GRPE - HALSA - GREMLIN Contacts

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GRPE - Protein GrpE

UniProt:	Q9HRY0	Sequences: MSDHAEHAADAADTDAPEGDDAGGDDGEQAGDDGTSALSERVRALDADNADALADDVAALEARVETLTDELADAEDEVADLTERVQTKQADFKNYKERAKRKQEEIRERATEDLVERLLDVRDNLDRALDQEESESDEDGIREGVELTRDEFDRVLETEGVTEIRPEPGDSVDAARHEVMMRVDSDQPAGTIVDVYRPGYEMSGRVVRAAQVTVSEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	217 (180)
Sequences:	4554 (3723)
Seq/√Len:	277.5

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
78_V	81_L	3.401	1.00
70_E	75_E	3.029	1.00
163_E	198_P	2.841	1.00
162_T	201_E	2.552	1.00
117_R	159_E	2.532	1.00
165_R	170_D	2.510	1.00
71_L	74_A	2.489	1.00
83_E	87_T	2.275	1.00
124_N	127_R	2.218	1.00
154_R	157_E	2.184	1.00
157_E	162_T	2.107	1.00
124_N	151_E	2.105	1.00
74_A	78_V	2.063	1.00
178_E	211_Q	2.058	1.00
77_E	82_T	2.023	1.00
197_R	211_Q	2.018	1.00
95_Y	99_A	1.967	1.00
194_D	213_T	1.927	1.00
181_M	213_T	1.852	1.00
115_V	161_V	1.844	1.00
117_R	158_T	1.838	1.00
73_D	77_E	1.802	1.00
75_E	79_A	1.800	1.00
183_V	193_V	1.796	1.00
92_F	95_Y	1.782	1.00
176_R	201_E	1.733	1.00
126_D	198_P	1.727	1.00
72_A	75_E	1.708	1.00
82_T	86_Q	1.702	1.00
93_K	96_K	1.697	1.00
166_P	195_V	1.661	1.00
154_R	158_T	1.656	1.00
97_E	101_R	1.643	1.00
76_D	80_D	1.620	1.00
146_E	150_D	1.612	1.00
101_R	105_E	1.573	1.00
115_V	207_V	1.553	1.00
188_P	191_T	1.553	1.00
193_V	215_S	1.503	1.00
127_R	130_D	1.488	1.00
70_E	73_D	1.486	1.00
173_D	176_R	1.467	1.00
126_D	149_R	1.461	1.00
93_K	97_E	1.454	1.00
111_T	114_L	1.445	1.00
67_L	71_L	1.444	1.00
112_E	205_R	1.436	1.00
128_A	145_V	1.390	1.00
187_Q	215_S	1.383	1.00
184_D	216_E	1.353	1.00
136_S	139_D	1.347	1.00
171_S	191_T	1.334	1.00
201_E	204_G	1.323	1.00
64_V	67_L	1.296	1.00
90_A	94_N	1.287	1.00
80_D	84_R	1.284	1.00
71_L	75_E	1.280	1.00
164_I	206_V	1.279	1.00
85_V	88_K	1.278	1.00
187_Q	193_V	1.274	1.00
162_T	204_G	1.272	1.00
69_D	73_D	1.271	1.00
140_G	143_E	1.260	1.00
183_V	213_T	1.238	1.00
100_K	104_E	1.238	1.00
88_K	92_F	1.237	1.00
143_E	146_E	1.234	1.00
103_Q	107_R	1.226	1.00
104_E	108_E	1.212	1.00
150_D	154_R	1.206	1.00
187_Q	191_T	1.167	1.00
79_A	83_E	1.165	1.00
183_V	194_D	1.156	1.00
166_P	170_D	1.156	1.00
168_P	195_V	1.152	1.00
63_R	68_T	1.136	1.00
165_R	168_P	1.131	1.00
196_Y	213_T	1.116	1.00
114_L	159_E	1.111	1.00
156_L	161_V	1.108	1.00
123_D	208_R	1.106	1.00
180_M	211_Q	1.102	1.00
