CCPA - BACSU - GREMLIN Contacts

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CCPA - Catabolite control protein A

UniProt:	P25144	Sequences: MSNITIYDVAREANVSMATVSRVVNGNPNVKPTTRKKVLEAIERLGYRPNAVARGLASKKTTTVGVIIPDISSIFYSELARGIEDIATMYKYNIILSNSDQNMEKELHLLNTMLGKQVDGIVFMGGNITDEHVAEFKRSPVPIVLAASVEEQEETPSVAIDYEQAIYDAVKLLVDKGHTDIAFVSGPMAEPINRSKKLQGYKRALEEANLPFNEQFVAEGDYTYDSGLEALQHLMSLDKKPTAILSATDEMALGIIHAAQDQGLSIPEDLDIIGFDNTRLSLMVRPQLSTVVQPTYDIGAVAMRLLTKLMNKEPVEEHIVELPHRIELRKSTKS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	334 (324)
Sequences:	36252 (26372)
Seq/√Len:	1465.1

ECOLI - LACI GALS GALR GNTR IDNR CYTR RBSR PURR CRA MALI ASCG YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF YPHF LSRB ARAF DGAL XYLR
BACSU - CCPA DEGA KDGR NTDR RBSR YKVZ EXUR GANR MSMR YVDE ARAR CCPB RBSB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
178_H	242_T	3.538	1.00
163_E	203_R	3.370	1.00
12_E	44_R	3.175	1.00
265_S	268_E	3.066	1.00
169_A	273_I	2.689	1.00
178_H	271_D	2.638	1.00
120_G	306_L	2.637	1.00
277_N	292_V	2.632	1.00
198_L	202_K	2.555	1.00
167_Y	207_E	2.381	1.00
156_P	309_L	2.331	1.00
228_L	261_D	2.267	1.00
86_I	89_M	2.224	1.00
32_P	36_K	2.214	1.00
40_E	44_R	2.192	1.00
36_K	40_E	2.175	1.00
86_I	304_R	2.154	1.00
232_Q	262_Q	2.130	1.00
301_V	304_R	2.063	1.00
167_Y	204_A	2.047	1.00
167_Y	203_R	2.046	1.00
174_V	208_A	2.027	1.00
87_A	303_M	2.017	1.00
171_K	204_A	2.016	1.00
164_Q	168_D	1.993	1.00
23_V	38_V	1.992	1.00
82_G	299_G	1.976	1.00
166_I	170_V	1.968	1.00
232_Q	258_A	1.966	1.00
165_A	275_F	1.962	1.00
24_V	42_I	1.941	1.00
35_R	39_L	1.930	1.00
227_G	254_G	1.920	1.00
163_E	199_Q	1.888	1.00
173_L	243_A	1.877	1.00
171_K	175_D	1.868	1.00
7_Y	17_M	1.845	1.00
86_I	300_A	1.834	1.00
166_I	245_L	1.827	1.00
259_A	270_L	1.785	1.00
236_S	262_Q	1.777	1.00
308_K	313_E	1.774	1.00
170_V	201_Y	1.772	1.00
292_V	325_R	1.771	1.00
85_D	296_Y	1.758	1.00
13_A	41_A	1.732	1.00
171_K	208_A	1.708	1.00
167_Y	171_K	1.686	1.00
228_L	258_A	1.680	1.00
287_Q	330_K	1.675	1.00
183_F	247_A	1.658	1.00
65_G	118_V	1.657	1.00
294_P	297_D	1.646	1.00
231_L	255_I	1.645	1.00
12_E	41_A	1.637	1.00
82_G	296_Y	1.634	1.00
182_A	241_P	1.619	1.00
246_S	255_I	1.617	1.00
168_D	324_H	1.605	1.00
301_V	320_V	1.596	1.00
277_N	329_R	1.592	1.00
264_L	269_D	1.580	1.00
172_L	176_K	1.576	1.00
180_D	213_N	1.575	1.00
146_A	302_A	1.553	1.00
86_I	90_Y	1.549	1.00
39_L	43_E	1.534	1.00
258_A	262_Q	1.534	1.00
265_S	269_D	1.532	1.00
23_V	42_I	1.526	1.00
180_D	240_K	1.518	1.00
