YPJA - BACSU - GREMLIN Contacts

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YPJA - Uncharacterized protein YpjA

UniProt:	P54392	Sequences: MLILVLAINFLGTVYGYYWYLPQLLETPARFLIFVPDSPTATFFFLFVLLAFLMKRNAPLLEALALVTLVKYGLWAVAMNFLVLAVTGDLPWEGYMLIASHFAMAVQGVLYSPYFRFSFWHLAIAAVWTLHNDVIDYLFDMMPQYSMLSDYMTEIGYGTFWLSIFSIALAYFLVVSKKQTKLELM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	185 (174)
Sequences:	361 (265)
Seq/√Len:	20.1

BACSU - YPJA
HALSA - Q9HP58

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_A	58_A	4.010	1.00
6_L	10_F	3.883	1.00
10_F	46_L	3.882	1.00
6_L	50_L	3.697	1.00
27_T	35_V	3.339	1.00
64_L	125_A	3.287	1.00
6_L	46_L	3.049	0.99
18_Y	21_L	2.951	0.99
8_I	103_A	2.447	0.97
30_R	33_I	2.260	0.95
48_V	62_E	2.251	0.95
74_L	102_F	2.235	0.95
131_H	157_Y	2.225	0.95
66_L	170_A	2.210	0.95
80_N	94_G	2.062	0.92
67_V	167_I	2.013	0.91
157_Y	161_W	1.991	0.91
78_A	158_G	1.916	0.89
13_T	43_F	1.875	0.88
67_V	122_L	1.828	0.86
68_T	128_W	1.804	0.86
131_H	161_W	1.785	0.85
95_Y	98_I	1.782	0.85
111_Y	114_Y	1.762	0.84
109_V	165_F	1.758	0.84
48_V	51_A	1.750	0.84
60_L	120_W	1.741	0.84
48_V	111_Y	1.689	0.82
70_V	109_V	1.670	0.81
26_E	144_Q	1.637	0.80
21_L	25_L	1.611	0.78
14_V	61_L	1.605	0.78
70_V	108_G	1.579	0.77
130_L	164_I	1.577	0.77
7_A	11_L	1.557	0.76
142_M	145_Y	1.530	0.75
14_V	18_Y	1.525	0.74
122_L	171_Y	1.514	0.74
67_V	129_T	1.508	0.74
71_K	133_D	1.475	0.72
28_P	141_M	1.454	0.71
31_F	135_I	1.453	0.71
60_L	124_I	1.449	0.70
130_L	163_S	1.433	0.70
90_L	95_Y	1.422	0.69
28_P	49_L	1.410	0.68
9_N	107_Q	1.406	0.68
47_F	61_L	1.379	0.67
68_T	129_T	1.371	0.66
70_V	169_L	1.351	0.65
46_L	50_L	1.346	0.65
126_A	167_I	1.331	0.64
81_F	98_I	1.323	0.63
84_L	94_G	1.321	0.63
47_F	51_A	1.278	0.60
91_P	95_Y	1.258	0.59
48_V	52_F	1.235	0.58
117_F	174_V	1.233	0.58
10_F	50_L	1.230	0.57
36_P	97_L	1.212	0.56
157_Y	160_F	1.211	0.56
70_V	166_S	1.210	0.56
139_F	154_E	1.192	0.55
47_F	92_W	1.188	0.55
28_P	166_S	1.183	0.54
120_W	124_I	1.157	0.53
80_N	84_L	1.150	0.52
10_F	174_V	1.149	0.52
163_S	167_I	1.121	0.50
46_L	54_M	1.120	0.50
131_H	138_L	1.088	0.48
23_Q	104_M	1.078	0.48
81_F	85_A	1.044	0.45
86_V	150_D	1.038	0.45
95_Y	118_S	1.035	0.45
49_L	110_L	1.033	0.45
51_A	59_P	1.031	0.45
118_S	121_H	1.005	0.43
111_Y	130_L	1.004	0.43
