GPMA - ECOLI - GREMLIN Contacts

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GPMA - 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

UniProt:	P62707	Sequences: MAVTKLVLVRHGESQWNKENRFTGWYDVDLSEKGVSEAKAAGKLLKEEGYSFDFAYTSVLKRAIHTLWNVLDELDQAWLPVEKSWKLNERHYGALQGLNKAETAEKYGDEQVKQWRRGFAVTPPELTKDDERYPGHDPRYAKLSEKELPLTESLALTIDRVIPYWNETILPRMKSGERVIIAAHGNSLRALVKYLDNMSEEEILELNIPTGVPLVYEFDENFKPLKRYYLGNADEIAAKAAAVANQGKAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11699
Length:	250 (192)
Sequences:	7922 (5352)
Seq/√Len:	386.2

ECOLI - GPMA COBC GPMB SIXA
BACSU - PHOE
SULSO - Q97WI1 Q97YV8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_V	65_H	2.988	1.00
86_K	167_E	2.849	1.00
13_E	33_K	2.809	1.00
64_I	83_K	2.734	1.00
5_K	215_V	2.641	1.00
94_A	150_L	2.617	1.00
59_V	88_N	2.604	1.00
54_F	82_E	2.415	1.00
5_K	217_E	2.363	1.00
5_K	178_R	2.333	1.00
9_V	70_V	2.311	1.00
98_L	106_K	2.259	1.00
86_K	163_P	2.195	1.00
55_A	71_L	2.122	1.00
29_D	65_H	2.098	1.00
162_I	194_Y	2.060	1.00
39_K	69_N	2.034	1.00
35_V	69_N	2.025	1.00
55_A	67_L	1.991	1.00
13_E	31_S	1.979	1.00
29_D	61_K	1.966	1.00
53_D	177_E	1.958	1.00
43_K	73_E	1.935	1.00
86_K	164_Y	1.900	1.00
65_H	68_W	1.872	1.00
87_L	164_Y	1.856	1.00
161_V	187_S	1.844	1.00
9_V	180_I	1.839	1.00
183_A	187_S	1.823	1.00
15_Q	19_E	1.817	1.00
32_E	35_V	1.809	1.00
9_V	41_A	1.792	1.00
15_Q	31_S	1.779	1.00
153_S	156_L	1.745	1.00
7_V	52_F	1.704	1.00
36_S	39_K	1.702	1.00
52_F	180_I	1.695	1.00
25_W	88_N	1.680	1.00
217_E	226_K	1.612	1.00
57_T	83_K	1.559	1.00
13_E	18_K	1.549	1.00
152_E	160_R	1.532	1.00
35_V	39_K	1.494	1.00
84_S	164_Y	1.489	1.00
188_L	208_I	1.489	1.00
183_A	188_L	1.468	1.00
84_S	167_E	1.466	1.00
53_D	178_R	1.465	1.00
25_W	91_H	1.452	1.00
36_S	40_A	1.425	1.00
33_K	36_S	1.423	1.00
16_W	28_V	1.404	1.00
70_V	182_A	1.370	1.00
16_W	21_R	1.347	1.00
7_V	178_R	1.337	1.00
107_Y	110_E	1.297	1.00
33_K	37_E	1.296	1.00
17_N	210_T	1.290	1.00
64_I	68_W	1.276	1.00
39_K	72_D	1.271	1.00
155_A	159_D	1.271	1.00
8_L	188_L	1.268	1.00
38_A	66_T	1.263	1.00
99_N	102_E	1.262	1.00
54_F	177_E	1.254	1.00
113_K	117_R	1.249	1.00
91_H	96_Q	1.248	1.00
59_V	85_W	1.240	1.00
156_L	159_D	1.234	1.00
39_K	73_E	1.230	1.00
68_W	72_D	1.218	1.00
40_A	43_K	1.212	1.00
58_S	63_A	1.207	1.00
162_I	166_N	1.202	1.00
16_W	23_T	1.199	1.00
98_L	102_E	1.198	1.00
27_D	61_K	1.185	1.00
147_E	156_L	1.185	1.00
32_E	36_S	1.172	1.00
164_Y	168_T	1.159	1.00
68_W	81_V	1.155	1.00
43_K	46_K	1.142	1.00
196_D	216_Y	1.139	1.00
56_Y	164_Y	1.126	1.00
161_V	191_L	1.125	1.00
