YAER - ECOLI - GREMLIN Contacts

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YAER - Uncharacterized protein YaeR

UniProt:	P52096	Sequences: MLGLKQVHHIAIIATDYAVSKAFYCDILGFTLQSEVYREARDSWKGDLALNGQYVIELFSFPFPPERPSRPEACGLRHLAFSVDDIDAAVAHLESHNVKCETIRVDPYTQKRFTFFNDPDGLPLELYEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13224
Length:	129 (119)
Sequences:	3590 (1936)
Seq/√Len:	177.5

ECOLI - YAER LGUL
BACSU - YWKD YWBC YURT YQJC YETH FOSB YYAH
HALSA - Q9HQK8 Q9HRQ2
SULSO - Q97W20

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_A	26_D	5.878	1.00
91_A	95_S	3.876	1.00
85_D	88_A	3.107	1.00
92_H	96_H	2.638	1.00
32_L	35_E	2.390	1.00
99_K	117_N	2.363	1.00
17_Y	46_G	2.153	1.00
93_L	98_V	2.026	1.00
16_D	19_V	2.008	1.00
112_R	128_E	1.956	1.00
32_L	46_G	1.858	1.00
90_V	94_E	1.851	1.00
22_A	27_I	1.805	1.00
36_V	108_Y	1.798	1.00
30_F	50_L	1.774	1.00
70_R	73_A	1.752	1.00
42_D	63_F	1.713	1.00
20_S	58_L	1.696	1.00
33_Q	49_A	1.681	1.00
87_D	112_R	1.680	1.00
94_E	100_C	1.590	1.00
37_Y	44_W	1.566	1.00
90_V	114_T	1.565	1.00
6_Q	82_S	1.552	1.00
89_A	92_H	1.530	1.00
25_C	31_T	1.463	1.00
117_N	121_G	1.449	1.00
15_T	64_P	1.435	1.00
64_P	74_C	1.417	1.00
27_I	96_H	1.383	1.00
115_F	125_E	1.367	1.00
26_D	96_H	1.342	1.00
81_F	124_L	1.304	1.00
117_N	123_P	1.288	1.00
87_D	91_A	1.280	1.00
19_V	22_A	1.276	1.00
19_V	120_D	1.267	1.00
21_K	48_L	1.223	1.00
39_E	42_D	1.213	1.00
8_H	82_S	1.211	1.00
114_T	126_L	1.194	1.00
42_D	62_P	1.183	1.00
18_A	22_A	1.173	1.00
113_F	127_Y	1.171	1.00
94_E	102_T	1.153	1.00
79_L	124_L	1.141	1.00
31_T	49_A	1.120	1.00
44_W	62_P	1.108	1.00
78_H	125_E	1.104	1.00
31_T	51_N	1.099	1.00
101_E	117_N	1.094	1.00
52_G	55_V	1.088	1.00
14_A	17_Y	1.085	1.00
30_F	81_F	1.083	1.00
37_Y	42_D	1.075	1.00
20_S	120_D	1.073	1.00
15_T	66_E	1.073	1.00
15_T	65_P	1.067	1.00
88_A	92_H	1.056	1.00
20_S	24_Y	1.050	1.00
38_R	43_S	1.038	1.00
88_A	91_A	1.028	0.99
50_L	81_F	1.024	0.99
93_L	126_L	1.023	0.99
116_F	124_L	1.014	0.99
101_E	123_P	1.002	0.99
37_Y	62_P	0.994	0.99
9_H	80_A	0.987	0.99
91_A	94_E	0.941	0.99
28_L	116_F	0.936	0.99
86_I	112_R	0.912	0.99
86_I	90_V	0.904	0.99
92_H	95_S	0.901	0.99
27_I	93_L	0.898	0.99
35_E	44_W	0.891	0.98
83_V	89_A	0.888	0.98
8_H	127_Y	0.870	0.98
35_E	46_G	0.866	0.98
9_H	57_E	0.854	0.98
43_S	61_F	0.850	0.98
38_R	41_R	0.849	0.98
24_Y	118_D	0.843	0.98
76_L	79_L	0.843	0.98
15_T	19_V	0.836	0.98
78_H	115_F	0.833	0.98
102_T	114_T	0.829	0.98
28_L	126_L	0.827	0.98
11_A	59_F	0.819	0.97
