CCPB - BACSU - GREMLIN Contacts

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CCPB - Catabolite control protein B

UniProt:	P37517	Sequences: MANIKEIARLANVSVSTVSRVLNHHPYVSEEKRKLVHQVMKELDYTPNRTAIDLIRGKTHTVGVILPYSDHPCFDKIVNGITKAAFQHEYATTLLPTNYNPDIEIKYLELLRTKKIDGLIITSRANHWDSILAYQEYGPVIACEDTGDIDVPCAFNDRKTAYAESFRYLKSRGHENIAFTCVREADRSPSTADKAAAYKAVCGRLEDRHMLSGCNDMNDGELAAEHFYMSGRVPTAIYANSDEVAAGIHLFAKKNNWDVEIIGEGNTSISRVLGFPSLDLNLEQLGIAAFSLFLQDEPADIKIQHKFKKKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	311 (298)
Sequences:	36063 (25996)
Seq/√Len:	1505.9

ECOLI - GALS GALR PURR RBSR ASCG MALI LACI CYTR YCJW CRA GNTR IDNR TRER EBGR TORT ALSB RBSB LSRB XYLF YTFQ YPHF ARAF DGAL
BACSU - CCPB NTDR YKVZ KDGR RBSR CCPA EXUR YVDE DEGA MSMR GANR ARAR 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
159_K	200_A	3.421	1.00
174_H	235_T	3.316	1.00
10_L	42_E	3.174	1.00
271_R	274_G	2.869	1.00
165_S	262_I	2.630	1.00
118_G	293_F	2.602	1.00
266_N	279_D	2.598	1.00
174_H	260_E	2.557	1.00
195_A	199_K	2.553	1.00
152_P	296_D	2.467	1.00
163_A	204_R	2.385	1.00
221_E	254_K	2.262	1.00
30_E	34_K	2.247	1.00
84_A	87_Q	2.219	1.00
38_Q	42_E	2.207	1.00
34_K	38_Q	2.200	1.00
84_A	291_S	2.189	1.00
225_E	255_N	2.134	1.00
163_A	200_A	2.126	1.00
288_A	291_S	2.075	1.00
160_T	164_E	2.058	1.00
163_A	201_V	2.020	1.00
167_R	201_V	1.999	1.00
162_Y	166_F	1.992	1.00
85_A	290_F	1.990	1.00
21_V	36_V	1.964	1.00
225_E	251_F	1.949	1.00
161_A	264_E	1.942	1.00
80_G	286_G	1.931	1.00
159_K	196_A	1.920	1.00
295_Q	300_D	1.915	1.00
33_R	37_H	1.911	1.00
252_A	259_V	1.887	1.00
22_L	40_M	1.859	1.00
229_M	255_N	1.858	1.00
169_L	236_A	1.852	1.00
5_K	15_V	1.842	1.00
84_A	287_I	1.839	1.00
220_G	247_G	1.822	1.00
162_Y	238_Y	1.805	1.00
167_R	171_S	1.804	1.00
83_K	283_E	1.787	1.00
166_F	198_Y	1.763	1.00
168_Y	172_R	1.752	1.00
11_A	39_V	1.697	1.00
63_G	116_I	1.693	1.00
163_A	167_R	1.682	1.00
221_E	251_F	1.666	1.00
281_N	284_Q	1.663	1.00
179_F	240_N	1.656	1.00
224_A	248_I	1.648	1.00
10_L	39_V	1.647	1.00
239_A	248_I	1.619	1.00
80_G	283_E	1.609	1.00
178_A	234_P	1.601	1.00
84_A	88_H	1.586	1.00
251_F	255_N	1.567	1.00
143_C	289_A	1.541	1.00
37_H	41_K	1.541	1.00
206_E	209_H	1.534	1.00
160_T	163_A	1.530	1.00
196_A	200_A	1.523	1.00
176_N	233_V	1.517	1.00
88_H	294_L	1.505	1.00
21_V	40_M	1.486	1.00
