YPUA - BACSU - GREMLIN Contacts

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YPUA - Uncharacterized protein YpuA

UniProt:	P31847	Sequences: MKKIWIGMLAAAVLLLMVPKVSLADAAVGDVIVTLGADLSESDKQKVLDEMNVPDNATTVTVTNKEEHEYLGKYISNAQIGSRAISSSSITIAKKGSGLNVETHNISGITDEMYLNALMTAGVKDAKVYVTAPFEVSGTAALTGLIKAYEVSSDEAISEDVKQVANQELVTTSELGDKIGNENAAALIAKIKEEFAKNGVPDNKADIEKQVDDAASDLNVTLTDSQKNQLVSLFNKMKNADIDWGQVSDQLDKAKDKITKFIESDEGKNFIQKVIDFFVSIWNAIVSIFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	290 (278)
Sequences:	449 (370)
Seq/√Len:	22.2

BACSU - YPUA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
277_F	281_I	4.925	1.00
272_Q	276_D	4.149	1.00
223_T	226_Q	4.049	1.00
284_A	288_I	3.451	1.00
178_K	226_Q	3.273	1.00
213_D	216_S	3.163	1.00
35_L	48_L	3.101	1.00
270_F	274_V	3.046	1.00
191_I	234_F	3.011	1.00
283_N	287_S	2.850	0.99
84_A	140_A	2.833	0.99
275_I	279_V	2.689	0.99
265_D	268_K	2.662	0.99
228_N	232_S	2.582	0.98
243_D	246_Q	2.576	0.98
268_K	276_D	2.570	0.98
282_W	286_V	2.520	0.98
33_V	53_V	2.506	0.98
100_N	127_K	2.474	0.98
105_N	135_E	2.454	0.98
230_L	234_F	2.420	0.98
66_E	147_K	2.332	0.97
278_F	281_I	2.246	0.96
272_Q	275_I	2.240	0.96
204_K	208_E	2.206	0.96
264_S	267_G	2.172	0.95
34_T	88_S	2.116	0.95
45_Q	49_D	2.071	0.94
106_I	130_V	2.049	0.94
9_L	13_V	2.045	0.94
106_I	114_Y	2.042	0.94
51_M	129_Y	1.962	0.92
269_N	272_Q	1.951	0.92
96_G	125_D	1.946	0.92
275_I	278_F	1.938	0.92
188_I	230_L	1.883	0.91
234_F	237_M	1.875	0.90
211_V	230_L	1.820	0.89
208_E	212_D	1.811	0.89
10_A	54_P	1.804	0.88
209_K	213_D	1.780	0.88
93_A	127_K	1.769	0.87
93_A	97_S	1.756	0.87
91_T	127_K	1.748	0.87
270_F	273_K	1.742	0.87
285_I	288_I	1.738	0.87
226_Q	229_Q	1.738	0.87
212_D	227_K	1.731	0.86
118_L	128_V	1.662	0.84
67_E	139_T	1.662	0.84
44_K	61_T	1.658	0.84
168_E	192_K	1.616	0.82
150_E	162_K	1.591	0.81
85_I	132_A	1.579	0.81
212_D	216_S	1.569	0.80
204_K	235_N	1.550	0.79
64_N	68_H	1.549	0.79
283_N	286_V	1.529	0.78
167_Q	236_K	1.528	0.78
224_D	228_N	1.472	0.76
108_G	173_S	1.447	0.74
234_F	247_V	1.442	0.74
113_M	133_P	1.432	0.74
50_E	131_T	1.431	0.74
223_T	227_K	1.406	0.72
271_I	275_I	1.389	0.71
114_Y	130_V	1.380	0.71
33_V	44_K	1.363	0.70
65_K	69_E	1.360	0.70
158_S	162_K	1.351	0.69
90_I	99_L	1.349	0.69
41_E	45_Q	1.326	0.68
276_D	279_V	1.314	0.67
269_N	274_V	1.302	0.66
120_T	192_K	1.298	0.66
120_T	168_E	1.295	0.66
233_L	237_M	1.289	0.65
253_K	256_D	1.286	0.65
67_E	137_S	1.281	0.65
95_K	125_D	1.267	0.64
278_F	282_W	1.260	0.64
69_E	281_I	1.259	0.63
108_G	177_D	1.259	0.63
104_H	131_T	1.252	0.63
128_V	195_F	1.237	0.62
164_V	237_M	1.235	0.62
188_I	233_L	1.224	0.61
221_T	225_S	1.220	0.61
67_E	80_I	1.213	0.60
