ISPA - ECOLI - GREMLIN Contacts

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ISPA - Farnesyl diphosphate synthase

UniProt:	P22939	Sequences: MDFPQQLEACVKQANQALSRFIAPLPFQNTPVVETMQYGALLGGKRLRPFLVYATGHMFGVSTNTLDAPAAAVECIHAYSLIHDDLPAMDDDDLRRGLPTCHVKFGEANAILAGDALQTLAFSILSDADMPEVSDRDRISMISELASASGIAGMCGGQALDLDAEGKHVPLDALERIHRHKTGALIRAAVRLGALSAGDKGRRALPVLDKYAESIGLAFQVQDDILDVVGDTATLGKRQGADQQLGKSTYPALLGLEQARKKARDLIDDARQSLKQLAEQSLDTSALEALADYIIQRNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10508
Length:	299 (264)
Sequences:	9707 (6620)
Seq/√Len:	407.4

ECOLI - ISPA ISPB
BACSU - ISPA HEPS2 COMQ
HALSA - Q9HQI3 Q9HND0
SULSO - GGPS HEXPP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_G	66_L	3.531	1.00
191_R	209_D	3.277	1.00
200_K	204_A	3.117	1.00
187_R	209_D	2.995	1.00
93_D	103_V	2.874	1.00
144_E	191_R	2.762	1.00
170_P	173_A	2.707	1.00
187_R	213_E	2.559	1.00
144_E	195_L	2.558	1.00
179_R	213_E	2.555	1.00
120_L	123_S	2.502	1.00
94_L	99_P	2.461	1.00
191_R	205_L	2.397	1.00
238_R	241_A	2.265	1.00
231_D	234_T	2.201	1.00
55_T	208_L	2.148	1.00
141_M	192_L	2.118	1.00
194_A	208_L	2.072	1.00
140_S	205_L	2.043	1.00
176_R	180_H	2.042	1.00
106_G	109_N	2.018	1.00
265_D	269_D	2.016	1.00
89_M	158_Q	1.987	1.00
55_T	190_V	1.965	1.00
264_R	268_D	1.917	1.00
262_K	265_D	1.889	1.00
210_K	214_S	1.873	1.00
190_V	212_A	1.866	1.00
59_F	204_A	1.844	1.00
126_S	142_I	1.833	1.00
171_L	254_L	1.770	1.00
206_P	210_K	1.759	1.00
266_L	269_D	1.689	1.00
109_N	159_A	1.669	1.00
83_H	115_D	1.665	1.00
199_D	204_A	1.655	1.00
276_Q	280_Q	1.649	1.00
83_H	114_G	1.633	1.00
68_A	127_D	1.625	1.00
188_A	192_L	1.625	1.00
140_S	202_R	1.623	1.00
200_K	203_R	1.605	1.00
284_T	288_E	1.591	1.00
167_K	173_A	1.589	1.00
241_A	245_L	1.577	1.00
127_D	143_S	1.564	1.00
82_I	101_C	1.530	1.00
254_L	258_Q	1.521	1.00
194_A	199_D	1.516	1.00
56_G	61_V	1.499	1.00
160_L	176_R	1.493	1.00
92_D	241_A	1.480	1.00
158_Q	161_D	1.467	1.00
37_Q	41_L	1.465	1.00
260_R	263_A	1.460	1.00
193_G	197_A	1.451	1.00
140_S	143_S	1.450	1.00
277_L	280_Q	1.445	1.00
54_A	57_H	1.442	1.00
232_T	239_Q	1.441	1.00
230_G	235_L	1.420	1.00
187_R	191_R	1.414	1.00
15_N	18_L	1.408	1.00
11_V	14_A	1.402	1.00
174_L	178_H	1.398	1.00
202_R	206_P	1.392	1.00
258_Q	261_K	1.383	1.00
285_S	288_E	1.366	1.00
42_L	98_L	1.361	1.00
11_V	15_N	1.353	1.00
285_S	289_A	1.351	1.00
268_D	272_Q	1.343	1.00
232_T	238_R	1.332	1.00
55_T	59_F	1.325	1.00
53_Y	70_A	1.323	1.00
80_S	154_M	1.319	1.00
69_P	141_M	1.318	1.00
86_L	107_E	1.305	1.00
179_R	217_L	1.304	1.00
75_C	124_I	1.283	1.00
214_S	269_D	1.275	1.00
