YEAP - ECOLI - GREMLIN Contacts

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YEAP - Probable diguanylate cyclase YeaP

UniProt:	P76245	Sequences: MSDQIIARVSQSLAKEQSLESLVRQLLEMLEMVTDMESTYLTKVDVEARLQHIMFARNSQKMYIPENFTVSWDYSLCKRAIDENCFFSDEVPDRWGDCIAARNLGITTFLSTPIHLPDGSFYGTLCAASSEKRQWSERAEQVLQLFAGLIAQYIQKEALVEQLREANAALIAQSYTDSLTGLPNRRAIFENLTTLFSLARHLNHKIMIAFIDLDNFKLINDRFGHNSGDLFLIQVGERLNTLQQNGEVIGRLGGDEFLVVSLNNENADISSLRERIQQQIRGEYHLGDVDLYYPGASLGIVEVDPETTDADSALHAADIAMYQEKKHKQKTPFVAHPALHS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13502
Length:	341 (306)
Sequences:	9701 (8665)
Seq/√Len:	495.4

ECOLI - YEAP YEGE YEDQ DOSC YDAM DOSP GMR YEAJ YEAI YCDT YFIN YLIF ADRA YNEF YDEH YFEA YFGF CSRD YLIE YHJK YLAB YJCC RTN
BACSU - YTRP YKOW YHCK YDAK

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
172_A	176_T	4.378	1.00
244_Q	247_E	3.962	1.00
215_N	329_Q	3.531	1.00
209_A	298_L	3.332	1.00
209_A	273_R	3.270	1.00
188_I	258_L	3.169	1.00
207_M	302_E	2.962	1.00
324_E	333_F	2.876	1.00
192_L	310_A	2.834	1.00
183_P	187_A	2.781	1.00
214_D	297_S	2.545	1.00
163_L	167_N	2.470	1.00
309_D	312_S	2.409	1.00
207_M	269_I	2.389	1.00
195_L	198_L	2.345	1.00
188_I	250_G	2.328	1.00
327_H	333_F	2.325	1.00
191_N	194_T	2.305	1.00
281_R	330_K	2.292	1.00
265_E	268_D	2.267	1.00
230_L	233_I	2.244	1.00
304_D	307_T	2.221	1.00
231_F	294_P	2.171	1.00
277_Q	332_P	2.162	1.00
182_L	236_G	2.076	1.00
243_Q	249_I	2.040	1.00
280_I	296_A	2.034	1.00
187_A	191_N	2.028	1.00
213_L	235_V	2.027	1.00
182_L	249_I	2.009	1.00
234_Q	237_E	1.994	1.00
234_Q	238_R	1.968	1.00
171_I	175_Y	1.961	1.00
239_L	249_I	1.954	1.00
274_E	277_Q	1.907	1.00
295_G	330_K	1.883	1.00
210_F	321_M	1.821	1.00
272_L	275_R	1.806	1.00
226_N	315_H	1.805	1.00
219_I	231_F	1.792	1.00
85_C	88_S	1.760	1.00
167_N	170_L	1.749	1.00
211_I	296_A	1.748	1.00
307_T	316_A	1.700	1.00
216_F	232_L	1.698	1.00
315_H	319_I	1.692	1.00
169_A	173_Q	1.691	1.00
252_L	258_L	1.645	1.00
242_L	279_Q	1.642	1.00
323_Q	327_H	1.636	1.00
261_S	272_L	1.627	1.00
323_Q	333_F	1.625	1.00
327_H	331_T	1.617	1.00
237_E	240_N	1.612	1.00
204_H	263_N	1.611	1.00
164_R	167_N	1.608	1.00
195_L	262_L	1.604	1.00
217_K	221_D	1.597	1.00
324_E	331_T	1.592	1.00
85_C	89_D	1.589	1.00
191_N	250_G	1.575	1.00
220_N	228_G	1.556	1.00
213_L	296_A	1.540	1.00
235_V	280_I	1.534	1.00
211_I	298_L	1.525	1.00
209_A	261_S	1.504	1.00
274_E	278_Q	1.487	1.00