170_K	201_V	1.484	1.00
284_Q	288_A	1.476	1.00
253_K	274_G	1.475	1.00
168_Y	171_S	1.460	1.00
193_D	196_A	1.448	1.00
7_I	39_V	1.441	1.00
166_F	170_K	1.441	1.00
251_F	254_K	1.434	1.00
37_H	40_M	1.425	1.00
199_K	203_G	1.411	1.00
157_D	160_T	1.409	1.00
284_Q	287_I	1.409	1.00
60_H	117_D	1.400	1.00
84_A	290_F	1.396	1.00
178_A	227_F	1.353	1.00
214_C	219_D	1.342	1.00
166_F	197_A	1.342	1.00
224_A	237_I	1.323	1.00
225_E	254_K	1.322	1.00
176_N	235_T	1.322	1.00
221_E	250_L	1.307	1.00
221_E	225_E	1.306	1.00
174_H	236_A	1.303	1.00
5_K	9_R	1.303	1.00
201_V	204_R	1.301	1.00
10_L	43_L	1.293	1.00
166_F	201_V	1.292	1.00
224_A	252_A	1.285	1.00
132_L	136_E	1.285	1.00
162_Y	197_A	1.282	1.00
6_E	9_R	1.281	1.00
60_H	90_Y	1.281	1.00
291_S	295_Q	1.276	1.00
20_R	25_H	1.270	1.00
30_E	33_R	1.267	1.00
197_A	201_V	1.255	1.00
294_L	298_P	1.253	1.00
225_E	229_M	1.251	1.00
29_S	32_K	1.251	1.00
167_R	204_R	1.245	1.00
35_L	39_V	1.244	1.00
62_V	85_A	1.241	1.00
164_E	167_R	1.239	1.00
176_N	209_H	1.239	1.00
7_I	11_A	1.233	1.00
249_H	261_I	1.230	1.00
63_G	111_L	1.228	1.00
211_L	226_H	1.227	1.00
159_K	163_A	1.220	1.00
120_I	289_A	1.218	1.00
95_L	111_L	1.216	1.00
95_L	107_Y	1.205	1.00
176_N	206_E	1.203	1.00
81_I	120_I	1.202	1.00
262_I	276_P	1.202	1.00
81_I	290_F	1.196	1.00
175_E	235_T	1.193	1.00
39_V	43_L	1.192	1.00
39_V	42_E	1.190	1.00
85_A	92_T	1.187	1.00
231_G	234_P	1.183	1.00
64_V	81_I	1.178	1.00
4_I	15_V	1.177	1.00
7_I	43_L	1.173	1.00
159_K	193_D	1.164	1.00
32_K	35_L	1.156	1.00
226_H	230_S	1.151	1.00
198_Y	202_C	1.147	1.00
109_E	133_A	1.141	1.00
218_N	222_L	1.139	1.00
64_V	92_T	1.130	1.00
283_E	287_I	1.129	1.00
247_G	251_F	1.127	1.00
88_H	291_S	1.126	1.00
180_T	248_I	1.124	1.00
207_D	210_M	1.121	1.00
177_I	202_C	1.115	1.00
159_K	197_A	1.113	1.00
200_A	204_R	1.110	1.00
21_V	28_V	1.101	1.00
242_D	277_S	1.101	1.00
38_Q	41_K	1.093	1.00
288_A	292_L	1.092	1.00
4_I	18_V	1.086	1.00
179_F	195_A	1.084	1.00
61_T	91_A	1.082	1.00
48_N	54_L	1.082	1.00
82_T	86_F	1.075	1.00
242_D	263_G	1.066	1.00
165_S	238_Y	1.063	1.00
205_L	208_R	1.058	1.00
61_T	93_T	1.052	1.00
34_K	37_H	1.048	1.00
237_I	248_I	1.048	1.00
105_I	109_E	1.046	1.00
176_N	232_R	1.042	1.00
216_D	219_D	1.040	1.00
286_G	290_F	1.036	1.00
24_H	33_R	1.034	1.00
196_A	199_K	1.033	1.00
86_F	103_I	1.029	1.00
223_A	226_H	1.028	1.00