267_I	271_R	1.275	1.00
144_E	188_A	1.273	1.00
72_A	125_L	1.273	1.00
12_K	15_N	1.272	1.00
14_A	18_L	1.259	1.00
140_S	195_L	1.255	1.00
141_M	196_S	1.235	1.00
225_I	229_V	1.228	1.00
31_P	163_D	1.226	1.00
153_G	180_H	1.222	1.00
31_P	106_G	1.220	1.00
185_L	189_A	1.211	1.00
59_F	197_A	1.201	1.00
194_A	205_L	1.200	1.00
176_R	179_R	1.183	1.00
123_S	149_S	1.178	1.00
286_A	289_A	1.176	1.00
254_L	257_E	1.172	1.00
160_L	180_H	1.166	1.00
261_K	265_D	1.166	1.00
226_L	235_L	1.166	1.00
16_Q	20_R	1.162	1.00
164_A	169_V	1.160	1.00
184_A	187_R	1.160	1.00
17_A	21_F	1.159	1.00
43_G	46_R	1.152	1.00
266_L	271_R	1.140	1.00
191_R	195_L	1.139	1.00
17_A	68_A	1.137	1.00
39_G	101_C	1.128	1.00
59_F	193_G	1.127	1.00
18_L	21_F	1.126	1.00
35_T	101_C	1.120	1.00
171_L	175_E	1.120	1.00
190_V	208_L	1.117	1.00
160_L	177_I	1.115	1.00
51_L	190_V	1.105	1.00
56_G	197_A	1.096	1.00
53_Y	67_D	1.090	1.00
261_K	264_R	1.089	1.00
69_P	192_L	1.086	1.00
13_Q	67_D	1.084	1.00
178_H	217_L	1.082	1.00
266_L	270_A	1.072	1.00
203_R	207_V	1.068	1.00
204_A	207_V	1.067	1.00
99_P	103_V	1.066	1.00
86_L	111_I	1.056	1.00
17_A	20_R	1.052	1.00
175_E	217_L	1.048	1.00
59_F	199_D	1.044	1.00
102_H	107_E	1.040	1.00
94_L	232_T	1.040	1.00
174_L	253_L	1.040	1.00
17_A	71_A	1.034	1.00
164_A	177_I	1.026	1.00
229_V	260_R	1.023	1.00
228_V	251_P	1.014	1.00
52_V	73_V	1.012	1.00
189_A	193_G	1.011	1.00
31_P	34_E	1.011	1.00
89_M	112_L	1.008	1.00
125_L	141_M	1.003	1.00
69_P	125_L	1.003	1.00
122_F	146_A	1.002	1.00
175_E	179_R	1.001	1.00
19_S	37_Q	0.994	1.00
99_P	104_K	0.993	1.00
30_T	34_E	0.992	1.00
228_V	243_Q	0.991	1.00
76_I	145_L	0.976	1.00
13_Q	16_Q	0.968	1.00
91_D	107_E	0.967	1.00
276_Q	279_E	0.965	1.00
62_S	65_T	0.962	1.00
207_V	211_Y	0.962	1.00
16_Q	19_S	0.950	1.00
34_E	38_Y	0.950	1.00
19_S	23_A	0.949	1.00
169_V	173_A	0.948	1.00
177_I	247_K	0.947	1.00
52_V	66_L	0.946	1.00
46_R	49_P	0.937	1.00
150_G	188_A	0.932	1.00
145_L	192_L	0.930	1.00
164_A	173_A	0.926	1.00
269_D	273_S	0.926	1.00
166_G	246_G	0.926	1.00
210_K	213_E	0.923	1.00
259_A	263_A	0.923	1.00
258_Q	262_K	0.917	1.00
53_Y	66_L	0.917	1.00
206_P	209_D	0.913	1.00
10_C	13_Q	0.907	1.00
13_Q	57_H	0.900	1.00
280_Q	284_T	0.897	1.00
75_C	120_L	0.897	1.00
69_P	196_S	0.890	1.00
33_V	37_Q	0.888	1.00
36_M	116_A	0.884	1.00
38_Y	104_K	0.883	1.00
235_L	239_Q	0.883	1.00
123_S	152_A	0.882	1.00
222_Q	263_A	0.874	1.00
187_R	212_A	0.873	1.00
14_A	17_A	0.871	1.00
20_R	23_A	0.871	1.00
12_K	16_Q	0.871	1.00
191_R	206_P	0.869	1.00
38_Y	105_F	0.868	1.00
190_V	211_Y	0.867	1.00
165_E	248_S	0.865	1.00
41_L	98_L	0.864	1.00
