54
29_E	34_I	1.136	0.54
85_N	111_Q	1.133	0.54
208_E	212_A	1.131	0.53
98_K	102_E	1.129	0.53
317_N	320_H	1.127	0.53
251_Y	258_G	1.125	0.53
109_K	261_V	1.124	0.53
80_S	159_V	1.122	0.53
216_K	219_A	1.108	0.52
44_S	106_A	1.100	0.51
46_L	200_G	1.085	0.50
302_A	310_L	1.079	0.50
290_Q	294_Y	1.075	0.50
249_H	253_E	1.074	0.50
249_H	255_E	1.074	0.50
213_E	296_G	1.067	0.49
294_Y	300_P	1.061	0.49
305_A	312_R	1.057	0.49
42_Y	263_V	1.055	0.48
154_A	261_V	1.045	0.48
44_S	265_T	1.040	0.47
312_R	316_K	1.039	0.47
51_Q	76_N	1.035	0.47
140_Y	154_A	1.031	0.47
286_S	291_H	1.025	0.46
162_Y	265_T	1.021	0.46
221_K	225_E	1.018	0.46
176_L	261_V	1.017	0.46
60_I	184_R	1.017	0.46
170_A	224_S	1.014	0.46
258_G	263_V	1.013	0.46
118_P	257_G	1.008	0.45
29_E	33_P	1.003	0.45
143_D	293_L	0.994	0.44
29_E	36_G	0.991	0.44
111_Q	261_V	0.984	0.44
51_Q	225_E	0.979	0.43
215_K	219_A	0.970	0.43
30_N	208_E	0.968	0.43
123_V	150_Y	0.964	0.42
38_L	204_F	0.958	0.42
90_W	275_P	0.953	0.42
191_P	194_V	0.951	0.42
28_A	31_R	0.948	0.41
79_L	186_D	0.942	0.41
290_Q	300_P	0.937	0.41
109_K	148_C	0.936	0.41
162_Y	297_M	0.935	0.40
284_A	303_V	0.931	0.40
61_N	200_G	0.930	0.40
277_L	280_L	0.928	0.40
272_L	275_P	0.925	0.40
69_G	117_D	0.924	0.40
128_A	144_V	0.922	0.40
84_N	172_H	0.920	0.40
30_N	34_I	0.919	0.39
42_Y	146_T	0.916	0.39
40_M	194_V	0.914	0.39
63_P	84_N	0.912	0.39
66_N	80_S	0.912	0.39
37_S	91_T	0.910	0.39
42_Y	109_K	0.910	0.39
74_S	170_A	0.907	0.39
42_Y	125_P	0.906	0.39
211_M	218_L	0.882	0.37
287_E	294_Y	0.874	0.37
290_Q	304_L	0.868	0.36
37_S	260_Q	0.866	0.36
90_W	273_D	0.863	0.36
122_S	287_E	0.857	0.36
80_S	264_L	0.850	0.35
129_L	140_Y	0.849	0.35
216_K	220_L	0.849	0.35
140_Y	169_G	0.846	0.35
256_G	274_L	0.845	0.35
287_E	291_H	0.843	0.35
304_L	307_L	0.840	0.35
195_E	221_K	0.831	0.34
63_P	66_N	0.827	0.34
61_N	84_N	0.826	0.34
279_D	321_D	0.824	0.34
218_L	264_L	0.824	0.34
298_M	301_L	0.823	0.33
132_D	137_I	0.822	0.33
312_R	319_H	0.817	0.33
35_P	100_Q	0.810	0.33
54_V	111_Q	0.809	0.33
310_L	315_T	0.807	0.33
52_A	59_D	0.802	0.32
72_T	88_Q	0.792	0.32
111_Q	152_M	0.783	0.31
121_V	199_A	0.780	0.31
32_P	142_K	0.778	0.31
141_D	144_V	0.778	0.31
218_L	223_G	0.777	0.31
135_T	139_H	0.777	0.31
170_A	209_E	0.775	0.31
122_S	286_S	0.772	0.31
38_L	176_L	0.769	0.30
48_V	161_K	0.769	0.30
36_G	206_T	0.768	0.30
131_K	200_G	0.765	0.30
81_P	162_Y	0.763	0.30
104_G	202_V	0.759	0.30
119_N	154_A	0.758	0.30
