YWBO - BACSU - GREMLIN Contacts

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YWBO - Uncharacterized protein YwbO

UniProt:	P39598	Sequences: MTVHIKVYSDYVCPFCFVGKAAFEEAIKGKDVEVEWMPFELRPSPSPQLDPVNDPSKQYMWQTSIQPMAEKLGVEINFPNVSPHPYTDLAFEGFHFAKEYNKGHEYNTRVFQAFFQEDQNIGDIDILTKLAEEVGLDGASFKSALETRTYQDVQRQALKHAYEEADITAVPTFIIGDTVIPGAAGKDVFEKAISDEQKKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	200 (189)
Sequences:	4554 (3530)
Seq/√Len:	256.8

BACSU - YWBO YJBH
HALSA - Q9HSL8
SULSO - Q97Z59

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
119_Q	129_K	3.524	1.00
29_G	190_E	3.001	1.00
112_Q	117_E	2.981	1.00
109_R	133_E	2.812	1.00
4_H	35_E	2.702	1.00
6_K	35_E	2.663	1.00
4_H	33_E	2.572	1.00
128_T	142_K	2.515	1.00
132_E	138_G	2.509	1.00
172_T	179_V	2.502	1.00
6_K	37_M	2.461	1.00
22_A	72_L	2.460	1.00
89_L	124_I	2.327	1.00
100_Y	140_S	2.208	1.00
106_Y	134_V	2.167	1.00
124_I	146_E	2.099	1.00
11_Y	94_F	2.045	1.00
11_Y	90_A	2.044	1.00
55_P	59_Y	2.018	1.00
159_K	164_E	2.011	1.00
20_K	24_E	1.910	1.00
99_E	153_V	1.900	1.00
119_Q	126_I	1.864	1.00
152_D	156_Q	1.815	1.00
21_A	108_T	1.811	1.00
102_K	105_E	1.808	1.00
88_D	155_R	1.800	1.00
120_N	123_D	1.769	1.00
131_A	141_F	1.745	1.00
113_A	130_L	1.697	1.00
106_Y	110_V	1.677	1.00
80_N	118_D	1.676	1.00
20_K	108_T	1.675	1.00
138_G	142_K	1.660	1.00
137_D	140_S	1.639	1.00
109_R	130_L	1.612	1.00
9_S	107_N	1.579	1.00
88_D	151_Q	1.578	1.00
93_G	106_Y	1.551	1.00
94_F	107_N	1.513	1.00
38_P	157_A	1.479	1.00
27_I	32_V	1.477	1.00
98_K	103_G	1.451	1.00
129_K	138_G	1.433	1.00
93_G	141_F	1.428	1.00
5_I	23_F	1.422	1.00
109_R	117_E	1.410	1.00
37_M	160_H	1.403	1.00
95_H	157_A	1.390	1.00
160_H	165_A	1.358	1.00
173_F	189_F	1.357	1.00
40_E	158_L	1.351	1.00
148_R	152_D	1.345	1.00
75_E	116_Q	1.308	1.00
97_A	101_N	1.301	1.00
77_N	80_N	1.300	1.00
113_A	119_Q	1.297	1.00
142_K	146_E	1.290	1.00
94_F	106_Y	1.281	1.00
112_Q	116_Q	1.280	1.00
37_M	157_A	1.278	1.00
36_W	104_H	1.243	1.00
125_D	142_K	1.239	1.00
113_A	126_I	1.238	1.00
107_N	111_F	1.237	1.00
190_E	194_S	1.225	1.00
35_E	98_K	1.212	1.00
6_K	177_D	1.195	1.00
53_N	57_K	1.157	1.00
156_Q	160_H	1.155	1.00
24_E	108_T	1.152	1.00
130_L	134_V	1.146	1.00
99_E	150_Y	1.132	1.00
175_I	192_A	1.121	1.00
54_D	57_K	1.119	1.00
128_T	138_G	1.112	1.00
25_E	72_L	1.109	1.00
124_I	128_T	1.092	1.00
11_Y	107_N	1.087	1.00
22_A	185_G	1.082	1.00
93_G	127_L	1.075	1.00
109_R	134_V	1.067	1.00
184_A	188_V	1.062	1.00
128_T	132_E	1.062	1.00
144_A	150_Y	1.061	1.00
