YBAP - ECOLI - GREMLIN Contacts

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YBAP - Uncharacterized protein YbaP

UniProt:	P77301	Sequences: MDLLYRVKTLWAALRGNHYTWPAIDITLPGNRHFHLIGSIHMGSHDMAPLPTRLLKKLKNADALIVEADVSTSDTPFANLPACEALEERISEEQLQNLQHISQEMGISPSLFSTQPLWQIAMVLQATQAQKLGLRAEYGIDYQLLQAAKQQHKPVIELEGAENQIAMLLQLPDKGLALLDDTLTHWHTNARLLQQMMSWWLNAPPQNNDITLPNTFSQSLYDVLMHQRNLAWRDKLRAMPPGRYVVAVGALHLYGEGNLPQMLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13244
Length:	264 (247)
Sequences:	1312 (1104)
Seq/√Len:	70.3

ECOLI - YBAP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_S	247_A	6.244	1.00
222_D	227_Q	5.653	1.00
91_S	94_Q	4.519	1.00
236_L	246_V	3.784	1.00
37_I	245_V	3.336	1.00
248_V	259_L	3.235	1.00
58_L	144_L	3.110	1.00
226_H	257_G	3.104	1.00
64_L	144_L	3.053	1.00
36_L	260_P	2.909	1.00
58_L	151_Q	2.809	1.00
222_D	226_H	2.703	1.00
163_N	231_A	2.640	1.00
116_P	169_L	2.592	1.00
66_V	145_L	2.519	1.00
61_A	245_V	2.487	1.00
204_P	207_N	2.471	1.00
157_E	160_G	2.465	1.00
84_E	89_R	2.432	1.00
236_L	239_M	2.420	1.00
87_E	113_S	2.380	1.00
230_L	262_M	2.348	1.00
163_N	167_M	2.335	1.00
175_G	179_L	2.298	1.00
24_I	37_I	2.225	1.00
65_I	156_I	2.221	1.00
233_R	259_L	2.186	1.00
225_M	251_L	2.178	1.00
163_N	235_K	2.161	1.00
66_V	141_D	2.114	1.00
212_L	251_L	2.101	1.00
221_Y	226_H	1.998	1.00
86_L	120_I	1.994	1.00
160_G	163_N	1.960	1.00
94_Q	180_D	1.933	1.00
144_L	247_A	1.929	1.00
57_K	245_V	1.900	1.00
37_I	54_L	1.899	1.00
34_F	236_L	1.828	1.00
249_G	252_H	1.790	1.00
65_I	232_W	1.732	1.00
38_G	41_H	1.692	1.00
258_N	262_M	1.671	1.00
199_W	207_N	1.653	0.99
62_D	243_R	1.630	0.99
41_H	249_G	1.624	0.99
228_R	249_G	1.591	0.99
66_V	157_E	1.586	0.99
66_V	155_V	1.561	0.99
121_A	178_L	1.553	0.99
65_I	246_V	1.518	0.99
102_S	112_F	1.509	0.99
43_G	47_M	1.486	0.99
80_L	89_R	1.475	0.99
228_R	252_H	1.474	0.99
85_A	88_E	1.414	0.98
41_H	252_H	1.393	0.98
29_P	32_R	1.391	0.98
63_A	244_Y	1.384	0.98
94_Q	97_N	1.365	0.98
87_E	95_L	1.345	0.98
26_I	33_H	1.343	0.98
232_W	259_L	1.297	0.97
63_A	156_I	1.276	0.97
233_R	258_N	1.262	0.97
99_Q	108_S	1.259	0.97
172_P	175_G	1.258	0.97
221_Y	257_G	1.255	0.96
115_Q	119_Q	1.251	0.96
233_R	237_R	1.243	0.96
116_P	175_G	1.204	0.96
97_N	184_T	1.197	0.95
41_H	228_R	1.192	0.95
23_A	37_I	1.180	0.95
63_A	154_P	1.176	0.95
78_A	119_Q	1.175	0.95
27_T	34_F	1.169	0.95
234_D	237_R	1.162	0.95
