RSPB - ECOLI - GREMLIN Contacts

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RSPB - Starvation-sensing protein RspB

UniProt:	P38105	Sequences: MKSILIEKPNQLAIVEREIPTPSAGEVRVKVKLAGICGSDSHIYRGHNPFAKYPRVIGHEFFGVIDAVGEGVESARVGERVAVDPVVSCGHCYPCSIGKPNVCTTLAVLGVHADGGFSEYAVVPAKNAWKIPEAVADQYAVMIEPFTIAANVTGHGQPTENDTVLVYGAGPIGLTIVQVLKGVYNVKNVIVADRIDERLEKAKESGADWAINNSQTPLGEIFTEKGIKPTLIIDAACHPSILKEAVTLASPAARIVLMGFSSEPSEVIQQGITGKELSIFSSRLNANKFPIVIDWLSKGLIKPEKLITHTFDFQHVADAISLFEQDQKHCCKVLLTFSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12452
Length:	339 (302)
Sequences:	52896 (36236)
Seq/√Len:	2085.1

ECOLI - RSPB YBDR YDJL GATD YDJJ TDH ADHP FRMA YJJN YPHC YGGP AHR YAHK IDND YCJQ QOR1 ACUI CURA
BACSU - YJMD DHSO BDHA ADHB TDH YYCR ADHA YOGA YHFP YFMJ
HALSA - Q9HMB6 Q9HP38 GLCDH Q9HQS8 Q9HR85
SULSO - Q97YT7 Q7LXK1 ADH Q97ZV3 Q97VV5 Q97XR4 Q97VW0 Q97WA1 GLCD2 Q97TZ4 GLCD1 Q97V32 Q97YM2 GLCD3 Q97W06 Q97VB8 Q97UW5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
315_H	318_D	2.966	1.00
32_K	137_D	2.915	1.00
30_K	66_D	2.829	1.00
32_K	64_V	2.736	1.00
28_R	66_D	2.648	1.00
7_E	15_V	2.636	1.00
27_V	128_A	2.573	1.00
163_T	188_N	2.542	1.00
136_A	139_Y	2.521	1.00
181_K	208_D	2.434	1.00
80_R	131_I	2.370	1.00
79_E	130_K	2.365	1.00
76_R	79_E	2.363	1.00
311_F	322_L	2.310	1.00
200_E	204_E	2.283	1.00
61_F	116_G	2.278	1.00
221_I	224_E	2.263	1.00
30_K	64_V	2.238	1.00
19_I	120_Y	2.209	1.00
188_N	209_W	2.185	1.00
138_Q	310_T	2.181	1.00
169_A	191_V	2.167	1.00
7_E	13_A	2.164	1.00
30_K	120_Y	2.149	1.00
294_D	298_K	2.092	1.00
199_L	203_K	2.084	1.00
164_V	180_L	2.083	1.00
309_H	322_L	2.075	1.00
74_S	125_A	2.048	1.00
159_T	162_D	2.018	1.00
312_D	315_H	2.013	1.00
24_A	70_E	2.011	1.00
5_L	15_V	2.004	1.00
23_S	26_E	1.978	1.00
134_A	297_S	1.974	1.00
61_F	83_V	1.951	1.00
177_V	207_A	1.949	1.00
24_A	71_G	1.933	1.00
80_R	137_D	1.929	1.00
25_G	71_G	1.910	1.00
321_S	325_Q	1.898	1.00
62_F	137_D	1.879	1.00
146_F	175_T	1.808	1.00
28_R	122_V	1.800	1.00
21_T	67_A	1.792	1.00
66_D	120_Y	1.781	1.00
45_R	324_E	1.779	1.00
200_E	203_K	1.767	1.00
318_D	321_S	1.746	1.00
165_L	192_A	1.736	1.00
165_L	229_P	1.729	1.00
196_D	200_E	1.727	1.00
199_L	210_A	1.723	1.00
162_D	254_R	1.700	1.00
230_T	250_S	1.663	1.00
190_I	229_P	1.656	1.00
131_I	137_D	1.655	1.00
322_L	327_Q	1.646	1.00
311_F	319_A	1.640	1.00
318_D	322_L	1.624	1.00
254_R	278_S	1.614	1.00