85_V	89_Q	1.101	1.00
69_D	72_A	1.097	1.00
182_R	190_G	1.097	1.00
65_E	69_D	1.092	1.00
68_T	72_A	1.091	1.00
78_V	82_T	1.084	1.00
166_P	210_A	1.049	1.00
168_P	194_D	1.043	1.00
139_D	143_E	1.041	1.00
122_R	156_L	1.040	1.00
125_L	149_R	1.035	1.00
149_R	153_D	1.030	1.00
84_R	89_Q	1.026	1.00
125_L	148_T	1.026	1.00
182_R	216_E	1.026	1.00
103_Q	106_I	1.018	1.00
99_A	103_Q	1.008	1.00
77_E	80_D	1.004	1.00
89_Q	93_K	1.003	1.00
109_R	205_R	1.003	1.00
87_T	90_A	0.997	1.00
195_V	210_A	0.991	1.00
57_V	60_L	0.989	1.00
191_T	215_S	0.985	1.00
81_L	85_V	0.983	1.00
108_E	203_S	0.975	1.00
109_R	203_S	0.964	1.00
121_V	155_V	0.963	1.00
189_A	215_S	0.961	1.00
83_E	91_D	0.955	1.00
63_R	66_T	0.944	1.00
163_E	195_V	0.932	1.00
39_S	42_V	0.925	1.00
153_D	163_E	0.920	1.00
161_V	202_M	0.920	1.00
65_E	68_T	0.912	1.00
77_E	81_L	0.903	1.00
41_R	44_A	0.899	1.00
64_V	68_T	0.895	1.00
126_D	130_D	0.888	1.00
122_R	200_Y	0.884	1.00
87_T	94_N	0.874	1.00
181_M	196_Y	0.871	1.00
178_E	197_R	0.870	1.00
88_K	95_Y	0.869	1.00
76_D	79_A	0.868	1.00
92_F	99_A	0.866	1.00
81_L	84_R	0.861	1.00
44_A	47_A	0.858	1.00
132_E	142_R	0.840	1.00
166_P	192_I	0.838	1.00
72_A	76_D	0.829	1.00
135_E	138_E	0.828	1.00
51_D	54_A	0.828	1.00
172_V	179_V	0.827	1.00
127_R	197_R	0.820	0.99
206_V	209_A	0.814	0.99
106_I	110_A	0.812	0.99
60_L	64_V	0.805	0.99
67_L	70_E	0.805	0.99
153_D	157_E	0.800	0.99
99_A	102_K	0.795	0.99
74_A	77_E	0.794	0.99
170_D	192_I	0.791	0.99
151_E	154_R	0.790	0.99
45_L	48_D	0.788	0.99
73_D	76_D	0.782	0.99
36_S	39_S	0.778	0.99
139_D	142_R	0.777	0.99
60_L	63_R	0.777	0.99
193_V	213_T	0.759	0.99
37_A	40_E	0.759	0.99
110_A	114_L	0.757	0.99
94_N	97_E	0.752	0.99
164_I	201_E	0.751	0.99
181_M	194_D	0.749	0.99
113_D	116_E	0.743	0.99
196_Y	211_Q	0.740	0.99
46_D	49_N	0.737	0.99
170_D	195_V	0.721	0.99
112_E	202_M	0.716	0.99
38_L	41_R	0.715	0.99
48_D	51_D	0.711	0.99
97_E	100_K	0.711	0.99
35_T	38_L	0.710	0.99
79_A	82_T	0.708	0.98
125_L	145_V	0.705	0.98
171_S	190_G	0.695	0.98
184_D	215_S	0.693	0.98
61_E	64_V	0.689	0.98
62_A	65_E	0.684	0.98
121_V	152_F	0.682	0.98
53_L	57_V	0.680	0.98
136_S	140_G	0.680	0.98
170_D	176_R	0.679	0.98
189_A	216_E	0.677	0.98
180_M	196_Y	0.676	0.98
177_H	192_I	0.676	0.98
111_T	159_E	0.672	0.98
102_K	105_E	0.670	0.98
102_K	106_I	0.669	0.98
91_D	95_Y	0.667	0.98
104_E	107_R	0.666	0.98
152_F	156_L	0.665	0.98
36_S	40_E	0.664	0.98