11_A	77_R	0.815	0.97
46_G	60_S	0.815	0.97
56_I	79_L	0.810	0.97
15_T	120_D	0.798	0.97
10_I	54_Y	0.798	0.97
36_V	45_K	0.791	0.97
27_I	98_V	0.777	0.96
9_H	78_H	0.775	0.96
50_L	53_Q	0.774	0.96
98_V	116_F	0.771	0.96
14_A	46_G	0.767	0.96
90_V	100_C	0.761	0.96
17_Y	60_S	0.752	0.96
51_N	54_Y	0.737	0.95
45_K	59_F	0.727	0.95
64_P	70_R	0.723	0.95
63_F	66_E	0.723	0.95
38_R	42_D	0.720	0.95
13_I	122_L	0.720	0.95
72_E	75_G	0.718	0.94
116_F	126_L	0.709	0.94
10_I	79_L	0.708	0.94
6_Q	53_Q	0.704	0.94
93_L	114_T	0.702	0.94
31_T	52_G	0.698	0.94
104_R	107_P	0.680	0.93
44_W	60_S	0.678	0.93
13_I	61_F	0.678	0.93
18_A	35_E	0.676	0.92
22_A	96_H	0.673	0.92
31_T	99_K	0.673	0.92
106_D	109_T	0.657	0.91
14_A	22_A	0.652	0.91
20_S	119_P	0.650	0.91
12_I	24_Y	0.649	0.91
107_P	110_Q	0.649	0.91
90_V	99_K	0.642	0.90
43_S	106_D	0.640	0.90
26_D	92_H	0.639	0.90
70_R	117_N	0.637	0.90
107_P	111_K	0.630	0.90
25_C	32_L	0.628	0.89
7_V	10_I	0.627	0.89
25_C	48_L	0.626	0.89
39_E	62_P	0.616	0.89
32_L	44_W	0.615	0.89
6_Q	52_G	0.610	0.88
100_C	116_F	0.605	0.88
66_E	71_P	0.600	0.87
37_Y	60_S	0.597	0.87
43_S	113_F	0.592	0.87
12_I	79_L	0.584	0.86
66_E	74_C	0.583	0.86
71_P	74_C	0.579	0.85
49_A	53_Q	0.577	0.85
60_S	64_P	0.575	0.85
22_A	25_C	0.570	0.84
86_I	113_F	0.569	0.84
43_S	59_F	0.567	0.84
11_A	61_F	0.566	0.84
57_E	61_F	0.560	0.83
70_R	80_A	0.559	0.83
7_V	54_Y	0.559	0.83
80_A	125_E	0.558	0.83
49_A	54_Y	0.555	0.83
82_S	127_Y	0.554	0.83
8_H	80_A	0.553	0.83
104_R	109_T	0.553	0.83
41_R	44_W	0.551	0.82
31_T	34_S	0.547	0.82
14_A	60_S	0.544	0.82
80_A	115_F	0.543	0.82
94_E	97_N	0.541	0.81
30_F	74_C	0.540	0.81
72_E	76_L	0.540	0.81
10_I	124_L	0.534	0.80
105_V	108_Y	0.527	0.80
108_Y	111_K	0.527	0.80
105_V	110_Q	0.527	0.80
118_D	122_L	0.526	0.79
38_R	45_K	0.524	0.79
21_K	46_G	0.515	0.78
45_K	57_E	0.514	0.78
102_T	109_T	0.513	0.78
51_N	55_V	0.513	0.78
26_D	84_D	0.512	0.78
21_K	25_C	0.510	0.77
61_F	76_L	0.505	0.77
14_A	30_F	0.503	0.76
20_S	118_D	0.500	0.76

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
2c21A	2	0.9225	99.9	0.364	Contact Map
2p25A	2	0.9767	99.9	0.365	Contact Map
1ss4A	4	0.9922	99.9	0.367	Contact Map
3l7tA	2	0.969	99.9	0.372	Contact Map
3w0tA	2	0.9922	99.9	0.374	Contact Map
3hdpA	2	0.9845	99.9	0.384	Contact Map
1jc4A	2	1	99.9	0.395	Contact Map
4mtsA	2	0.9457	99.9	0.398	Contact Map
3gm5A	2	0.9767	99.8	0.399	Contact Map
3kolA	2	0.9845	99.8	0.401	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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