175_Y	187_A	1.485	1.00
183_P	248_V	1.485	1.00
191_N	248_V	1.472	1.00
285_H	290_D	1.458	1.00
198_L	262_L	1.441	1.00
187_A	190_E	1.434	1.00
169_A	172_A	1.425	1.00
270_S	274_E	1.417	1.00
188_I	260_V	1.406	1.00
243_Q	259_V	1.401	1.00
300_I	332_P	1.396	1.00
318_D	322_Y	1.364	1.00
323_Q	326_K	1.364	1.00
230_L	234_Q	1.358	1.00
277_Q	281_R	1.354	1.00
187_A	248_V	1.352	1.00
210_F	252_L	1.338	1.00
277_Q	330_K	1.318	1.00
178_S	186_R	1.317	1.00
269_I	273_R	1.313	1.00
167_N	171_I	1.299	1.00
191_N	195_L	1.297	1.00
269_I	300_I	1.291	1.00
90_E	93_D	1.288	1.00
234_Q	284_Y	1.287	1.00
303_V	313_A	1.286	1.00
225_H	318_D	1.282	1.00
209_A	259_V	1.275	1.00
199_A	206_I	1.269	1.00
227_S	230_L	1.268	1.00
210_F	314_L	1.261	1.00
215_N	218_L	1.256	1.00
236_G	249_I	1.252	1.00
202_L	263_N	1.251	1.00
238_R	283_E	1.245	1.00
206_I	303_V	1.238	1.00
175_Y	183_P	1.234	1.00
145_L	149_L	1.234	1.00
273_R	298_L	1.225	1.00
279_Q	282_G	1.223	1.00
242_L	275_R	1.220	1.00
206_I	260_V	1.215	1.00
168_A	171_I	1.212	1.00
324_E	328_K	1.206	1.00
218_L	222_R	1.205	1.00
185_R	189_F	1.194	1.00
221_D	322_Y	1.193	1.00
301_V	313_A	1.191	1.00
256_E	318_D	1.190	1.00
308_T	316_A	1.190	1.00
273_R	332_P	1.186	1.00
175_Y	190_E	1.183	1.00
233_I	237_E	1.174	1.00
201_H	244_Q	1.170	1.00
297_S	324_E	1.164	1.00
180_T	232_L	1.164	1.00
252_L	314_L	1.162	1.00
217_K	322_Y	1.161	1.00
221_D	225_H	1.145	1.00
193_T	197_S	1.142	1.00
243_Q	276_I	1.138	1.00
244_Q	275_R	1.137	1.00
214_D	329_Q	1.115	1.00
300_I	334_V	1.115	1.00
227_S	286_L	1.113	1.00
78_K	82_D	1.110	1.00
273_R	300_I	1.106	1.00
176_T	183_P	1.103	1.00
312_S	316_A	1.101	1.00
270_S	332_P	1.101	1.00
210_F	258_L	1.099	1.00
258_L	314_L	1.098	1.00
192_L	260_V	1.098	1.00
264_N	268_D	1.092	1.00
230_L	287_G	1.088	1.00
244_Q	272_L	1.086	1.00
215_N	255_D	1.081	1.00
189_F	311_D	1.081	1.00
163_L	166_A	1.077	1.00
225_H	322_Y	1.076	1.00
221_D	318_D	1.071	1.00
176_T	187_A	1.055	1.00
211_I	239_L	1.054	1.00
270_S	334_V	1.051	1.00
205_K	305_P	1.050	1.00
199_A	303_V	1.050	1.00
301_V	316_A	1.045	1.00
253_G	256_E	1.045	1.00
213_L	232_L	1.038	1.00
27_L	39_T	1.035	1.00
212_D	325_K	1.033	1.00
301_V	317_A	1.033	1.00
172_A	181_G	1.029	1.00
185_R	229_D	1.029	1.00
179_L	232_L	1.025	1.00
278_Q	281_R	1.018	1.00
173_Q	186_R	1.018	1.00
316_A	320_A	1.012	1.00
87_F	91_V	1.011	1.00
166_A	170_L	1.010	1.00
31_E	39_T	1.009	1.00
195_L	206_I	1.008	1.00