180_D	183_L	1.161	0.95
141_D	148_A	1.158	0.94
47_M	201_L	1.156	0.94
28_L	33_H	1.131	0.94
162_E	166_A	1.128	0.94
84_E	88_E	1.105	0.93
231_A	235_K	1.103	0.93
98_L	183_L	1.097	0.93
146_Q	150_Q	1.092	0.93
239_M	246_V	1.092	0.93
232_W	235_K	1.090	0.92
54_L	245_V	1.072	0.92
58_L	153_K	1.056	0.91
147_A	150_Q	1.052	0.91
140_I	200_W	1.049	0.91
200_W	203_A	1.045	0.91
83_C	117_L	1.041	0.91
36_L	259_L	1.040	0.91
40_I	140_I	1.037	0.90
52_T	55_L	1.036	0.90
226_H	230_L	1.035	0.90
27_T	30_G	1.031	0.90
68_A	157_E	1.030	0.90
139_G	200_W	1.030	0.90
188_T	219_S	1.028	0.90
223_V	227_Q	1.027	0.90
82_A	85_A	1.019	0.90
65_I	158_L	1.017	0.90
258_N	261_Q	1.005	0.89
28_L	31_N	0.993	0.88
35_H	245_V	0.992	0.88
43_G	139_G	0.986	0.88
148_A	153_K	0.981	0.88
34_F	258_N	0.980	0.88
199_W	204_P	0.979	0.88
54_L	57_K	0.977	0.88
24_I	57_K	0.968	0.87
204_P	208_N	0.959	0.87
230_L	257_G	0.957	0.87
23_A	200_W	0.953	0.86
81_P	84_E	0.949	0.86
26_I	35_H	0.948	0.86
34_F	239_M	0.945	0.86
121_A	182_T	0.942	0.86
49_P	143_Q	0.938	0.85
47_M	197_M	0.937	0.85
79_N	115_Q	0.935	0.85
40_I	197_M	0.933	0.85
160_G	164_Q	0.928	0.85
206_Q	209_D	0.926	0.85
53_R	56_K	0.925	0.85
118_W	175_G	0.920	0.84
27_T	263_L	0.919	0.84
158_L	232_W	0.917	0.84
232_W	248_V	0.913	0.84
22_P	232_W	0.910	0.84
31_N	34_F	0.910	0.84
67_E	249_G	0.910	0.84
110_S	113_S	0.910	0.84
32_R	241_P	0.903	0.83
61_A	243_R	0.898	0.83
221_Y	225_M	0.897	0.83
59_K	151_Q	0.893	0.83
57_K	61_A	0.891	0.82
44_S	47_M	0.886	0.82
100_H	104_E	0.882	0.82
64_L	155_V	0.881	0.82
55_L	147_A	0.876	0.81
48_A	143_Q	0.868	0.81
58_L	247_A	0.867	0.81
235_K	238_A	0.865	0.80
191_R	195_Q	0.865	0.80
27_T	246_V	0.858	0.80
254_Y	258_N	0.852	0.79
95_L	99_Q	0.849	0.79
236_L	263_L	0.845	0.79
227_Q	231_A	0.845	0.79
256_E	261_Q	0.840	0.79
94_Q	184_T	0.839	0.78
22_P	200_W	0.838	0.78
45_H	138_Y	0.836	0.78
233_R	262_M	0.831	0.78
58_L	147_A	0.827	0.77
40_I	43_G	0.825	0.77
99_Q	109_P	0.820	0.77
166_A	170_Q	0.819	0.77
250_A	254_Y	0.815	0.76
121_A	175_G	0.813	0.76
66_V	70_V	0.813	0.76
38_G	228_R	0.812	0.76
34_F	244_Y	0.806	0.76
55_L	246_V	0.802	0.75
86_L	141_D	0.796	0.75
80_L	84_E	0.792	0.74
69_D	72_T	0.790	0.74
257_G	261_Q	0.787	0.74
94_Q	176_L	0.786	0.74
117_L	175_G	0.786	0.74
213_P	221_Y	0.784	0.74
185_H	188_T	0.781	0.73
21_W	204_P	0.779	0.73
167_M	223_V	0.775	0.73
118_W	169_L	0.773	0.73
50_L	54_L	0.773	0.73
170_Q	223_V	0.770	0.72
97_N	187_H	0.768	0.72