222_L	226_H	1.026	1.00
198_Y	238_Y	1.025	1.00
50_T	53_D	1.025	1.00
168_Y	276_P	1.018	1.00
40_M	43_L	1.013	1.00
239_A	245_A	1.009	1.00
293_F	297_E	1.007	1.00
220_G	224_A	1.006	1.00
88_H	298_P	0.998	1.00
217_M	250_L	0.998	1.00
287_I	291_S	0.987	1.00
172_R	260_E	0.975	1.00
224_A	228_Y	0.973	1.00
156_N	281_N	0.972	1.00
239_A	244_V	0.970	1.00
48_N	51_A	0.969	1.00
103_I	106_K	0.967	1.00
177_I	236_A	0.964	1.00
219_D	222_L	0.963	1.00
11_A	18_V	0.958	1.00
90_Y	294_L	0.956	1.00
165_S	278_L	0.947	1.00
87_Q	287_I	0.947	1.00
189_P	193_D	0.942	1.00
192_A	196_A	0.939	1.00
152_P	292_L	0.939	1.00
170_K	175_E	0.933	1.00
166_F	202_C	0.933	1.00
51_A	54_L	0.927	1.00
109_E	113_T	0.910	1.00
83_K	287_I	0.910	1.00
120_I	293_F	0.907	1.00
182_V	215_N	0.903	1.00
47_P	52_I	0.903	1.00
154_A	292_L	0.897	1.00
112_R	137_Y	0.895	1.00
79_N	83_K	0.894	1.00
184_E	212_S	0.892	1.00
128_W	132_L	0.887	1.00
62_V	120_I	0.885	1.00
187_R	192_A	0.882	1.00
24_H	37_H	0.882	1.00
205_L	209_H	0.870	1.00
222_L	225_E	0.856	1.00
242_D	266_N	0.854	1.00
237_I	259_V	0.854	1.00
64_V	78_V	0.848	1.00
21_V	37_H	0.848	1.00
178_A	237_I	0.845	1.00
78_V	82_T	0.843	1.00
81_I	286_G	0.843	1.00
213_G	244_V	0.842	1.00
31_E	34_K	0.841	1.00
252_A	261_I	0.836	1.00
266_N	270_S	0.835	1.00
263_G	277_S	0.835	1.00
118_G	297_E	0.831	1.00
169_L	262_I	0.831	1.00
228_Y	251_F	0.830	1.00
17_T	20_R	0.822	1.00
156_N	280_L	0.818	1.00
181_C	195_A	0.816	1.00
81_I	92_T	0.813	1.00
170_K	202_C	0.813	1.00
73_C	282_L	0.812	1.00
200_A	203_G	0.812	1.00
292_L	295_Q	0.810	1.00
219_D	223_A	0.804	1.00
193_D	197_A	0.804	1.00
290_F	294_L	0.800	1.00
83_K	87_Q	0.798	1.00
76_K	283_E	0.792	1.00
13_V	36_V	0.792	1.00
59_T	117_D	0.791	1.00
224_A	227_F	0.787	1.00
242_D	245_A	0.785	1.00
80_G	287_I	0.785	1.00
158_R	194_K	0.783	1.00
77_I	143_C	0.782	1.00
100_N	103_I	0.782	1.00
49_R	52_I	0.778	1.00
235_T	260_E	0.775	1.00
180_T	239_A	0.774	1.00
265_G	280_L	0.771	1.00
16_S	20_R	0.764	1.00
31_E	35_L	0.763	1.00
58_K	298_P	0.762	1.00
67_P	74_F	0.761	1.00
80_G	84_A	0.757	1.00
61_T	114_K	0.755	1.00
179_F	238_Y	0.753	1.00
164_E	278_L	0.753	1.00
82_T	92_T	0.749	1.00
133_A	136_E	0.748	1.00
20_R	26_P	0.746	1.00
238_Y	262_I	0.744	1.00
224_A	251_F	0.743	1.00
46_T	113_T	0.743	1.00
228_Y	255_N	0.738	1.00
58_K	117_D	0.737	1.00
134_Y	140_V	0.736	1.00