183_P	250_G	1.008	1.00
162_Q	165_E	1.004	1.00
219_I	291_L	1.004	1.00
241_T	279_Q	1.001	1.00
271_S	275_R	0.998	1.00
166_A	169_A	0.995	1.00
88_S	92_P	0.993	1.00
328_K	331_T	0.988	1.00
206_I	313_A	0.984	1.00
86_F	90_E	0.982	1.00
177_D	251_R	0.982	1.00
212_D	322_Y	0.980	1.00
235_V	239_L	0.980	1.00
85_C	90_E	0.979	1.00
193_T	310_A	0.979	1.00
249_I	259_V	0.955	1.00
277_Q	298_L	0.955	1.00
211_I	259_V	0.950	1.00
285_H	288_D	0.947	1.00
207_M	300_I	0.947	1.00
253_G	322_Y	0.936	1.00
79_R	83_E	0.934	1.00
273_R	277_Q	0.933	1.00
175_Y	186_R	0.932	1.00
238_R	284_Y	0.919	1.00
223_F	289_V	0.913	1.00
24_R	28_E	0.911	1.00
238_R	279_Q	0.906	1.00
239_L	276_I	0.906	1.00
240_N	249_I	0.906	1.00
188_I	192_L	0.905	1.00
190_E	194_T	0.899	1.00
243_Q	272_L	0.896	1.00
306_E	334_V	0.894	1.00
212_D	255_D	0.892	1.00
208_I	313_A	0.889	1.00
214_D	328_K	0.889	1.00
27_L	31_E	0.885	1.00
208_I	314_L	0.878	1.00
170_L	173_Q	0.872	1.00
254_G	322_Y	0.866	1.00
227_S	289_V	0.865	1.00
71_S	74_Y	0.863	1.00
231_F	284_Y	0.855	1.00
67_N	71_S	0.848	1.00
40_Y	126_C	0.847	1.00
227_S	291_L	0.837	1.00
268_D	271_S	0.836	1.00
187_A	250_G	0.833	1.00
23_V	27_L	0.832	1.00
243_Q	247_E	0.832	1.00
283_E	286_L	0.825	1.00
55_F	58_N	0.821	1.00
196_F	303_V	0.816	1.00
233_I	236_G	0.812	1.00
74_Y	78_K	0.812	1.00
201_H	246_G	0.811	1.00
85_C	93_D	0.807	1.00
220_N	254_G	0.803	1.00
209_A	300_I	0.801	1.00
247_E	272_L	0.800	1.00
220_N	229_D	0.799	1.00
261_S	269_I	0.798	1.00
50_L	54_M	0.798	1.00
295_G	328_K	0.797	1.00
266_N	302_E	0.796	1.00
165_E	169_A	0.796	1.00
45_D	49_R	0.795	1.00
256_E	322_Y	0.792	1.00
27_L	53_I	0.789	1.00
212_D	220_N	0.789	1.00
214_D	330_K	0.787	1.00
304_D	316_A	0.786	1.00
286_L	289_V	0.785	1.00
188_I	314_L	0.777	1.00
46_V	49_R	0.771	1.00
67_N	70_V	0.767	1.00
269_I	302_E	0.763	1.00
114_I	123_G	0.761	1.00
189_F	250_G	0.760	1.00
255_D	295_G	0.756	1.00
198_L	201_H	0.748	1.00
109_F	113_P	0.745	1.00
310_A	314_L	0.740	1.00
176_T	182_L	0.739	1.00
225_H	254_G	0.736	1.00
217_K	225_H	0.735	1.00
231_F	255_D	0.732	1.00
191_N	260_V	0.731	1.00
37_E	130_S	0.731	1.00
217_K	254_G	0.728	1.00
218_L	255_D	0.727	1.00
250_G	258_L	0.725	1.00
129_S	132_K	0.723	1.00
235_V	294_P	0.723	1.00
38_S	128_A	0.723	1.00
226_N	230_L	0.721	1.00
212_D	221_D	0.721	1.00
26_L	150_I	0.718	1.00
75_S	78_K	0.716	1.00
221_D	254_G	0.715	1.00
255_D	329_Q	0.714	1.00
207_M	273_R	0.711	1.00
217_K	256_E	0.701	1.00
