YIGI - ECOLI - GREMLIN Contacts

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YIGI - Uncharacterized protein YigI

UniProt:	P0ADP2	Sequences: MSAVLTAEQALKLVGEMFVYHMPFNRALGMELERYEKEFAQLAFKNQPMMVGNWAQSILHGGVIASALDVAAGLVCVGSTLTRHETISEDELRQRLSRMGTIDLRVDYLRPGRGERFTATSSLLRAGNKVAVARVELHNEEQLYIASATATYMVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11467
Length:	155 (125)
Sequences:	3197 (2217)
Seq/√Len:	198.3

ECOLI - YIGI MENI ENTH PAAI
BACSU - COMA2
HALSA - Y1336
SULSO - Q97UX9 Y1253 Y2140 Q97VK2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_E	43_A	3.405	1.00
43_A	116_R	3.391	1.00
102_I	130_V	3.198	1.00
41_Q	120_T	2.652	1.00
72_A	135_V	2.476	1.00
120_T	138_H	2.381	1.00
34_R	41_Q	2.334	1.00
44_F	63_V	2.301	1.00
68_L	135_V	2.218	1.00
34_R	39_F	2.180	1.00
42_L	71_A	2.148	1.00
76_C	131_A	1.990	1.00
39_F	122_S	1.979	1.00
31_E	43_A	1.942	1.00
65_A	104_L	1.936	1.00
122_S	134_R	1.892	1.00
65_A	108_Y	1.849	1.00
38_E	78_G	1.799	1.00
103_D	107_D	1.790	1.00
136_E	144_Y	1.785	1.00
36_E	39_F	1.772	1.00
43_A	118_T	1.763	1.00
134_R	147_S	1.727	1.00
122_S	136_E	1.705	1.00
68_L	148_A	1.683	1.00
39_F	120_T	1.630	1.00
71_A	119_A	1.616	1.00
68_L	137_L	1.611	1.00
33_E	41_Q	1.582	1.00
41_Q	118_T	1.510	1.00
112_G	145_I	1.508	1.00
45_K	116_R	1.414	1.00
124_L	147_S	1.390	1.00
110_R	143_L	1.377	1.00
76_C	133_A	1.364	1.00
79_S	126_A	1.363	1.00
27_A	49_M	1.351	1.00
59_L	117_F	1.311	1.00
115_E	140_E	1.291	1.00
72_A	150_A	1.283	1.00
16_E	20_Y	1.269	1.00
124_L	134_R	1.244	1.00
61_G	108_Y	1.242	1.00
136_E	147_S	1.238	1.00
46_N	59_L	1.235	1.00
139_N	143_L	1.217	1.00
64_I	112_G	1.174	1.00
112_G	117_F	1.162	1.00
125_R	130_V	1.156	1.00
65_A	106_V	1.153	1.00
24_F	66_S	1.137	1.00
47_Q	50_M	1.135	1.00
67_A	119_A	1.135	1.00
120_T	142_Q	1.132	1.00
123_L	126_A	1.130	1.00
107_D	132_V	1.128	1.00
64_I	146_A	1.126	1.00
117_F	145_I	1.118	1.00
45_K	50_M	1.116	1.00
75_V	123_L	1.098	1.00
64_I	108_Y	1.096	1.00
31_E	116_R	1.092	1.00
138_H	142_Q	1.091	1.00
117_F	137_L	1.072	1.00
79_S	123_L	1.061	1.00
24_F	63_V	1.032	1.00
81_L	97_S	1.009	1.00
17_M	20_Y	1.006	1.00
20_Y	26_R	1.003	1.00
138_H	144_Y	0.987	1.00
119_A	135_V	0.983	1.00
31_E	45_K	0.978	0.99
14_V	17_M	0.967	0.99
46_N	50_M	0.956	0.99
69_D	101_T	0.949	0.99
144_Y	147_S	0.943	0.99
50_M	63_V	0.923	0.99
109_L	147_S	0.921	0.99
125_R	132_V	0.905	0.99
72_A	152_Y	0.894	0.99
38_E	75_V	0.870	0.99
109_L	125_R	0.858	0.99
120_T	136_E	0.854	0.99
68_L	106_V	0.851	0.99
15_G	19_V	0.848	0.99
44_F	67_A	0.841	0.98
60_H	70_V	0.839	0.98
37_K	79_S	0.833	0.98
46_N	51_V	0.827	0.98
107_D	149_T	0.813	0.98
132_V	151_T	0.812	0.98
77_V	98_R	0.809	0.98
67_A	137_L	0.804	0.98