164_Q	167_Y	1.518	1.00
199_Q	203_R	1.513	1.00
260_Q	285_R	1.512	1.00
161_D	164_Q	1.473	1.00
90_Y	307_T	1.470	1.00
174_V	204_A	1.463	1.00
297_D	301_V	1.458	1.00
172_L	175_D	1.455	1.00
258_A	261_D	1.444	1.00
9_V	41_A	1.437	1.00
218_A	233_H	1.436	1.00
39_L	42_I	1.422	1.00
196_K	199_Q	1.417	1.00
62_T	119_D	1.409	1.00
273_I	289_S	1.387	1.00
297_D	300_A	1.385	1.00
202_K	206_E	1.380	1.00
165_A	324_H	1.377	1.00
166_I	200_G	1.376	1.00
86_I	303_M	1.372	1.00
170_V	174_V	1.361	1.00
172_L	328_L	1.356	1.00
170_V	200_G	1.351	1.00
178_H	243_A	1.336	1.00
259_A	264_L	1.332	1.00
204_A	207_E	1.332	1.00
9_V	13_A	1.316	1.00
228_L	257_H	1.314	1.00
180_D	242_T	1.302	1.00
232_Q	261_D	1.291	1.00
62_T	92_Y	1.287	1.00
12_E	45_L	1.285	1.00
170_V	204_A	1.285	1.00
182_A	234_L	1.282	1.00
22_R	27_N	1.280	1.00
231_L	244_I	1.274	1.00
228_L	232_Q	1.271	1.00
7_Y	11_R	1.264	1.00
307_T	311_N	1.264	1.00
32_P	35_R	1.261	1.00
31_K	34_T	1.259	1.00
304_R	308_K	1.258	1.00
213_N	216_F	1.253	1.00
231_L	259_A	1.251	1.00
200_G	204_A	1.246	1.00
64_V	87_A	1.242	1.00
8_D	11_R	1.241	1.00
97_S	113_M	1.240	1.00
232_Q	236_S	1.233	1.00
65_G	113_M	1.227	1.00
134_A	138_R	1.224	1.00
37_K	41_A	1.223	1.00
97_S	109_L	1.221	1.00
122_V	302_A	1.218	1.00
6_I	17_M	1.214	1.00
168_D	171_K	1.203	1.00
221_D	226_S	1.201	1.00
163_E	167_Y	1.199	1.00
87_A	94_I	1.197	1.00
256_I	272_I	1.189	1.00
83_I	303_M	1.183	1.00
179_T	242_T	1.181	1.00
9_V	45_L	1.180	1.00
41_A	44_R	1.179	1.00
238_D	241_P	1.173	1.00
163_E	196_K	1.172	1.00
41_A	45_L	1.172	1.00
66_V	83_I	1.172	1.00
233_H	237_L	1.166	1.00
83_I	122_V	1.156	1.00
254_G	258_A	1.151	1.00
171_K	207_E	1.147	1.00
34_T	37_K	1.132	1.00
111_N	135_E	1.131	1.00
201_Y	205_L	1.121	1.00
6_I	20_V	1.120	1.00
296_Y	300_A	1.119	1.00
249_D	290_T	1.113	1.00
225_D	229_E	1.106	1.00
176_K	328_L	1.106	1.00
90_Y	304_R	1.104	1.00
249_D	274_G	1.099	1.00
63_T	93_N	1.099	1.00
23_V	30_V	1.098	1.00
66_V	94_I	1.097	1.00
181_I	205_L	1.095	1.00
40_E	43_E	1.094	1.00
299_G	303_M	1.092	1.00
183_F	198_L	1.086	1.00
184_V	255_I	1.081	1.00
244_I	255_I	1.079	1.00
169_A	245_L	1.077	1.00
203_R	207_E	1.071	1.00
163_E	200_G	1.070	1.00
84_E	88_T	1.065	1.00
36_K	39_L	1.054	1.00
301_V	305_L	1.052	1.00
204_A	208_A	1.044	1.00
230_A	233_H	1.036	1.00
223_T	226_S	1.032	1.00
42_I	45_L	1.025	1.00
50_N	56_L	1.024	1.00
26_G	35_R	1.023	1.00
107_L	111_N	1.022	1.00
175_D	208_A	1.021	1.00
63_T	95_I	1.021	1.00
174_V	210_L	1.013	1.00
227_G	231_L	1.006	1.00
300_A	304_R	1.004	1.00
88_T	105_K	1.001	1.00