7_G	11_A	1.212	0.60
32_I	88_S	1.202	0.60
109_I	113_M	1.196	0.59
32_I	149_Y	1.189	0.59
158_S	161_V	1.183	0.59
19_P	24_A	1.182	0.58
67_E	84_A	1.178	0.58
109_I	166_N	1.174	0.58
84_A	139_T	1.173	0.58
274_V	278_F	1.166	0.57
67_E	81_G	1.158	0.57
199_G	213_D	1.158	0.57
123_V	126_A	1.152	0.56
137_S	140_A	1.143	0.56
71_L	172_T	1.125	0.55
39_L	120_T	1.120	0.54
207_I	211_V	1.102	0.53
81_G	139_T	1.101	0.53
280_S	283_N	1.099	0.53
206_D	209_K	1.099	0.53
191_I	211_V	1.097	0.53
282_W	285_I	1.095	0.53
51_M	131_T	1.095	0.53
99_L	112_E	1.089	0.52
157_I	161_V	1.083	0.52
43_D	46_K	1.076	0.51
193_E	255_K	1.073	0.51
281_I	284_A	1.071	0.51
48_L	59_T	1.070	0.51
182_E	222_L	1.069	0.51
132_A	150_E	1.068	0.51
206_D	219_N	1.062	0.50
179_I	184_A	1.056	0.50
159_E	162_K	1.053	0.50
88_S	145_L	1.052	0.50
39_L	168_E	1.047	0.49
260_K	263_E	1.038	0.49
130_V	196_A	1.036	0.49
213_D	219_N	1.036	0.49
283_N	288_I	1.035	0.49
107_S	135_E	1.031	0.48
194_E	197_K	1.029	0.48
47_V	51_M	1.029	0.48
191_I	210_Q	1.026	0.48
275_I	283_N	1.018	0.47
103_T	131_T	1.013	0.47
210_Q	213_D	0.984	0.45
64_N	67_E	0.983	0.45
56_N	241_D	0.982	0.45
38_D	81_G	0.976	0.45
279_V	288_I	0.976	0.45
12_A	22_S	0.972	0.44
109_I	136_V	0.967	0.44
39_L	192_K	0.961	0.43
212_D	224_D	0.961	0.43
52_N	272_Q	0.957	0.43
87_S	114_Y	0.949	0.43
114_Y	196_A	0.949	0.43
85_I	140_A	0.942	0.42
208_E	228_N	0.941	0.42
80_I	137_S	0.935	0.42
279_V	282_W	0.932	0.42
108_G	139_T	0.931	0.41
34_T	129_Y	0.931	0.41
6_I	14_L	0.925	0.41
210_Q	219_N	0.917	0.41
16_L	249_D	0.911	0.40
57_A	251_L	0.906	0.40
68_H	72_G	0.905	0.40
80_I	170_V	0.905	0.40
27_A	123_V	0.898	0.39
132_A	166_N	0.894	0.39
225_S	232_S	0.894	0.39
64_N	80_I	0.883	0.38
56_N	263_E	0.882	0.38
81_G	137_S	0.876	0.38
97_S	125_D	0.873	0.38
174_E	248_S	0.868	0.37
43_D	134_F	0.866	0.37
276_D	280_S	0.866	0.37
116_N	120_T	0.865	0.37
74_Y	137_S	0.865	0.37
23_L	243_D	0.862	0.37
155_E	258_I	0.861	0.37
266_E	274_V	0.859	0.37
112_E	115_L	0.858	0.37
32_I	148_A	0.857	0.37
42_S	167_Q	0.857	0.37
51_M	89_S	0.854	0.36
112_E	185_A	0.849	0.36
113_M	118_L	0.849	0.36
116_N	168_E	0.847	0.36
205_A	209_K	0.845	0.36
10_A	13_V	0.837	0.35
124_K	246_Q	0.834	0.35
128_V	185_A	0.831	0.35
139_T	172_T	0.830	0.35
177_D	285_I	0.825	0.35
228_N	248_S	0.823	0.35
115_L	211_V	0.819	0.34
70_Y	121_A	0.814	0.34
16_L	49_D	0.814	0.34
249_D	281_I	0.812	0.34
67_E	74_Y	0.812	0.34
207_I	230_L	0.811	0.34
278_F	286_V	0.809	0.34
47_V	114_Y	0.808	0.34
118_L	187_L	0.805	0.33
224_D	227_K	0.801	0.33
8_M	13_V	0.801	0.33
20_K	177_D	0.800	0.33
81_G	84_A	0.796	0.33
139_T	176_G	0.796	0.33
248_S	281_I	0.795	0.33
143_T	170_V	0.794	0.33
187_L	220_V	0.793	0.33
163_Q	278_F	0.793	0.33
