YNBB - ECOLI - GREMLIN Contacts

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YNBB - Uncharacterized protein YnbB

UniProt:	P76091	Sequences: MLEKSLATLFALLILATLINRFLLWRLPERKGGEVTLRIRTWWGIVICFSMVISGPRWMTLTFFALISFLALKEYCTLISVHFPRWLYWGIPLNYLLIGFNCFELFLLFIPLAGFLILATGQVLVGDPSGFLHTVSAIFWGWIMTVFALSHAAWLLMLPTTNIQGGALLVLFLLALTESNDIAQYLWGKSCGRRKVVPKVSPGKTLEGLMGGVITIMIASLIIGPLLTPLNTLQALLAGLLIGISGFCGDVVMSAIKRDIGVKDSGKLLPGHGGLLDRIDSLIFTAPVFFYFIRYCCY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13749
Length:	298 (256)
Sequences:	4752 (3605)
Seq/√Len:	225.3

ECOLI - YNBB CDSA
BACSU - CDSA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_T	269_L	6.215	1.00
183_A	215_T	5.135	1.00
194_R	207_E	4.134	1.00
187_W	211_G	4.086	1.00
209_L	247_F	3.668	1.00
179_S	219_A	3.280	1.00
253_M	265_S	3.040	1.00
187_W	215_T	2.954	1.00
189_K	205_T	2.840	1.00
193_R	207_E	2.813	1.00
71_A	275_L	2.805	1.00
75_Y	141_G	2.777	1.00
187_W	191_C	2.746	1.00
174_L	178_E	2.605	1.00
52_V	63_F	2.237	1.00
42_W	47_I	2.234	1.00
180_N	247_F	2.218	1.00
39_I	186_L	2.161	1.00
173_L	286_A	2.099	1.00
35_V	39_I	2.098	1.00
196_V	209_L	2.055	1.00
78_L	262_V	2.025	1.00
78_L	265_S	2.024	1.00
172_F	239_G	2.014	1.00
220_S	239_G	1.980	1.00
70_L	275_L	1.977	1.00
180_N	243_G	1.967	1.00
194_R	206_L	1.958	1.00
42_W	46_V	1.941	1.00
272_H	278_R	1.934	1.00
35_V	186_L	1.898	1.00
55_G	59_M	1.892	1.00
180_N	246_G	1.877	1.00
186_L	190_S	1.866	1.00
196_V	206_L	1.803	1.00
73_K	77_T	1.790	1.00
206_L	210_M	1.784	1.00
210_M	214_I	1.764	1.00
222_I	226_L	1.724	1.00
184_Q	212_G	1.721	1.00
235_A	239_G	1.672	1.00
196_V	251_V	1.664	1.00
177_T	285_T	1.655	1.00
245_S	288_V	1.651	1.00
187_W	190_S	1.638	1.00
72_L	76_C	1.629	1.00
279_I	282_L	1.617	1.00
40_R	44_G	1.578	1.00
148_A	151_H	1.573	1.00
175_A	219_A	1.561	1.00
234_Q	292_F	1.555	1.00
67_I	275_L	1.539	1.00
62_T	66_L	1.521	1.00
238_A	292_F	1.498	1.00
217_M	236_L	1.487	1.00
195_K	203_G	1.466	1.00
187_W	214_I	1.459	1.00
136_S	140_W	1.458	1.00
43_W	47_I	1.456	1.00
218_I	222_I	1.413	1.00
36_T	40_R	1.394	1.00
66_L	70_L	1.377	1.00
179_S	215_T	1.377	1.00
173_L	289_F	1.376	1.00
213_V	243_G	1.352	1.00
213_V	240_L	1.351	1.00
176_L	220_S	1.330	1.00
151_H	286_A	1.313	1.00
78_L	260_I	1.307	1.00
73_K	266_G	1.294	1.00
148_A	152_A	1.287	1.00