199_Q	202_K	1.001	1.00
305_L	320_V	1.000	1.00
90_Y	311_N	0.999	1.00
52_V	55_G	0.998	1.00
246_S	251_M	0.994	1.00
218_A	230_A	0.994	1.00
201_Y	245_L	0.989	1.00
188_M	219_E	0.989	1.00
50_N	53_A	0.987	1.00
229_E	233_H	0.986	1.00
246_S	252_A	0.978	1.00
180_D	239_K	0.977	1.00
13_A	20_V	0.977	1.00
205_L	210_L	0.975	1.00
306_L	310_M	0.974	1.00
92_Y	307_T	0.972	1.00
301_V	322_L	0.963	1.00
224_Y	257_H	0.962	1.00
226_S	229_E	0.953	1.00
172_L	289_S	0.949	1.00
231_L	235_M	0.943	1.00
164_Q	323_P	0.943	1.00
195_S	199_Q	0.937	1.00
169_A	291_V	0.932	1.00
89_M	300_A	0.929	1.00
160_I	294_P	0.920	1.00
256_I	284_V	0.917	1.00
176_K	271_D	0.915	1.00
186_G	222_Y	0.907	1.00
170_V	205_L	0.907	1.00
122_V	306_L	0.906	1.00
81_R	85_D	0.900	1.00
85_D	300_A	0.899	1.00
294_P	322_L	0.896	1.00
111_N	115_G	0.896	1.00
181_I	243_A	0.895	1.00
325_R	328_L	0.887	1.00
49_P	54_R	0.886	1.00
64_V	122_V	0.885	1.00
180_D	216_F	0.885	1.00
83_I	299_G	0.877	1.00
249_D	277_N	0.875	1.00
292_V	327_E	0.870	1.00
105_K	108_H	0.868	1.00
202_K	212_F	0.865	1.00
256_I	266_I	0.858	1.00
26_G	39_L	0.858	1.00
164_Q	324_H	0.856	1.00
53_A	56_L	0.855	1.00
260_Q	287_Q	0.855	1.00
174_V	179_T	0.852	1.00
66_V	80_A	0.848	1.00
259_A	272_I	0.848	1.00
235_M	258_A	0.844	1.00
274_G	290_T	0.843	1.00
23_V	39_L	0.843	1.00
161_D	321_E	0.840	1.00
229_E	232_Q	0.837	1.00
75_F	295_T	0.834	1.00
160_I	324_H	0.833	1.00
182_A	244_I	0.832	1.00
158_V	305_L	0.827	1.00
157_S	319_I	0.824	1.00
19_T	22_R	0.824	1.00
159_A	321_E	0.822	1.00
161_D	323_P	0.822	1.00
162_Y	197_K	0.819	1.00
244_I	270_L	0.818	1.00
276_D	293_Q	0.816	1.00
220_G	251_M	0.815	1.00
160_I	293_Q	0.814	1.00
80_A	84_E	0.813	1.00
79_L	146_A	0.813	1.00
277_N	327_E	0.810	1.00
264_L	270_L	0.803	1.00
305_L	308_K	0.802	1.00
120_G	310_M	0.800	1.00
33_T	36_K	0.795	1.00
61_T	119_D	0.793	1.00
15_V	38_V	0.793	1.00
179_T	210_L	0.792	1.00
203_R	206_E	0.790	1.00
69_P	76_Y	0.790	1.00
183_F	245_L	0.783	1.00
240_K	264_L	0.783	1.00
294_P	325_R	0.781	1.00
184_V	246_S	0.780	1.00
78_E	296_Y	0.778	1.00
198_L	217_V	0.777	1.00
185_S	198_L	0.777	1.00
249_D	252_A	0.775	1.00
51_A	54_R	0.775	1.00
205_L	212_F	0.772	1.00
303_M	307_T	0.771	1.00
216_F	237_L	0.771	1.00
135_E	138_R	0.770	1.00
281_S	284_V	0.770	1.00
156_P	305_L	0.770	1.00
82_G	300_A	0.767	1.00
22_R	28_P	0.766	1.00
83_I	94_I	0.761	1.00
102_N	105_K	0.761	1.00
85_D	89_M	0.759	1.00
196_K	200_G	0.759	1.00
226_S	230_A	0.759	1.00
173_L	273_I	0.756	1.00
189_A	195_S	0.756	1.00
253_L	284_V	0.753	1.00
63_T	116_K	0.753	1.00