110_T	228_N	0.793	0.33
6_I	167_Q	0.792	0.33
41_E	225_S	0.791	0.33
64_N	84_A	0.791	0.33
64_N	81_G	0.788	0.32
35_L	134_F	0.788	0.32
272_Q	279_V	0.782	0.32
177_D	265_D	0.782	0.32
279_V	286_V	0.779	0.32
278_F	285_I	0.777	0.32
39_L	116_N	0.772	0.31
11_A	14_L	0.768	0.31
13_V	279_V	0.764	0.31
47_V	153_S	0.764	0.31
245_G	249_D	0.761	0.31
45_Q	156_A	0.756	0.31
88_S	214_A	0.752	0.30
201_P	206_D	0.751	0.30
71_L	84_A	0.750	0.30
99_L	102_E	0.746	0.30
47_V	131_T	0.744	0.30
260_K	271_I	0.744	0.30
87_S	106_I	0.742	0.30
117_A	242_I	0.740	0.30
24_A	27_A	0.739	0.30
195_F	210_Q	0.736	0.29
26_A	31_V	0.735	0.29
225_S	279_V	0.734	0.29
184_A	187_L	0.732	0.29
15_L	223_T	0.731	0.29
38_D	134_F	0.728	0.29
269_N	279_V	0.727	0.29
47_V	133_P	0.725	0.29
80_I	139_T	0.725	0.29
31_V	92_I	0.724	0.29
98_G	125_D	0.721	0.29
8_M	12_A	0.711	0.28
6_I	17_M	0.710	0.28
158_S	223_T	0.710	0.28
272_Q	288_I	0.709	0.28
262_I	268_K	0.706	0.28
45_Q	52_N	0.705	0.28
164_V	240_A	0.703	0.28
274_V	277_F	0.700	0.27
159_E	167_Q	0.698	0.27
67_E	71_L	0.697	0.27
12_A	15_L	0.696	0.27
51_M	87_S	0.696	0.27
81_G	170_V	0.696	0.27
90_I	148_A	0.693	0.27
99_L	119_M	0.691	0.27
29_G	164_V	0.691	0.27
118_L	236_K	0.689	0.27
175_L	184_A	0.689	0.27
113_M	185_A	0.688	0.27
31_V	87_S	0.688	0.27
132_A	136_V	0.688	0.27
169_L	225_S	0.687	0.27
271_I	274_V	0.683	0.26
156_A	163_Q	0.679	0.26
44_K	197_K	0.676	0.26
46_K	282_W	0.676	0.26
70_Y	143_T	0.672	0.26
158_S	171_T	0.672	0.26
40_S	43_D	0.672	0.26
113_M	184_A	0.670	0.26
196_A	242_I	0.668	0.26
85_I	149_Y	0.668	0.26
275_I	282_W	0.662	0.25
203_N	206_D	0.661	0.25
34_T	71_L	0.659	0.25
176_G	179_I	0.656	0.25
84_A	137_S	0.656	0.25
90_I	149_Y	0.654	0.25
53_V	147_K	0.653	0.25
13_V	124_K	0.651	0.25
99_L	219_N	0.651	0.25
116_N	258_I	0.651	0.25
29_G	125_D	0.650	0.25
38_D	84_A	0.649	0.25
10_A	22_S	0.649	0.25
28_V	92_I	0.648	0.25
48_L	81_G	0.644	0.24
208_E	219_N	0.644	0.24
28_V	94_K	0.643	0.24
188_I	191_I	0.642	0.24
111_D	115_L	0.641	0.24
7_G	18_V	0.641	0.24
34_T	140_A	0.640	0.24
114_Y	148_A	0.639	0.24
178_K	188_I	0.639	0.24
242_I	247_V	0.638	0.24
109_I	176_G	0.638	0.24
53_V	89_S	0.637	0.24
60_V	83_R	0.634	0.24
169_L	183_N	0.631	0.24
113_M	128_V	0.629	0.24
96_G	237_M	0.628	0.24
54_P	256_D	0.628	0.24
14_L	17_M	0.627	0.24
12_A	42_S	0.623	0.23
132_A	162_K	0.620	0.23
282_W	288_I	0.620	0.23
53_V	57_A	0.619	0.23
168_E	222_L	0.619	0.23
195_F	230_L	0.617	0.23
271_I	282_W	0.616	0.23
211_V	261_F	0.615	0.23
17_M	177_D	0.615	0.23
119_M	250_Q	0.615	0.23
186_A	235_N	0.614	0.23
239_N	249_D	0.614	0.23
282_W	287_S	0.612	0.23
278_F	288_I	0.610	0.23
41_E	44_K	0.609	0.23
148_A	218_L	0.608	0.23
115_L	157_I	0.608	0.23
