YGXA - BACSU - GREMLIN Contacts

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YGXA - Uncharacterized protein YgxA

UniProt:	Q04385	Sequences: MENLLRPIYQERASHPNTLAVIMIERRNKTSSLTDNFDAALLVIVKDADEPVFIKHYEFDHQTASLHVVTDSQIQEWILLGTNRRIIDWIVNGRVLFDRNEYVVELIDRLNTFPFAERKLKIGLEYGKLIRRYVEGKAFFEANQFLDAYNAVVHALHHLARIEVIDRGFHPETTVWSQVRQMEPQVYKLYSELIESHESLEKRLELLFLANDFLIHSKAEIGSAHLFEVMKEKDIWQFGELLQHHDLKHFTQDLGVMLDYLTEKGLINVCQIETKGQAVYHRGYSFKKGVDSDS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	294 (281)
Sequences:	231 (195)
Seq/√Len:	11.6

BACSU - YGXA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
227_F	267_I	4.744	1.00
130_I	204_L	3.832	0.99
225_H	250_F	2.948	0.95
188_K	192_E	2.674	0.91
22_I	70_T	2.609	0.90
204_L	208_F	2.571	0.89
230_M	241_L	2.454	0.87
130_I	233_K	2.424	0.86
23_M	96_L	2.160	0.79
172_E	178_Q	2.160	0.79
103_V	232_E	2.149	0.79
136_G	222_G	2.088	0.77
155_A	218_K	2.082	0.76
40_A	237_Q	2.038	0.75
133_Y	149_Y	2.037	0.75
162_I	204_L	2.037	0.75
120_L	267_I	2.030	0.74
153_V	221_I	2.013	0.74
165_I	237_Q	1.979	0.72
188_K	206_L	1.978	0.72
148_A	266_L	1.959	0.72
272_I	283_G	1.948	0.71
21_V	43_V	1.936	0.71
246_D	257_M	1.899	0.69
133_Y	196_S	1.897	0.69
9_Y	18_T	1.880	0.68
206_L	213_F	1.866	0.68
132_R	154_H	1.865	0.68
28_N	138_A	1.847	0.67
188_K	213_F	1.837	0.67
21_V	271_Q	1.833	0.66
170_H	238_F	1.833	0.66
241_L	267_I	1.832	0.66
52_V	139_F	1.819	0.66
171_P	178_Q	1.798	0.65
95_V	118_R	1.795	0.65
44_I	75_Q	1.776	0.64
123_G	204_L	1.754	0.63
137_K	183_E	1.750	0.63
20_A	166_D	1.745	0.62
141_E	215_I	1.718	0.61
157_H	172_E	1.717	0.61
4_L	59_F	1.686	0.60
41_L	230_M	1.685	0.60
109_R	133_Y	1.684	0.60
134_V	256_V	1.682	0.59
102_Y	226_L	1.643	0.58
192_E	206_L	1.634	0.57
35_D	114_P	1.576	0.54
132_R	158_H	1.566	0.54
94_R	241_L	1.556	0.53
61_H	152_V	1.554	0.53
188_K	209_L	1.545	0.53
211_N	215_I	1.533	0.52
206_L	209_L	1.491	0.50
127_G	212_D	1.479	0.50
170_H	173_T	1.477	0.49
201_E	223_S	1.476	0.49
130_I	212_D	1.467	0.49
241_L	258_L	1.453	0.48
205_E	209_L	1.451	0.48
87_I	240_E	1.450	0.48
28_N	280_Y	1.447	0.48
20_A	77_W	1.446	0.48
260_Y	269_V	1.426	0.47
241_L	254_L	1.411	0.46
61_H	280_Y	1.408	0.46
74_I	183_E	1.397	0.45
198_E	206_L	1.385	0.45
89_W	114_P	1.384	0.45
22_I	230_M	1.383	0.45
103_V	237_Q	1.369	0.44
206_L	210_A	1.369	0.44
51_P	204_L	1.351	0.43
143_N	268_N	1.339	0.43
8_I	11_E	1.325	0.42
76_E	230_M	1.313	0.41
271_Q	282_R	1.309	0.41
61_H	270_C	1.307	0.41
248_K	280_Y	1.307	0.41
176_W	192_E	1.300	0.41
135_E	138_A	1.296	0.41
103_V	265_G	1.293	0.40
228_E	258_L	1.291	0.40
40_A	180_R	1.281	0.40
44_I	254_L	1.280	0.40
58_E	224_A	1.261	0.39
3_N	244_H	1.249	0.38
120_L	133_Y	1.248	0.38
43_V	226_L	1.244	0.38
