YMAB - BACSU - GREMLIN Contacts

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YMAB - Uncharacterized protein YmaB

UniProt:	P50619	Sequences: MGKMDEMILVAPRDDVFKKESLTFQGVYSEDSRVAEIMAQIEAAYREMRRGDAEEDPRFKQPIPYVVIKREDEVFLYERLAGGGESRLHNKLSLGFGGHMNAIEGAASFAEVLKLNTDRELEEELQINEEDKQAIVTLGLINDDENSVGKVHIGILSALQLKPGAQVEVKEKEQIAGKWMKVSELKQDDIYNRLETWSQFVVDILE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	206 (192)
Sequences:	131 (103)
Seq/√Len:	7.4

BACSU - YMAB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
191_Y	203_D	3.352	0.91
69_K	160_Q	3.234	0.89
75_F	177_G	3.076	0.87
60_K	149_G	3.059	0.86
67_V	90_N	2.976	0.85
141_I	179_W	2.835	0.82
60_K	142_N	2.689	0.78
77_Y	93_S	2.664	0.77
10_V	171_E	2.574	0.75
83_G	89_H	2.386	0.69
26_G	143_D	2.375	0.68
24_F	144_D	2.339	0.67
28_Y	35_A	2.149	0.60
93_S	151_V	2.086	0.58
13_R	142_N	2.032	0.56
136_V	160_Q	2.016	0.55
48_M	53_A	2.001	0.55
80_L	113_L	1.990	0.54
83_G	141_I	1.980	0.54
173_E	185_L	1.978	0.54
94_L	186_K	1.853	0.49
143_D	149_G	1.825	0.48
78_E	176_A	1.811	0.47
77_Y	149_G	1.794	0.46
10_V	53_A	1.785	0.46
113_L	167_V	1.755	0.45
54_E	63_I	1.748	0.45
194_L	202_V	1.742	0.44
151_V	154_G	1.737	0.44
61_Q	151_V	1.648	0.41
96_F	155_I	1.608	0.39
6_E	101_N	1.587	0.38
5_D	100_M	1.569	0.38
62_P	125_L	1.568	0.38
91_K	146_N	1.553	0.37
61_Q	95_G	1.533	0.36
62_P	200_F	1.517	0.36
61_Q	93_S	1.509	0.36
67_V	156_L	1.508	0.35
105_G	110_A	1.507	0.35
64_P	75_F	1.501	0.35
161_L	185_L	1.477	0.34
13_R	83_G	1.444	0.33
60_K	143_D	1.442	0.33
62_P	156_L	1.439	0.33
64_P	85_E	1.439	0.33
64_P	194_L	1.436	0.33
60_K	144_D	1.425	0.33
12_P	16_V	1.413	0.32
104_E	116_N	1.405	0.32
117_T	177_G	1.401	0.32
48_M	56_D	1.394	0.31
72_D	181_K	1.392	0.31
82_G	200_F	1.384	0.31
85_E	154_G	1.383	0.31
155_I	185_L	1.381	0.31
113_L	157_S	1.375	0.31
46_R	179_W	1.349	0.30
20_E	24_F	1.346	0.30
87_R	154_G	1.339	0.30
7_M	101_N	1.325	0.29
76_L	179_W	1.321	0.29
60_K	201_V	1.310	0.29
70_R	73_E	1.308	0.29
80_L	89_H	1.288	0.28
58_R	103_I	1.286	0.28
83_G	149_G	1.263	0.27
16_V	167_V	1.241	0.26
13_R	179_W	1.230	0.26
196_T	199_Q	1.230	0.26
65_Y	95_G	1.229	0.26
93_S	185_L	1.225	0.26
24_F	142_N	1.208	0.25
50_R	148_V	1.204	0.25
82_G	173_E	1.197	0.25
13_R	60_K	1.182	0.25
24_F	60_K	1.181	0.25
10_V	26_G	1.175	0.25
50_R	54_E	1.171	0.24
114_K	127_I	1.168	0.24
91_K	131_D	1.160	0.24
55_E	175_I	1.147	0.24
155_I	182_V	1.141	0.24
26_G	142_N	1.084	0.22
66_V	184_E	1.082	0.22
181_K	184_E	1.068	0.22
169_V	177_G	1.064	0.21
58_R	73_E	1.055	0.21