48_V	114_Y	1.001	0.43
69_L	107_Q	0.992	0.42
3_I	55_K	0.992	0.42
23_Q	35_V	0.984	0.42
82_L	87_T	0.964	0.40
122_L	167_I	0.963	0.40
135_I	139_F	0.962	0.40
33_I	168_A	0.950	0.40
111_Y	159_T	0.950	0.40
102_F	119_F	0.949	0.39
171_Y	175_V	0.937	0.39
59_P	130_L	0.936	0.39
70_V	173_L	0.928	0.38
95_Y	171_Y	0.926	0.38
50_L	57_N	0.921	0.38
23_Q	100_S	0.919	0.38
131_H	141_M	0.916	0.37
61_L	133_D	0.908	0.37
66_L	169_L	0.901	0.37
17_Y	79_M	0.899	0.36
76_A	80_N	0.896	0.36
103_A	164_I	0.896	0.36
6_L	53_L	0.896	0.36
29_A	153_T	0.889	0.36
142_M	152_M	0.885	0.36
66_L	108_G	0.883	0.35
103_A	170_A	0.876	0.35
83_V	147_M	0.873	0.35
84_L	145_Y	0.867	0.34
89_D	124_I	0.861	0.34
53_L	116_R	0.861	0.34
168_A	172_F	0.861	0.34
38_S	65_A	0.861	0.34
33_I	134_V	0.859	0.34
102_F	106_V	0.855	0.34
7_A	153_T	0.853	0.34
78_A	82_L	0.849	0.33
135_I	141_M	0.839	0.33
84_L	108_G	0.836	0.33
44_F	69_L	0.830	0.32
95_Y	117_F	0.821	0.32
148_L	151_Y	0.814	0.31
8_I	107_Q	0.813	0.31
16_G	136_D	0.810	0.31
110_L	115_F	0.809	0.31
62_E	111_Y	0.806	0.31
30_R	107_Q	0.798	0.31
138_L	157_Y	0.796	0.30
146_S	149_S	0.793	0.30
123_A	126_A	0.792	0.30
15_Y	19_W	0.792	0.30
51_A	57_N	0.790	0.30
18_Y	77_V	0.789	0.30
89_D	106_V	0.782	0.30
51_A	120_W	0.776	0.29
94_G	145_Y	0.770	0.29
169_L	175_V	0.768	0.29
119_F	127_V	0.765	0.29
31_F	141_M	0.765	0.29
127_V	155_I	0.760	0.29
17_Y	40_T	0.759	0.28
42_T	62_E	0.755	0.28
134_V	138_L	0.752	0.28
32_L	141_M	0.751	0.28
147_M	150_D	0.749	0.28
13_T	42_T	0.747	0.28
8_I	114_Y	0.745	0.28
22_P	25_L	0.740	0.27
52_F	108_G	0.730	0.27
19_W	96_M	0.728	0.27
82_L	145_Y	0.724	0.27
17_Y	43_F	0.724	0.27
84_L	102_F	0.723	0.27
46_L	51_A	0.723	0.27
35_V	104_M	0.721	0.26
47_F	58_A	0.719	0.26
159_T	167_I	0.719	0.26
12_G	97_L	0.718	0.26
116_R	139_F	0.717	0.26
131_H	160_F	0.709	0.26
51_A	56_R	0.707	0.26
11_L	33_I	0.705	0.26
59_P	62_E	0.699	0.25
29_A	74_L	0.692	0.25
24_L	72_Y	0.688	0.25
93_E	148_L	0.683	0.25
65_A	71_K	0.681	0.25
140_D	153_T	0.674	0.24
55_K	106_V	0.672	0.24
92_W	98_I	0.671	0.24
99_A	102_F	0.669	0.24
123_A	169_L	0.668	0.24
90_L	130_L	0.664	0.24
138_L	161_W	0.656	0.23
86_V	151_Y	0.654	0.23
109_V	169_L	0.653	0.23
156_G	160_F	0.652	0.23
149_S	152_M	0.647	0.23
42_T	68_T	0.641	0.23
143_P	146_S	0.640	0.23
64_L	103_A	0.640	0.23
8_I	32_L	0.635	0.22
127_V	131_H	0.633	0.22
