GRPE - ECOLI - GREMLIN Contacts

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GRPE - Protein GrpE

UniProt:	P09372	Sequences: MSSKEQKTPEGQAPEEIIMDQHEEIEAVEPEASAEQVDPRDEKVANLEAQLAEAQTRERDGILRVKAEMENLRRRTELDIEKAHKFALEKFINELLPVIDSLDRALEVADKANPDMSAMVEGIELTLKSMLDVVRKFGVEVIAETNVPLDPNVHQAIAMVESDDVAPGNVLGIMQKGYTLNGRTIRAAMVTVAKAKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10416
Length:	197 (174)
Sequences:	4769 (3748)
Seq/√Len:	284.1

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
55_Q	58_E	3.468	1.00
47_L	52_A	2.986	1.00
141_V	176_K	2.983	1.00
94_E	137_F	2.546	1.00
143_A	147_V	2.470	1.00
140_E	179_T	2.457	1.00
48_E	51_L	2.393	1.00
60_D	64_R	2.282	1.00
101_S	104_R	2.250	1.00
101_S	129_S	2.170	1.00
175_Q	189_M	2.161	1.00
155_Q	189_M	2.127	1.00
162_S	165_V	2.091	1.00
51_L	55_Q	2.083	1.00
135_R	140_E	2.000	1.00
72_L	76_T	1.990	1.00
132_D	135_R	1.985	1.00
54_A	59_R	1.939	1.00
94_E	136_K	1.912	1.00
172_G	191_T	1.879	1.00
158_A	191_T	1.854	1.00
92_I	139_V	1.847	1.00
69_M	72_L	1.829	1.00
153_V	179_T	1.811	1.00
50_Q	54_A	1.797	1.00
160_V	171_L	1.757	1.00
70_E	73_R	1.708	1.00
132_D	136_K	1.700	1.00
59_R	63_L	1.695	1.00
52_A	56_T	1.660	1.00
103_D	176_K	1.659	1.00
144_E	173_I	1.617	1.00
103_D	127_L	1.572	1.00
104_R	107_E	1.556	1.00
124_E	128_K	1.555	1.00
78_L	82_K	1.550	1.00
53_E	57_R	1.549	1.00
166_A	169_N	1.515	1.00
49_A	52_A	1.508	1.00
171_L	193_A	1.494	1.00
150_D	153_V	1.492	1.00
74_R	78_L	1.476	1.00
47_L	50_Q	1.475	1.00
88_L	91_F	1.474	1.00
48_E	52_A	1.464	1.00
89_E	183_R	1.459	1.00
44_V	48_E	1.424	1.00
92_I	185_I	1.412	1.00
70_E	74_R	1.397	1.00
179_T	182_G	1.371	1.00
161_E	194_K	1.357	1.00
148_P	169_N	1.343	1.00
67_A	71_N	1.342	1.00
62_I	65_V	1.342	1.00
160_V	191_T	1.329	1.00
56_T	60_D	1.329	1.00
118_A	121_E	1.327	1.00
162_S	193_A	1.309	1.00
121_E	124_E	1.288	1.00
105_A	123_I	1.282	1.00
114_P	117_S	1.272	1.00
165_V	193_A	1.247	1.00
140_E	182_G	1.241	1.00
46_N	50_Q	1.227	1.00
160_V	172_G	1.225	1.00
165_V	171_L	1.217	1.00
65_V	69_M	1.215	1.00
77_E	81_E	1.214	1.00
81_E	85_K	1.206	1.00
142_I	184_T	1.203	1.00
128_K	132_D	1.197	1.00
46_N	49_A	1.179	1.00
57_R	61_G	1.169	1.00
80_I	84_H	1.168	1.00
159_M	194_K	1.156	1.00
174_M	191_T	1.151	1.00
100_D	186_R	1.149	1.00
42_E	46_N	1.149	1.00
62_I	66_K	1.143	1.00
