YAHA - ECOLI - GREMLIN Contacts

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YAHA - Cyclic di-GMP phosphodiesterase YahA

UniProt:	P21514	Sequences: MNSCDFRVFLQEFGTTVHLSLPGSVSEKERLLLKLLMQGMSVTEISQYRNRSAKTISHQKKQLFEKLGIQSDITFWRDIFFQYNPEIISATGSNSHRYINDNHYHHIVTPEAISLALENHEFKPWIQPVFCAQTGVLTGCEVLVRWEHPQTGIIPPDQFIPLAESSGLIVIMTRQLMKQTADILMPVKHLLPDNFHIGINVSAGCFLAAGFEKECLNLVNKLGNDKIKLVLELTERNPIPVTPEARAIFDSLHQHNITFALDDFGTGYATYRYLQAFPVDFIKIDKSFVQMASVDEISGHIVDNIVELARKPGLSIVAEGVETQEQADLMIGKGVHFLQGYLYSPPVPGNKFISEWVMKAGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11236
Length:	362 (352)
Sequences:	20076 (16071)
Seq/√Len:	856.6

ECOLI - YAHA YFEA YHJK GMR YFGF CSRD YLIE YEGE YLAB YJCC RTN DOSP YCGG ADRB BLUF YHJH YDIV
BACSU - YKOW YKUI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_C	352_F	3.860	1.00
132_A	338_L	3.800	1.00
174_R	214_E	3.377	1.00
216_L	255_H	3.106	1.00
173_T	205_C	3.066	1.00
286_K	290_Q	2.895	1.00
126_I	183_I	2.838	1.00
230_V	281_F	2.798	1.00
123_K	147_E	2.781	1.00
16_T	19_L	2.774	1.00
253_H	280_D	2.764	1.00
178_K	221_K	2.746	1.00
344_S	347_V	2.727	1.00
131_C	134_T	2.572	1.00
105_H	158_Q	2.534	1.00
188_K	228_K	2.528	1.00
329_L	333_K	2.482	1.00
310_R	336_H	2.415	1.00
185_M	189_H	2.356	1.00
324_Q	328_D	2.306	1.00
112_A	148_H	2.256	1.00
327_A	343_Y	2.214	1.00
183_I	349_G	2.206	1.00
175_Q	179_Q	2.186	1.00
260_A	281_F	2.132	1.00
303_D	311_K	2.099	1.00
148_H	152_G	2.077	1.00
275_Q	298_S	2.006	1.00
179_Q	182_D	1.989	1.00
115_L	119_N	1.960	1.00
163_A	172_M	1.954	1.00
147_E	153_I	1.939	1.00
321_V	338_L	1.938	1.00
299_G	329_L	1.903	1.00
144_V	176_L	1.887	1.00
323_T	326_Q	1.885	1.00
129_V	337_F	1.871	1.00
179_Q	183_I	1.821	1.00
181_A	218_L	1.814	1.00
327_A	338_L	1.813	1.00
123_K	153_I	1.812	1.00
125_W	348_P	1.799	1.00
120_H	179_Q	1.797	1.00
230_V	260_A	1.782	1.00
303_D	333_K	1.777	1.00
106_H	165_S	1.775	1.00
178_K	218_L	1.758	1.00
201_V	211_F	1.733	1.00
348_P	351_K	1.727	1.00
281_F	317_V	1.718	1.00
129_V	281_F	1.710	1.00
225_D	228_K	1.707	1.00
249_F	259_F	1.696	1.00
183_I	187_V	1.679	1.00
327_A	331_I	1.677	1.00
196_H	258_T	1.671	1.00
124_P	176_L	1.667	1.00
184_L	224_N	1.667	1.00
73_I	76_W	1.637	1.00
130_F	343_Y	1.634	1.00
303_D	307_E	1.623	1.00
