YLBO - BACSU - GREMLIN Contacts

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YLBO - Uncharacterized protein YlbO

UniProt:	O34549	Sequences: MTITRQDAWTQDEDLLLAEVVLRHIREGGTQLSAFEEVGRALTRTAAACGFRWNSYVRKQYQSGIELAKKQRKELRKQIGVHSVNMPNSMKQTASASSEGKRDLSIQDVIQFLEQFKETPSAQEFQLEREKLKEQIQSLQKELEDLRSENQTLRNQLEMTEEDYKALIDIMDRARKMVVSKEDGRMKKAAQET	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	193 (179)
Sequences:	344 (257)
Seq/√Len:	19.2

BACSU - YLBO RSFA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
25_I	65_I	4.293	1.00
142_E	147_R	4.139	1.00
24_H	29_G	3.640	1.00
135_Q	140_Q	3.440	1.00
129_R	132_L	3.420	1.00
105_S	112_F	3.041	0.99
107_Q	117_K	2.870	0.99
141_K	145_D	2.693	0.98
13_E	43_T	2.650	0.98
149_E	154_R	2.344	0.96
64_G	67_L	2.262	0.95
64_G	71_Q	2.239	0.94
163_D	173_R	2.229	0.94
12_D	55_S	2.205	0.94
109_V	112_F	2.124	0.92
104_L	109_V	1.966	0.89
23_R	64_G	1.960	0.89
4_T	10_T	1.945	0.89
19_E	23_R	1.919	0.88
119_T	184_G	1.868	0.86
3_I	55_S	1.862	0.86
67_L	71_Q	1.764	0.83
56_Y	172_D	1.710	0.81
20_V	38_V	1.708	0.81
6_Q	51_F	1.705	0.81
12_D	43_T	1.691	0.80
147_R	151_Q	1.659	0.79
137_Q	141_K	1.644	0.78
62_Q	66_E	1.621	0.77
51_F	72_R	1.533	0.73
33_S	36_E	1.530	0.73
16_L	74_E	1.524	0.73
23_R	67_L	1.498	0.71
143_L	146_L	1.490	0.71
23_R	26_R	1.469	0.70
20_V	55_S	1.458	0.69
112_F	116_F	1.450	0.69
29_G	109_V	1.438	0.68
20_V	77_K	1.431	0.68
6_Q	72_R	1.421	0.67
136_I	139_L	1.397	0.66
15_L	23_R	1.393	0.66
43_T	55_S	1.387	0.65
38_V	51_F	1.387	0.65
11_Q	25_I	1.386	0.65
106_I	116_F	1.365	0.64
20_V	43_T	1.336	0.62
19_E	64_G	1.333	0.62
21_V	73_K	1.331	0.62
108_D	144_E	1.328	0.62
137_Q	151_Q	1.325	0.62
3_I	12_D	1.297	0.60
31_Q	58_R	1.296	0.60
115_Q	135_Q	1.281	0.59
26_R	71_Q	1.280	0.59
170_I	173_R	1.275	0.58
3_I	43_T	1.267	0.58
20_V	40_R	1.262	0.58
126_Q	130_E	1.257	0.57
94_A	97_S	1.255	0.57
40_R	55_S	1.249	0.57
25_I	172_D	1.236	0.56
123_Q	126_Q	1.211	0.54
43_T	59_K	1.209	0.54
85_N	88_N	1.202	0.54
10_T	46_A	1.181	0.53
16_L	51_F	1.165	0.52
25_I	76_R	1.161	0.51
150_N	153_L	1.149	0.51
156_Q	161_E	1.144	0.50
55_S	77_K	1.124	0.49
40_R	62_Q	1.123	0.49
6_Q	55_S	1.104	0.48
15_L	71_Q	1.102	0.48
74_E	116_F	1.096	0.47
13_E	62_Q	1.092	0.47
46_A	77_K	1.088	0.47
170_I	176_K	1.086	0.47
108_D	148_S	1.080	0.46
138_S	142_E	1.078	0.46
6_Q	164_Y	1.074	0.46
13_E	63_S	1.067	0.45
