YCBJ - BACSU - GREMLIN Contacts

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YCBJ - Uncharacterized protein YcbJ

UniProt:	P42242	Sequences: MTNLNEKQLITEIVGLARSQGLTVHSENAQLNETGMDFQVVFAKDDTGMPWVLRKPRRSDVVERASAEGITLAFLRANLTADVPDWRIHTPELIAYPMLKGTPAAGIDLEQKQYVWNMDHQPPSDDFVRTLADILAELHGTDQISAGQSGIEVIRPEDFRQMTADSMVDVKNKLGVSTTLWERWQKWVDDDAYWPGFSSLIHGDLHPPHILIDQNGRVTGLLDWTEAKVADPAKDFVLYQTIFGEKETARLLEYYDQAGGRIWAKMQEHISEMQAAYPVEIAKLALQTQQEEHINMALEALGVTSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	306 (271)
Sequences:	5507 (4158)
Seq/√Len:	252.6

ECOLI - RDOA YCBJ
BACSU - YCBJ YERI
HALSA - Q9HNB3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
85_D	97_P	3.951	1.00
80_T	137_E	3.883	1.00
133_D	254_Y	3.843	1.00
99_L	220_G	3.624	1.00
72_L	86_W	3.375	1.00
42_F	98_M	3.246	1.00
50_P	98_M	3.035	1.00
131_L	210_I	2.996	1.00
130_T	133_D	2.953	1.00
42_F	50_P	2.914	1.00
53_L	95_A	2.885	1.00
14_V	18_R	2.845	1.00
187_W	191_D	2.814	1.00
129_R	254_Y	2.773	1.00
69_G	86_W	2.766	1.00
139_H	255_Y	2.712	1.00
44_K	50_P	2.654	1.00
134_I	221_L	2.650	1.00
76_R	85_D	2.604	1.00
99_L	219_T	2.572	1.00
125_D	250_R	2.497	1.00
28_N	44_K	2.483	1.00
119_D	123_P	2.477	1.00
133_D	258_A	2.462	1.00
132_A	254_Y	2.361	1.00
125_D	129_R	2.309	1.00
160_R	164_A	2.306	1.00
103_P	211_L	2.257	1.00
213_D	217_R	2.223	1.00
30_Q	42_F	2.031	1.00
239_Y	251_L	1.897	1.00
247_E	250_R	1.895	1.00
144_I	149_S	1.891	1.00
132_A	251_L	1.889	1.00
130_T	217_R	1.876	1.00
201_I	230_A	1.824	1.00
211_L	219_T	1.798	1.00
287_Q	291_E	1.762	1.00
186_K	190_D	1.760	1.00
252_L	267_Q	1.743	1.00
137_E	258_A	1.737	1.00
253_E	257_Q	1.730	1.00
199_S	232_P	1.710	1.00
99_L	211_L	1.708	1.00
12_E	15_G	1.701	1.00
263_W	266_M	1.630	1.00
211_L	222_L	1.628	1.00
50_P	100_K	1.627	1.00
72_L	84_P	1.597	1.00
141_T	146_A	1.595	1.00
135_L	205_L	1.557	1.00
100_K	213_D	1.522	1.00
140_G	259_G	1.512	1.00
130_T	134_I	1.510	1.00
76_R	86_W	1.510	1.00
167_M	171_K	1.510	1.00
168_V	172_N	1.505	1.00
159_F	162_M	1.503	1.00
164_A	168_V	1.464	1.00
130_T	218_V	1.458	1.00
37_D	225_T	1.444	1.00
30_Q	44_K	1.425	1.00
163_T	167_M	1.422	1.00
71_T	227_A	1.411	1.00
249_A	253_E	1.404	1.00
11_T	14_V	1.389	1.00
134_I	218_V	1.375	1.00
254_Y	257_Q	1.363	1.00
10_I	29_A	1.353	1.00
180_L	183_R	1.345	1.00
42_F	52_V	1.338	1.00
55_K	91_P	1.336	1.00
237_V	274_Q	1.331	1.00
286_L	290_Q	1.310	1.00
213_D	219_T	1.305	1.00
204_D	209_H	1.303	1.00
129_R	250_R	1.301	1.00
143_Q	200_L	1.295	1.00
167_M	189_D	1.272	1.00
52_V	98_M	1.266	1.00
133_D	137_E	1.246	1.00
38_F	54_R	1.241	1.00
158_D	162_M	1.241	1.00
142_D	145_S	1.234	1.00
100_K	214_Q	1.229	1.00