293_S	299_G	1.622	1.00
218_L	222_L	1.608	1.00
258_T	280_D	1.604	1.00
178_K	222_L	1.593	1.00
282_I	309_A	1.587	1.00
71_S	80_F	1.580	1.00
148_H	151_T	1.570	1.00
306_V	335_V	1.561	1.00
4_C	7_R	1.561	1.00
324_Q	342_L	1.560	1.00
129_V	230_V	1.559	1.00
91_T	97_R	1.549	1.00
125_W	153_I	1.546	1.00
196_H	230_V	1.545	1.00
219_V	257_I	1.538	1.00
88_I	97_R	1.521	1.00
327_A	342_L	1.514	1.00
293_S	325_E	1.511	1.00
315_S	336_H	1.507	1.00
138_T	337_F	1.506	1.00
8_V	56_I	1.497	1.00
315_S	337_F	1.491	1.00
286_K	320_G	1.487	1.00
306_V	333_K	1.475	1.00
190_L	353_I	1.474	1.00
57_S	62_Q	1.448	1.00
24_S	30_R	1.446	1.00
122_F	144_V	1.444	1.00
187_V	349_G	1.430	1.00
201_V	231_L	1.419	1.00
275_Q	291_M	1.418	1.00
121_E	148_H	1.407	1.00
8_V	11_Q	1.401	1.00
261_L	279_V	1.400	1.00
341_Y	346_P	1.387	1.00
281_F	315_S	1.372	1.00
144_V	172_M	1.368	1.00
188_K	225_D	1.360	1.00
5_D	65_E	1.345	1.00
129_V	139_G	1.338	1.00
293_S	329_L	1.323	1.00
124_P	175_Q	1.320	1.00
217_N	221_K	1.312	1.00
182_D	222_L	1.309	1.00
170_V	208_A	1.309	1.00
246_R	250_D	1.295	1.00
318_A	335_V	1.285	1.00
186_P	190_L	1.257	1.00
11_Q	14_G	1.253	1.00
9_F	52_S	1.245	1.00
180_T	197_I	1.243	1.00
292_A	329_L	1.243	1.00
121_E	146_W	1.238	1.00
219_V	226_K	1.232	1.00
82_Q	86_E	1.231	1.00
4_C	59_Q	1.225	1.00
87_I	90_A	1.225	1.00
131_C	138_T	1.219	1.00
214_E	218_L	1.215	1.00
338_L	343_Y	1.211	1.00
194_N	228_K	1.209	1.00
309_A	316_I	1.208	1.00
246_R	276_A	1.200	1.00
105_H	151_T	1.194	1.00
33_L	44_E	1.191	1.00
184_L	197_I	1.189	1.00
112_A	151_T	1.189	1.00
151_T	158_Q	1.185	1.00
8_V	12_E	1.183	1.00
80_F	104_Y	1.175	1.00
328_D	331_I	1.174	1.00
216_L	251_S	1.174	1.00
183_I	186_P	1.171	1.00
87_I	91_T	1.168	1.00
230_V	258_T	1.164	1.00
115_L	121_E	1.153	1.00
307_E	311_K	1.152	1.00
76_W	80_F	1.146	1.00
293_S	323_T	1.144	1.00
135_G	331_I	1.135	1.00
216_L	220_N	1.131	1.00
129_V	198_G	1.129	1.00
198_G	230_V	1.129	1.00
212_E	216_L	1.123	1.00
144_V	175_Q	1.123	1.00
347_V	351_K	1.122	1.00
87_I	97_R	1.119	1.00
139_G	196_H	1.119	1.00
131_C	136_V	1.118	1.00
295_D	298_S	1.114	1.00
51_R	54_K	1.114	1.00
324_Q	327_A	1.112	1.00
88_I	95_S	1.106	1.00
38_Q	41_S	1.103	1.00
4_C	8_V	1.100	1.00
187_V	353_I	1.099	1.00
132_A	327_A	1.095	1.00
281_F	337_F	1.084	1.00
250_D	254_Q	1.082	1.00