113_D	117_R	0.663	0.98
122_R	149_R	0.659	0.98
75_E	78_V	0.658	0.98
43_R	46_D	0.656	0.97
42_V	45_L	0.656	0.97
171_S	188_P	0.646	0.97
144_G	147_L	0.643	0.97
108_E	112_E	0.641	0.97
129_L	146_E	0.640	0.97
143_E	150_D	0.637	0.97
105_E	108_E	0.632	0.97
47_A	50_A	0.630	0.97
39_S	48_D	0.630	0.97
172_V	192_I	0.629	0.97
111_T	115_V	0.629	0.97
55_D	58_A	0.626	0.97
109_R	112_E	0.625	0.97
164_I	210_A	0.625	0.97
145_V	148_T	0.624	0.97
165_R	192_I	0.624	0.97
106_I	109_R	0.623	0.97
66_T	69_D	0.623	0.97
183_V	215_S	0.622	0.97
122_R	153_D	0.616	0.96
126_D	153_D	0.616	0.96
160_G	203_S	0.613	0.96
54_A	57_V	0.611	0.96
36_S	42_V	0.608	0.96
111_T	202_M	0.608	0.96
40_E	43_R	0.606	0.96
120_D	197_R	0.606	0.96
52_A	55_D	0.605	0.96
117_R	120_D	0.604	0.96
202_M	207_V	0.602	0.96
86_Q	93_K	0.601	0.96
108_E	204_G	0.598	0.96
100_K	103_Q	0.598	0.96
127_R	131_Q	0.590	0.95
53_L	56_D	0.589	0.95
155_V	159_E	0.586	0.95
147_L	150_D	0.583	0.95
78_V	85_V	0.581	0.95
58_A	61_E	0.581	0.95
112_E	207_V	0.580	0.95
119_L	208_R	0.580	0.95
111_T	203_S	0.578	0.95
83_E	86_Q	0.578	0.95
70_E	74_A	0.574	0.95
92_F	96_K	0.564	0.94
112_E	116_E	0.562	0.94
128_A	131_Q	0.560	0.94
46_D	53_L	0.559	0.94
137_D	140_G	0.555	0.94
63_R	67_L	0.554	0.94
141_I	145_V	0.554	0.94
121_V	151_E	0.543	0.93
84_R	88_K	0.542	0.93
151_E	155_V	0.541	0.93
129_L	149_R	0.541	0.93
49_N	57_V	0.540	0.93
39_S	45_L	0.537	0.93
195_V	198_P	0.535	0.92
149_R	163_E	0.532	0.92
56_D	60_L	0.532	0.92
91_D	213_T	0.530	0.92
129_L	142_R	0.530	0.92
127_R	151_E	0.529	0.92
130_D	194_D	0.527	0.92
85_V	92_F	0.526	0.92
36_S	43_R	0.521	0.91
132_E	141_I	0.520	0.91
115_V	202_M	0.517	0.91
138_E	141_I	0.516	0.91
120_D	151_E	0.516	0.91
107_R	111_T	0.510	0.90
50_A	53_L	0.509	0.90
92_F	103_Q	0.508	0.90
44_A	48_D	0.508	0.90
107_R	113_D	0.507	0.90
126_D	163_E	0.506	0.90
171_S	192_I	0.506	0.90
138_E	143_E	0.502	0.90
170_D	201_E	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	0.7143	100	0.137	Contact Map
3a6mA	2	0.765	100	0.171	Contact Map
1dkgA	2	0.7143	100	0.179	Contact Map
4etpB	1	0.6267	55.4	0.928	Contact Map
3swyA	3	0.212	50.2	0.93	Contact Map
4rsiB	1	0.8249	48	0.931	Contact Map
3mkbB	1	0.5991	37.5	0.935	Contact Map
4rsiA	1	0.7373	37.5	0.935	Contact Map
3swfA	3	0.2719	36.4	0.936	Contact Map
2aa1B	1	0.6129	32	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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