61_V	66_L	0.862	1.00
209_D	213_E	0.860	1.00
171_L	257_E	0.860	1.00
161_D	247_K	0.859	1.00
213_E	217_L	0.851	1.00
93_D	102_H	0.850	1.00
205_L	209_D	0.846	1.00
271_R	288_E	0.844	1.00
123_S	127_D	0.844	1.00
71_A	124_I	0.843	1.00
195_L	205_L	0.837	1.00
265_D	268_D	0.837	1.00
10_C	14_A	0.836	1.00
38_Y	98_L	0.833	1.00
123_S	143_S	0.832	1.00
273_S	276_Q	0.831	1.00
126_S	143_S	0.831	1.00
275_K	288_E	0.827	1.00
82_I	110_A	0.823	1.00
22_I	37_Q	0.821	1.00
225_I	256_L	0.817	1.00
68_A	128_A	0.817	1.00
172_D	175_E	0.815	1.00
101_C	105_F	0.808	1.00
18_L	46_R	0.807	1.00
79_Y	118_Q	0.804	1.00
163_D	167_K	0.801	1.00
49_P	78_A	0.800	1.00
24_P	127_D	0.799	1.00
277_L	284_T	0.796	1.00
130_M	140_S	0.791	1.00
226_L	230_G	0.788	1.00
58_M	208_L	0.787	1.00
144_E	209_D	0.785	1.00
66_L	196_S	0.784	1.00
101_C	104_K	0.781	1.00
100_T	103_V	0.781	1.00
278_A	284_T	0.779	1.00
150_G	153_G	0.779	1.00
284_T	287_L	0.778	1.00
255_G	259_A	0.777	1.00
207_V	276_Q	0.771	1.00
210_K	273_S	0.771	1.00
48_R	219_F	0.770	1.00
13_Q	63_T	0.769	1.00
116_A	155_C	0.765	1.00
15_N	19_S	0.759	1.00
219_F	223_D	0.759	1.00
18_L	25_L	0.759	1.00
221_V	225_I	0.758	1.00
10_C	57_H	0.755	1.00
51_L	215_I	0.755	1.00
36_M	117_L	0.747	1.00
171_L	250_Y	0.745	1.00
227_D	241_A	0.745	1.00
52_V	70_A	0.739	1.00
160_L	164_A	0.739	1.00
108_A	162_L	0.736	1.00
67_D	71_A	0.732	1.00
39_G	78_A	0.731	1.00
118_Q	155_C	0.730	1.00
179_R	184_A	0.730	1.00
272_Q	275_K	0.729	1.00
230_G	234_T	0.729	1.00
251_P	254_L	0.727	1.00
39_G	82_I	0.725	1.00
223_D	226_L	0.721	1.00
119_T	155_C	0.720	1.00
68_A	71_A	0.716	1.00
57_H	63_T	0.715	1.00
128_A	131_P	0.712	1.00
31_P	109_N	0.707	1.00
69_P	128_A	0.702	1.00
89_M	155_C	0.701	1.00
68_A	124_I	0.696	1.00
154_M	186_I	0.693	1.00
98_L	104_K	0.693	1.00
222_Q	225_I	0.693	1.00
214_S	266_L	0.690	1.00
274_L	277_L	0.680	1.00
197_A	200_K	0.677	0.99
52_V	193_G	0.675	0.99
73_V	192_L	0.670	0.99
35_T	113_A	0.663	0.99
171_L	253_L	0.659	0.99
35_T	109_N	0.659	0.99
36_M	113_A	0.658	0.99
52_V	189_A	0.657	0.99
20_R	68_A	0.657	0.99
177_I	180_H	0.657	0.99
186_I	215_I	0.656	0.99
10_C	50_F	0.654	0.99
252_A	271_R	0.654	0.99
77_H	80_S	0.653	0.99
45_K	219_F	0.653	0.99
235_L	238_R	0.648	0.99
172_D	176_R	0.646	0.99
13_Q	17_A	0.645	0.99
80_S	185_L	0.645	0.99
214_S	217_L	0.645	0.99
250_Y	254_L	0.644	0.99
28_Q	176_R	0.643	0.99
182_T	219_F	0.642	0.99
211_Y	214_S	0.641	0.99
73_V	189_A	0.639	0.99
230_G	239_Q	0.638	0.99
82_I	117_L	0.638	0.99
180_H	184_A	0.637	0.99
29_N	33_V	0.637	0.99
169_V	248_S	0.633	0.99
183_G	217_L	0.631	0.99
86_L	108_A	0.629	0.99