85_E	151_V	1.045	0.21
109_F	112_V	1.032	0.21
53_A	194_L	1.027	0.20
60_K	96_F	1.027	0.20
14_D	33_R	1.023	0.20
100_M	116_N	1.022	0.20
130_E	180_M	1.022	0.20
87_R	151_V	1.005	0.20
84_G	143_D	1.005	0.20
50_R	87_R	0.995	0.20
174_Q	177_G	0.983	0.19
44_A	162_K	0.963	0.19
28_Y	137_T	0.961	0.19
13_R	17_F	0.954	0.19
40_Q	146_N	0.946	0.18
83_G	113_L	0.939	0.18
85_E	93_S	0.934	0.18
67_V	111_E	0.930	0.18
117_T	141_I	0.928	0.18
87_R	93_S	0.927	0.18
40_Q	136_V	0.927	0.18
7_M	14_D	0.922	0.18
28_Y	145_E	0.918	0.18
7_M	86_S	0.918	0.18
7_M	23_T	0.916	0.18
103_I	187_Q	0.908	0.18
32_S	58_R	0.899	0.17
72_D	130_E	0.886	0.17
8_I	106_A	0.880	0.17
125_L	193_R	0.879	0.17
49_R	52_D	0.876	0.17
57_P	144_D	0.875	0.17
64_P	177_G	0.871	0.17
64_P	87_R	0.865	0.17
65_Y	154_G	0.856	0.16
54_E	148_V	0.855	0.16
73_E	111_E	0.853	0.16
5_D	8_I	0.850	0.16
91_K	184_E	0.835	0.16
5_D	20_E	0.834	0.16
12_P	57_P	0.829	0.16
27_V	53_A	0.828	0.16
94_L	202_V	0.825	0.16
32_S	155_I	0.822	0.16
67_V	141_I	0.807	0.15
81_A	122_E	0.807	0.15
185_L	194_L	0.806	0.15
71_E	106_A	0.801	0.15
72_D	182_V	0.799	0.15
27_V	125_L	0.788	0.15
13_R	80_L	0.782	0.15
101_N	142_N	0.782	0.15
72_D	105_G	0.781	0.15
141_I	148_V	0.765	0.15
20_E	55_E	0.763	0.14
69_K	158_A	0.761	0.14
125_L	161_L	0.756	0.14
185_L	202_V	0.755	0.14
178_K	182_V	0.753	0.14
27_V	150_K	0.749	0.14
45_Y	149_G	0.748	0.14
26_G	84_G	0.743	0.14
62_P	161_L	0.742	0.14
50_R	139_G	0.739	0.14
93_S	143_D	0.739	0.14
117_T	174_Q	0.738	0.14
86_S	191_Y	0.738	0.14
94_L	130_E	0.733	0.14
35_A	112_V	0.729	0.14
28_Y	34_V	0.723	0.14
52_D	127_I	0.721	0.14
89_H	139_G	0.721	0.14
121_L	139_G	0.715	0.14
41_I	69_K	0.713	0.14
93_S	149_G	0.713	0.14
68_I	121_L	0.712	0.14
16_V	38_M	0.695	0.13
6_E	142_N	0.694	0.13
97_G	123_E	0.691	0.13
97_G	124_E	0.691	0.13
97_G	152_H	0.691	0.13
97_G	195_E	0.691	0.13
97_G	197_W	0.691	0.13
98_G	119_R	0.691	0.13
97_G	120_E	0.691	0.13
97_G	119_R	0.691	0.13
120_E	124_E	0.691	0.13
120_E	123_E	0.691	0.13
99_H	152_H	0.691	0.13
119_R	197_W	0.691	0.13
120_E	152_H	0.691	0.13
119_R	195_E	0.691	0.13
99_H	197_W	0.691	0.13
120_E	195_E	0.691	0.13
98_G	120_E	0.691	0.13
119_R	152_H	0.691	0.13
120_E	197_W	0.691	0.13
119_R	123_E	0.691	0.13
152_H	195_E	0.691	0.13
98_G	197_W	0.691	0.13
99_H	119_R	0.691	0.13
99_H	120_E	0.691	0.13
99_H	123_E	0.691	0.13
99_H	124_E	0.691	0.13
99_H	195_E	0.691	0.13
124_E	197_W	0.691	0.13
124_E	195_E	0.691	0.13
124_E	152_H	0.691	0.13
98_G	123_E	0.691	0.13
123_E	152_H	0.691	0.13
98_G	124_E	0.691	0.13
123_E	195_E	0.691	0.13