136_G	158_H	1.240	0.38
32_S	125_E	1.237	0.38
103_V	247_L	1.230	0.37
48_A	155_A	1.226	0.37
146_L	269_V	1.209	0.37
32_S	110_L	1.206	0.36
105_E	220_E	1.206	0.36
20_A	126_Y	1.199	0.36
196_S	209_L	1.194	0.36
161_R	164_V	1.190	0.36
43_V	229_V	1.177	0.35
33_L	234_D	1.174	0.35
229_V	258_L	1.165	0.35
81_G	230_M	1.163	0.34
216_H	222_G	1.162	0.34
8_I	153_V	1.159	0.34
47_D	224_A	1.159	0.34
39_A	252_Q	1.158	0.34
64_A	140_F	1.155	0.34
170_H	255_G	1.152	0.34
12_R	18_T	1.152	0.34
61_H	76_E	1.146	0.34
34_T	173_T	1.145	0.34
192_E	209_L	1.145	0.34
171_P	176_W	1.141	0.33
117_E	155_A	1.140	0.33
221_I	231_K	1.139	0.33
8_I	64_A	1.130	0.33
156_L	175_V	1.129	0.33
35_D	173_T	1.122	0.33
143_N	218_K	1.121	0.33
198_E	209_L	1.119	0.32
64_A	254_L	1.117	0.32
70_T	265_G	1.117	0.32
38_D	97_F	1.114	0.32
201_E	242_L	1.112	0.32
224_A	264_K	1.107	0.32
20_A	135_E	1.106	0.32
24_I	241_L	1.104	0.32
84_R	109_R	1.101	0.32
40_A	155_A	1.099	0.32
230_M	267_I	1.093	0.31
35_D	131_R	1.092	0.31
148_A	204_L	1.089	0.31
60_D	278_A	1.083	0.31
133_Y	209_L	1.081	0.31
242_L	257_M	1.080	0.31
272_I	280_Y	1.073	0.31
89_W	171_P	1.070	0.30
209_L	212_D	1.067	0.30
18_T	225_H	1.063	0.30
4_L	243_Q	1.061	0.30
10_Q	101_E	1.058	0.30
156_L	189_L	1.056	0.30
189_L	206_L	1.051	0.30
96_L	223_S	1.046	0.29
95_V	244_H	1.032	0.29
203_R	206_L	1.020	0.28
221_I	277_Q	1.019	0.28
95_V	269_V	1.013	0.28
202_K	207_L	1.003	0.28
108_D	243_Q	0.994	0.27
203_R	209_L	0.994	0.27
86_I	111_N	0.993	0.27
144_Q	179_V	0.990	0.27
83_N	100_N	0.984	0.27
29_K	39_A	0.982	0.27
176_W	206_L	0.981	0.27
176_W	209_L	0.981	0.27
278_A	283_G	0.980	0.27
39_A	278_A	0.978	0.27
43_V	72_S	0.977	0.27
98_D	104_V	0.972	0.26
204_L	211_N	0.972	0.26
6_R	18_T	0.971	0.26
213_F	216_H	0.971	0.26
94_R	230_M	0.967	0.26
17_N	133_Y	0.963	0.26
44_I	96_L	0.961	0.26
54_I	231_K	0.961	0.26
96_L	141_E	0.960	0.26
180_R	228_E	0.959	0.26
7_P	64_A	0.955	0.26
54_I	244_H	0.955	0.26
189_L	198_E	0.953	0.26
162_I	246_D	0.951	0.26
52_V	208_F	0.950	0.26
212_D	240_E	0.946	0.25
90_I	201_E	0.942	0.25
140_F	216_H	0.942	0.25
119_K	228_E	0.941	0.25
192_E	203_R	0.938	0.25
171_P	241_L	0.938	0.25
27_R	30_T	0.937	0.25
40_A	65_S	0.935	0.25
123_G	131_R	0.930	0.25
21_V	94_R	0.925	0.25
131_R	257_M	0.925	0.25
136_G	205_E	0.924	0.25
91_V	96_L	0.923	0.25
81_G	208_F	0.920	0.25
87_I	135_E	0.919	0.24
87_I	179_V	0.918	0.24
44_I	234_D	0.914	0.24
20_A	155_A	0.913	0.24
248_K	273_E	0.911	0.24
145_F	230_M	0.904	0.24
204_L	214_L	0.898	0.24
140_F	159_L	0.898	0.24
134_V	199_S	0.894	0.24
166_D	212_D	0.890	0.23
213_F	217_S	0.887	0.23
19_L	139_F	0.885	0.23
147_D	171_P	0.880	0.23
192_E	210_A	0.878	0.23
50_E	260_Y	0.874	0.23
17_N	270_C	0.873	0.23
204_L	240_E	0.871	0.23
69_V	90_I	0.871	0.23