67_L	81_V	1.125	1.00
199_S	202_E	1.112	1.00
59_V	83_K	1.108	1.00
192_V	214_L	1.087	1.00
7_V	215_V	1.074	1.00
208_I	214_L	1.069	1.00
101_A	104_A	1.064	1.00
98_L	103_T	1.059	1.00
23_T	28_V	1.052	1.00
42_G	69_N	1.027	1.00
159_D	163_P	1.024	1.00
198_M	202_E	1.023	1.00
71_L	81_V	1.014	1.00
58_S	184_H	1.010	1.00
166_N	170_L	1.010	1.00
37_E	210_T	1.003	1.00
52_F	178_R	1.000	1.00
174_K	177_E	0.994	1.00
157_T	187_S	0.992	1.00
67_L	182_A	0.987	1.00
25_W	59_V	0.984	1.00
101_A	105_E	0.971	1.00
95_L	103_T	0.961	1.00
202_E	205_E	0.931	1.00
8_L	191_L	0.928	1.00
171_P	174_K	0.926	1.00
104_A	112_V	0.926	1.00
219_D	223_K	0.925	1.00
26_Y	96_Q	0.924	1.00
69_N	72_D	0.910	1.00
61_K	64_I	0.908	1.00
57_T	81_V	0.908	1.00
61_K	65_H	0.907	1.00
57_T	64_I	0.907	1.00
14_S	31_S	0.904	1.00
102_E	105_E	0.902	1.00
63_A	184_H	0.892	1.00
193_K	200_E	0.890	1.00
17_N	23_T	0.887	1.00
4_T	176_G	0.883	1.00
4_T	174_K	0.882	1.00
30_L	38_A	0.879	1.00
157_T	161_V	0.870	1.00
4_T	175_S	0.865	1.00
54_F	179_V	0.861	1.00
219_D	222_F	0.856	1.00
109_D	113_K	0.855	1.00
65_H	69_N	0.853	1.00
94_A	149_P	0.852	1.00
56_Y	82_E	0.852	1.00
158_I	162_I	0.848	1.00
144_S	147_E	0.845	1.00
12_G	30_L	0.844	1.00
7_V	50_Y	0.840	1.00
52_F	74_L	0.837	1.00
56_Y	174_K	0.834	1.00
38_A	211_G	0.834	1.00
14_S	23_T	0.832	1.00
28_V	31_S	0.828	1.00
50_Y	178_R	0.828	1.00
14_S	17_N	0.824	1.00
56_Y	168_T	0.819	1.00
15_Q	18_K	0.816	1.00
192_V	196_D	0.813	1.00
218_F	223_K	0.807	1.00
57_T	63_A	0.807	1.00
157_T	186_N	0.806	1.00
208_I	212_V	0.805	1.00
55_A	79_L	0.805	1.00
41_A	211_G	0.803	1.00
15_Q	29_D	0.803	1.00
85_W	88_N	0.798	1.00
56_Y	84_S	0.795	1.00
192_V	216_Y	0.786	1.00
21_R	99_N	0.779	1.00
23_T	210_T	0.776	1.00
13_E	37_E	0.772	1.00
87_L	168_T	0.771	1.00
167_E	171_P	0.765	1.00
42_G	73_E	0.765	1.00
168_T	181_I	0.762	1.00
157_T	190_A	0.758	1.00
82_E	171_P	0.750	1.00
34_G	38_A	0.746	1.00
8_L	181_I	0.744	1.00
16_W	26_Y	0.739	1.00
9_V	213_P	0.735	1.00
22_F	100_K	0.734	1.00
90_R	157_T	0.734	1.00
114_Q	118_G	0.732	1.00
196_D	206_L	0.731	1.00
42_G	70_V	0.729	1.00
57_T	67_L	0.726	1.00
60_L	88_N	0.724	1.00
170_L	174_K	0.722	1.00
18_K	33_K	0.714	1.00
8_L	216_Y	0.714	1.00
4_T	220_E	0.709	1.00
102_E	106_K	0.703	1.00
55_A	180_I	0.699	1.00
158_I	190_A	0.698	1.00
46_K	73_E	0.694	0.99
89_E	185_G	0.693	0.99
69_N	73_E	0.693	0.99
44_L	213_P	0.692	0.99
31_S	34_G	0.690	0.99
166_N	194_Y	0.690	0.99
185_G	207_N	0.683	0.99
165_W	191_L	0.682	0.99
56_Y	179_V	0.676	0.99
38_A	69_N	0.666	0.99
41_A	213_P	0.665	0.99
110_E	149_P	0.663	0.99