178_K	182_D	1.082	1.00
279_V	314_L	1.077	1.00
185_M	222_L	1.073	1.00
328_D	332_G	1.067	1.00
49_R	96_H	1.067	1.00
300_H	311_K	1.065	1.00
108_V	112_A	1.064	1.00
292_A	302_V	1.064	1.00
207_L	240_P	1.064	1.00
52_S	67_L	1.059	1.00
185_M	188_K	1.057	1.00
212_E	251_S	1.053	1.00
215_C	231_L	1.049	1.00
156_P	159_F	1.045	1.00
122_F	175_Q	1.037	1.00
215_C	252_L	1.037	1.00
113_I	163_A	1.036	1.00
149_P	152_G	1.036	1.00
231_L	257_I	1.035	1.00
329_L	332_G	1.032	1.00
212_E	248_I	1.024	1.00
304_N	311_K	1.014	1.00
46_S	50_N	1.014	1.00
248_I	251_S	1.013	1.00
141_E	200_N	1.012	1.00
109_T	162_L	1.010	1.00
244_E	248_I	1.008	1.00
166_S	170_V	1.006	1.00
123_K	348_P	0.999	1.00
184_L	188_K	0.999	1.00
242_T	277_F	0.997	1.00
306_V	316_I	0.990	1.00
349_G	353_I	0.985	1.00
129_V	196_H	0.981	1.00
12_E	56_I	0.977	1.00
129_V	317_V	0.969	1.00
112_A	150_Q	0.969	1.00
181_A	229_L	0.966	1.00
164_E	169_I	0.966	1.00
49_R	69_I	0.964	1.00
36_L	41_S	0.964	1.00
171_I	174_R	0.963	1.00
203_A	236_R	0.962	1.00
142_V	197_I	0.961	1.00
180_T	199_I	0.955	1.00
218_L	221_K	0.953	1.00
38_Q	42_V	0.953	1.00
120_H	175_Q	0.951	1.00
133_Q	336_H	0.950	1.00
239_I	273_Y	0.949	1.00
110_P	114_S	0.948	1.00
317_V	337_F	0.944	1.00
26_S	86_E	0.940	1.00
251_S	254_Q	0.935	1.00
182_D	186_P	0.934	1.00
131_C	336_H	0.933	1.00
168_L	171_I	0.933	1.00
7_R	11_Q	0.933	1.00
185_M	223_G	0.928	1.00
151_T	154_I	0.927	1.00
118_E	171_I	0.926	1.00
293_S	326_Q	0.921	1.00
110_P	166_S	0.920	1.00
13_F	21_L	0.917	1.00
183_I	353_I	0.916	1.00
157_D	286_K	0.916	1.00
114_S	168_L	0.915	1.00
68_G	93_S	0.913	1.00
177_M	218_L	0.909	1.00
99_I	103_H	0.908	1.00
53_A	94_N	0.905	1.00
140_C	195_F	0.905	1.00
45_I	69_I	0.905	1.00
210_G	214_E	0.902	1.00
45_I	96_H	0.901	1.00
66_K	70_Q	0.899	1.00
124_P	180_T	0.896	1.00
44_E	47_Q	0.895	1.00
76_W	79_I	0.892	1.00
208_A	214_E	0.892	1.00
37_M	41_S	0.891	1.00
160_I	169_I	0.891	1.00
148_H	154_I	0.891	1.00
83_Y	103_H	0.890	1.00
27_E	89_S	0.888	1.00
115_L	118_E	0.888	1.00
211_F	215_C	0.888	1.00
126_I	349_G	0.888	1.00
120_H	178_K	0.887	1.00
241_V	244_E	0.885	1.00
66_K	94_N	0.879	1.00
306_V	310_R	0.869	1.00
114_S	171_I	0.864	1.00
45_I	49_R	0.863	1.00
50_N	53_A	0.859	1.00
124_P	142_V	0.858	1.00
126_I	142_V	0.857	1.00