91_F	137_F	1.135	1.00
61_G	66_K	1.133	1.00
145_T	173_I	1.121	1.00
165_V	169_N	1.110	1.00
41_D	44_V	1.106	1.00
144_E	147_V	1.098	1.00
55_Q	59_R	1.094	1.00
159_M	168_G	1.081	1.00
127_L	131_L	1.077	1.00
76_T	80_I	1.044	1.00
145_T	172_G	1.040	1.00
117_S	121_E	1.025	1.00
134_V	139_V	1.018	1.00
86_F	183_R	1.013	1.00
53_E	56_T	1.004	1.00
44_V	47_L	0.996	1.00
86_F	181_N	0.994	1.00
80_I	83_A	0.994	1.00
169_N	193_A	0.993	1.00
102_L	126_T	0.985	1.00
144_E	188_A	0.984	1.00
98_V	133_V	0.978	1.00
58_E	62_I	0.974	1.00
64_R	67_A	0.966	1.00
102_L	127_L	0.960	1.00
85_K	181_N	0.960	1.00
99_I	134_V	0.954	1.00
99_I	178_Y	0.951	1.00
141_V	173_I	0.944	1.00
139_V	180_L	0.935	1.00
66_K	70_E	0.933	1.00
54_A	57_R	0.923	1.00
157_I	189_M	0.921	1.00
40_R	45_A	0.921	1.00
173_I	188_A	0.914	1.00
45_A	49_A	0.902	1.00
131_L	141_V	0.869	1.00
103_D	107_E	0.864	1.00
184_T	187_A	0.863	1.00
54_A	58_E	0.858	1.00
109_A	120_V	0.858	1.00
69_M	76_T	0.857	1.00
34_A	37_V	0.857	1.00
158_A	174_M	0.856	1.00
58_E	61_G	0.855	1.00
129_S	132_D	0.853	1.00
149_L	156_A	0.846	1.00
65_V	72_L	0.846	1.00
104_R	175_Q	0.840	1.00
155_Q	175_Q	0.835	1.00
71_N	74_R	0.817	1.00
167_P	193_A	0.812	0.99
60_D	68_E	0.808	0.99
171_L	191_T	0.793	0.99
41_D	45_A	0.791	0.99
49_A	53_E	0.787	0.99
23_E	26_E	0.782	0.99
42_E	45_A	0.780	0.99
79_D	82_K	0.767	0.99
56_T	59_R	0.766	0.99
98_V	130_M	0.763	0.99
131_L	135_R	0.759	0.99
64_R	71_N	0.756	0.99
37_V	40_R	0.754	0.99
144_E	170_V	0.752	0.99
38_D	41_D	0.741	0.99
29_E	32_A	0.739	0.99
24_E	27_A	0.739	0.99
83_A	87_A	0.739	0.99
40_R	43_K	0.736	0.99
50_Q	53_E	0.734	0.99
19_M	22_H	0.734	0.99
158_A	172_G	0.733	0.99
51_L	54_A	0.731	0.99
117_S	120_V	0.731	0.99
113_N	116_M	0.723	0.99
147_V	173_I	0.722	0.99
90_K	93_N	0.721	0.99
174_M	189_M	0.720	0.99
28_V	31_E	0.717	0.99
39_P	42_E	0.711	0.99
22_H	25_I	0.710	0.99
87_A	91_F	0.697	0.98
149_L	170_V	0.693	0.98
81_E	84_H	0.686	0.98
37_V	41_D	0.684	0.98
147_V	153_V	0.683	0.98
74_R	77_E	0.679	0.98
20_D	23_E	0.675	0.98
167_P	194_K	0.669	0.98
97_P	175_Q	0.669	0.98
52_A	55_Q	0.667	0.98
85_K	89_E	0.662	0.98
89_E	180_L	0.661	0.98
154_H	170_V	0.661	0.98
76_T	79_D	0.660	0.98
68_E	72_L	0.658	0.98
88_L	137_F	0.658	0.98
99_I	127_L	0.655	0.98
30_P	34_A	0.652	0.98
121_E	128_K	0.649	0.98
142_I	179_T	0.645	0.97
99_I	131_L	0.645	0.97