90_A	121_I	1.055	1.00
38_P	95_H	1.048	1.00
42_R	45_P	1.014	1.00
23_F	34_V	1.013	1.00
66_Q	70_E	1.013	1.00
64_S	67_P	1.012	1.00
165_A	174_I	1.008	1.00
89_L	92_E	1.001	1.00
139_A	143_S	0.999	1.00
129_K	133_E	0.993	1.00
25_E	28_K	0.986	1.00
140_S	143_S	0.985	1.00
60_M	64_S	0.971	1.00
169_A	172_T	0.967	1.00
63_T	67_P	0.964	1.00
110_V	127_L	0.956	1.00
95_H	98_K	0.952	1.00
97_A	136_L	0.951	1.00
12_V	87_T	0.951	1.00
16_C	170_V	0.951	1.00
109_R	112_Q	0.950	1.00
69_A	76_I	0.948	1.00
180_I	192_A	0.947	1.00
11_Y	110_V	0.945	1.00
159_K	163_E	0.941	1.00
92_E	148_R	0.941	1.00
40_E	88_D	0.939	1.00
126_I	129_K	0.928	1.00
96_F	144_A	0.926	1.00
25_E	29_G	0.923	1.00
8_Y	161_A	0.922	1.00
129_K	132_E	0.920	1.00
77_N	118_D	0.919	1.00
15_F	68_M	0.913	1.00
59_Y	63_T	0.912	1.00
61_W	65_I	0.912	1.00
174_I	179_V	0.907	1.00
87_T	91_F	0.906	1.00
153_V	156_Q	0.905	1.00
140_S	144_A	0.904	1.00
64_S	68_M	0.898	1.00
160_H	164_E	0.898	1.00
26_A	186_K	0.896	1.00
69_A	74_V	0.886	1.00
57_K	60_M	0.882	1.00
175_I	189_F	0.881	1.00
24_E	104_H	0.878	1.00
143_S	149_T	0.876	1.00
17_F	116_Q	0.870	1.00
140_S	149_T	0.860	1.00
155_R	158_L	0.855	0.99
96_F	150_Y	0.852	0.99
65_I	76_I	0.849	0.99
36_W	107_N	0.844	0.99
47_P	89_L	0.844	0.99
110_V	121_I	0.843	0.99
186_K	190_E	0.828	0.99
22_A	68_M	0.826	0.99
25_E	186_K	0.817	0.99
188_V	191_K	0.816	0.99
58_Q	62_Q	0.815	0.99
19_G	173_F	0.810	0.99
96_F	100_Y	0.807	0.99
67_P	70_E	0.807	0.99
40_E	155_R	0.803	0.99
21_A	24_E	0.802	0.99
106_Y	131_A	0.801	0.99
8_Y	174_I	0.799	0.99
81_V	118_D	0.798	0.99
39_F	170_V	0.798	0.99
18_V	65_I	0.798	0.99
70_E	75_E	0.793	0.99
20_K	104_H	0.781	0.99
17_F	74_V	0.776	0.99
123_D	126_I	0.774	0.99
109_R	113_A	0.767	0.99
110_V	130_L	0.763	0.99
160_H	177_D	0.762	0.99
20_K	36_W	0.762	0.99
39_F	44_S	0.760	0.99
142_K	145_L	0.754	0.99
169_A	181_P	0.742	0.99
61_W	64_S	0.741	0.99
63_T	66_Q	0.738	0.98
95_H	150_Y	0.738	0.98
9_S	111_F	0.729	0.98
175_I	193_I	0.728	0.98
57_K	61_W	0.723	0.98
100_Y	136_L	0.723	0.98
85_P	122_G	0.723	0.98
143_S	146_E	0.722	0.98
27_I	34_V	0.718	0.98
30_K	190_E	0.714	0.98
124_I	142_K	0.711	0.98
94_F	103_G	0.708	0.98
151_Q	155_R	0.707	0.98
181_P	184_A	0.707	0.98
143_S	147_T	0.704	0.98
45_P	49_L	0.704	0.98
172_T	181_P	0.702	0.98
175_I	180_I	0.700	0.98
40_E	86_Y	0.699	0.98
22_A	186_K	0.697	0.98
55_P	58_Q	0.697	0.98
96_F	141_F	0.694	0.98
21_A	74_V	0.694	0.98
139_A	142_K	0.693	0.98
44_S	47_P	0.684	0.98
41_L	87_T	0.681	0.97
93_G	110_V	0.676	0.97
