GRPE - BACSU - GREMLIN Contacts

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GRPE - Protein GrpE

UniProt:	P15874	Sequences: MSEEKQTVEQNETEEQEIIEEQAAADEQQEETNESELLQNQINELQGLLEEKENKLLRVQADFENYKRRSRLEMEASQKYRSQNIVTDLLPALDSFERALQVEADNEQTKSLLQGMEMVHRQLVEALKKEGVEAIEAVGQEFDPNLHQAVMQAEDENYGSNIVVEEMQKGYKLKDRVIRPSMVKVNQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	187 (170)
Sequences:	4804 (3738)
Seq/√Len:	286.7

ECOLI - GRPE
BACSU - GRPE
HALSA - GRPE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_L	52_K	3.361	1.00
134_A	169_K	2.915	1.00
41_Q	46_Q	2.832	1.00
88_D	130_E	2.522	1.00
133_E	172_K	2.417	1.00
136_E	140_Q	2.376	1.00
42_I	45_L	2.370	1.00
54_N	58_R	2.148	1.00
95_S	122_Q	2.122	1.00
168_Q	182_M	2.102	1.00
95_S	98_R	2.085	1.00
45_L	49_L	2.058	1.00
128_K	133_E	2.037	1.00
148_Q	182_M	2.014	1.00
66_Y	70_S	1.986	1.00
48_L	53_E	1.962	1.00
155_D	158_Y	1.958	1.00
125_E	128_K	1.885	1.00
88_D	129_K	1.883	1.00
151_M	184_K	1.825	1.00
165_E	184_K	1.806	1.00
86_V	132_V	1.783	1.00
146_L	172_K	1.780	1.00
63_F	66_Y	1.767	1.00
44_E	48_L	1.764	1.00
53_E	57_L	1.742	1.00
153_A	164_V	1.683	1.00
125_E	129_K	1.646	1.00
46_Q	50_E	1.613	1.00
97_E	169_K	1.604	1.00
137_A	166_E	1.593	1.00
47_G	51_E	1.569	1.00
64_E	67_K	1.560	1.00
97_E	120_H	1.554	1.00
159_G	162_I	1.537	1.00
117_E	121_R	1.536	1.00
143_D	146_L	1.512	1.00
43_N	46_Q	1.506	1.00
41_Q	44_E	1.504	1.00
72_L	76_A	1.499	1.00
83_Q	176_R	1.453	1.00
98_R	101_Q	1.448	1.00
42_I	46_Q	1.444	1.00
86_V	178_I	1.405	1.00
164_V	186_N	1.393	1.00
172_K	175_D	1.378	1.00
68_R	72_L	1.376	1.00
82_S	85_I	1.368	1.00
141_E	162_I	1.348	1.00
56_L	59_V	1.329	1.00
111_S	114_Q	1.322	1.00
153_A	184_K	1.317	1.00
64_E	68_R	1.315	1.00
155_D	186_N	1.275	1.00
61_A	65_N	1.263	1.00
153_A	165_E	1.260	1.00
99_A	116_M	1.257	1.00
40_N	44_E	1.251	1.00
38_L	42_I	1.250	1.00
135_I	177_V	1.243	1.00
35_S	38_L	1.240	1.00
133_E	175_D	1.235	1.00
114_Q	117_E	1.222	1.00
59_V	63_F	1.213	1.00
167_M	184_K	1.205	1.00
71_R	75_E	1.204	1.00
158_Y	186_N	1.203	1.00
51_E	55_K	1.194	1.00
121_R	125_E	1.194	1.00
75_E	79_K	1.192	1.00
158_Y	164_V	1.182	1.00
74_M	78_Q	1.145	1.00
50_E	54_N	1.143	1.00
120_H	124_V	1.138	1.00
49_L	53_E	1.130	1.00
56_L	60_Q	1.123	1.00
138_V	166_E	1.114	1.00