19_W	97_L	0.630	0.22
51_A	54_M	0.628	0.22
169_L	172_F	0.628	0.22
80_N	83_V	0.625	0.22
19_W	111_Y	0.624	0.22
52_F	166_S	0.622	0.22
85_A	99_A	0.618	0.22
27_T	36_P	0.617	0.22
125_A	129_T	0.616	0.22
34_F	105_A	0.615	0.21
96_M	100_S	0.614	0.21
38_S	104_M	0.614	0.21
81_F	173_L	0.613	0.21
12_G	104_M	0.613	0.21
10_F	89_D	0.612	0.21
45_F	105_A	0.610	0.21
62_E	115_F	0.607	0.21
29_A	115_F	0.606	0.21
115_F	129_T	0.603	0.21
18_Y	24_L	0.601	0.21
83_V	145_Y	0.598	0.21
61_L	123_A	0.597	0.21
12_G	23_Q	0.593	0.21
147_M	170_A	0.591	0.20
131_H	135_I	0.590	0.20
22_P	26_E	0.589	0.20
28_P	83_V	0.589	0.20
97_L	100_S	0.586	0.20
5_V	45_F	0.584	0.20
19_W	76_A	0.582	0.20
140_D	152_M	0.582	0.20
48_V	57_N	0.580	0.20
8_I	91_P	0.580	0.20
32_L	42_T	0.580	0.20
129_T	159_T	0.575	0.20
80_N	145_Y	0.575	0.20
30_R	140_D	0.575	0.20
163_S	166_S	0.573	0.20
145_Y	161_W	0.573	0.20
85_A	149_S	0.572	0.20
134_V	160_F	0.570	0.20
66_L	109_V	0.570	0.20
131_H	134_V	0.569	0.20
13_T	44_F	0.569	0.20
110_L	114_Y	0.565	0.19
91_P	99_A	0.560	0.19
97_L	104_M	0.560	0.19
46_L	61_L	0.557	0.19
29_A	126_A	0.556	0.19
78_A	127_V	0.556	0.19
119_F	122_L	0.554	0.19
141_M	145_Y	0.552	0.19
50_L	102_F	0.552	0.19
2_L	53_L	0.545	0.19
36_P	104_M	0.543	0.18
10_F	124_I	0.542	0.18
125_A	139_F	0.542	0.18
13_T	104_M	0.535	0.18
159_T	166_S	0.532	0.18
15_Y	96_M	0.532	0.18
7_A	99_A	0.526	0.18
94_G	125_A	0.523	0.18
12_G	36_P	0.521	0.18
76_A	111_Y	0.520	0.18
67_V	175_V	0.520	0.18
42_T	100_S	0.518	0.18
52_F	122_L	0.517	0.17
59_P	139_F	0.515	0.17
22_P	147_M	0.514	0.17
111_Y	115_F	0.514	0.17
19_W	45_F	0.513	0.17
9_N	12_G	0.512	0.17
47_F	173_L	0.511	0.17
129_T	133_D	0.511	0.17
11_L	21_L	0.508	0.17
68_T	133_D	0.505	0.17
32_L	166_S	0.502	0.17
57_N	135_I	0.501	0.17
50_L	164_I	0.500	0.17

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
2jp3A	1	0.2865	9.3	0.963	Contact Map
2l6wA	2	0.2108	6.8	0.965	Contact Map
2m20A	2	0.2	5.1	0.967	Contact Map
2kluA	1	0.2054	5	0.967	Contact Map
2mkvA	1	0.3243	3.7	0.969	Contact Map
3wguG	1	0.1838	3.5	0.969	Contact Map
4qndA	2	0.2378	3.4	0.97	Contact Map
2kv5A	1	0.1784	3.1	0.97	Contact Map
2l2tA	2	0.227	2.6	0.971	Contact Map
2jwaA	2	0.2162	2.4	0.972	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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