91_T	103_N	0.758	0.30
199_A	291_H	0.758	0.30
54_V	71_Q	0.757	0.30
62_F	65_R	0.756	0.30
315_T	318_D	0.755	0.30
101_E	264_L	0.754	0.30
296_G	302_A	0.754	0.30
51_Q	74_S	0.752	0.29
70_E	73_W	0.750	0.29
163_D	170_A	0.749	0.29
215_K	254_K	0.746	0.29
214_A	217_R	0.746	0.29
44_S	48_V	0.744	0.29
59_D	159_V	0.737	0.29
118_P	259_T	0.737	0.29
42_Y	274_L	0.728	0.28
295_K	311_V	0.728	0.28
34_I	37_S	0.727	0.28
75_N	89_V	0.727	0.28
308_T	312_R	0.725	0.28
305_A	318_D	0.714	0.27
55_T	166_N	0.713	0.27
45_T	217_R	0.713	0.27
185_L	192_G	0.710	0.27
141_D	216_K	0.701	0.27
52_A	196_V	0.699	0.27
111_Q	263_V	0.697	0.26
39_G	204_F	0.697	0.26
297_M	300_P	0.696	0.26
163_D	169_G	0.695	0.26
118_P	280_L	0.692	0.26
42_Y	106_A	0.691	0.26
126_V	154_A	0.688	0.26
54_V	127_S	0.686	0.26
190_L	302_A	0.681	0.26
309_V	313_R	0.679	0.26
87_I	132_D	0.679	0.26
299_L	302_A	0.675	0.25
123_V	146_T	0.674	0.25
64_E	79_L	0.674	0.25
44_S	263_V	0.672	0.25
190_L	194_V	0.672	0.25
54_V	86_I	0.671	0.25
168_F	201_A	0.671	0.25
32_P	36_G	0.667	0.25
221_K	264_L	0.662	0.25
139_H	178_N	0.655	0.24
81_P	322_G	0.654	0.24
311_V	320_H	0.653	0.24
146_T	202_V	0.651	0.24
185_L	302_A	0.650	0.24
141_D	178_N	0.647	0.24
52_A	161_K	0.647	0.24
162_Y	212_A	0.647	0.24
152_M	261_V	0.645	0.24
85_N	88_Q	0.645	0.24
60_I	74_S	0.644	0.24
52_A	60_I	0.639	0.24
297_M	309_V	0.639	0.24
58_Q	295_K	0.637	0.23
175_E	224_S	0.636	0.23
170_A	284_A	0.633	0.23
92_S	162_Y	0.630	0.23
277_L	313_R	0.630	0.23
82_Y	167_P	0.629	0.23
277_L	283_G	0.627	0.23
159_V	248_P	0.626	0.23
79_L	129_L	0.625	0.23
198_P	202_V	0.625	0.23
79_L	161_K	0.622	0.23
28_A	60_I	0.622	0.23
226_Y	269_Y	0.621	0.23
208_E	320_H	0.620	0.23
287_E	292_T	0.619	0.23
290_Q	296_G	0.618	0.23
186_D	250_L	0.615	0.22
149_R	153_V	0.615	0.22
158_N	202_V	0.612	0.22
109_K	263_V	0.611	0.22
249_H	266_G	0.610	0.22
79_L	175_E	0.609	0.22
69_G	72_T	0.609	0.22
33_P	134_K	0.607	0.22
69_G	319_H	0.607	0.22
129_L	202_V	0.606	0.22
222_P	225_E	0.606	0.22
269_Y	272_L	0.601	0.22
219_A	250_L	0.598	0.22
122_S	201_A	0.593	0.21
135_T	260_Q	0.593	0.21
169_G	225_E	0.592	0.21
31_R	142_K	0.589	0.21
63_P	82_Y	0.589	0.21
102_E	322_G	0.587	0.21
98_K	298_M	0.585	0.21
207_R	262_L	0.585	0.21
137_I	178_N	0.584	0.21
149_R	253_E	0.584	0.21
305_A	309_V	0.582	0.21
149_R	294_Y	0.580	0.21
46_L	98_K	0.579	0.21
134_K	200_G	0.577	0.21
87_I	137_I	0.572	0.20
41_L	264_L	0.569	0.20
280_L	283_G	0.569	0.20