115_D	118_A	0.645	0.97
130_M	134_V	0.644	0.97
96_L	186_R	0.638	0.97
43_K	46_N	0.636	0.97
166_A	193_A	0.635	0.97
69_M	73_R	0.632	0.97
88_L	92_I	0.631	0.97
161_E	193_A	0.629	0.97
180_L	185_I	0.628	0.97
31_E	34_A	0.626	0.97
63_L	70_E	0.623	0.97
60_D	63_L	0.620	0.97
25_I	28_V	0.619	0.97
20_D	24_E	0.619	0.97
94_E	97_P	0.614	0.97
55_Q	62_I	0.613	0.97
106_L	124_E	0.609	0.96
148_P	168_G	0.608	0.96
79_D	83_A	0.607	0.96
83_A	86_F	0.607	0.96
88_L	181_N	0.606	0.96
119_M	123_I	0.604	0.96
97_P	129_S	0.600	0.96
173_I	176_K	0.597	0.96
86_F	89_E	0.596	0.96
90_K	94_E	0.590	0.96
82_K	85_K	0.588	0.96
77_E	80_I	0.588	0.96
157_I	174_M	0.586	0.96
148_P	166_A	0.586	0.96
109_A	116_M	0.585	0.95
110_D	116_M	0.582	0.95
32_A	38_D	0.581	0.95
21_Q	24_E	0.581	0.95
142_I	188_A	0.574	0.95
89_E	93_N	0.574	0.95
104_R	108_V	0.573	0.95
102_L	123_I	0.570	0.95
26_E	29_E	0.567	0.95
160_V	193_A	0.566	0.95
107_E	172_G	0.565	0.95
19_M	25_I	0.564	0.94
123_I	126_T	0.563	0.94
30_P	33_S	0.562	0.94
129_S	133_V	0.562	0.94
89_E	185_I	0.558	0.94
122_G	125_L	0.557	0.94
45_A	48_E	0.556	0.94
109_A	119_M	0.551	0.94
19_M	39_P	0.545	0.93
138_G	181_N	0.545	0.93
23_E	30_P	0.541	0.93
147_V	170_V	0.541	0.93
88_L	180_L	0.540	0.93
33_S	37_V	0.540	0.93
35_E	38_D	0.539	0.93
162_S	166_A	0.537	0.93
38_D	42_E	0.536	0.93
26_E	30_P	0.535	0.93
85_K	182_G	0.528	0.92
148_P	170_V	0.528	0.92
125_L	128_K	0.527	0.92
21_Q	25_I	0.526	0.92
84_H	90_K	0.525	0.92
67_A	74_R	0.525	0.92
62_I	69_M	0.523	0.92
110_D	113_N	0.523	0.92
106_L	120_V	0.521	0.92
58_E	65_V	0.519	0.92
103_D	131_L	0.517	0.92
141_V	144_E	0.514	0.91
133_V	137_F	0.514	0.91
61_G	65_V	0.512	0.91
156_A	192_V	0.511	0.91
106_L	127_L	0.510	0.91
75_R	79_D	0.508	0.91
20_D	30_P	0.506	0.91
27_A	30_P	0.505	0.91
92_I	180_L	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
1dkgA	2	0.7817	100	0.094	Contact Map
4aniA	2	0.7919	100	0.111	Contact Map
3a6mA	2	0.8528	100	0.14	Contact Map
3swyA	3	0.2335	50.5	0.928	Contact Map
4etpB	1	0.6904	41.6	0.931	Contact Map
3swfA	3	0.2995	33.6	0.935	Contact Map
3vkgA	2	0.9086	32.6	0.935	Contact Map
3mkbB	1	0.665	30.4	0.936	Contact Map
1gcvB	1	0.665	28.5	0.937	Contact Map
3ojaB	1	0.3909	27.8	0.937	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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