18_A	22_R	0.752	1.00
231_L	234_L	0.749	1.00
22_R	29_N	0.749	1.00
231_L	258_A	0.746	1.00
64_V	303_M	0.742	1.00
82_G	86_I	0.742	1.00
33_T	37_K	0.742	1.00
137_K	154_E	0.738	1.00
65_G	121_I	0.737	1.00
235_M	262_Q	0.737	1.00
172_L	326_I	0.737	1.00
108_H	111_N	0.735	1.00
80_A	96_L	0.735	1.00
242_T	271_D	0.733	1.00
114_L	139_S	0.730	1.00
159_A	319_I	0.730	1.00
218_A	234_L	0.726	1.00
212_F	215_Q	0.725	1.00
60_K	119_D	0.721	1.00
257_H	260_Q	0.721	1.00
237_L	241_P	0.719	1.00
95_I	118_V	0.712	1.00
81_R	84_E	0.711	1.00
48_R	115_G	0.710	1.00
237_L	240_K	0.707	1.00
168_D	291_V	0.706	1.00
277_N	281_S	0.701	1.00
84_E	94_I	0.701	1.00
280_L	284_V	0.698	1.00
252_A	274_G	0.697	1.00
245_L	273_I	0.697	1.00
167_Y	200_G	0.696	1.00
105_K	109_L	0.693	1.00
149_V	319_I	0.692	1.00
84_E	98_N	0.691	1.00
104_E	108_H	0.690	1.00
120_G	144_V	0.688	1.00
60_K	311_N	0.687	1.00
67_I	109_L	0.686	1.00
136_F	143_I	0.680	1.00
194_R	222_Y	0.677	1.00
100_D	105_K	0.677	1.00
145_L	155_T	0.676	1.00
231_L	254_G	0.676	1.00
134_A	137_K	0.675	1.00
248_T	276_D	0.675	1.00
257_H	287_Q	0.672	1.00
233_H	236_S	0.670	1.00
308_K	312_K	0.670	1.00
259_A	266_I	0.669	1.00
181_I	242_T	0.667	1.00
7_Y	57_A	0.665	1.00
23_V	35_R	0.664	1.00
122_V	146_A	0.662	1.00
227_G	230_A	0.659	1.00
36_K	43_E	0.657	1.00
220_G	226_S	0.653	1.00
174_V	205_L	0.649	1.00
147_A	162_Y	0.648	1.00
257_H	261_D	0.647	1.00
145_L	150_E	0.647	1.00
137_K	143_I	0.642	1.00
218_A	237_L	0.638	1.00
9_V	20_V	0.638	1.00
20_V	23_V	0.635	1.00
287_Q	329_R	0.635	1.00
29_N	34_T	0.634	1.00
289_S	326_I	0.634	1.00
183_F	201_Y	0.629	1.00
73_S	250_E	0.628	1.00
156_P	317_E	0.626	1.00
48_R	111_N	0.624	1.00
43_E	46_G	0.624	1.00
37_K	40_E	0.623	1.00
20_V	42_I	0.622	1.00
186_G	194_R	0.620	1.00
222_Y	247_A	0.620	1.00
168_D	172_L	0.620	1.00
181_I	201_Y	0.619	1.00
182_A	216_F	0.617	1.00
120_G	302_A	0.617	1.00
143_I	155_T	0.617	1.00
296_Y	299_G	0.616	1.00
82_G	295_T	0.613	1.00
15_V	34_T	0.612	1.00
95_I	116_K	0.612	1.00
79_L	295_T	0.610	1.00
78_E	295_T	0.610	1.00
253_L	278_T	0.609	1.00
144_V	158_V	0.607	1.00
22_R	30_V	0.606	1.00
222_Y	251_M	0.605	1.00
147_A	193_N	0.601	1.00
132_H	135_E	0.601	1.00
173_L	245_L	0.600	1.00
92_Y	119_D	0.600	1.00
110_L	121_I	0.599	1.00
114_L	141_V	0.598	1.00
27_N	30_V	0.597	1.00
201_Y	212_F	0.596	1.00
144_V	306_L	0.595	1.00
257_H	285_R	0.594	1.00
198_L	219_E	0.593	1.00
169_A	243_A	0.592	1.00
275_F	293_Q	0.591	1.00
81_R	296_Y	0.590	1.00
259_A	262_Q	0.589	1.00
75_F	79_L	0.588	1.00
245_L	275_F	0.588	1.00