13_C	16_C	0.672	0.97
5_I	32_V	0.667	0.97
158_L	163_E	0.662	0.97
191_K	194_S	0.660	0.97
10_D	87_T	0.659	0.97
7_V	36_W	0.654	0.97
17_F	112_Q	0.647	0.97
7_V	173_F	0.646	0.97
21_A	25_E	0.646	0.97
54_D	58_Q	0.645	0.96
8_Y	37_M	0.644	0.96
69_A	78_F	0.642	0.96
8_Y	38_P	0.642	0.96
147_T	150_Y	0.641	0.96
56_S	59_Y	0.641	0.96
53_N	58_Q	0.641	0.96
68_M	183_A	0.641	0.96
101_N	105_E	0.638	0.96
17_F	111_F	0.635	0.96
93_G	145_L	0.632	0.96
156_Q	164_E	0.627	0.96
144_A	147_T	0.624	0.96
189_F	192_A	0.623	0.96
167_I	172_T	0.620	0.96
100_Y	137_D	0.618	0.96
98_K	157_A	0.617	0.95
85_P	114_F	0.617	0.95
7_V	23_F	0.609	0.95
156_Q	159_K	0.605	0.95
11_Y	15_F	0.604	0.95
92_E	151_Q	0.602	0.95
37_M	98_K	0.602	0.95
68_M	72_L	0.599	0.95
150_Y	153_V	0.599	0.95
108_T	112_Q	0.596	0.95
23_F	27_I	0.594	0.94
22_A	25_E	0.592	0.94
26_A	190_E	0.589	0.94
40_E	43_P	0.586	0.94
100_Y	144_A	0.579	0.94
185_G	188_V	0.578	0.94
114_F	121_I	0.578	0.94
79_P	82_S	0.577	0.94
92_E	154_Q	0.576	0.94
102_K	134_V	0.574	0.93
105_E	134_V	0.573	0.93
48_Q	52_V	0.571	0.93
5_I	175_I	0.570	0.93
130_L	133_E	0.568	0.93
49_L	52_V	0.568	0.93
94_F	110_V	0.563	0.93
12_V	81_V	0.562	0.93
88_D	154_Q	0.560	0.93
157_A	160_H	0.555	0.92
9_S	16_C	0.554	0.92
165_A	177_D	0.551	0.92
45_P	48_Q	0.551	0.92
11_Y	121_I	0.551	0.92
95_H	153_V	0.549	0.92
32_V	193_I	0.549	0.92
90_A	122_G	0.547	0.92
68_M	71_K	0.546	0.92
45_P	50_D	0.545	0.92
64_S	185_G	0.545	0.92
53_N	61_W	0.543	0.91
79_P	118_D	0.539	0.91
22_A	183_A	0.536	0.91
8_Y	39_F	0.534	0.91
58_Q	61_W	0.534	0.91
92_E	149_T	0.530	0.90
87_T	114_F	0.526	0.90
153_V	157_A	0.525	0.90
6_K	165_A	0.525	0.90
128_T	131_A	0.523	0.90
99_E	149_T	0.516	0.89
90_A	127_L	0.515	0.89
95_H	99_E	0.515	0.89
5_I	173_F	0.514	0.89
126_I	130_L	0.514	0.89
81_V	85_P	0.513	0.89
21_A	112_Q	0.507	0.88
119_Q	130_L	0.507	0.88
29_G	186_K	0.505	0.88
85_P	120_N	0.505	0.88
119_Q	133_E	0.504	0.88
87_T	121_I	0.503	0.88
8_Y	160_H	0.503	0.88
17_F	21_A	0.501	0.88
67_P	71_K	0.500	0.88

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
2imfA	2	0.97	100	0.255	Contact Map
3fz5A	2	0.93	100	0.262	Contact Map
1r4wA	2	0.99	100	0.263	Contact Map
3rppA	2	0.98	100	0.265	Contact Map
3gl5A	2	0.985	100	0.287	Contact Map
3kzqA	3	0.97	100	0.301	Contact Map
2in3A	1	0.945	100	0.339	Contact Map
4nxiA	2	0.86	100	0.456	Contact Map
3f4sA	1	0.785	99.9	0.488	Contact Map
3c7mA	1	0.855	99.9	0.492	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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