232_E	283_K	0.856	1.00
177_M	215_C	0.852	1.00
196_H	228_K	0.852	1.00
126_I	140_C	0.852	1.00
321_V	330_M	0.851	1.00
174_R	178_K	0.847	1.00
214_E	217_N	0.845	1.00
116_A	121_E	0.845	1.00
133_Q	331_I	0.845	1.00
186_P	349_G	0.837	1.00
57_S	60_K	0.836	1.00
174_R	218_L	0.836	1.00
247_A	251_S	0.833	1.00
100_N	103_H	0.824	1.00
186_P	189_H	0.820	1.00
213_K	251_S	0.819	1.00
128_P	344_S	0.815	1.00
52_S	56_I	0.814	1.00
121_E	149_P	0.814	1.00
213_K	217_N	0.813	1.00
124_P	144_V	0.812	1.00
130_F	137_L	0.810	1.00
250_D	278_P	0.808	1.00
142_V	180_T	0.808	1.00
25_V	28_K	0.806	1.00
36_L	42_V	0.804	1.00
170_V	205_C	0.803	1.00
144_V	159_F	0.802	1.00
91_T	95_S	0.799	1.00
116_A	122_F	0.799	1.00
321_V	327_A	0.794	1.00
181_A	224_N	0.789	1.00
28_K	82_Q	0.788	1.00
163_A	169_I	0.787	1.00
71_S	77_R	0.784	1.00
10_L	21_L	0.781	1.00
276_A	297_I	0.780	1.00
135_G	327_A	0.780	1.00
300_H	303_D	0.780	1.00
113_I	122_F	0.777	1.00
58_H	63_L	0.776	1.00
15_T	51_R	0.775	1.00
62_Q	115_L	0.775	1.00
290_Q	326_Q	0.774	1.00
275_Q	301_I	0.774	1.00
307_E	310_R	0.771	1.00
247_A	250_D	0.769	1.00
291_M	298_S	0.769	1.00
177_M	199_I	0.767	1.00
244_E	247_A	0.767	1.00
181_A	222_L	0.765	1.00
258_T	315_S	0.763	1.00
318_A	330_M	0.762	1.00
330_M	335_V	0.759	1.00
224_N	229_L	0.752	1.00
128_P	347_V	0.750	1.00
289_V	292_A	0.747	1.00
291_M	294_V	0.744	1.00
234_T	263_D	0.743	1.00
110_P	162_L	0.742	1.00
263_D	319_E	0.740	1.00
299_G	303_D	0.739	1.00
310_R	316_I	0.734	1.00
264_F	305_I	0.734	1.00
188_K	194_N	0.731	1.00
242_T	246_R	0.731	1.00
30_R	78_D	0.728	1.00
246_R	278_P	0.727	1.00
209_A	244_E	0.723	1.00
117_L	175_Q	0.720	1.00
5_D	56_I	0.719	1.00
296_E	299_G	0.712	1.00
80_F	99_I	0.710	1.00
46_S	49_R	0.707	1.00
341_Y	345_P	0.706	1.00
192_P	195_F	0.706	1.00
157_D	161_P	0.704	1.00
70_Q	84_N	0.701	1.00
347_V	352_F	0.700	1.00
155_P	158_Q	0.698	1.00
298_S	326_Q	0.697	1.00
16_T	44_E	0.697	1.00
92_G	95_S	0.695	1.00
186_P	353_I	0.690	1.00
16_T	47_Q	0.689	1.00
108_V	151_T	0.683	1.00
128_P	137_L	0.682	1.00
166_S	169_I	0.679	1.00
284_I	335_V	0.677	1.00
19_L	33_L	0.675	1.00
113_I	116_A	0.671	1.00
9_F	13_F	0.671	1.00
147_E	152_G	0.670	1.00
330_M	338_L	0.668	1.00
113_I	168_L	0.666	1.00
258_T	281_F	0.664	1.00
306_V	330_M	0.664	1.00
178_K	214_E	0.660	1.00