127_G	199_S	0.871	0.23
34_T	57_Y	0.870	0.23
209_L	213_F	0.869	0.23
211_N	216_H	0.866	0.23
78_I	95_V	0.864	0.23
114_P	118_R	0.860	0.22
86_I	90_I	0.848	0.22
66_L	275_K	0.847	0.22
194_I	248_K	0.844	0.22
130_I	208_F	0.844	0.22
158_H	222_G	0.840	0.22
154_H	169_F	0.839	0.22
61_H	211_N	0.837	0.22
147_D	176_W	0.836	0.22
192_E	202_K	0.835	0.22
148_A	232_E	0.834	0.22
8_I	254_L	0.833	0.21
61_H	87_I	0.830	0.21
131_R	146_L	0.829	0.21
95_V	104_V	0.823	0.21
49_D	98_D	0.823	0.21
108_D	143_N	0.823	0.21
127_G	146_L	0.821	0.21
251_T	258_L	0.818	0.21
170_H	223_S	0.815	0.21
166_D	206_L	0.815	0.21
201_E	224_A	0.814	0.21
30_T	40_A	0.814	0.21
152_V	191_S	0.807	0.21
60_D	280_Y	0.800	0.20
95_V	107_I	0.798	0.20
245_H	265_G	0.798	0.20
3_N	259_D	0.797	0.20
45_V	259_D	0.790	0.20
91_V	283_G	0.790	0.20
21_V	170_H	0.787	0.20
171_P	190_Y	0.786	0.20
61_H	115_F	0.786	0.20
65_S	281_H	0.785	0.20
108_D	191_S	0.785	0.20
130_I	251_T	0.778	0.20
61_H	137_K	0.769	0.19
78_I	205_E	0.767	0.19
31_S	142_A	0.761	0.19
32_S	255_G	0.759	0.19
230_M	243_Q	0.758	0.19
106_L	156_L	0.756	0.19
122_I	160_A	0.756	0.19
149_Y	193_L	0.754	0.19
79_L	117_E	0.751	0.19
273_E	277_Q	0.750	0.19
95_V	201_E	0.750	0.19
60_D	231_K	0.747	0.19
23_M	181_Q	0.745	0.19
212_D	238_F	0.744	0.19
104_V	230_M	0.742	0.19
3_N	27_R	0.740	0.19
246_D	258_L	0.740	0.19
72_S	143_N	0.740	0.19
102_Y	220_E	0.738	0.18
147_D	206_L	0.738	0.18
148_A	215_I	0.737	0.18
16_P	141_E	0.737	0.18
73_Q	122_I	0.733	0.18
109_R	196_S	0.733	0.18
64_A	175_V	0.733	0.18
149_Y	221_I	0.731	0.18
192_E	213_F	0.730	0.18
159_L	275_K	0.727	0.18
147_D	203_R	0.726	0.18
69_V	113_F	0.722	0.18
196_S	216_H	0.718	0.18
197_H	211_N	0.715	0.18
69_V	74_I	0.713	0.18
251_T	280_Y	0.713	0.18
200_L	264_K	0.712	0.18
28_N	199_S	0.707	0.18
55_K	281_H	0.702	0.17
202_K	259_D	0.701	0.17
200_L	245_H	0.701	0.17
28_N	277_Q	0.699	0.17
69_V	234_D	0.696	0.17
42_L	122_I	0.695	0.17
180_R	190_Y	0.695	0.17
52_V	207_L	0.693	0.17
22_I	66_L	0.691	0.17
143_N	235_I	0.688	0.17
199_S	237_Q	0.687	0.17
32_S	37_F	0.684	0.17
61_H	68_V	0.684	0.17
129_L	211_N	0.684	0.17
37_F	65_S	0.683	0.17
126_Y	147_D	0.680	0.17
88_D	111_N	0.678	0.17
109_R	155_A	0.678	0.17
106_L	110_L	0.677	0.17
35_D	264_K	0.674	0.17
163_E	183_E	0.665	0.16
235_I	283_G	0.661	0.16
11_E	64_A	0.661	0.16
199_S	256_V	0.659	0.16
20_A	221_I	0.657	0.16
81_G	158_H	0.655	0.16
69_V	86_I	0.654	0.16
209_L	233_K	0.652	0.16
54_I	230_M	0.649	0.16
65_S	159_L	0.647	0.16
98_D	209_L	0.647	0.16
28_N	40_A	0.644	0.16
176_W	203_R	0.643	0.16
24_I	169_F	0.643	0.16
56_H	121_K	0.642	0.16
127_G	226_L	0.641	0.16
36_N	63_T	0.640	0.16
11_E	106_L	0.640	0.16
179_V	206_L	0.638	0.16
190_Y	205_E	0.638	0.16
6_R	9_Y	0.637	0.16