107_E	110_K	1.107	1.00
40_N	43_N	1.106	1.00
85_I	130_E	1.103	1.00
137_A	140_Q	1.094	1.00
152_Q	161_N	1.079	1.00
94_D	179_R	1.074	1.00
55_K	60_Q	1.055	1.00
138_V	165_E	1.049	1.00
127_L	132_V	1.044	1.00
80_Y	174_K	1.039	1.00
28_Q	31_E	1.029	1.00
60_Q	64_E	1.025	1.00
70_S	74_M	1.024	1.00
158_Y	162_I	1.021	1.00
34_E	39_Q	1.013	1.00
47_G	50_E	0.998	1.00
162_I	186_N	0.990	1.00
110_K	114_Q	0.989	1.00
48_L	52_K	0.989	1.00
74_M	77_S	0.988	1.00
80_Y	176_R	0.984	1.00
36_E	39_Q	0.981	1.00
36_E	40_N	0.977	1.00
48_L	51_E	0.964	1.00
93_L	127_L	0.962	1.00
92_A	126_A	0.957	1.00
150_V	182_M	0.956	1.00
79_K	174_K	0.952	1.00
96_F	120_H	0.951	1.00
93_L	171_Y	0.950	1.00
97_E	101_Q	0.947	1.00
96_F	119_V	0.935	1.00
132_V	173_L	0.932	1.00
52_K	56_L	0.924	1.00
58_R	61_A	0.921	1.00
151_M	167_M	0.920	1.00
137_A	181_S	0.915	1.00
35_S	39_Q	0.899	1.00
59_V	66_Y	0.899	1.00
63_F	70_S	0.897	1.00
124_V	134_A	0.891	1.00
142_F	149_A	0.884	1.00
92_A	123_L	0.880	1.00
177_V	180_P	0.878	1.00
52_K	55_K	0.867	1.00
39_Q	43_N	0.864	1.00
44_E	47_G	0.859	1.00
122_Q	125_E	0.856	1.00
134_A	166_E	0.854	1.00
54_N	62_D	0.852	1.00
166_E	181_S	0.848	1.00
34_E	37_L	0.840	1.00
98_R	168_Q	0.832	1.00
31_E	35_S	0.825	1.00
65_N	68_R	0.818	1.00
103_E	106_N	0.817	1.00
140_Q	166_E	0.812	1.00
148_Q	168_Q	0.810	0.99
45_L	48_L	0.796	0.99
160_S	186_N	0.791	0.99
17_E	20_E	0.787	0.99
73_E	76_A	0.786	0.99
110_K	113_L	0.780	0.99
124_V	128_K	0.780	0.99
50_E	53_E	0.775	0.99
167_M	182_M	0.770	0.99
24_A	28_Q	0.749	0.99
84_N	87_T	0.745	0.99
58_R	65_N	0.742	0.99
31_E	34_E	0.741	0.99
77_S	81_R	0.738	0.99
70_S	73_E	0.738	0.99
137_A	163_V	0.737	0.99
81_R	85_I	0.735	0.99
19_I	22_Q	0.734	0.99
43_N	47_G	0.733	0.99
140_Q	146_L	0.731	0.99
115_G	118_M	0.729	0.99
68_R	71_R	0.726	0.99
164_V	184_K	0.725	0.99
100_L	117_E	0.723	0.99
25_A	28_Q	0.721	0.99
75_E	78_Q	0.719	0.99
83_Q	173_L	0.719	0.99
18_I	21_E	0.703	0.99
38_L	41_Q	0.703	0.99
33_N	36_E	0.698	0.98
151_M	165_E	0.697	0.98
21_E	24_A	0.693	0.98
135_I	172_K	0.692	0.98
77_S	80_Y	0.685	0.98
82_S	130_E	0.682	0.98
91_P	122_Q	0.680	0.98
26_D	29_Q	0.679	0.98
93_L	124_V	0.677	0.98
88_D	91_P	0.676	0.98
16_Q	19_I	0.676	0.98
91_P	168_Q	0.672	0.98
46_Q	49_L	0.671	0.98
22_Q	25_A	0.668	0.98
82_S	174_K	0.666	0.98