66_S	70_I	1.220	1.00
69_G	73_A	1.215	1.00
187_W	272_E	1.213	1.00
166_S	170_V	1.191	1.00
254_Y	258_A	1.179	1.00
167_M	185_Q	1.177	1.00
240_Q	267_Q	1.169	1.00
104_A	127_F	1.162	1.00
162_M	166_S	1.147	1.00
119_D	122_P	1.145	1.00
171_K	174_L	1.137	1.00
105_A	208_P	1.128	1.00
197_F	261_R	1.114	1.00
70_I	74_F	1.112	1.00
131_L	205_L	1.106	1.00
10_I	14_V	1.099	1.00
73_A	86_W	1.097	1.00
128_V	246_K	1.087	1.00
134_I	137_E	1.086	1.00
164_A	189_D	1.083	1.00
131_L	239_Y	1.083	1.00
205_L	221_L	1.083	1.00
168_V	171_K	1.081	1.00
102_T	123_P	1.067	1.00
174_L	177_S	1.067	1.00
269_H	273_M	1.046	1.00
230_A	235_D	1.045	1.00
37_D	40_V	1.038	1.00
17_A	95_A	1.038	1.00
273_M	277_Y	1.033	1.00
138_L	221_L	1.027	1.00
163_T	166_S	1.025	1.00
138_L	200_L	1.024	1.00
43_A	95_A	1.023	1.00
132_A	258_A	1.021	1.00
285_A	289_Q	1.020	1.00
70_I	73_A	1.010	1.00
286_L	289_Q	0.999	1.00
49_M	97_P	0.997	1.00
171_K	182_E	0.996	1.00
97_P	220_G	0.991	1.00
129_R	133_D	0.990	1.00
71_T	200_L	0.983	1.00
165_D	169_D	0.980	1.00
198_S	229_V	0.979	1.00
143_Q	149_S	0.977	1.00
127_F	212_I	0.975	1.00
201_I	228_K	0.975	1.00
185_Q	189_D	0.973	1.00
17_A	21_G	0.961	1.00
250_R	253_E	0.943	1.00
136_A	256_D	0.935	1.00
146_A	149_S	0.934	1.00
126_D	129_R	0.934	1.00
184_W	187_W	0.934	1.00
84_P	96_Y	0.934	1.00
236_F	252_L	0.932	1.00
209_H	223_D	0.930	1.00
123_P	126_D	0.926	1.00
123_P	216_G	0.924	1.00
129_R	258_A	0.914	1.00
132_A	136_A	0.913	1.00
51_W	87_R	0.908	1.00
81_A	134_I	0.907	1.00
162_M	169_D	0.905	1.00
195_P	231_D	0.903	1.00
252_L	256_D	0.889	1.00
143_Q	229_V	0.889	1.00
35_G	223_D	0.887	1.00
40_V	222_L	0.886	1.00
15_G	18_R	0.879	1.00
14_V	26_S	0.877	1.00
147_G	150_G	0.875	1.00
72_L	94_I	0.871	1.00
69_G	94_I	0.871	1.00
185_Q	188_V	0.869	1.00
155_R	158_D	0.868	1.00
63_E	66_S	0.867	1.00
82_D	134_I	0.867	1.00
90_T	93_L	0.867	1.00
43_A	53_L	0.866	1.00
16_L	93_L	0.865	0.99
135_L	139_H	0.858	0.99
54_R	224_W	0.854	0.99
248_T	252_L	0.848	0.99
87_R	92_E	0.846	0.99
282_A	285_A	0.843	0.99
156_P	160_R	0.843	0.99
76_R	83_V	0.842	0.99
183_R	187_W	0.836	0.99
133_D	136_A	0.836	0.99
281_I	285_A	0.834	0.99
265_K	268_E	0.830	0.99
136_A	259_G	0.829	0.99
176_V	283_K	0.827	0.99
285_A	288_T	0.825	0.99
170_V	173_K	0.824	0.99
156_P	159_F	0.820	0.99
240_Q	271_S	0.819	0.99
169_D	173_K	0.813	0.99
18_R	25_H	0.813	0.99
266_M	269_H	0.813	0.99
74_F	146_A	0.809	0.99
143_Q	146_A	0.806	0.99
21_G	24_V	0.805	0.99
213_D	216_G	0.805	0.99
183_R	186_K	0.805	0.99
35_G	209_H	0.803	0.99
250_R	254_Y	0.802	0.99
278_P	281_I	0.799	0.99
73_A	77_A	0.798	0.99
70_I	150_G	0.797	0.99
134_I	205_L	0.790	0.99
228_K	234_K	0.788	0.99
73_A	76_R	0.787	0.99