78_V	94_L	0.736	1.00
93_T	116_I	0.735	1.00
63_G	119_L	0.733	1.00
245_A	263_G	0.729	1.00
98_N	103_I	0.729	1.00
62_V	290_F	0.729	1.00
79_N	82_T	0.727	1.00
226_H	229_M	0.726	1.00
132_L	135_Q	0.720	1.00
250_L	253_K	0.719	1.00
106_K	109_E	0.717	1.00
213_G	219_D	0.717	1.00
163_A	197_A	0.712	1.00
118_G	141_I	0.709	1.00
164_E	168_Y	0.708	1.00
295_Q	299_A	0.705	1.00
209_H	230_S	0.704	1.00
103_I	107_Y	0.703	1.00
230_S	233_V	0.700	1.00
220_G	223_A	0.693	1.00
102_D	106_K	0.691	1.00
230_S	234_P	0.686	1.00
299_A	302_K	0.686	1.00
65_I	107_Y	0.683	1.00
207_D	211_L	0.682	1.00
241_S	265_G	0.681	1.00
34_K	41_K	0.681	1.00
120_I	143_C	0.677	1.00
246_A	269_I	0.676	1.00
191_T	215_N	0.674	1.00
211_L	223_A	0.673	1.00
135_Q	151_V	0.672	1.00
21_V	33_R	0.670	1.00
270_S	277_S	0.670	1.00
82_T	96_P	0.669	1.00
183_R	187_R	0.668	1.00
224_A	247_G	0.666	1.00
135_Q	140_V	0.663	1.00
177_I	235_T	0.662	1.00
118_G	289_A	0.657	1.00
144_E	190_S	0.654	1.00
141_I	154_A	0.654	1.00
252_A	255_N	0.648	1.00
108_L	119_L	0.646	1.00
41_K	44_D	0.642	1.00
140_V	151_V	0.640	1.00
142_A	151_V	0.639	1.00
20_R	28_V	0.637	1.00
5_K	55_I	0.637	1.00
46_T	109_E	0.637	1.00
71_H	243_E	0.636	1.00
249_H	253_K	0.635	1.00
35_L	38_Q	0.633	1.00
27_Y	32_K	0.633	1.00
250_L	254_K	0.631	1.00
177_I	198_Y	0.630	1.00
141_I	296_D	0.627	1.00
217_M	269_I	0.627	1.00
205_L	210_M	0.627	1.00
260_E	276_P	0.624	1.00
76_K	282_L	0.622	1.00
18_V	21_V	0.622	1.00
7_I	18_V	0.621	1.00
250_L	274_G	0.621	1.00
163_A	166_F	0.621	1.00
77_I	282_L	0.618	1.00
283_E	286_G	0.617	1.00
135_Q	138_G	0.616	1.00
179_F	198_Y	0.614	1.00
169_L	238_Y	0.613	1.00
18_V	40_M	0.611	1.00
93_T	114_K	0.610	1.00
62_V	90_Y	0.606	1.00
182_V	191_T	0.606	1.00
264_E	280_L	0.605	1.00
144_E	158_R	0.604	1.00
218_N	221_E	0.603	1.00
13_V	32_K	0.603	1.00
141_I	293_F	0.603	1.00
130_S	133_A	0.602	1.00
211_L	227_F	0.601	1.00
241_S	244_V	0.598	1.00
59_T	91_A	0.597	1.00
199_K	205_L	0.596	1.00
176_N	234_P	0.593	1.00
80_G	282_L	0.590	1.00
211_L	230_S	0.588	1.00
239_A	263_G	0.588	1.00
79_N	283_E	0.587	1.00
135_Q	150_D	0.587	1.00
62_V	118_G	0.586	1.00
215_N	240_N	0.586	1.00
73_C	77_I	0.585	1.00
165_S	236_A	0.584	1.00
158_R	193_D	0.583	1.00
141_I	292_L	0.582	1.00
129_D	132_L	0.582	1.00
90_Y	117_D	0.582	1.00
246_A	267_T	0.577	1.00
238_Y	264_E	0.577	1.00