79_K	83_Q	0.665	0.98
154_E	186_N	0.663	0.98
84_N	88_D	0.663	0.98
123_L	127_L	0.663	0.98
141_E	161_N	0.661	0.98
90_L	179_R	0.652	0.98
173_L	178_I	0.652	0.98
93_L	120_H	0.643	0.97
32_T	35_S	0.641	0.97
141_E	159_G	0.639	0.97
106_N	110_K	0.639	0.97
112_L	116_M	0.637	0.97
56_L	63_F	0.636	0.97
83_Q	87_T	0.632	0.97
147_H	163_V	0.631	0.97
114_Q	121_R	0.629	0.97
80_Y	83_Q	0.628	0.97
83_Q	178_I	0.628	0.97
106_N	109_T	0.627	0.97
98_R	102_V	0.626	0.97
63_F	67_K	0.624	0.97
166_E	169_K	0.623	0.97
100_L	115_G	0.620	0.97
23_A	26_D	0.620	0.97
96_F	116_M	0.619	0.97
104_A	113_L	0.617	0.97
150_V	167_M	0.615	0.97
78_Q	84_N	0.613	0.97
34_E	38_L	0.612	0.97
62_D	66_Y	0.607	0.96
49_L	56_L	0.602	0.96
54_N	57_L	0.601	0.96
20_E	23_A	0.600	0.96
57_L	64_E	0.598	0.96
71_R	74_M	0.596	0.96
142_F	163_V	0.595	0.96
76_A	79_K	0.593	0.96
100_L	120_H	0.592	0.96
79_K	175_D	0.587	0.96
106_N	113_L	0.587	0.96
135_I	181_S	0.581	0.95
69_R	73_E	0.575	0.95
126_A	130_E	0.573	0.95
122_Q	126_A	0.572	0.95
86_V	173_L	0.570	0.95
131_G	174_K	0.569	0.95
82_S	86_V	0.568	0.95
16_Q	27_E	0.566	0.95
20_E	24_A	0.557	0.94
140_Q	163_V	0.556	0.94
32_T	36_E	0.555	0.94
118_M	121_R	0.552	0.94
24_A	27_E	0.552	0.94
155_D	159_G	0.544	0.94
61_A	68_R	0.544	0.94
103_E	113_L	0.543	0.93
92_A	122_Q	0.542	0.93
101_Q	165_E	0.540	0.93
16_Q	20_E	0.537	0.93
37_L	40_N	0.530	0.93
55_K	59_V	0.528	0.93
116_M	119_V	0.527	0.92
21_E	28_Q	0.526	0.92
16_Q	21_E	0.524	0.92
159_G	186_N	0.521	0.92
89_L	123_L	0.516	0.92
52_K	59_V	0.516	0.92
73_E	77_S	0.514	0.91
141_E	163_V	0.513	0.91
63_F	74_M	0.512	0.91
39_Q	42_I	0.507	0.91
153_A	186_N	0.505	0.91
137_A	147_H	0.504	0.91
20_E	28_Q	0.502	0.91
100_L	116_M	0.501	0.90
19_I	32_T	0.501	0.90
148_Q	180_P	0.500	0.90

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
4aniA	2	0.8342	100	0.086	Contact Map
1dkgA	2	0.8075	100	0.086	Contact Map
3a6mA	2	0.8824	100	0.121	Contact Map
4rsiB	1	0.9305	62.2	0.919	Contact Map
3swyA	3	0.246	45.9	0.927	Contact Map
3he5A	1	0.2513	44.2	0.928	Contact Map
4etpB	1	0.7112	43.6	0.928	Contact Map
1i84S	2	0	38.1	0.93	Contact Map
3swfA	3	0.3155	35.5	0.931	Contact Map
3ojaB	1	0.3797	34.5	0.932	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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