131_I	140_A	1.594	1.00
167_Y	245_A	1.582	1.00
216_T	221_I	1.577	1.00
193_D	199_L	1.556	1.00
69_G	72_V	1.552	1.00
75_A	130_K	1.539	1.00
4_I	316_V	1.538	1.00
201_K	204_E	1.531	1.00
188_N	208_D	1.527	1.00
196_D	212_N	1.525	1.00
156_G	231_L	1.525	1.00
249_A	255_I	1.516	1.00
254_R	280_F	1.505	1.00
68_V	77_V	1.490	1.00
182_G	300_L	1.483	1.00
28_R	120_Y	1.482	1.00
67_A	77_V	1.469	1.00
196_D	215_Q	1.467	1.00
217_P	220_E	1.463	1.00
26_E	124_P	1.456	1.00
31_V	61_F	1.454	1.00
212_N	215_Q	1.452	1.00
249_A	277_L	1.451	1.00
117_F	320_I	1.444	1.00
22_P	122_V	1.441	1.00
75_A	79_E	1.435	1.00
249_A	253_A	1.406	1.00
25_G	124_P	1.401	1.00
64_V	80_R	1.393	1.00
80_R	133_E	1.382	1.00
22_P	28_R	1.381	1.00
26_E	122_V	1.371	1.00
232_I	245_A	1.364	1.00
33_L	138_Q	1.355	1.00
232_I	249_A	1.353	1.00
317_A	321_S	1.349	1.00
65_I	75_A	1.341	1.00
44_Y	320_I	1.339	1.00
308_T	322_L	1.320	1.00
28_R	67_A	1.303	1.00
27_V	75_A	1.301	1.00
220_E	224_E	1.291	1.00
294_D	297_S	1.276	1.00
64_V	137_D	1.269	1.00
177_V	191_V	1.268	1.00
4_I	14_I	1.252	1.00
163_T	190_I	1.248	1.00
176_I	233_I	1.247	1.00
194_R	213_N	1.241	1.00
167_Y	192_A	1.235	1.00
154_G	288_K	1.226	1.00
154_G	291_I	1.225	1.00
3_S	17_R	1.220	1.00
75_A	128_A	1.177	1.00
8_K	11_Q	1.176	1.00
32_K	80_R	1.176	1.00
143_I	296_L	1.166	1.00
203_K	210_A	1.157	1.00
158_P	186_V	1.151	1.00
196_D	199_L	1.151	1.00
199_L	212_N	1.148	1.00
19_I	28_R	1.147	1.00
163_T	230_T	1.129	1.00
25_G	125_A	1.112	1.00
291_I	294_D	1.104	1.00
31_V	121_A	1.102	1.00
22_P	26_E	1.101	1.00
123_V	128_A	1.095	1.00
286_A	290_P	1.092	1.00
178_Q	302_K	1.091	1.00
162_D	230_T	1.076	1.00
66_D	77_V	1.075	1.00
191_V	207_A	1.058	1.00
156_G	256_V	1.058	1.00
14_I	314_Q	1.051	1.00
29_V	63_G	1.049	1.00
36_I	319_A	1.047	1.00
217_P	221_I	1.039	1.00
4_I	313_F	1.038	1.00
151_N	288_K	1.037	1.00
139_Y	302_K	1.031	1.00
316_V	335_L	1.025	1.00
44_Y	324_E	1.024	1.00
203_K	209_W	1.022	1.00
201_K	330_C	1.021	1.00
155_H	278_S	1.019	1.00
33_L	137_D	1.017	1.00
247_T	271_G	1.013	1.00
29_V	81_V	1.012	1.00
295_W	300_L	1.006	1.00
149_A	176_I	1.005	1.00
290_P	294_D	0.998	1.00
215_Q	221_I	0.990	1.00
149_A	179_V	0.989	1.00
34_A	117_F	0.989	1.00
236_A	241_I	0.986	1.00
219_G	247_T	0.976	1.00
204_E	305_K	0.974	1.00
37_C	60_E	0.969	1.00
5_L	17_R	0.964	1.00
37_C	59_H	0.961	1.00
158_P	162_D	0.959	1.00
302_K	305_K	0.959	1.00
32_K	62_F	0.954	1.00