147_A	151_A	0.701	1.00
217_K	220_N	0.692	1.00
213_L	295_G	0.691	1.00
220_N	225_H	0.691	1.00
239_L	259_V	0.687	1.00
123_G	126_C	0.687	1.00
266_N	270_S	0.685	1.00
210_F	317_A	0.685	1.00
253_G	318_D	0.685	1.00
223_F	291_L	0.684	1.00
210_F	255_D	0.684	1.00
95_W	99_I	0.682	1.00
25_Q	29_M	0.681	1.00
219_I	227_S	0.680	1.00
266_N	334_V	0.679	1.00
135_W	140_E	0.678	1.00
198_L	202_L	0.678	1.00
278_Q	282_G	0.671	1.00
188_I	252_L	0.671	1.00
56_A	59_S	0.669	1.00
189_F	314_L	0.668	1.00
235_V	296_A	0.668	1.00
225_H	228_G	0.667	1.00
311_D	315_H	0.666	1.00
29_M	32_M	0.665	1.00
214_D	321_M	0.664	1.00
87_F	90_E	0.662	1.00
220_N	325_K	0.662	1.00
38_S	42_T	0.662	1.00
303_V	307_T	0.661	1.00
30_L	33_V	0.661	1.00
189_F	193_T	0.660	1.00
152_Q	156_K	0.660	1.00
213_L	216_F	0.659	1.00
199_A	204_H	0.658	1.00
239_L	243_Q	0.656	1.00
242_L	276_I	0.652	1.00
217_K	318_D	0.649	1.00
226_N	311_D	0.647	1.00
26_L	30_L	0.642	1.00
81_I	84_N	0.642	1.00
126_C	135_W	0.642	1.00
302_E	334_V	0.638	1.00
283_E	292_Y	0.638	1.00
196_F	313_A	0.636	1.00
89_D	93_D	0.633	1.00
231_F	286_L	0.633	1.00
164_R	168_A	0.632	1.00
221_D	256_E	0.630	1.00
283_E	290_D	0.630	1.00
216_F	231_F	0.629	1.00
99_I	102_R	0.628	1.00
43_K	122_Y	0.627	1.00
273_R	296_A	0.627	1.00
54_M	58_N	0.626	1.00
197_S	200_R	0.626	1.00
301_V	320_A	0.624	1.00
247_E	275_R	0.624	1.00
31_E	37_E	0.622	1.00
54_M	60_Q	0.622	1.00
308_T	312_S	0.619	1.00
89_D	92_P	0.619	1.00
258_L	317_A	0.619	1.00
28_E	32_M	0.618	1.00
200_R	303_V	0.618	1.00
45_D	52_H	0.615	1.00
172_A	175_Y	0.615	1.00
286_L	291_L	0.615	1.00
204_H	262_L	0.613	0.99
306_E	316_A	0.612	0.99
284_Y	294_P	0.611	0.99
226_N	287_G	0.610	0.99
223_F	255_D	0.609	0.99
86_F	91_V	0.608	0.99
168_A	172_A	0.607	0.99
54_M	57_R	0.607	0.99
200_R	308_T	0.606	0.99
199_A	202_L	0.606	0.99
174_S	318_D	0.604	0.99
45_D	48_A	0.603	0.99
320_A	324_E	0.603	0.99
94_R	97_D	0.602	0.99
254_G	318_D	0.602	0.99
84_N	115_H	0.602	0.99
312_S	315_H	0.601	0.99
235_V	284_Y	0.600	0.99
129_S	135_W	0.598	0.99
196_F	206_I	0.592	0.99
216_F	255_D	0.591	0.99
195_L	201_H	0.591	0.99
152_Q	155_Q	0.590	0.99
51_Q	54_M	0.589	0.99
205_K	302_E	0.588	0.99
218_L	223_F	0.587	0.99
228_G	254_G	0.582	0.99
298_L	332_P	0.581	0.99
142_V	150_I	0.581	0.99
280_I	294_P	0.579	0.99
248_V	260_V	0.579	0.99
102_R	106_I	0.578	0.99
140_E	144_Q	0.578	0.99
136_S	139_A	0.576	0.99
237_E	241_T	0.575	0.99
220_N	255_D	0.572	0.99
230_L	286_L	0.572	0.99