245_S	285_T	1.285	1.00
252_V	284_F	1.280	1.00
216_I	243_G	1.272	1.00
88_Y	92_P	1.271	1.00
196_V	210_M	1.256	1.00
50_S	54_S	1.255	1.00
172_F	223_I	1.253	1.00
71_A	276_L	1.248	1.00
195_K	205_T	1.248	1.00
222_I	225_P	1.241	1.00
120_T	123_V	1.237	1.00
177_T	282_L	1.226	1.00
212_G	243_G	1.211	1.00
72_L	141_G	1.199	1.00
41_T	270_P	1.196	1.00
217_M	240_L	1.181	1.00
192_G	207_E	1.178	1.00
99_G	102_C	1.176	1.00
242_I	289_F	1.175	1.00
231_N	234_Q	1.161	1.00
209_L	244_I	1.161	1.00
221_L	236_L	1.156	1.00
176_L	216_I	1.152	1.00
47_I	51_M	1.140	1.00
151_H	291_Y	1.138	1.00
183_A	211_G	1.131	1.00
243_G	247_F	1.130	1.00
41_T	44_G	1.116	1.00
95_Y	102_C	1.115	1.00
246_G	281_S	1.111	1.00
152_A	170_V	1.102	1.00
59_M	62_T	1.099	1.00
45_I	279_I	1.099	1.00
242_I	285_T	1.096	1.00
216_I	219_A	1.095	1.00
252_V	256_I	1.089	1.00
75_Y	79_I	1.083	1.00
177_T	246_G	1.079	1.00
71_A	279_I	1.077	1.00
39_I	182_I	1.073	1.00
144_M	148_A	1.063	1.00
67_I	279_I	1.062	1.00
197_V	200_V	1.061	1.00
35_V	185_Y	1.061	1.00
56_P	59_M	1.055	1.00
206_L	209_L	1.054	1.00
51_M	55_G	1.050	1.00
145_T	283_I	1.049	1.00
45_I	269_L	1.041	1.00
71_A	145_T	1.024	1.00
189_K	203_G	1.021	1.00
151_H	290_F	1.017	1.00
58_W	62_T	1.010	1.00
269_L	275_L	1.008	1.00
90_G	94_N	1.008	1.00
87_L	93_L	1.001	1.00
174_L	282_L	0.997	1.00
52_V	56_P	0.996	1.00
41_T	271_G	0.995	1.00
42_W	186_L	0.994	1.00
145_T	276_L	0.991	1.00
87_L	94_N	0.984	1.00
233_L	237_L	0.979	1.00
144_M	253_M	0.968	1.00
172_F	289_F	0.966	1.00
285_T	289_F	0.960	1.00
37_L	41_T	0.937	1.00
140_W	144_M	0.933	1.00
39_I	43_W	0.926	1.00
230_L	234_Q	0.926	1.00
86_W	91_I	0.918	1.00
60_T	170_V	0.911	0.99
70_L	73_K	0.909	0.99
108_L	111_P	0.902	0.99
195_K	198_P	0.900	0.99
64_F	153_A	0.895	0.99
178_E	272_H	0.895	0.99
86_W	89_W	0.892	0.99
156_L	167_A	0.889	0.99
91_I	95_Y	0.886	0.99
154_W	290_F	0.886	0.99
221_L	225_P	0.880	0.99
194_R	210_M	0.877	0.99
124_L	127_D	0.876	0.99
144_M	147_F	0.871	0.99
196_V	247_F	0.869	0.99
132_L	136_S	0.867	0.99
152_A	286_A	0.860	0.99
113_A	117_I	0.859	0.99
180_N	212_G	0.854	0.99
89_W	92_P	0.851	0.99
87_L	95_Y	0.845	0.99
45_I	48_C	0.842	0.99
215_T	219_A	0.840	0.99
172_F	220_S	0.840	0.99
88_Y	103_F	0.836	0.99
266_G	269_L	0.836	0.99
37_L	40_R	0.834	0.99
180_N	216_I	0.830	0.99
151_H	154_W	0.827	0.99
253_M	276_L	0.824	0.99