9_P	53_Y	0.954	1.00
7_E	11_Q	0.954	1.00
117_F	316_V	0.952	1.00
194_R	199_L	0.950	1.00
169_A	193_D	0.946	1.00
146_F	292_V	0.939	1.00
34_A	116_G	0.938	1.00
190_I	209_W	0.937	1.00
322_L	333_V	0.930	1.00
321_S	324_E	0.925	1.00
243_K	247_T	0.918	1.00
19_I	67_A	0.913	1.00
234_D	237_C	0.912	1.00
244_E	247_T	0.912	1.00
68_V	72_V	0.910	1.00
152_V	258_M	0.910	1.00
180_L	186_V	0.907	1.00
150_A	291_I	0.906	1.00
5_L	56_V	0.905	1.00
219_G	244_E	0.903	1.00
72_V	125_A	0.903	1.00
166_V	176_I	0.898	1.00
166_V	180_L	0.896	1.00
177_V	189_V	0.895	1.00
25_G	69_G	0.893	1.00
41_S	323_F	0.893	1.00
195_I	198_R	0.892	1.00
182_G	295_W	0.892	1.00
33_L	334_L	0.890	1.00
135_V	140_A	0.890	1.00
222_F	229_P	0.886	1.00
169_A	202_A	0.886	1.00
192_A	213_N	0.883	1.00
190_I	211_I	0.881	1.00
55_R	114_D	0.880	1.00
272_I	279_I	0.878	1.00
167_Y	232_I	0.876	1.00
73_E	125_A	0.875	1.00
165_L	248_L	0.873	1.00
194_R	214_S	0.873	1.00
152_V	233_I	0.871	1.00
3_S	56_V	0.871	1.00
76_R	130_K	0.869	1.00
219_G	223_T	0.867	1.00
30_K	119_E	0.865	1.00
179_V	292_V	0.865	1.00
17_R	114_D	0.861	1.00
174_L	201_K	0.859	1.00
271_G	275_K	0.858	1.00
35_G	60_E	0.858	1.00
197_E	200_E	0.855	1.00
21_T	28_R	0.854	1.00
117_F	335_L	0.854	1.00
19_I	66_D	0.851	1.00
169_A	177_V	0.843	1.00
198_R	330_C	0.842	1.00
61_F	121_A	0.842	1.00
82_A	293_I	0.839	1.00
163_T	229_P	0.836	1.00
4_I	12_L	0.833	1.00
323_F	333_V	0.833	1.00
162_D	231_L	0.832	1.00
191_V	202_A	0.828	1.00
311_F	315_H	0.821	1.00
287_N	291_I	0.821	1.00
193_D	210_A	0.821	1.00
195_I	212_N	0.815	1.00
133_E	297_S	0.812	1.00
291_I	295_W	0.812	1.00
147_T	288_K	0.805	1.00
36_I	323_F	0.804	1.00
4_I	317_A	0.799	1.00
179_V	295_W	0.797	1.00
252_A	276_E	0.797	1.00
220_E	223_T	0.793	1.00
155_H	280_F	0.791	1.00
268_I	271_G	0.790	1.00
37_C	40_D	0.788	1.00
287_N	290_P	0.782	1.00
81_V	128_A	0.779	1.00
202_A	207_A	0.778	1.00
153_T	180_L	0.776	1.00
190_I	222_F	0.770	1.00
23_S	122_V	0.769	1.00
152_V	176_I	0.764	1.00
218_L	244_E	0.762	1.00
149_A	175_T	0.762	1.00
135_V	296_L	0.759	1.00
245_A	255_I	0.756	1.00
10_N	44_Y	0.752	1.00
14_I	313_F	0.752	1.00
164_V	186_V	0.751	1.00
83_V	123_V	0.750	1.00
219_G	248_L	0.748	1.00
39_S	59_H	0.746	1.00
232_I	255_I	0.743	1.00
184_Y	291_I	0.741	1.00
217_P	244_E	0.740	1.00
25_G	70_E	0.740	1.00
129_W	290_P	0.738	1.00
167_Y	241_I	0.737	1.00
27_V	125_A	0.734	1.00
68_V	76_R	0.733	1.00
163_T	227_I	0.731	1.00