242_L	272_L	0.568	0.99
225_H	253_G	0.566	0.99
44_V	49_R	0.565	0.99
231_F	234_Q	0.564	0.99
225_H	256_E	0.564	0.99
198_L	246_G	0.563	0.99
196_F	307_T	0.562	0.99
303_V	306_E	0.561	0.99
212_D	253_G	0.560	0.99
135_W	139_A	0.560	0.99
72_W	75_S	0.558	0.99
319_I	323_Q	0.557	0.99
153_Y	156_K	0.557	0.99
295_G	329_Q	0.556	0.99
304_D	308_T	0.555	0.99
137_E	158_A	0.553	0.99
45_D	50_L	0.551	0.99
49_R	53_I	0.550	0.99
70_V	73_D	0.550	0.99
113_P	124_T	0.549	0.99
214_D	295_G	0.548	0.99
252_L	255_D	0.547	0.99
277_Q	324_E	0.547	0.99
216_F	297_S	0.547	0.99
192_L	196_F	0.547	0.99
196_F	310_A	0.547	0.99
140_E	152_Q	0.547	0.99
88_S	91_V	0.546	0.99
77_C	81_I	0.546	0.99
275_R	279_Q	0.545	0.99
195_L	248_V	0.544	0.99
68_F	71_S	0.538	0.99
137_E	163_L	0.538	0.99
277_Q	295_G	0.537	0.99
307_T	312_S	0.537	0.99
44_V	48_A	0.537	0.99
162_Q	166_A	0.536	0.99
101_A	105_G	0.535	0.99
27_L	30_L	0.534	0.99
40_Y	54_M	0.534	0.99
77_C	109_F	0.532	0.99
238_R	242_L	0.532	0.99
70_V	74_Y	0.531	0.99
190_E	193_T	0.530	0.99
116_L	122_Y	0.527	0.98
212_D	318_D	0.527	0.98
199_A	203_N	0.527	0.98
166_A	173_Q	0.526	0.98
212_D	228_G	0.526	0.98
219_I	286_L	0.522	0.98
29_M	33_V	0.520	0.98
142_V	152_Q	0.519	0.98
205_K	265_E	0.519	0.98
78_K	81_I	0.517	0.98
127_A	136_S	0.517	0.98
277_Q	296_A	0.517	0.98
255_D	331_T	0.516	0.98
185_R	256_E	0.515	0.98
75_S	79_R	0.514	0.98
149_L	153_Y	0.513	0.98
70_V	76_L	0.513	0.98
100_A	103_N	0.512	0.98
189_F	310_A	0.512	0.98
106_I	128_A	0.511	0.98
113_P	116_L	0.511	0.98
212_D	217_K	0.510	0.98
301_V	307_T	0.509	0.98
316_A	319_I	0.509	0.98
111_S	126_C	0.509	0.98
37_E	40_Y	0.508	0.98
115_H	121_F	0.508	0.98
201_H	247_E	0.507	0.98
145_L	151_A	0.507	0.98
223_F	227_S	0.507	0.98
183_P	191_N	0.506	0.98
284_Y	291_L	0.504	0.98
225_H	229_D	0.503	0.98
101_A	106_I	0.503	0.98
229_D	254_G	0.503	0.98
86_F	89_D	0.501	0.98
255_D	325_K	0.500	0.98

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
1w25A	2	0.9501	100	0.356	Contact Map
4j40A	2	0	100	0.389	Contact Map
4h54A	2	0.8094	100	0.393	Contact Map
3ezuA	2	0.9326	100	0.403	Contact Map
4rnhA	2	0.4751	100	0.405	Contact Map
3pjxA	1	0.5191	100	0.409	Contact Map
3mtkA	2	0.4751	100	0.418	Contact Map
3ignA	1	0.4839	100	0.424	Contact Map
3i5cA	2	0.563	100	0.426	Contact Map
3hvaA	1	0.4721	100	0.436	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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