CBPA - ECOLI - GREMLIN Contacts

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CBPA - Curved DNA-binding protein

UniProt:	P36659	Sequences: MELKDYYAIMGVKPTDDLKTIKTAYRRLARKYHPDVSKEPDAEARFKEVAEAWEVLSDEQRRAEYDQMWQHRNDPQFNRQFHHGDGQSFNAEDFDDIFSSIFGQHARQSRQRPATRGHDIEIEVAVFLEETLTEHKRTISYNLPVYNAFGMIEQEIPKTLNVKIPAGVGNGQRIRLKGQGTPGENGGPNGDLWLVIHIAPHPLFDIVGQDLEIVVPVSPWEAALGAKVTVPTLKESILLTIPPGSQAGQRLRVKGKGLVSKKQTGDLYAVLKIVMPPKPDENTAALWQQLADAQSSFDPRKDWGKA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12193
Length:	306 (276)
Sequences:	3323 (2335)
Seq/√Len:	140.6

ECOLI - CBPA DNAJ
BACSU - DNAJ
HALSA - DNAJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_D	20_T	4.673	1.00
43_E	47_K	3.762	1.00
127_F	130_E	2.976	1.00
245_S	271_L	2.825	1.00
129_E	201_H	2.761	1.00
218_S	221_E	2.708	1.00
18_L	59_E	2.677	1.00
123_E	197_H	2.669	1.00
280_D	283_T	2.628	1.00
130_E	137_R	2.546	1.00
170_N	197_H	2.542	1.00
158_K	179_Q	2.527	1.00
227_K	240_T	2.329	1.00
214_V	270_V	2.325	1.00
214_V	272_K	2.318	1.00
132_L	258_L	2.285	1.00
4_K	48_E	2.280	1.00
136_K	163_K	2.226	1.00
30_R	36_V	2.215	1.00
5_D	8_A	2.213	1.00
212_E	270_V	2.195	1.00
282_N	285_A	2.183	1.00
127_F	199_A	2.110	1.00
63_A	67_Q	2.091	1.00
125_A	197_H	2.089	1.00
286_L	289_Q	2.078	1.00
221_E	226_A	2.048	1.00
173_R	193_W	2.039	1.00
216_P	272_K	2.007	1.00
211_L	267_L	1.990	1.00
207_V	212_E	1.979	1.00
170_N	198_I	1.959	1.00
285_A	289_Q	1.950	1.00
250_R	268_Y	1.932	1.00
125_A	199_A	1.932	1.00
138_T	161_N	1.919	1.00
41_D	44_A	1.881	1.00
234_K	264_T	1.851	1.00
284_A	288_Q	1.841	1.00
136_K	161_N	1.829	1.00
251_L	271_L	1.796	1.00
19_K	23_T	1.794	1.00
282_N	289_Q	1.783	1.00
209_Q	260_S	1.768	1.00
255_G	266_D	1.744	1.00
121_E	173_R	1.715	1.00
58_D	61_R	1.698	1.00
168_V	196_I	1.684	1.00
40_P	43_E	1.646	1.00
252_R	266_D	1.622	1.00
229_T	236_S	1.581	1.00
243_P	284_A	1.567	1.00
286_L	290_L	1.565	1.00
45_R	48_E	1.557	1.00
60_Q	63_A	1.538	1.00
6_Y	55_V	1.520	1.00
227_K	238_L	1.494	1.00
212_E	250_R	1.481	1.00
216_P	274_V	1.481	1.00
233_L	267_L	1.464	1.00
123_E	195_V	1.455	1.00
203_L	213_I	1.451	1.00
250_R	270_V	1.447	1.00
239_L	269_A	1.441	1.00
288_Q	292_D	1.437	1.00
229_T	238_L	1.434	1.00
126_V	131_T	1.422	1.00
207_V	210_D	1.422	1.00
131_T	198_I	1.418	1.00
130_E	135_H	1.416	1.00
44_A	48_E	1.415	1.00
281_E	285_A	1.410	1.00
168_V	172_Q	1.395	1.00
37_S	42_A	1.390	1.00
206_I	258_L	1.386	1.00
205_D	214_V	1.384	1.00
219_P	275_M	1.372	1.00
25_Y	50_A	1.364	1.00
279_P	283_T	1.358	1.00
32_Y	49_V	1.355	1.00
95_D	98_F	1.345	1.00
12_V	21_I	1.344	1.00
29_A	46_F	1.326	1.00
160_L	179_Q	1.323	1.00
210_D	268_Y	1.317	1.00
285_A	288_Q	1.315	1.00