272_I	277_L	0.731	1.00
295_W	298_K	0.728	1.00
151_N	276_E	0.727	1.00
157_Q	254_R	0.725	1.00
309_H	318_D	0.725	1.00
149_A	172_I	0.724	1.00
158_P	231_L	0.722	1.00
235_A	258_M	0.722	1.00
322_L	325_Q	0.721	1.00
82_A	131_I	0.718	1.00
295_W	299_G	0.711	1.00
22_P	69_G	0.711	1.00
204_E	302_K	0.709	1.00
180_L	189_V	0.707	1.00
189_V	208_D	0.706	1.00
17_R	56_V	0.703	1.00
62_F	141_V	0.702	1.00
36_I	117_F	0.701	1.00
179_V	184_Y	0.701	1.00
257_L	279_I	0.700	1.00
22_P	67_A	0.694	1.00
129_W	289_F	0.693	1.00
33_L	310_T	0.691	1.00
311_F	335_L	0.685	1.00
150_A	292_V	0.685	1.00
311_F	333_V	0.684	1.00
149_A	153_T	0.684	1.00
186_V	231_L	0.684	1.00
272_I	281_S	0.683	1.00
166_V	191_V	0.680	1.00
116_G	121_A	0.679	1.00
229_P	232_I	0.678	1.00
231_L	256_V	0.676	1.00
186_V	189_V	0.674	1.00
307_I	310_T	0.674	1.00
243_K	264_P	0.670	1.00
309_H	333_V	0.668	1.00
54_P	58_G	0.668	1.00
80_R	134_A	0.666	1.00
227_I	250_S	0.665	1.00
242_L	255_I	0.664	1.00
132_P	297_S	0.661	1.00
74_S	286_A	0.660	1.00
150_A	295_W	0.656	1.00
251_P	275_K	0.656	1.00
293_I	297_S	0.656	1.00
222_F	248_L	0.655	1.00
209_W	221_I	0.654	1.00
157_Q	280_F	0.654	1.00
201_K	205_S	0.653	1.00
148_I	172_I	0.652	1.00
145_P	171_P	0.652	1.00
79_E	133_E	0.651	1.00
62_F	131_I	0.649	1.00
129_W	293_I	0.648	1.00
20_P	122_V	0.647	1.00
25_G	126_K	0.645	1.00
37_C	145_P	0.643	1.00
193_D	213_N	0.641	1.00
177_V	205_S	0.640	1.00
74_S	130_K	0.639	1.00
38_G	42_H	0.638	1.00
8_K	13_A	0.632	1.00
33_L	62_F	0.630	1.00
320_I	324_E	0.630	1.00
27_V	65_I	0.629	1.00
74_S	77_V	0.627	1.00
234_D	255_I	0.624	1.00
243_K	271_G	0.624	1.00
199_L	202_A	0.624	1.00
51_A	55_R	0.621	1.00
243_K	266_E	0.620	1.00
157_Q	278_S	0.620	1.00
223_T	228_K	0.617	1.00
39_S	43_I	0.617	1.00
62_F	80_R	0.616	1.00
144_E	148_I	0.615	1.00
178_Q	205_S	0.612	1.00
31_V	34_A	0.611	1.00
229_P	248_L	0.611	1.00
192_A	211_I	0.610	1.00
193_D	212_N	0.610	1.00
238_H	241_I	0.609	1.00
29_V	83_V	0.609	1.00
41_S	324_E	0.605	1.00
84_D	129_W	0.605	1.00
150_A	288_K	0.602	1.00
156_G	254_R	0.601	1.00
154_G	184_Y	0.600	1.00
176_I	258_M	0.597	1.00
218_L	222_F	0.597	1.00
239_P	243_K	0.595	1.00
231_L	254_R	0.594	1.00
181_K	189_V	0.594	1.00
199_L	213_N	0.592	1.00
82_A	144_E	0.591	1.00
232_I	248_L	0.590	1.00
201_K	306_L	0.588	1.00
143_I	292_V	0.584	1.00
202_A	210_A	0.582	1.00
129_W	286_A	0.579	1.00
20_P	120_Y	0.578	1.00
38_G	170_G	0.578	1.00