23_R	27_E	1.054	0.45
171_M	174_A	1.048	0.44
163_D	171_M	1.047	0.44
154_R	160_T	1.046	0.44
144_E	147_R	1.041	0.44
35_F	44_R	1.034	0.43
2_T	129_R	1.032	0.43
100_G	103_D	1.024	0.43
73_K	153_L	1.022	0.43
36_E	59_K	1.012	0.42
40_R	77_K	1.005	0.41
3_I	56_Y	0.989	0.41
44_R	49_C	0.981	0.40
58_R	68_A	0.980	0.40
51_F	55_S	0.975	0.40
152_T	156_Q	0.970	0.39
66_E	149_E	0.961	0.39
10_T	167_L	0.944	0.38
4_T	169_D	0.944	0.38
18_A	57_V	0.944	0.38
153_L	178_V	0.938	0.37
83_S	182_E	0.931	0.37
55_S	59_K	0.925	0.37
31_Q	68_A	0.924	0.37
12_D	20_V	0.922	0.36
10_T	84_V	0.914	0.36
128_E	133_K	0.912	0.36
177_M	180_S	0.906	0.36
163_D	168_I	0.906	0.36
3_I	40_R	0.900	0.35
118_E	121_S	0.899	0.35
32_L	37_E	0.899	0.35
170_I	174_A	0.888	0.34
150_N	183_D	0.884	0.34
177_M	181_K	0.882	0.34
7_D	47_A	0.870	0.33
164_Y	171_M	0.864	0.33
11_Q	76_R	0.860	0.33
78_Q	136_I	0.858	0.33
177_M	182_E	0.858	0.33
125_F	167_L	0.845	0.32
33_S	80_G	0.839	0.32
29_G	33_S	0.838	0.32
15_L	64_G	0.834	0.31
159_M	162_E	0.826	0.31
95_S	98_S	0.825	0.31
163_D	170_I	0.825	0.31
30_T	58_R	0.813	0.30
15_L	26_R	0.812	0.30
152_T	155_N	0.808	0.30
21_V	132_L	0.805	0.30
65_I	165_K	0.798	0.30
103_D	107_Q	0.796	0.29
160_T	171_M	0.794	0.29
130_E	134_E	0.793	0.29
36_E	46_A	0.792	0.29
35_F	49_C	0.791	0.29
43_T	70_K	0.791	0.29
44_R	50_G	0.790	0.29
75_L	79_I	0.776	0.28
5_R	44_R	0.775	0.28
165_K	177_M	0.769	0.28
118_E	127_L	0.761	0.28
171_M	176_K	0.761	0.28
115_Q	142_E	0.753	0.27
39_G	51_F	0.749	0.27
34_A	38_V	0.749	0.27
163_D	174_A	0.745	0.27
13_E	25_I	0.744	0.27
32_L	58_R	0.743	0.27
5_R	45_T	0.742	0.27
103_D	138_S	0.742	0.27
143_L	147_R	0.736	0.26
145_D	148_S	0.735	0.26
96_A	127_L	0.729	0.26
151_Q	155_N	0.724	0.26
7_D	45_T	0.720	0.26
106_I	114_E	0.720	0.26
125_F	129_R	0.718	0.25
46_A	139_L	0.717	0.25
62_Q	65_I	0.715	0.25
130_E	185_R	0.711	0.25
58_R	69_K	0.707	0.25
18_A	47_A	0.700	0.25
33_S	76_R	0.699	0.25
76_R	116_F	0.699	0.25
2_T	36_E	0.697	0.24
168_I	173_R	0.685	0.24
151_Q	158_E	0.683	0.24
85_N	107_Q	0.682	0.24
31_Q	69_K	0.668	0.23
32_L	65_I	0.663	0.23
8_A	32_L	0.663	0.23
104_L	120_P	0.662	0.23
114_E	132_L	0.662	0.23
36_E	174_A	0.659	0.23
100_G	141_K	0.657	0.23
141_K	148_S	0.656	0.23
22_L	26_R	0.651	0.22
128_E	160_T	0.646	0.22
33_S	41_A	0.644	0.22
150_N	180_S	0.643	0.22
36_E	71_Q	0.643	0.22
15_L	38_V	0.640	0.22
76_R	85_N	0.639	0.22