59_E	63_A	1.310	1.00
132_L	233_L	1.304	1.00
138_T	159_T	1.298	1.00
98_F	102_F	1.295	1.00
118_H	181_T	1.286	1.00
219_P	287_W	1.286	1.00
289_Q	292_D	1.276	1.00
215_V	228_V	1.275	1.00
169_G	209_Q	1.263	1.00
246_Q	249_Q	1.260	1.00
117_G	183_G	1.256	1.00
16_D	21_I	1.253	1.00
121_E	195_V	1.250	1.00
213_I	269_A	1.244	1.00
4_K	9_I	1.244	1.00
6_Y	51_E	1.243	1.00
13_K	20_T	1.238	1.00
7_Y	66_D	1.237	1.00
44_A	47_K	1.231	1.00
200_P	205_D	1.226	1.00
203_L	231_P	1.216	1.00
182_P	189_N	1.205	1.00
288_Q	291_A	1.203	1.00
212_E	268_Y	1.200	1.00
237_I	253_V	1.191	1.00
210_D	266_D	1.185	1.00
80_Q	83_H	1.174	1.00
28_L	49_V	1.172	1.00
281_E	284_A	1.167	1.00
223_A	275_M	1.163	0.99
247_A	273_I	1.150	0.99
14_P	69_W	1.129	0.99
219_P	223_A	1.114	0.99
246_Q	277_P	1.098	0.99
260_S	263_Q	1.097	0.99
75_P	78_N	1.095	0.99
239_L	251_L	1.089	0.99
15_T	20_T	1.088	0.99
236_S	256_K	1.081	0.99
94_F	97_I	1.080	0.99
78_N	81_F	1.057	0.99
78_N	82_H	1.055	0.99
228_V	241_I	1.049	0.99
228_V	231_P	1.026	0.99
223_A	279_P	1.026	0.99
128_L	131_T	1.025	0.99
128_L	211_L	1.025	0.99
198_I	206_I	1.023	0.99
169_G	172_Q	1.023	0.99
204_F	213_I	1.019	0.99
131_T	258_L	1.016	0.99
119_D	190_G	1.015	0.99
213_I	216_P	1.009	0.99
114_A	185_N	1.006	0.99
222_A	273_I	1.001	0.98
128_L	233_L	0.999	0.98
172_Q	261_K	0.999	0.98
211_L	258_L	0.993	0.98
70_Q	74_D	0.989	0.98
98_F	101_I	0.976	0.98
95_D	99_S	0.975	0.98
6_Y	65_Y	0.972	0.98
64_E	69_W	0.966	0.98
180_G	191_D	0.964	0.98
247_A	275_M	0.961	0.98
9_I	48_E	0.959	0.98
204_F	233_L	0.955	0.98
128_L	258_L	0.950	0.98
281_E	288_Q	0.949	0.98
119_D	175_R	0.949	0.98
46_F	50_A	0.949	0.98
119_D	193_W	0.945	0.98
176_L	179_Q	0.942	0.98
128_L	132_L	0.936	0.98
111_Q	114_A	0.925	0.97
120_I	181_T	0.923	0.97
140_S	159_T	0.921	0.97
234_K	256_K	0.921	0.97
117_G	190_G	0.916	0.97
245_S	251_L	0.915	0.97
178_G	190_G	0.913	0.97
79_R	83_H	0.911	0.97
84_G	90_N	0.908	0.97
96_D	99_S	0.907	0.97
124_V	196_I	0.902	0.97
54_E	61_R	0.902	0.97
217_V	271_L	0.902	0.97
5_D	14_P	0.901	0.97
287_W	290_L	0.899	0.97
60_Q	64_E	0.898	0.97
131_T	166_A	0.895	0.97
84_G	87_Q	0.890	0.97
283_T	290_L	0.890	0.97
28_L	31_K	0.882	0.97
205_D	212_E	0.882	0.97
209_Q	258_L	0.881	0.97
132_L	264_T	0.879	0.96
128_L	206_I	0.877	0.96
50_A	53_W	0.876	0.96
260_S	264_T	0.876	0.96
259_V	264_T	0.870	0.96
122_I	194_L	0.870	0.96
69_W	72_R	0.866	0.96
38_K	41_D	0.862	0.96
244_G	275_M	0.857	0.96
96_D	100_S	0.857	0.96
37_S	41_D	0.857	0.96
79_R	82_H	0.854	0.96
71_H	74_D	0.851	0.96
90_N	93_D	0.851	0.96
4_K	8_A	0.848	0.96
32_Y	45_R	0.846	0.96
223_A	287_W	0.842	0.96
55_V	69_W	0.839	0.95
129_E	133_T	0.835	0.95
11_G	24_A	0.835	0.95
169_G	206_I	0.834	0.95
142_N	157_P	0.832	0.95