148_I	258_M	0.577	1.00
164_V	231_L	0.577	1.00
145_P	175_T	0.576	1.00
37_C	332_K	0.576	1.00
329_H	333_V	0.575	1.00
234_D	259_G	0.575	1.00
264_P	268_I	0.575	1.00
73_E	76_R	0.574	1.00
174_L	306_L	0.573	1.00
241_I	245_A	0.573	1.00
19_I	22_P	0.572	1.00
83_V	128_A	0.571	1.00
18_E	21_T	0.570	1.00
42_H	47_H	0.569	1.00
211_I	221_I	0.568	1.00
9_P	46_G	0.567	1.00
39_S	42_H	0.566	1.00
299_G	302_K	0.562	1.00
20_P	26_E	0.559	1.00
194_R	202_A	0.558	1.00
51_A	54_P	0.557	1.00
177_V	202_A	0.556	1.00
165_L	232_I	0.553	1.00
19_I	122_V	0.552	1.00
58_G	117_F	0.552	1.00
34_A	335_L	0.552	1.00
75_A	125_A	0.550	1.00
153_T	179_V	0.550	1.00
68_V	79_E	0.549	1.00
322_L	329_H	0.547	1.00
12_L	320_I	0.547	1.00
154_G	287_N	0.546	1.00
160_E	184_Y	0.546	1.00
309_H	330_C	0.544	1.00
125_A	128_A	0.542	1.00
274_G	283_R	0.542	1.00
264_P	267_V	0.542	1.00
160_E	185_N	0.541	1.00
142_M	334_L	0.539	1.00
132_P	140_A	0.536	1.00
137_D	140_A	0.536	1.00
14_I	316_V	0.536	1.00
157_Q	162_D	0.536	1.00
154_G	157_Q	0.535	1.00
60_E	332_K	0.534	1.00
31_V	83_V	0.533	1.00
150_A	184_Y	0.533	1.00
22_P	71_G	0.533	1.00
41_S	45_R	0.533	1.00
175_T	179_V	0.532	1.00
308_T	331_C	0.532	1.00
136_A	310_T	0.531	1.00
181_K	184_Y	0.529	1.00
288_K	291_I	0.527	1.00
211_I	216_T	0.525	1.00
20_P	28_R	0.525	1.00
228_K	250_S	0.522	1.00
174_L	205_S	0.519	1.00
163_T	209_W	0.519	1.00
256_V	282_S	0.519	1.00
130_K	133_E	0.518	1.00
36_I	335_L	0.517	1.00
136_A	140_A	0.515	1.00
83_V	116_G	0.515	1.00
194_R	212_N	0.514	1.00
83_V	121_A	0.514	1.00
56_V	115_G	0.514	1.00
29_V	128_A	0.511	1.00
178_Q	301_I	0.511	1.00
26_E	113_A	0.510	1.00
311_F	318_D	0.510	1.00
271_G	274_G	0.509	1.00
203_K	207_A	0.509	1.00
62_F	140_A	0.509	1.00
273_T	281_S	0.505	1.00
296_L	301_I	0.502	1.00
153_T	176_I	0.501	1.00
68_V	75_A	0.501	1.00
163_T	228_K	0.500	1.00
43_I	48_N	0.500	1.00
265_S	269_Q	0.500	1.00

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
4ilkA	2	0.9882	100	0.106	Contact Map
4ej6A	1	0.9853	100	0.135	Contact Map
2dq4A	4	0.9853	100	0.137	Contact Map
3ukoA	4	0.9882	100	0.148	Contact Map
4oh1A	4	0.9735	100	0.15	Contact Map
4gkvA	4	0.9823	100	0.154	Contact Map
3m6iA	4	0.9882	100	0.156	Contact Map
4uejA	2	0.9823	100	0.157	Contact Map
1f8fA	4	0.9794	100	0.16	Contact Map
1e3iA	2	0.9794	100	0.161	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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