123_E	197_W	0.691	0.13
98_G	152_H	0.691	0.13
119_R	124_E	0.691	0.13
98_G	195_E	0.691	0.13
152_H	197_W	0.691	0.13
88_L	120_E	0.691	0.13
88_L	195_E	0.691	0.13
88_L	97_G	0.691	0.13
88_L	98_G	0.691	0.13
88_L	99_H	0.691	0.13
88_L	119_R	0.691	0.13
88_L	123_E	0.691	0.13
88_L	124_E	0.691	0.13
88_L	152_H	0.691	0.13
88_L	197_W	0.691	0.13
28_Y	111_E	0.688	0.13
7_M	184_E	0.688	0.13
160_Q	199_Q	0.688	0.13
136_V	187_Q	0.685	0.13
114_K	163_P	0.683	0.13
84_G	171_E	0.683	0.13
49_R	116_N	0.682	0.13
140_L	157_S	0.682	0.13
110_A	150_K	0.681	0.13
5_D	52_D	0.677	0.13
80_L	159_L	0.676	0.13
50_R	63_I	0.675	0.13
94_L	182_V	0.672	0.13
53_A	109_F	0.668	0.13
121_L	159_L	0.666	0.13
83_G	175_I	0.664	0.13
12_P	24_F	0.661	0.13
87_R	148_V	0.659	0.13
77_Y	151_V	0.656	0.13
174_Q	194_L	0.641	0.12
162_K	166_Q	0.636	0.12
105_G	167_V	0.628	0.12
49_R	80_L	0.627	0.12
60_K	93_S	0.626	0.12
69_K	108_S	0.626	0.12
54_E	87_R	0.624	0.12
68_I	166_Q	0.621	0.12
61_Q	77_Y	0.616	0.12
131_D	166_Q	0.615	0.12
13_R	51_G	0.613	0.12
92_L	125_L	0.613	0.12
52_D	200_F	0.612	0.12
125_L	186_K	0.608	0.12
76_L	157_S	0.607	0.12
22_L	34_V	0.601	0.12
25_Q	28_Y	0.599	0.12
8_I	100_M	0.596	0.12
25_Q	48_M	0.592	0.11
35_A	58_R	0.583	0.11
86_S	122_E	0.576	0.11
42_E	64_P	0.575	0.11
67_V	185_L	0.574	0.11
13_R	149_G	0.572	0.11
73_E	138_L	0.570	0.11
16_V	146_N	0.569	0.11
13_R	24_F	0.568	0.11
95_G	151_V	0.567	0.11
78_E	142_N	0.558	0.11
20_E	49_R	0.557	0.11
92_L	193_R	0.556	0.11
10_V	125_L	0.552	0.11
56_D	63_I	0.546	0.11
80_L	175_I	0.543	0.11
27_V	140_L	0.542	0.11
59_F	72_D	0.541	0.11
43_A	74_V	0.538	0.11
80_L	157_S	0.535	0.11
58_R	180_M	0.530	0.10
73_E	183_S	0.530	0.10
114_K	118_D	0.527	0.10
141_I	172_K	0.523	0.10
158_A	201_V	0.521	0.10
127_I	131_D	0.518	0.10
34_V	62_P	0.515	0.10
146_N	192_N	0.513	0.10
81_A	91_K	0.513	0.10
62_P	77_Y	0.511	0.10
45_Y	169_V	0.511	0.10
38_M	146_N	0.510	0.10
13_R	48_M	0.509	0.10
68_I	94_L	0.508	0.10
7_M	49_R	0.501	0.10
101_N	116_N	0.500	0.10

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
3e57A	2	0.8689	100	0.608	Contact Map
1hztA	1	0.6553	98.9	0.845	Contact Map
1q27A	1	0.7961	98.8	0.853	Contact Map
2b0vA	2	0.6262	98.7	0.855	Contact Map
1sjyA	2	0.665	98.7	0.857	Contact Map
3f6aA	2	0.6165	98.7	0.859	Contact Map
2pnyA	1	0.8738	98.6	0.862	Contact Map
3dupA	2	0.9563	98.5	0.864	Contact Map
4kyxA	2	0.6165	98.5	0.865	Contact Map
4nfwA	6	0.6311	98.5	0.865	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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