165_P	168_V	0.829	0.95
248_G	273_I	0.828	0.95
126_V	130_E	0.826	0.95
8_A	13_K	0.826	0.95
282_N	286_L	0.824	0.95
162_V	194_L	0.823	0.95
175_R	193_W	0.813	0.95
252_R	268_Y	0.804	0.94
92_E	97_I	0.793	0.94
132_L	234_K	0.792	0.94
97_I	101_I	0.789	0.94
131_T	134_E	0.788	0.94
247_A	272_K	0.787	0.94
78_N	83_H	0.787	0.94
140_S	157_P	0.786	0.94
32_Y	42_A	0.783	0.93
22_K	26_R	0.781	0.93
182_P	186_G	0.776	0.93
105_H	108_Q	0.774	0.93
64_E	73_N	0.771	0.93
77_F	80_Q	0.769	0.93
201_H	213_I	0.767	0.93
86_G	89_F	0.766	0.93
246_Q	274_V	0.765	0.93
217_V	222_A	0.761	0.92
126_V	135_H	0.760	0.92
205_D	270_V	0.751	0.92
210_D	265_G	0.750	0.92
206_I	209_Q	0.749	0.92
45_R	49_V	0.748	0.92
178_G	188_P	0.747	0.92
106_A	109_S	0.746	0.92
70_Q	73_N	0.743	0.92
209_Q	264_T	0.741	0.91
95_D	102_F	0.739	0.91
116_R	188_P	0.738	0.91
65_Y	192_L	0.737	0.91
116_R	119_D	0.736	0.91
226_A	241_I	0.734	0.91
94_F	98_F	0.726	0.91
237_I	256_K	0.718	0.90
241_I	271_L	0.716	0.90
12_V	62_R	0.716	0.90
242_P	251_L	0.711	0.90
85_D	88_S	0.711	0.90
7_Y	65_Y	0.708	0.89
97_I	100_S	0.707	0.89
245_S	249_Q	0.706	0.89
64_E	71_H	0.706	0.89
18_L	62_R	0.706	0.89
127_F	137_R	0.703	0.89
256_K	264_T	0.697	0.89
213_I	231_P	0.690	0.88
33_H	46_F	0.687	0.88
93_D	96_D	0.685	0.88
220_W	291_A	0.677	0.87
114_A	186_G	0.676	0.87
88_S	91_A	0.670	0.87
27_R	30_R	0.669	0.87
178_G	191_D	0.668	0.87
162_V	165_P	0.667	0.86
166_A	259_V	0.667	0.86
163_K	179_Q	0.667	0.86
32_Y	39_E	0.665	0.86
257_G	265_G	0.660	0.86
164_I	167_G	0.658	0.86
204_F	267_L	0.658	0.86
128_L	204_F	0.657	0.86
94_F	99_S	0.657	0.86
160_L	176_L	0.655	0.85
105_H	110_R	0.654	0.85
128_L	201_H	0.653	0.85
64_E	68_M	0.651	0.85
51_E	55_V	0.648	0.85
184_E	188_P	0.647	0.85
223_A	244_G	0.647	0.85
206_I	219_P	0.646	0.85
133_T	234_K	0.646	0.85
53_W	57_S	0.646	0.85
232_T	237_I	0.645	0.85
131_T	168_V	0.641	0.84
5_D	69_W	0.641	0.84
183_G	186_G	0.639	0.84
73_N	76_Q	0.635	0.84
31_K	37_S	0.634	0.84
224_L	288_Q	0.630	0.83
47_K	51_E	0.629	0.83
117_G	182_P	0.629	0.83
204_F	230_V	0.627	0.83
6_Y	70_Q	0.626	0.83
84_G	88_S	0.626	0.83
73_N	78_N	0.625	0.83
274_V	277_P	0.623	0.83
10_M	49_V	0.621	0.82
231_P	267_L	0.621	0.82
231_P	236_S	0.621	0.82
68_M	71_H	0.619	0.82
71_H	76_Q	0.619	0.82
41_D	45_R	0.618	0.82
74_D	77_F	0.618	0.82
139_I	159_T	0.617	0.82
92_E	96_D	0.615	0.82
174_I	196_I	0.614	0.82
287_W	291_A	0.613	0.82
222_A	275_M	0.613	0.82
221_E	228_V	0.612	0.81
135_H	164_I	0.611	0.81
31_K	39_E	0.610	0.81
126_V	196_I	0.609	0.81
173_R	195_V	0.607	0.81
64_E	76_Q	0.605	0.81
223_A	247_A	0.605	0.81
201_H	204_F	0.604	0.81
128_L	198_I	0.604	0.81
116_R	178_G	0.601	0.80
12_V	29_A	0.600	0.80
158_K	189_N	0.595	0.80
