YBEY - ECOLI - GREMLIN Contacts

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YBEY - Endoribonuclease YbeY

UniProt:	P0A898	Sequences: MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIAEKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13655
Length:	155 (133)
Sequences:	3758 (2714)
Seq/√Len:	235.3

ECOLI - YBEY
BACSU - YBEY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_T	89_C	3.095	1.00
52_H	62_D	3.079	1.00
48_T	95_K	2.562	1.00
134_E	137_E	2.389	1.00
92_V	95_K	2.241	1.00
52_H	63_K	2.228	1.00
53_S	57_T	2.178	1.00
56_L	62_D	2.166	1.00
48_T	92_V	2.144	1.00
52_H	56_L	2.090	1.00
45_V	90_R	2.006	1.00
48_T	91_Q	1.925	1.00
44_R	87_V	1.727	1.00
28_L	116_S	1.720	1.00
66_N	96_E	1.716	1.00
30_A	143_A	1.706	1.00
125_I	129_E	1.653	1.00
46_V	50_E	1.623	1.00
106_A	146_Y	1.621	1.00
52_H	64_P	1.611	1.00
93_V	111_M	1.584	1.00
126_E	129_E	1.582	1.00
34_Q	143_A	1.537	1.00
54_L	68_L	1.532	1.00
24_F	43_I	1.526	1.00
138_T	142_L	1.485	1.00
34_Q	139_E	1.485	1.00
136_L	139_E	1.470	1.00
94_E	104_L	1.466	1.00
46_V	87_V	1.465	1.00
50_E	53_S	1.454	1.00
46_V	51_S	1.452	1.00
93_V	108_W	1.451	1.00
130_A	134_E	1.450	1.00
54_L	87_V	1.444	1.00
51_S	64_P	1.436	1.00
88_I	112_V	1.424	1.00
135_A	139_E	1.409	1.00
66_N	107_H	1.399	1.00
88_I	93_V	1.399	1.00
25_Q	29_N	1.339	1.00
89_C	92_V	1.289	1.00
96_E	107_H	1.286	1.00
110_H	130_A	1.279	1.00
75_P	78_M	1.244	1.00
24_F	112_V	1.223	1.00
93_V	104_L	1.217	1.00
73_E	81_S	1.212	1.00
47_D	50_E	1.209	1.00
90_R	94_E	1.208	1.00
23_Q	105_E	1.205	1.00
67_V	86_L	1.196	1.00
127_D	131_E	1.176	1.00
44_R	50_E	1.175	1.00
94_E	98_Q	1.169	1.00
103_P	106_A	1.166	1.00
122_Y	136_L	1.158	1.00
110_H	137_E	1.144	1.00
109_A	146_Y	1.140	1.00
95_K	99_E	1.130	1.00
21_E	25_Q	1.111	1.00
71_P	74_V	1.104	1.00
69_S	84_G	1.094	1.00
28_L	112_V	1.084	1.00
31_V	113_V	1.084	1.00
30_A	34_Q	1.075	1.00
132_E	136_L	1.071	1.00
23_Q	27_W	1.058	1.00
42_T	85_D	1.043	1.00
22_S	26_T	1.032	1.00
61_K	68_L	1.029	1.00
113_V	140_I	0.983	1.00
55_N	59_R	0.981	1.00
122_Y	132_E	0.973	1.00
45_V	108_W	0.970	1.00
131_E	135_A	0.969	1.00
32_I	116_S	0.966	1.00
43_I	112_V	0.964	1.00
139_E	143_A	0.947	1.00
55_N	61_K	0.947	1.00
72_F	82_L	0.946	1.00
27_W	109_A	0.939	1.00
64_P	89_C	0.934	1.00
23_Q	26_T	0.929	1.00
110_H	134_E	0.919	1.00
96_E	102_K	0.918	1.00
84_G	119_L	0.915	1.00
130_A	137_E	0.901	1.00
30_A	144_L	0.892	0.99
102_K	107_H	0.884	0.99
16_S	19_P	0.884	0.99
40_E	82_L	0.873	0.99
31_V	116_S	0.857	0.99
43_I	86_L	0.857	0.99
90_R	108_W	0.854	0.99
41_V	116_S	0.852	0.99
104_L	108_W	0.841	0.99
52_H	61_K	0.836	0.99
47_D	91_Q	0.830	0.99
59_R	68_L	0.830	0.99
29_N	33_P	0.830	0.99
83_L	120_L	0.828	0.99
39_S	81_S	0.827	0.99