135_L	235_D	0.787	0.99
102_T	214_Q	0.786	0.99
287_Q	290_Q	0.783	0.99
164_A	167_M	0.782	0.99
181_W	185_Q	0.777	0.99
210_I	221_L	0.776	0.99
11_T	15_G	0.773	0.99
167_M	170_V	0.770	0.99
152_E	155_R	0.770	0.99
166_S	169_D	0.767	0.99
202_H	224_W	0.766	0.99
68_E	72_L	0.766	0.99
147_G	152_E	0.764	0.99
182_E	185_Q	0.763	0.99
77_A	80_T	0.763	0.99
131_L	135_L	0.760	0.99
182_E	186_K	0.759	0.99
24_V	51_W	0.758	0.99
32_N	52_V	0.752	0.99
153_V	157_E	0.750	0.99
167_M	174_L	0.748	0.99
185_Q	276_A	0.747	0.99
241_T	274_Q	0.741	0.98
256_D	264_A	0.740	0.98
284_L	288_T	0.738	0.98
186_K	189_D	0.731	0.98
206_H	226_E	0.728	0.98
27_E	43_A	0.724	0.98
160_R	192_A	0.723	0.98
163_T	170_V	0.721	0.98
74_F	77_A	0.721	0.98
128_V	245_E	0.719	0.98
40_V	206_H	0.719	0.98
210_I	218_V	0.719	0.98
167_M	172_N	0.717	0.98
79_L	82_D	0.717	0.98
100_K	219_T	0.717	0.98
46_D	51_W	0.715	0.98
281_I	284_L	0.715	0.98
38_F	56_P	0.713	0.98
104_A	212_I	0.712	0.98
157_E	160_R	0.708	0.98
201_I	234_K	0.700	0.98
166_S	173_K	0.700	0.98
171_K	185_Q	0.698	0.98
158_D	166_S	0.697	0.98
268_E	271_S	0.697	0.98
126_D	217_R	0.695	0.98
129_R	132_A	0.691	0.98
52_V	96_Y	0.690	0.98
37_D	57_R	0.690	0.98
264_A	267_Q	0.686	0.97
54_R	68_E	0.683	0.97
102_T	106_G	0.682	0.97
71_T	224_W	0.681	0.97
248_T	271_S	0.679	0.97
102_T	213_D	0.679	0.97
267_Q	271_S	0.679	0.97
103_P	222_L	0.678	0.97
44_K	48_G	0.672	0.97
283_K	286_L	0.671	0.97
17_A	51_W	0.669	0.97
191_D	269_H	0.667	0.97
36_M	206_H	0.667	0.97
87_R	90_T	0.663	0.97
44_K	47_T	0.660	0.97
181_W	280_E	0.659	0.97
153_V	156_P	0.658	0.97
65_A	94_I	0.658	0.97
117_N	120_H	0.657	0.97
81_A	141_T	0.657	0.97
236_F	239_Y	0.656	0.97
272_E	275_A	0.655	0.97
234_K	237_V	0.655	0.97
276_A	280_E	0.654	0.97
127_F	130_T	0.654	0.97
74_F	141_T	0.654	0.97
226_E	281_I	0.653	0.97
204_D	223_D	0.652	0.97
205_L	210_I	0.652	0.97
126_D	130_T	0.647	0.96
239_Y	243_F	0.647	0.96
253_E	256_D	0.647	0.96
156_P	164_A	0.646	0.96
118_M	123_P	0.646	0.96
37_D	226_E	0.645	0.96
261_R	264_A	0.645	0.96
32_N	42_F	0.644	0.96
163_T	174_L	0.642	0.96
81_A	138_L	0.640	0.96
56_P	65_A	0.638	0.96
178_T	182_E	0.637	0.96
139_H	201_I	0.637	0.96
15_G	19_S	0.636	0.96
179_T	183_R	0.636	0.96
37_D	64_R	0.636	0.96
271_S	275_A	0.632	0.96
269_H	272_E	0.631	0.96
27_E	47_T	0.630	0.96
81_A	86_W	0.629	0.96
103_P	106_G	0.627	0.96
189_D	192_A	0.625	0.96
270_I	274_Q	0.624	0.96
122_P	125_D	0.620	0.95
61_V	64_R	0.615	0.95
20_Q	25_H	0.613	0.95
177_S	182_E	0.613	0.95
151_I	227_A	0.612	0.95
202_H	235_D	0.611	0.95
277_Y	280_E	0.611	0.95
175_G	283_K	0.610	0.95
126_D	215_N	0.610	0.95
27_E	46_D	0.609	0.95
136_A	258_A	0.609	0.95
285_A	290_Q	0.608	0.95