217_M	247_G	0.577	1.00
202_C	205_L	0.576	1.00
46_T	50_T	0.576	1.00
105_I	130_S	0.575	1.00
52_I	56_R	0.574	1.00
228_Y	252_A	0.573	1.00
242_D	267_T	0.572	1.00
195_A	210_M	0.571	1.00
168_Y	262_I	0.571	1.00
178_A	209_H	0.568	1.00
270_S	275_F	0.568	1.00
141_I	289_A	0.561	1.00
101_P	105_I	0.561	1.00
95_L	110_L	0.560	1.00
142_A	153_C	0.560	1.00
221_E	224_A	0.560	1.00
248_I	252_A	0.559	1.00
249_H	273_L	0.559	1.00
18_V	36_V	0.559	1.00
90_Y	297_E	0.558	1.00
154_A	288_A	0.557	1.00
191_T	240_N	0.557	1.00
223_A	227_F	0.556	1.00
292_L	296_D	0.556	1.00
85_A	294_L	0.556	1.00
13_V	18_V	0.555	1.00
11_A	21_V	0.552	1.00
62_V	297_E	0.550	1.00
156_N	161_A	0.545	1.00
213_G	220_G	0.544	1.00
84_A	294_L	0.544	1.00
161_A	164_E	0.540	1.00
205_L	211_L	0.536	1.00
61_T	117_D	0.536	1.00
167_R	170_K	0.535	1.00
215_N	244_V	0.535	1.00
116_I	119_L	0.534	1.00
221_E	247_G	0.533	1.00
85_A	90_Y	0.532	1.00
25_H	28_V	0.531	1.00
234_P	237_I	0.530	1.00
79_N	98_N	0.528	1.00
109_E	112_R	0.527	1.00
118_G	139_P	0.527	1.00
142_A	146_T	0.527	1.00
111_L	116_I	0.525	1.00
72_P	243_E	0.521	1.00
208_R	211_L	0.521	1.00
172_R	235_T	0.520	1.00
159_K	162_Y	0.519	1.00
24_H	27_Y	0.518	1.00
81_I	85_A	0.516	1.00
170_K	205_L	0.516	1.00
53_D	56_R	0.515	1.00
76_K	268_S	0.515	1.00
59_T	90_Y	0.515	1.00
233_V	258_D	0.512	1.00
180_T	223_A	0.511	1.00
176_N	231_G	0.511	1.00
188_S	191_T	0.511	1.00
28_V	33_R	0.510	1.00
71_H	74_F	0.510	1.00
236_A	260_E	0.509	1.00
158_R	190_S	0.509	1.00
296_D	302_K	0.508	1.00
266_N	277_S	0.508	1.00
26_P	33_R	0.505	1.00
242_D	270_S	0.504	1.00
74_F	122_T	0.504	1.00
16_S	25_H	0.501	1.00
133_A	137_Y	0.501	1.00
6_E	10_L	0.501	1.00
288_A	295_Q	0.501	1.00
105_I	133_A	0.501	1.00
110_L	113_T	0.501	1.00
102_D	105_I	0.500	1.00
219_D	244_V	0.500	1.00
208_R	230_S	0.500	1.00
281_N	285_L	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	0.8135	100	0.122	Contact Map
2hsgA	1	0.9839	100	0.124	Contact Map
4o5aA	2	0.8006	100	0.133	Contact Map
3h5oA	2	0.8006	100	0.134	Contact Map
3bilA	2	0.7556	100	0.134	Contact Map
2o20A	2	0.8167	100	0.135	Contact Map
1qpzA	2	0.9904	100	0.136	Contact Map
3kjxA	2	0.9968	100	0.136	Contact Map
3ctpA	2	0.791	100	0.137	Contact Map
1jyeA	2	0.8039	100	0.142	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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