189_L	203_R	0.636	0.16
38_D	265_G	0.635	0.16
64_A	263_E	0.634	0.16
60_D	163_E	0.634	0.16
20_A	127_G	0.631	0.16
174_T	204_L	0.630	0.15
105_E	109_R	0.629	0.15
123_G	214_L	0.628	0.15
205_E	213_F	0.628	0.15
37_F	149_Y	0.622	0.15
90_I	151_A	0.620	0.15
108_D	112_T	0.619	0.15
212_D	272_I	0.619	0.15
132_R	204_L	0.616	0.15
176_W	212_D	0.614	0.15
80_L	140_F	0.614	0.15
170_H	239_G	0.610	0.15
32_S	102_Y	0.604	0.15
74_I	164_V	0.602	0.15
231_K	270_C	0.601	0.15
31_S	240_E	0.597	0.15
50_E	103_V	0.595	0.15
66_L	139_F	0.595	0.15
95_V	199_S	0.594	0.15
159_L	260_Y	0.592	0.15
143_N	176_W	0.590	0.14
88_D	107_I	0.590	0.14
20_A	129_L	0.590	0.14
33_L	227_F	0.590	0.14
239_G	243_Q	0.587	0.14
6_R	225_H	0.581	0.14
128_K	149_Y	0.578	0.14
228_E	278_A	0.578	0.14
19_L	164_V	0.575	0.14
30_T	170_H	0.575	0.14
75_Q	248_K	0.573	0.14
119_K	143_N	0.572	0.14
155_A	232_E	0.570	0.14
202_K	209_L	0.570	0.14
152_V	239_G	0.570	0.14
11_E	18_T	0.567	0.14
23_M	143_N	0.565	0.14
146_L	152_V	0.565	0.14
131_R	161_R	0.563	0.14
74_I	80_L	0.561	0.14
139_F	208_F	0.560	0.14
9_Y	19_L	0.559	0.14
136_G	164_V	0.559	0.14
188_K	217_S	0.558	0.14
70_T	81_G	0.558	0.14
220_E	255_G	0.556	0.14
229_V	247_L	0.555	0.14
200_L	203_R	0.553	0.14
10_Q	281_H	0.550	0.14
125_E	236_W	0.550	0.14
130_I	155_A	0.549	0.14
48_A	237_Q	0.549	0.14
29_K	165_I	0.548	0.13
25_E	100_N	0.548	0.13
133_Y	203_R	0.547	0.13
197_H	208_F	0.544	0.13
244_H	262_T	0.544	0.13
188_K	198_E	0.542	0.13
153_V	215_I	0.540	0.13
231_K	258_L	0.540	0.13
177_S	266_L	0.539	0.13
148_A	168_G	0.536	0.13
70_T	278_A	0.536	0.13
134_V	186_V	0.534	0.13
47_D	280_Y	0.533	0.13
32_S	220_E	0.533	0.13
167_R	220_E	0.530	0.13
188_K	203_R	0.529	0.13
42_L	74_I	0.529	0.13
147_D	189_L	0.528	0.13
52_V	85_R	0.528	0.13
43_V	258_L	0.525	0.13
119_K	257_M	0.525	0.13
61_H	142_A	0.524	0.13
74_I	258_L	0.523	0.13
155_A	249_H	0.523	0.13
51_P	95_V	0.522	0.13
248_K	256_V	0.521	0.13
43_V	239_G	0.519	0.13
50_E	194_I	0.517	0.13
183_E	234_D	0.515	0.13
92_N	173_T	0.515	0.13
163_E	181_Q	0.511	0.13
3_N	22_I	0.511	0.13
154_H	242_L	0.508	0.13
19_L	97_F	0.507	0.13
78_I	177_S	0.507	0.13
33_L	94_R	0.502	0.12
112_T	248_K	0.500	0.12
34_T	131_R	0.500	0.12

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
3c18A	2	0.9796	100	0.127	Contact Map
1knyA	2	0.7891	99.4	0.843	Contact Map
3jz0A	2	0.8027	99	0.874	Contact Map
2pbeA	1	0.7041	98.8	0.883	Contact Map
4ebjA	2	0.8061	97.6	0.915	Contact Map
2rffA	1	0.3129	97.2	0.921	Contact Map
1no5A	4	0.3095	96.5	0.928	Contact Map
1ylqA	2	0.2891	95.6	0.933	Contact Map
1wotA	1	0.2959	93.9	0.939	Contact Map
4cs6A	1	0.6701	93.9	0.939	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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