256_I	260_Q	0.586	1.00
202_K	217_V	0.586	1.00
64_V	120_G	0.582	1.00
167_Y	170_V	0.582	1.00
224_Y	254_G	0.581	1.00
20_V	38_V	0.580	1.00
92_Y	310_M	0.580	1.00
107_L	132_H	0.579	1.00
248_T	251_M	0.578	1.00
162_Y	196_K	0.576	1.00
144_V	309_L	0.575	1.00
260_Q	265_S	0.573	1.00
212_F	217_V	0.573	1.00
131_E	134_A	0.572	1.00
312_K	315_V	0.568	1.00
228_L	254_G	0.568	1.00
172_L	273_I	0.565	1.00
246_S	274_G	0.565	1.00
180_D	211_P	0.564	1.00
121_I	141_V	0.563	1.00
225_D	228_L	0.562	1.00
64_V	92_Y	0.561	1.00
13_A	23_V	0.560	1.00
282_L	287_Q	0.556	1.00
305_L	309_L	0.554	1.00
64_V	310_M	0.549	1.00
202_K	214_E	0.548	1.00
285_R	330_K	0.548	1.00
185_S	219_E	0.545	1.00
15_V	20_V	0.543	1.00
144_V	302_A	0.542	1.00
48_R	52_V	0.542	1.00
180_D	241_P	0.541	1.00
298_I	322_L	0.541	1.00
144_V	305_L	0.541	1.00
97_S	112_T	0.541	1.00
197_K	293_Q	0.539	1.00
103_M	107_L	0.539	1.00
18_A	27_N	0.538	1.00
87_A	307_T	0.536	1.00
158_V	301_V	0.535	1.00
54_R	58_S	0.535	1.00
284_V	287_Q	0.535	1.00
135_E	139_S	0.532	1.00
76_Y	124_M	0.532	1.00
235_M	259_A	0.531	1.00
198_L	212_F	0.529	1.00
281_S	288_L	0.528	1.00
249_D	278_T	0.528	1.00
309_L	312_K	0.527	1.00
253_L	280_L	0.526	1.00
260_Q	286_P	0.526	1.00
87_A	92_Y	0.524	1.00
81_R	100_D	0.524	1.00
291_V	324_H	0.523	1.00
255_I	259_A	0.523	1.00
74_I	250_E	0.523	1.00
257_H	282_L	0.522	1.00
113_M	118_V	0.522	1.00
277_N	282_L	0.521	1.00
241_P	264_L	0.520	1.00
277_N	290_T	0.516	1.00
149_V	157_S	0.516	1.00
289_S	328_L	0.515	1.00
61_T	93_N	0.513	1.00
99_S	106_E	0.512	1.00
194_R	247_A	0.511	1.00
160_I	275_F	0.511	1.00
184_V	230_A	0.511	1.00
224_Y	280_L	0.509	1.00
145_L	157_S	0.509	1.00
55_G	58_S	0.508	1.00
13_A	38_V	0.508	1.00
160_I	165_A	0.508	1.00
220_G	227_G	0.508	1.00
243_A	271_D	0.507	1.00
228_L	231_L	0.507	1.00
137_K	155_T	0.507	1.00
281_S	290_T	0.506	1.00
63_T	119_D	0.505	1.00
83_I	87_A	0.505	1.00
230_A	234_L	0.504	1.00
185_S	217_V	0.502	1.00
112_T	115_G	0.501	1.00
301_V	308_K	0.501	1.00
241_P	244_I	0.501	1.00
26_G	29_N	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
3dbiA	2	0.8204	100	0.044	Contact Map
2hsgA	1	0.979	100	0.05	Contact Map
2o20A	2	0.8234	100	0.054	Contact Map
1qpzA	2	0.988	100	0.062	Contact Map
4o5aA	2	0.7994	100	0.063	Contact Map
3kjxA	2	0.997	100	0.065	Contact Map
3e3mA	2	0.8024	100	0.068	Contact Map
3bilA	2	0.7635	100	0.069	Contact Map
3h5oA	2	0.8084	100	0.073	Contact Map
1jyeA	2	0.7994	100	0.077	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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