183_G	188_P	0.595	0.80
117_G	189_N	0.594	0.79
124_V	137_R	0.594	0.79
181_T	184_E	0.594	0.79
220_W	287_W	0.593	0.79
222_A	225_G	0.592	0.79
198_I	258_L	0.591	0.79
69_W	73_N	0.591	0.79
139_I	160_L	0.591	0.79
206_I	265_G	0.589	0.79
248_G	270_V	0.589	0.79
206_I	287_W	0.588	0.79
120_I	141_Y	0.585	0.78
248_G	272_K	0.584	0.78
254_K	266_D	0.580	0.78
36_V	39_E	0.580	0.78
242_P	271_L	0.578	0.78
221_E	291_A	0.577	0.78
124_V	194_L	0.576	0.77
40_P	44_A	0.576	0.77
101_I	104_Q	0.572	0.77
241_I	251_L	0.571	0.77
215_V	271_L	0.570	0.77
91_A	101_I	0.570	0.77
224_L	291_A	0.567	0.76
58_D	196_I	0.566	0.76
98_F	104_Q	0.564	0.76
271_L	275_M	0.563	0.76
91_A	97_I	0.560	0.75
25_Y	233_L	0.557	0.75
117_G	186_G	0.557	0.75
28_L	32_Y	0.556	0.75
18_L	57_S	0.555	0.75
101_I	106_A	0.554	0.75
129_E	233_L	0.551	0.74
111_Q	115_T	0.550	0.74
128_L	259_V	0.549	0.74
237_I	267_L	0.548	0.74
142_N	155_E	0.548	0.74
209_Q	263_Q	0.547	0.74
20_T	23_T	0.547	0.74
76_Q	82_H	0.546	0.74
64_E	72_R	0.544	0.73
232_T	236_S	0.544	0.73
58_D	66_D	0.543	0.73
134_E	164_I	0.543	0.73
54_E	72_R	0.543	0.73
38_K	42_A	0.541	0.73
88_S	92_E	0.541	0.73
165_P	261_K	0.539	0.73
116_R	183_G	0.538	0.73
51_E	70_Q	0.538	0.73
213_I	267_L	0.536	0.72
164_I	174_I	0.534	0.72
69_W	76_Q	0.533	0.72
220_W	223_A	0.533	0.72
244_G	279_P	0.531	0.72
230_V	269_A	0.526	0.71
134_E	167_G	0.526	0.71
139_I	194_L	0.526	0.71
233_L	264_T	0.524	0.71
9_I	28_L	0.524	0.71
55_V	75_P	0.524	0.71
51_E	68_M	0.522	0.70
169_G	207_V	0.521	0.70
168_V	194_L	0.520	0.70
224_L	286_L	0.520	0.70
10_M	23_T	0.517	0.70
128_L	200_P	0.517	0.70
206_I	220_W	0.517	0.70
231_P	239_L	0.515	0.69
22_K	35_D	0.515	0.69
113_P	185_N	0.514	0.69
168_V	174_I	0.513	0.69
32_Y	37_S	0.512	0.69
168_V	173_R	0.511	0.69
133_T	236_S	0.511	0.69
52_A	56_L	0.510	0.69
72_R	76_Q	0.509	0.68
112_R	116_R	0.509	0.68
85_D	90_N	0.508	0.68
113_P	184_E	0.507	0.68
117_G	188_P	0.507	0.68
37_S	95_D	0.506	0.68
6_Y	68_M	0.505	0.68
22_K	246_Q	0.505	0.68
116_R	191_D	0.505	0.68
127_F	135_H	0.504	0.68
132_L	259_V	0.504	0.68
279_P	291_A	0.504	0.68
204_F	232_T	0.504	0.68
174_I	194_L	0.503	0.67
18_L	22_K	0.500	0.67

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
3lz8A	2	0.6176	100	0.155	Contact Map
4j80A	2	0.8824	100	0.205	Contact Map
1nltA	1	0.5327	100	0.518	Contact Map
3agxA	2	0.5621	100	0.523	Contact Map
2q2gA	3	0.5621	100	0.525	Contact Map
1c3gA	2	0.5425	100	0.536	Contact Map
4j7zA	1	0.3464	100	0.679	Contact Map
1bq0A	1	0.2484	99.9	0.695	Contact Map
3i38A	5	0.3399	99.9	0.708	Contact Map
2ctrA	1	0.2778	99.9	0.714	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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