38_F	209_H	0.605	0.95
257_Q	260_G	0.604	0.95
28_N	43_A	0.604	0.95
64_R	226_E	0.603	0.95
18_R	23_T	0.603	0.95
129_R	246_K	0.600	0.95
169_D	172_N	0.598	0.94
57_R	226_E	0.598	0.94
66_S	92_E	0.597	0.94
12_E	17_A	0.597	0.94
139_H	235_D	0.597	0.94
236_F	251_L	0.595	0.94
285_A	291_E	0.590	0.94
25_H	46_D	0.588	0.94
152_E	157_E	0.588	0.94
202_H	205_L	0.587	0.94
129_R	257_Q	0.584	0.94
181_W	184_W	0.583	0.94
83_V	86_W	0.580	0.93
155_R	162_M	0.579	0.93
170_V	174_L	0.577	0.93
128_V	132_A	0.577	0.93
57_R	206_H	0.575	0.93
209_H	220_G	0.575	0.93
79_L	141_T	0.573	0.93
102_T	117_N	0.573	0.93
233_A	266_M	0.570	0.93
156_P	163_T	0.569	0.93
67_A	71_T	0.567	0.93
240_Q	243_F	0.566	0.93
238_L	242_I	0.563	0.92
177_S	184_W	0.562	0.92
38_F	41_V	0.561	0.92
35_G	52_V	0.561	0.92
240_Q	248_T	0.561	0.92
67_A	148_Q	0.561	0.92
118_M	127_F	0.560	0.92
31_L	41_V	0.559	0.92
203_G	235_D	0.559	0.92
46_D	49_M	0.558	0.92
165_D	168_V	0.556	0.92
56_P	66_S	0.554	0.92
158_D	161_Q	0.553	0.92
178_T	185_Q	0.553	0.92
237_V	271_S	0.551	0.92
22_L	25_H	0.551	0.92
61_V	65_A	0.549	0.92
208_P	238_L	0.548	0.91
137_E	140_G	0.547	0.91
159_F	167_M	0.547	0.91
29_A	43_A	0.547	0.91
136_A	254_Y	0.547	0.91
170_V	175_G	0.546	0.91
142_D	147_G	0.546	0.91
231_D	270_I	0.544	0.91
196_G	231_D	0.542	0.91
142_D	229_V	0.541	0.91
126_D	133_D	0.540	0.91
176_V	179_T	0.539	0.91
277_Y	284_L	0.537	0.91
75_L	224_W	0.537	0.91
40_V	57_R	0.535	0.90
146_A	150_G	0.535	0.90
231_D	236_F	0.535	0.90
163_T	171_K	0.534	0.90
106_G	109_L	0.534	0.90
64_R	225_T	0.533	0.90
160_R	163_T	0.532	0.90
277_Y	281_I	0.532	0.90
75_L	79_L	0.529	0.90
161_Q	165_D	0.528	0.90
131_L	251_L	0.526	0.90
181_W	187_W	0.521	0.89
208_P	211_L	0.521	0.89
136_A	255_Y	0.520	0.89
177_S	180_L	0.518	0.89
134_I	138_L	0.518	0.89
160_R	217_R	0.511	0.88
184_W	188_V	0.511	0.88
159_F	273_M	0.510	0.88
220_G	238_L	0.508	0.88
158_D	164_A	0.507	0.88
143_Q	198_S	0.507	0.88
139_H	199_S	0.506	0.88
197_F	259_G	0.506	0.88
272_E	278_P	0.506	0.88
14_V	24_V	0.503	0.88
231_D	269_H	0.502	0.87
266_M	270_I	0.502	0.87
159_F	163_T	0.500	0.87
147_G	151_I	0.500	0.87

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
3tdwA	1	0.9183	100	0.376	Contact Map
3dxpA	2	0.9248	100	0.388	Contact Map
4orkA	1	0.9281	100	0.396	Contact Map
4dcaA	1	0.9052	100	0.419	Contact Map
3atsA	1	0.9575	100	0.421	Contact Map
3sg8A	2	0.9314	100	0.435	Contact Map
3w0oA	1	0.8431	100	0.461	Contact Map
3jr1A	1	0.8987	100	0.479	Contact Map
3csvA	2	0.8889	100	0.481	Contact Map
3f7wA	1	0.8791	100	0.484	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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