93_G	151_T	0.662	0.99
92_Y	186_N	0.659	0.99
39_K	43_K	0.658	0.99
71_L	74_L	0.653	0.99
188_L	214_L	0.651	0.99
87_L	181_I	0.644	0.99
6_L	169_I	0.643	0.99
167_E	170_L	0.642	0.99
170_L	222_F	0.637	0.99
55_A	81_V	0.637	0.99
92_Y	96_Q	0.636	0.99
220_E	223_K	0.634	0.99
53_D	180_I	0.617	0.99
103_T	107_Y	0.613	0.99
28_V	92_Y	0.612	0.99
20_N	99_N	0.610	0.99
166_N	169_I	0.610	0.99
29_D	35_V	0.606	0.99
154_L	190_A	0.604	0.99
6_L	218_F	0.600	0.99
154_L	189_R	0.597	0.98
56_Y	171_P	0.595	0.98
185_G	210_T	0.594	0.98
209_P	212_V	0.594	0.98
60_L	63_A	0.594	0.98
22_F	92_Y	0.593	0.98
51_S	178_R	0.591	0.98
158_I	194_Y	0.591	0.98
103_T	112_V	0.587	0.98
219_D	224_P	0.587	0.98
112_V	115_W	0.586	0.98
34_G	37_E	0.579	0.98
18_K	31_S	0.579	0.98
71_L	79_L	0.577	0.98
24_G	60_L	0.575	0.98
38_A	42_G	0.575	0.98
14_S	96_Q	0.572	0.98
143_L	148_L	0.571	0.98
162_I	191_L	0.571	0.98
154_L	203_I	0.570	0.98
50_Y	74_L	0.569	0.98
87_L	187_S	0.567	0.98
193_K	203_I	0.567	0.98
90_R	95_L	0.565	0.98
183_A	208_I	0.562	0.98
43_K	47_E	0.560	0.98
45_L	50_Y	0.557	0.98
24_G	27_D	0.554	0.98
142_K	145_E	0.552	0.97
52_F	55_A	0.549	0.97
104_A	109_D	0.544	0.97
164_Y	181_I	0.544	0.97
42_G	46_K	0.544	0.97
45_L	74_L	0.543	0.97
10_R	89_E	0.542	0.97
168_T	179_V	0.541	0.97
15_Q	28_V	0.537	0.97
13_E	17_N	0.537	0.97
7_V	45_L	0.536	0.97
164_Y	167_E	0.535	0.97
193_K	198_M	0.533	0.97
191_L	195_L	0.532	0.97
4_T	177_E	0.530	0.97
58_S	62_R	0.528	0.97
143_L	146_K	0.527	0.97
6_L	165_W	0.525	0.97
159_D	162_I	0.525	0.97
7_V	213_P	0.522	0.96
165_W	195_L	0.519	0.96
25_W	60_L	0.519	0.96
159_D	175_S	0.518	0.96
203_I	206_L	0.518	0.96
161_V	194_Y	0.516	0.96
20_N	101_A	0.516	0.96
46_K	75_D	0.515	0.96
21_R	102_E	0.515	0.96
9_V	182_A	0.515	0.96
11_H	89_E	0.515	0.96
148_L	151_T	0.514	0.96
93_G	152_E	0.513	0.96
75_D	79_L	0.513	0.96
54_F	174_K	0.511	0.96
66_T	211_G	0.510	0.96
23_T	185_G	0.510	0.96
63_A	67_L	0.507	0.96
82_E	168_T	0.506	0.96
10_R	17_N	0.506	0.96
90_R	189_R	0.505	0.96
90_R	154_L	0.500	0.95
30_L	34_G	0.500	0.95

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
4odiA	3	0.976	100	0.164	Contact Map
3kkkA	3	0.92	100	0.165	Contact Map
2hhjA	2	0.996	100	0.171	Contact Map
3gp3A	1	0.916	100	0.171	Contact Map
3d8hA	2	0.928	100	0.18	Contact Map
1e58A	2	0.988	100	0.19	Contact Map
1riiA	4	0.964	100	0.198	Contact Map
4gpzA	2	0.952	100	0.209	Contact Map
4embA	2	0.98	100	0.21	Contact Map
4pzaA	2	0.812	100	0.242	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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