35_T	105_F	0.628	0.99
279_E	285_S	0.625	0.99
30_T	33_V	0.623	0.99
275_K	280_Q	0.618	0.99
192_L	196_S	0.614	0.99
202_R	205_L	0.613	0.99
124_I	127_D	0.612	0.99
241_A	244_Q	0.611	0.99
207_V	273_S	0.611	0.99
149_S	153_G	0.610	0.99
275_K	278_A	0.607	0.99
227_D	235_L	0.607	0.99
89_M	162_L	0.606	0.99
82_I	113_A	0.606	0.99
82_I	86_L	0.603	0.99
119_T	122_F	0.599	0.99
56_G	196_S	0.594	0.99
153_G	156_G	0.594	0.99
120_L	152_A	0.593	0.99
182_T	186_I	0.593	0.99
207_V	210_K	0.592	0.99
153_G	179_R	0.590	0.99
269_D	272_Q	0.590	0.99
174_L	250_Y	0.589	0.99
42_L	78_A	0.587	0.99
140_S	144_E	0.586	0.99
232_T	235_L	0.584	0.99
47_L	186_I	0.581	0.98
279_E	284_T	0.578	0.98
159_A	163_D	0.577	0.98
156_G	180_H	0.577	0.98
61_V	193_G	0.576	0.98
48_R	77_H	0.573	0.98
32_V	35_T	0.572	0.98
175_E	221_V	0.572	0.98
27_F	33_V	0.572	0.98
107_E	111_I	0.571	0.98
59_F	208_L	0.568	0.98
91_D	102_H	0.564	0.98
79_Y	119_T	0.563	0.98
161_D	165_E	0.561	0.98
53_Y	57_H	0.559	0.98
222_Q	229_V	0.559	0.98
271_R	274_L	0.559	0.98
120_L	124_I	0.558	0.98
65_T	130_M	0.556	0.98
155_C	162_L	0.556	0.98
35_T	38_Y	0.555	0.98
262_K	266_L	0.551	0.98
13_Q	64_N	0.549	0.98
259_A	262_K	0.549	0.98
20_R	24_P	0.547	0.98
65_T	128_A	0.544	0.98
276_Q	284_T	0.544	0.98
274_L	287_L	0.543	0.98
270_A	273_S	0.543	0.98
256_L	260_R	0.542	0.98
64_N	67_D	0.542	0.98
14_A	22_I	0.542	0.98
46_R	50_F	0.540	0.98
75_C	117_L	0.538	0.97
165_E	245_L	0.537	0.97
160_L	173_A	0.535	0.97
227_D	238_R	0.534	0.97
270_A	274_L	0.533	0.97
184_A	213_E	0.533	0.97
255_G	287_L	0.530	0.97
164_A	167_K	0.529	0.97
76_I	121_A	0.528	0.97
28_Q	31_P	0.527	0.97
257_E	260_R	0.526	0.97
223_D	237_K	0.526	0.97
92_D	238_R	0.525	0.97
254_L	262_K	0.521	0.97
20_R	67_D	0.516	0.97
18_L	41_L	0.514	0.97
126_S	146_A	0.513	0.97
141_M	195_L	0.513	0.97
273_S	280_Q	0.513	0.97
260_R	264_R	0.510	0.97
50_F	54_A	0.510	0.97
23_A	26_P	0.510	0.97
21_F	24_P	0.509	0.96
122_F	125_L	0.502	0.96
94_L	100_T	0.502	0.96
21_F	25_L	0.501	0.96
199_D	205_L	0.501	0.96
17_A	67_D	0.500	0.96
39_G	42_L	0.500	0.96
56_G	193_G	0.500	0.96

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
4jxyA	5	0.893	100	0.119	Contact Map
1rqjA	2	0.99	100	0.122	Contact Map
3oyrA	2	0.9565	100	0.124	Contact Map
3lsnA	2	0.9264	100	0.124	Contact Map
3pdeA	2	0.9465	100	0.126	Contact Map
3ts7A	2	0.9431	100	0.126	Contact Map
1wy0A	2	0.9632	100	0.129	Contact Map
3wjkA	2	0.9331	100	0.129	Contact Map
3mzvA	2	0.9565	100	0.132	Contact Map
2h8oA	2	0.9097	100	0.133	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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