80_S	170_A	0.568	0.20
64_E	172_H	0.568	0.20
31_R	208_E	0.566	0.20
198_P	259_T	0.566	0.20
30_N	35_P	0.564	0.20
295_K	298_M	0.564	0.20
39_G	44_S	0.558	0.20
148_C	157_Y	0.557	0.20
67_P	80_S	0.557	0.20
253_E	262_L	0.556	0.20
35_P	141_D	0.550	0.20
265_T	268_P	0.548	0.19
253_E	286_S	0.548	0.19
48_V	76_N	0.546	0.19
118_P	160_P	0.546	0.19
213_E	219_A	0.545	0.19
80_S	320_H	0.543	0.19
30_N	36_G	0.542	0.19
303_V	311_V	0.541	0.19
215_K	262_L	0.537	0.19
212_A	270_E	0.536	0.19
64_E	84_N	0.536	0.19
86_I	194_V	0.531	0.19
252_G	258_G	0.531	0.19
52_A	116_V	0.530	0.19
58_Q	108_I	0.529	0.19
109_K	198_P	0.526	0.19
156_P	193_C	0.525	0.18
125_P	300_P	0.524	0.18
299_L	307_L	0.523	0.18
312_R	318_D	0.522	0.18
81_P	153_V	0.520	0.18
304_L	308_T	0.518	0.18
55_T	301_L	0.517	0.18
40_M	111_Q	0.515	0.18
163_D	256_G	0.512	0.18
293_L	306_G	0.511	0.18
194_V	201_A	0.510	0.18
40_M	152_M	0.506	0.18
59_D	317_N	0.506	0.18
281_S	287_E	0.506	0.18
41_L	135_T	0.505	0.18
313_R	316_K	0.501	0.18
47_C	197_C	0.500	0.18
124_C	155_C	0.500	0.18
47_C	50_C	0.500	0.18
47_C	53_C	0.500	0.18
47_C	57_C	0.500	0.18
47_C	120_C	0.500	0.18
47_C	174_C	0.500	0.18
47_C	173_K	0.500	0.18
47_C	155_C	0.500	0.18
47_C	112_C	0.500	0.18
47_C	151_C	0.500	0.18
47_C	115_C	0.500	0.18
47_C	124_C	0.500	0.18
47_C	145_C	0.500	0.18
145_C	155_C	0.500	0.18
124_C	174_C	0.500	0.18
124_C	173_K	0.500	0.18
124_C	145_C	0.500	0.18
53_C	197_C	0.500	0.18
120_C	197_C	0.500	0.18
120_C	174_C	0.500	0.18
120_C	173_K	0.500	0.18
120_C	155_C	0.500	0.18
120_C	151_C	0.500	0.18
120_C	145_C	0.500	0.18
124_C	197_C	0.500	0.18
53_C	174_C	0.500	0.18
145_C	151_C	0.500	0.18
53_C	112_C	0.500	0.18
53_C	115_C	0.500	0.18
57_C	197_C	0.500	0.18
53_C	120_C	0.500	0.18
53_C	124_C	0.500	0.18
53_C	145_C	0.500	0.18
53_C	151_C	0.500	0.18
53_C	155_C	0.500	0.18
53_C	173_K	0.500	0.18
57_C	173_K	0.500	0.18
115_C	197_C	0.500	0.18

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
1kqfB	3	0.8445	100	0.529	Contact Map
1h0hB	1	0.6341	100	0.629	Contact Map
2ivfB	1	0.7927	100	0.655	Contact Map
1ti6B	2	0.7591	100	0.68	Contact Map
2vpzB	2	0.5884	100	0.704	Contact Map
1q16B	2	0.8628	100	0.715	Contact Map
4z3xE	2	0.5183	99.9	0.783	Contact Map
3mm5B	2	0.7256	99.8	0.831	Contact Map
2fgoA	1	0.2317	99.4	0.88	Contact Map
1rgvA	1	0.2409	99.3	0.884	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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