36_E	39_G	0.637	0.22
38_V	64_G	0.631	0.22
33_S	181_K	0.631	0.22
15_L	19_E	0.629	0.21
145_D	149_E	0.628	0.21
42_L	139_L	0.627	0.21
26_R	72_R	0.627	0.21
124_E	127_L	0.625	0.21
123_Q	133_K	0.624	0.21
95_S	141_K	0.623	0.21
32_L	50_G	0.622	0.21
23_R	36_E	0.621	0.21
75_L	81_V	0.617	0.21
35_F	50_G	0.615	0.21
134_E	151_Q	0.614	0.21
33_S	86_M	0.612	0.21
5_R	35_F	0.611	0.21
94_A	99_E	0.608	0.21
115_Q	120_P	0.607	0.20
124_E	155_N	0.603	0.20
40_R	43_T	0.602	0.20
31_Q	37_E	0.601	0.20
6_Q	32_L	0.600	0.20
6_Q	38_V	0.599	0.20
55_S	164_Y	0.591	0.20
129_R	133_K	0.590	0.20
82_H	158_E	0.590	0.20
26_R	61_Y	0.589	0.20
56_Y	76_R	0.588	0.20
29_G	150_N	0.583	0.20
108_D	112_F	0.582	0.19
29_G	175_R	0.581	0.19
123_Q	151_Q	0.578	0.19
94_A	116_F	0.576	0.19
119_T	122_A	0.574	0.19
73_K	132_L	0.570	0.19
12_D	64_G	0.570	0.19
137_Q	140_Q	0.569	0.19
150_N	154_R	0.568	0.19
41_A	145_D	0.567	0.19
84_V	88_N	0.566	0.19
55_S	63_S	0.566	0.19
24_H	37_E	0.566	0.19
19_E	67_L	0.564	0.19
176_K	182_E	0.563	0.19
83_S	86_M	0.559	0.19
18_A	31_Q	0.557	0.19
88_N	101_K	0.557	0.19
38_V	46_A	0.550	0.18
128_E	132_L	0.549	0.18
102_R	115_Q	0.547	0.18
82_H	85_N	0.547	0.18
117_K	142_E	0.544	0.18
63_S	74_E	0.543	0.18
144_E	148_S	0.540	0.18
87_P	94_A	0.537	0.18
84_V	156_Q	0.533	0.18
127_L	147_R	0.532	0.18
106_I	117_K	0.530	0.17
10_T	150_N	0.529	0.17
57_V	73_K	0.529	0.17
25_I	168_I	0.528	0.17
10_T	184_G	0.527	0.17
5_R	49_C	0.527	0.17
114_E	142_E	0.523	0.17
5_R	32_L	0.522	0.17
161_E	166_A	0.522	0.17
157_L	185_R	0.521	0.17
42_L	73_K	0.520	0.17
144_E	149_E	0.518	0.17
18_A	58_R	0.518	0.17
4_T	12_D	0.516	0.17
150_N	160_T	0.515	0.17
32_L	35_F	0.513	0.17
41_A	139_L	0.513	0.17
134_E	145_D	0.510	0.17
131_K	135_Q	0.509	0.17
13_E	70_K	0.505	0.17
130_E	149_E	0.503	0.17
5_R	42_L	0.502	0.16
106_I	134_E	0.500	0.16

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
2ltpA	1	0.3212	98.1	0.875	Contact Map
1gv2A	1	0.2642	97.8	0.882	Contact Map
1guuA	1	0.2539	97.7	0.886	Contact Map
2dinA	1	0.3264	97.7	0.886	Contact Map
1h8aC	1	0.2694	97.7	0.886	Contact Map
1gvdA	1	0.2642	97.6	0.887	Contact Map
2d9aA	1	0.2953	97.6	0.887	Contact Map
2k9nA	1	0.3057	97.5	0.891	Contact Map
2m2eA	1	0.3627	97.5	0.891	Contact Map
2dimA	1	0.342	97.4	0.892	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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