30_M	44_F	0.794	0.98
48_P	51_V	0.794	0.98
72_A	133_A	0.791	0.98
72_A	148_A	0.783	0.98
58_I	100_G	0.777	0.97
42_L	121_S	0.770	0.97
69_D	73_G	0.766	0.97
119_A	137_L	0.751	0.97
135_V	148_A	0.751	0.97
104_L	108_Y	0.751	0.97
30_M	42_L	0.745	0.97
50_M	59_L	0.717	0.96
134_R	149_T	0.715	0.96
118_T	138_H	0.715	0.96
109_L	144_Y	0.714	0.96
126_A	131_A	0.706	0.96
129_K	153_M	0.703	0.95
33_E	116_R	0.696	0.95
25_N	30_M	0.695	0.95
59_L	112_G	0.693	0.95
24_F	60_H	0.689	0.95
76_C	99_M	0.688	0.95
40_A	75_V	0.681	0.95
121_S	135_V	0.679	0.94
105_R	149_T	0.677	0.94
118_T	142_Q	0.675	0.94
110_R	125_R	0.662	0.94
75_V	121_S	0.660	0.94
26_R	49_M	0.651	0.93
64_I	137_L	0.647	0.93
123_L	133_A	0.647	0.93
75_V	78_G	0.647	0.93
62_G	66_S	0.642	0.93
101_T	150_A	0.639	0.93
139_N	145_I	0.638	0.92
115_E	139_N	0.634	0.92
73_G	152_Y	0.627	0.92
35_Y	78_G	0.620	0.91
103_D	151_T	0.616	0.91
14_V	18_F	0.615	0.91
123_L	131_A	0.603	0.90
80_T	97_S	0.603	0.90
104_L	150_A	0.596	0.90
121_S	133_A	0.592	0.89
110_R	153_M	0.591	0.89
22_M	55_A	0.590	0.89
116_R	140_E	0.588	0.89
130_V	153_M	0.587	0.89
15_G	18_F	0.586	0.89
16_E	31_E	0.585	0.89
116_R	139_N	0.583	0.89
22_M	74_L	0.579	0.88
32_L	42_L	0.577	0.88
78_G	123_L	0.571	0.88
17_M	21_H	0.571	0.88
23_P	51_V	0.571	0.88
103_D	149_T	0.568	0.87
65_A	148_A	0.567	0.87
68_L	104_L	0.562	0.87
100_G	150_A	0.558	0.86
76_C	152_Y	0.556	0.86
55_A	74_L	0.555	0.86
132_V	147_S	0.555	0.86
52_G	56_Q	0.553	0.86
21_H	26_R	0.553	0.86
29_G	49_M	0.552	0.86
32_L	40_A	0.551	0.86
102_I	153_M	0.547	0.85
76_C	126_A	0.544	0.85
23_P	26_R	0.543	0.85
124_L	144_Y	0.542	0.85
25_N	70_V	0.541	0.85
69_D	100_G	0.540	0.85
109_L	130_V	0.539	0.85
43_A	140_E	0.538	0.84
29_G	44_F	0.535	0.84
135_V	150_A	0.534	0.84
112_G	115_E	0.533	0.84
74_L	77_V	0.523	0.83
107_D	130_V	0.521	0.83
63_V	117_F	0.521	0.83
76_C	80_T	0.520	0.82
46_N	114_G	0.519	0.82
52_G	62_G	0.516	0.82
55_A	73_G	0.516	0.82
14_V	19_V	0.515	0.82
35_Y	40_A	0.514	0.82
46_N	117_F	0.513	0.82
22_M	52_G	0.513	0.82
28_L	63_V	0.510	0.81
30_M	119_A	0.509	0.81
56_Q	100_G	0.508	0.81
61_G	127_G	0.507	0.81
52_G	60_H	0.503	0.80
56_Q	99_M	0.500	0.80

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
3e8pA	3	0.9806	100	0.362	Contact Map
4rmmA	2	0.8452	99.9	0.385	Contact Map
3f1tA	2	0.871	99.9	0.395	Contact Map
3lmbA	2	0.9097	99.9	0.405	Contact Map
1yocA	4	0.8968	99.9	0.413	Contact Map
3hduA	4	0.9677	99.9	0.418	Contact Map
3gekA	3	0.7677	99.9	0.422	Contact Map
1t82A	2	0.871	99.9	0.423	Contact Map
1sh8A	2	0.8516	99.9	0.424	Contact Map
1vh5A	2	0.8839	99.9	0.433	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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