63_A	242_G	0.765	0.72
72_T	157_E	0.756	0.71
209_D	254_Y	0.754	0.71
70_V	145_L	0.752	0.70
59_K	62_D	0.752	0.70
27_T	153_K	0.746	0.70
231_A	234_D	0.740	0.69
198_S	202_N	0.738	0.69
97_N	180_D	0.737	0.69
117_L	176_L	0.734	0.69
43_G	140_I	0.734	0.69
99_Q	103_Q	0.733	0.68
42_M	126_A	0.733	0.68
24_I	245_V	0.724	0.68
24_I	27_T	0.722	0.67
229_N	253_L	0.719	0.67
96_Q	100_H	0.719	0.67
24_I	54_L	0.718	0.67
46_D	140_I	0.715	0.67
254_Y	260_P	0.715	0.67
44_S	141_D	0.711	0.66
49_P	200_W	0.710	0.66
138_Y	143_Q	0.708	0.66
43_G	141_D	0.705	0.65
248_V	253_L	0.705	0.65
50_L	55_L	0.702	0.65
163_N	166_A	0.701	0.65
199_W	211_T	0.700	0.65
38_G	229_N	0.699	0.65
171_L	220_L	0.698	0.65
90_I	176_L	0.696	0.64
150_Q	154_P	0.696	0.64
54_L	58_L	0.694	0.64
89_R	94_Q	0.689	0.64
145_L	157_E	0.688	0.64
55_L	59_K	0.687	0.63
30_G	211_T	0.687	0.63
171_L	178_L	0.683	0.63
57_K	153_K	0.682	0.63
58_L	148_A	0.681	0.63
134_L	225_M	0.681	0.63
75_T	256_E	0.679	0.63
143_Q	236_L	0.676	0.62
50_L	140_I	0.674	0.62
118_W	168_L	0.670	0.62
170_Q	204_P	0.670	0.62
22_P	51_P	0.668	0.61
232_W	253_L	0.667	0.61
168_L	171_L	0.666	0.61
159_E	228_R	0.664	0.61
66_V	71_S	0.663	0.61
24_I	35_H	0.662	0.61
159_E	252_H	0.657	0.60
44_S	232_W	0.657	0.60
37_I	149_K	0.656	0.60
176_L	179_L	0.652	0.59
29_P	33_H	0.651	0.59
46_D	194_Q	0.648	0.59
79_N	114_T	0.644	0.59
232_W	236_L	0.642	0.58
253_L	258_N	0.639	0.58
142_Y	146_Q	0.639	0.58
64_L	220_L	0.634	0.57
86_L	118_W	0.630	0.57
47_M	140_I	0.627	0.56
162_E	193_L	0.625	0.56
90_I	94_Q	0.621	0.56
176_L	180_D	0.621	0.56
133_G	139_G	0.619	0.56
174_K	219_S	0.618	0.55
159_E	249_G	0.616	0.55
229_N	232_W	0.616	0.55
253_L	260_P	0.613	0.55
200_W	254_Y	0.607	0.54
71_S	75_T	0.606	0.54
97_N	100_H	0.605	0.54
133_G	136_A	0.603	0.54
26_I	54_L	0.602	0.53
222_D	259_L	0.601	0.53
234_D	238_A	0.601	0.53
212_L	259_L	0.599	0.53
25_D	153_K	0.599	0.53
55_L	58_L	0.599	0.53
43_G	232_W	0.598	0.53
96_Q	99_Q	0.596	0.53
33_H	243_R	0.595	0.53
158_L	262_M	0.594	0.53
25_D	253_L	0.594	0.53
66_V	140_I	0.592	0.52
83_C	176_L	0.591	0.52
52_T	256_E	0.588	0.52
44_S	131_K	0.588	0.52
236_L	254_Y	0.586	0.52
118_W	179_L	0.585	0.51
46_D	127_T	0.585	0.51
47_M	66_V	0.583	0.51
125_Q	186_W	0.582	0.51
68_A	164_Q	0.582	0.51
56_K	60_N	0.581	0.51
43_G	200_W	0.581	0.51
58_L	245_V	0.581	0.51
29_P	34_F	0.580	0.51
229_N	258_N	0.577	0.50
105_M	112_F	0.577	0.50
64_L	153_K	0.575	0.50