195_F	228_K	0.658	1.00
49_R	94_N	0.657	1.00
184_L	228_K	0.656	1.00
229_L	257_I	0.654	1.00
282_I	314_L	0.654	1.00
289_V	318_A	0.653	1.00
9_F	56_I	0.652	1.00
322_E	341_Y	0.649	1.00
242_T	245_A	0.648	1.00
19_L	44_E	0.648	1.00
206_F	248_I	0.646	1.00
235_E	265_G	0.644	1.00
299_G	333_K	0.644	1.00
12_E	55_T	0.643	1.00
135_G	324_Q	0.639	1.00
291_M	295_D	0.637	1.00
316_I	336_H	0.637	1.00
206_F	237_N	0.636	1.00
251_S	255_H	0.636	1.00
200_N	262_D	0.634	1.00
213_K	216_L	0.634	1.00
125_W	147_E	0.634	1.00
70_Q	81_F	0.633	1.00
140_C	197_I	0.632	1.00
14_G	21_L	0.632	1.00
169_I	204_G	0.629	1.00
43_T	47_Q	0.622	1.00
261_L	273_Y	0.622	1.00
4_C	58_H	0.619	1.00
23_G	27_E	0.618	1.00
130_F	135_G	0.615	1.00
174_R	205_C	0.614	1.00
212_E	255_H	0.614	1.00
289_V	302_V	0.614	1.00
296_E	300_H	0.613	1.00
199_I	229_L	0.612	1.00
219_V	222_L	0.610	1.00
132_A	331_I	0.609	1.00
122_F	146_W	0.609	1.00
137_L	344_S	0.608	1.00
2_N	26_S	0.606	1.00
305_I	309_A	0.605	1.00
64_F	114_S	0.604	1.00
300_H	304_N	0.600	1.00
187_V	352_F	0.599	1.00
215_C	218_L	0.597	1.00
163_A	167_G	0.597	1.00
37_M	40_M	0.597	1.00
139_G	198_G	0.597	1.00
215_C	257_I	0.596	1.00
197_I	224_N	0.596	1.00
31_L	48_Y	0.595	1.00
266_T	288_F	0.595	1.00
99_I	104_Y	0.594	1.00
113_I	172_M	0.594	1.00
125_W	346_P	0.594	1.00
184_L	194_N	0.594	1.00
112_A	146_W	0.590	1.00
174_R	217_N	0.590	1.00
112_A	115_L	0.589	1.00
114_S	118_E	0.588	1.00
141_E	283_K	0.587	1.00
188_K	191_L	0.585	1.00
170_V	174_R	0.583	1.00
204_G	207_L	0.581	1.00
109_T	112_A	0.580	1.00
12_E	51_R	0.580	1.00
58_H	61_K	0.579	1.00
39_G	42_V	0.578	1.00
49_R	53_A	0.578	1.00
266_T	287_S	0.577	1.00
11_Q	15_T	0.576	1.00
147_E	151_T	0.575	1.00
107_I	111_E	0.572	1.00
177_M	181_A	0.572	1.00
143_L	200_N	0.571	1.00
86_E	89_S	0.570	1.00
322_E	326_Q	0.570	1.00
224_N	228_K	0.569	1.00
203_A	237_N	0.569	1.00
55_T	62_Q	0.568	1.00
184_L	229_L	0.568	1.00
242_T	276_A	0.567	1.00
309_A	314_L	0.567	1.00
83_Y	104_Y	0.566	1.00
231_L	259_F	0.566	1.00
248_I	252_L	0.565	1.00
275_Q	295_D	0.564	1.00
72_D	76_W	0.564	1.00
259_F	280_D	0.563	1.00
68_G	88_I	0.562	1.00
87_I	103_H	0.561	1.00
2_N	6_F	0.559	1.00
177_M	201_V	0.559	1.00
82_Q	85_P	0.558	1.00
123_K	179_Q	0.558	1.00
284_I	305_I	0.556	1.00
7_R	10_L	0.556	1.00