116_S	120_L	0.825	0.99
67_V	115_G	0.823	0.99
26_T	30_A	0.822	0.99
69_S	119_L	0.816	0.99
44_R	85_D	0.816	0.99
64_P	92_V	0.815	0.99
28_L	31_V	0.812	0.99
135_A	138_T	0.802	0.99
28_L	32_I	0.800	0.99
24_F	108_W	0.798	0.99
94_E	97_A	0.798	0.99
107_H	110_H	0.796	0.99
69_S	83_L	0.786	0.99
67_V	111_M	0.782	0.99
66_N	134_E	0.782	0.99
35_F	39_S	0.782	0.99
48_T	64_P	0.781	0.99
58_Y	70_F	0.779	0.99
51_S	63_K	0.772	0.98
97_A	103_P	0.767	0.98
136_L	140_I	0.764	0.98
127_D	130_A	0.764	0.98
59_R	63_K	0.760	0.98
71_P	115_G	0.760	0.98
110_H	138_T	0.759	0.98
96_E	110_H	0.752	0.98
51_S	65_T	0.749	0.98
51_S	89_C	0.747	0.98
68_L	71_P	0.746	0.98
54_L	58_Y	0.745	0.98
66_N	102_K	0.738	0.98
28_L	43_I	0.738	0.98
86_L	115_G	0.733	0.98
71_P	85_D	0.728	0.98
106_A	145_G	0.727	0.98
66_N	110_H	0.726	0.98
34_Q	140_I	0.713	0.97
138_T	141_M	0.712	0.97
55_N	62_D	0.710	0.97
102_K	110_H	0.700	0.97
51_S	86_L	0.690	0.97
117_L	140_I	0.682	0.97
112_V	116_S	0.681	0.97
106_A	110_H	0.680	0.97
71_P	75_P	0.679	0.97
51_S	87_V	0.675	0.97
72_F	119_L	0.665	0.96
98_Q	104_L	0.658	0.96
51_S	92_V	0.656	0.96
105_E	146_Y	0.656	0.96
23_Q	109_A	0.655	0.96
30_A	33_P	0.649	0.96
27_W	144_L	0.647	0.96
113_V	141_M	0.645	0.95
106_A	147_E	0.640	0.95
56_L	63_K	0.632	0.95
72_F	83_L	0.631	0.95
141_M	146_Y	0.631	0.95
117_L	133_M	0.619	0.94
66_N	138_T	0.616	0.94
55_N	68_L	0.608	0.94
53_S	56_L	0.605	0.94
67_V	93_V	0.602	0.94
142_L	147_E	0.595	0.93
20_E	23_Q	0.593	0.93
30_A	140_I	0.591	0.93
98_Q	101_G	0.584	0.92
15_N	18_L	0.580	0.92
113_V	117_L	0.579	0.92
71_P	125_I	0.577	0.92
129_E	132_E	0.575	0.92
102_K	106_A	0.566	0.91
111_M	124_H	0.565	0.91
36_Q	39_S	0.561	0.91
72_F	87_V	0.559	0.91
46_V	89_C	0.555	0.90
100_Q	146_Y	0.553	0.90
42_T	82_L	0.553	0.90
24_F	27_W	0.552	0.90
100_Q	107_H	0.546	0.90
49_A	53_S	0.543	0.89
72_F	85_D	0.543	0.89
107_H	138_T	0.541	0.89
59_R	124_H	0.540	0.89
35_F	38_E	0.537	0.89
63_K	92_V	0.536	0.89
54_L	86_L	0.535	0.89
52_H	57_T	0.535	0.89
38_E	81_S	0.527	0.88
75_P	81_S	0.524	0.88
126_E	131_E	0.521	0.88
110_H	141_M	0.516	0.87
96_E	111_M	0.515	0.87
131_E	134_E	0.509	0.86
106_A	109_A	0.505	0.86
139_E	142_L	0.501	0.85
37_E	81_S	0.500	0.85

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
1xaxA	1	0.929	100	0.106	Contact Map
1xm5A	1	0.9806	100	0.107	Contact Map
1oz9A	1	0.8968	100	0.187	Contact Map
1tviA	1	0.9161	100	0.214	Contact Map
1hv5A	2	0.9097	86.7	0.899	Contact Map
1cgeA	1	0.9032	82	0.905	Contact Map
3ayuA	1	0.9161	81.4	0.905	Contact Map
1su3A	4	0.9161	80.7	0.906	Contact Map
3ma2D	1	0.9226	79.4	0.907	Contact Map
4xctA	1	0.8968	78	0.908	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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