229_N	252_H	0.574	0.50
23_A	157_E	0.574	0.50
140_I	145_L	0.574	0.50
60_N	153_K	0.574	0.50
47_M	129_A	0.572	0.50
22_P	43_G	0.570	0.50
72_T	76_P	0.570	0.50
48_A	201_L	0.570	0.50
29_P	251_L	0.569	0.49
41_H	229_N	0.568	0.49
93_E	210_I	0.568	0.49
112_F	120_I	0.567	0.49
21_W	53_R	0.566	0.49
26_I	57_K	0.566	0.49
257_G	262_M	0.565	0.49
27_T	35_H	0.563	0.49
207_N	210_I	0.562	0.49
196_M	205_P	0.562	0.49
203_A	254_Y	0.561	0.48
91_S	176_L	0.558	0.48
132_L	190_A	0.557	0.48
42_M	190_A	0.556	0.48
209_D	213_P	0.555	0.48
121_A	126_A	0.554	0.48
222_D	230_L	0.553	0.48
155_V	180_D	0.551	0.47
40_I	258_N	0.551	0.47
24_I	34_F	0.551	0.47
87_E	110_S	0.550	0.47
91_S	95_L	0.550	0.47
169_L	204_P	0.549	0.47
48_A	58_L	0.549	0.47
200_W	239_M	0.547	0.47
46_D	89_R	0.546	0.47
81_P	114_T	0.545	0.47
24_I	51_P	0.545	0.47
169_L	175_G	0.545	0.47
37_I	58_L	0.544	0.46
248_V	252_H	0.544	0.46
172_P	176_L	0.543	0.46
143_Q	147_A	0.543	0.46
78_A	83_C	0.535	0.45
91_S	235_K	0.535	0.45
123_V	136_A	0.534	0.45
84_E	95_L	0.534	0.45
43_G	49_P	0.532	0.45
40_I	196_M	0.532	0.45
59_K	207_N	0.531	0.45
68_A	161_A	0.528	0.45
229_N	249_G	0.527	0.44
59_K	147_A	0.527	0.44
190_A	198_S	0.526	0.44
188_T	196_M	0.522	0.44
56_K	202_N	0.522	0.44
253_L	261_Q	0.522	0.44
170_Q	188_T	0.522	0.44
195_Q	207_N	0.521	0.44
172_P	179_L	0.519	0.43
94_Q	183_L	0.518	0.43
135_R	138_Y	0.518	0.43
51_P	203_A	0.517	0.43
70_V	142_Y	0.516	0.43
44_S	66_V	0.516	0.43
194_Q	198_S	0.516	0.43
28_L	32_R	0.515	0.43
68_A	160_G	0.515	0.43
96_Q	194_Q	0.514	0.43
206_Q	245_V	0.513	0.43
56_K	59_K	0.513	0.43
197_M	201_L	0.512	0.43
178_L	186_W	0.511	0.42
207_N	211_T	0.508	0.42
234_D	240_P	0.508	0.42
45_H	74_D	0.506	0.42
36_L	123_V	0.505	0.42
41_H	248_V	0.505	0.42
98_L	134_L	0.504	0.42
183_L	216_F	0.503	0.42
146_Q	224_L	0.501	0.41
189_N	196_M	0.501	0.41
121_A	160_G	0.500	0.41

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
2g5gX	1	0.7311	92.2	0.917	Contact Map
2o7aA	1	0.3902	25.7	0.952	Contact Map
4lmiA	2	0.3106	24.1	0.953	Contact Map
3f14A	2	0.1894	18.2	0.955	Contact Map
3unoA	6	0.3258	17.7	0.956	Contact Map
5aigA	1	0.2917	16.1	0.957	Contact Map
5aihA	1	0.2765	15.3	0.957	Contact Map
1vqqA	1	0.2841	14.4	0.957	Contact Map
4cydA	2	0.3371	13.4	0.958	Contact Map
3ehcA	2	0.1856	12.8	0.958	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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