272_R	287_S	0.555	1.00
304_N	308_L	0.555	1.00
325_E	328_D	0.554	1.00
20_S	32_L	0.554	1.00
252_L	257_I	0.551	1.00
141_E	262_D	0.550	1.00
174_R	210_G	0.550	1.00
135_G	343_Y	0.548	1.00
23_G	26_S	0.547	1.00
219_V	224_N	0.547	1.00
174_R	208_A	0.547	1.00
105_H	109_T	0.546	1.00
273_Y	276_A	0.546	1.00
124_P	179_Q	0.545	1.00
123_K	350_N	0.545	1.00
250_D	253_H	0.543	1.00
120_H	182_D	0.542	1.00
227_I	258_T	0.542	1.00
49_R	67_L	0.541	1.00
185_M	224_N	0.541	1.00
217_N	220_N	0.540	1.00
273_Y	277_F	0.540	1.00
292_A	330_M	0.540	1.00
304_N	307_E	0.538	1.00
167_G	204_G	0.538	1.00
181_A	219_V	0.538	1.00
164_E	236_R	0.538	1.00
210_G	213_K	0.536	1.00
111_E	115_L	0.536	1.00
275_Q	297_I	0.536	1.00
154_I	161_P	0.534	1.00
25_V	86_E	0.533	1.00
117_L	172_M	0.532	1.00
20_S	34_K	0.531	1.00
234_T	319_E	0.531	1.00
113_I	146_W	0.530	1.00
343_Y	346_P	0.528	1.00
97_R	103_H	0.528	1.00
226_K	257_I	0.527	1.00
200_N	283_K	0.527	1.00
173_T	176_L	0.527	1.00
308_L	312_P	0.527	1.00
209_A	248_I	0.525	1.00
172_M	176_L	0.525	1.00
112_A	149_P	0.524	1.00
56_I	65_E	0.524	1.00
239_I	242_T	0.523	1.00
173_T	202_S	0.522	1.00
220_N	255_H	0.521	1.00
211_F	214_E	0.520	1.00
164_E	202_S	0.520	1.00
203_A	239_I	0.519	1.00
239_I	245_A	0.519	1.00
302_V	318_A	0.518	1.00
46_S	96_H	0.516	1.00
108_V	150_Q	0.514	1.00
249_F	278_P	0.514	1.00
259_F	279_V	0.514	1.00
243_P	276_A	0.513	1.00
296_E	313_G	0.512	1.00
130_F	344_S	0.512	1.00
350_N	353_I	0.511	1.00
184_L	222_L	0.511	1.00
71_S	76_W	0.511	1.00
243_P	247_A	0.510	1.00
299_G	332_G	0.510	1.00
177_M	214_E	0.509	1.00
331_I	338_L	0.506	1.00
170_V	204_G	0.506	1.00
42_V	45_I	0.505	1.00
108_V	111_E	0.504	1.00
297_I	313_G	0.502	1.00
203_A	273_Y	0.502	1.00
253_H	259_F	0.501	1.00
205_C	211_F	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
4rnhA	2	0.9862	100	0.091	Contact Map
4j40A	2	0.6878	100	0.106	Contact Map
3pjxA	1	0.9392	100	0.124	Contact Map
4hjfA	1	0.7072	100	0.191	Contact Map
3gfzA	2	0.9006	100	0.236	Contact Map
4kieA	1	0.721	100	0.264	Contact Map
4hu4A	1	0.674	100	0.269	Contact Map
2r6oA	2	0.7072	100	0.275	Contact Map
4rniA	2	0.6961	100	0.275	Contact Map
3sy8A	6	0.8978	100	0.287	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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