193_E	272_Q	0.606	0.23
208_E	211_V	0.604	0.23
95_K	273_K	0.604	0.23
274_V	279_V	0.602	0.22
85_I	136_V	0.601	0.22
176_G	184_A	0.599	0.22
121_A	196_A	0.597	0.22
62_V	70_Y	0.596	0.22
25_D	29_G	0.594	0.22
94_K	220_V	0.593	0.22
268_K	272_Q	0.589	0.22
190_K	218_L	0.589	0.22
162_K	167_Q	0.587	0.22
273_K	280_S	0.584	0.22
182_E	239_N	0.581	0.21
195_F	199_G	0.581	0.21
146_I	153_S	0.577	0.21
10_A	219_N	0.577	0.21
71_L	121_A	0.575	0.21
31_V	131_T	0.575	0.21
99_L	140_A	0.575	0.21
100_N	205_A	0.572	0.21
107_S	145_L	0.571	0.21
187_L	218_L	0.567	0.21
35_L	268_K	0.566	0.21
114_Y	146_I	0.564	0.21
143_T	163_Q	0.564	0.21
198_N	204_K	0.561	0.21
91_T	242_I	0.560	0.20
39_L	43_D	0.559	0.20
120_T	133_P	0.553	0.20
176_G	181_N	0.553	0.20
42_S	197_K	0.553	0.20
266_E	271_I	0.552	0.20
149_Y	233_L	0.552	0.20
256_D	281_I	0.550	0.20
225_S	262_I	0.546	0.20
121_A	147_K	0.544	0.20
108_G	176_G	0.543	0.20
109_I	185_A	0.543	0.20
63_T	252_D	0.542	0.20
42_S	124_K	0.541	0.20
26_A	34_T	0.541	0.20
137_S	222_L	0.540	0.20
265_D	276_D	0.539	0.20
139_T	179_I	0.537	0.19
32_I	152_S	0.537	0.19
65_K	95_K	0.535	0.19
181_N	185_A	0.534	0.19
70_Y	98_G	0.533	0.19
66_E	84_A	0.532	0.19
78_A	107_S	0.532	0.19
11_A	18_V	0.531	0.19
214_A	278_F	0.530	0.19
50_E	157_I	0.530	0.19
99_L	126_A	0.530	0.19
37_A	63_T	0.530	0.19
143_T	162_K	0.529	0.19
116_N	192_K	0.529	0.19
199_G	238_K	0.529	0.19
81_G	108_G	0.528	0.19
160_D	259_T	0.528	0.19
105_N	126_A	0.527	0.19
50_E	104_H	0.524	0.19
213_D	217_D	0.523	0.19
114_Y	117_A	0.522	0.19
230_L	237_M	0.522	0.19
266_E	288_I	0.522	0.19
85_I	281_I	0.521	0.19
52_N	279_V	0.521	0.19
281_I	285_I	0.519	0.19
99_L	237_M	0.517	0.19
169_L	173_S	0.517	0.19
269_N	273_K	0.516	0.19
85_I	134_F	0.516	0.19
21_V	188_I	0.515	0.19
44_K	216_S	0.515	0.19
136_V	139_T	0.513	0.18
18_V	110_T	0.513	0.18
88_S	130_V	0.512	0.18
40_S	287_S	0.512	0.18
71_L	82_S	0.509	0.18
41_E	280_S	0.509	0.18
33_V	147_K	0.508	0.18
263_E	270_F	0.508	0.18
7_G	10_A	0.506	0.18
67_E	109_I	0.505	0.18
113_M	176_G	0.504	0.18
274_V	286_V	0.504	0.18
149_Y	234_F	0.502	0.18
279_V	287_S	0.501	0.18
230_L	247_V	0.501	0.18
177_D	203_N	0.500	0.18
221_T	224_D	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
1m5yA	1	0.4414	52	0.96	Contact Map
1y1xA	2	0.6069	40	0.963	Contact Map
1iojA	1	0.1862	33.7	0.965	Contact Map
2w9yA	1	0.2862	29.9	0.965	Contact Map
4il1A	1	0	24.1	0.967	Contact Map
2o36A	1	0.6207	23.8	0.967	Contact Map
3eabG	1	0.1448	22.6	0.967	Contact Map
3sjsA	2	0.6724	22.4	0.968	Contact Map
2fcgF	1	0.0586	21.7	0.968	Contact Map
1k8uA	2	0.2966	21.2	0.968	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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