183_A	212_G	0.824	0.99
234_Q	238_A	0.820	0.99
121_G	124_L	0.813	0.99
120_T	124_L	0.812	0.99
183_A	187_W	0.809	0.99
88_Y	91_I	0.806	0.99
176_L	239_G	0.804	0.99
147_F	151_H	0.804	0.99
36_T	39_I	0.803	0.99
86_W	99_G	0.798	0.99
87_L	91_I	0.797	0.99
152_A	156_L	0.796	0.99
179_S	183_A	0.793	0.99
61_L	153_A	0.793	0.99
262_V	265_S	0.793	0.99
92_P	95_Y	0.792	0.99
42_W	178_E	0.791	0.99
241_L	292_F	0.788	0.98
59_M	63_F	0.783	0.98
201_S	204_K	0.781	0.98
117_I	120_T	0.781	0.98
178_E	278_R	0.781	0.98
191_C	207_E	0.779	0.98
131_F	140_W	0.777	0.98
244_I	247_F	0.774	0.98
224_G	235_A	0.773	0.98
44_G	47_I	0.771	0.98
69_F	73_K	0.764	0.98
203_G	206_L	0.764	0.98
223_I	227_L	0.759	0.98
123_V	127_D	0.757	0.98
75_Y	276_L	0.753	0.98
76_C	138_I	0.752	0.98
200_V	255_A	0.752	0.98
127_D	246_G	0.749	0.98
144_M	149_L	0.749	0.98
198_P	209_L	0.748	0.98
88_Y	93_L	0.746	0.98
188_G	263_K	0.745	0.98
47_I	50_S	0.740	0.98
40_R	47_I	0.739	0.98
156_L	166_G	0.734	0.98
53_I	170_V	0.734	0.98
130_G	133_H	0.734	0.98
47_I	178_E	0.728	0.97
78_L	256_I	0.722	0.97
98_I	101_N	0.721	0.97
91_I	96_L	0.719	0.97
96_L	101_N	0.716	0.97
109_F	112_L	0.714	0.97
113_A	120_T	0.713	0.97
89_W	96_L	0.713	0.97
177_T	281_S	0.712	0.97
131_F	134_T	0.705	0.97
252_V	255_A	0.703	0.97
89_W	94_N	0.703	0.97
95_Y	99_G	0.698	0.97
183_A	186_L	0.696	0.97
219_A	223_I	0.695	0.97
97_L	101_N	0.695	0.97
244_I	248_C	0.691	0.97
236_L	240_L	0.688	0.96
187_W	205_T	0.686	0.96
48_C	51_M	0.686	0.96
221_L	232_T	0.684	0.96
197_V	251_V	0.681	0.96
192_G	205_T	0.681	0.96
176_L	242_I	0.679	0.96
116_L	119_A	0.678	0.96
217_M	221_L	0.678	0.96
94_N	101_N	0.675	0.96
250_D	263_K	0.674	0.96
94_N	98_I	0.671	0.96
151_H	155_L	0.671	0.96
72_L	75_Y	0.668	0.96
115_F	122_Q	0.667	0.96
54_S	167_A	0.667	0.96
216_I	223_I	0.664	0.96
87_L	98_I	0.664	0.96
95_Y	100_F	0.663	0.96
239_G	243_G	0.661	0.96
87_L	92_P	0.660	0.95
188_G	201_S	0.658	0.95
234_Q	237_L	0.655	0.95
68_S	149_L	0.654	0.95
196_V	205_T	0.648	0.95
89_W	99_G	0.647	0.95
144_M	283_I	0.647	0.95
125_V	129_S	0.646	0.95
63_F	67_I	0.645	0.95
178_E	182_I	0.645	0.95
204_K	263_K	0.642	0.95
87_L	100_F	0.639	0.95
201_S	263_K	0.639	0.95
67_I	149_L	0.637	0.95
48_C	52_V	0.636	0.95
87_L	90_G	0.634	0.94
78_L	253_M	0.633	0.94
92_P	96_L	0.632	0.94
193_R	281_S	0.631	0.94
220_S	235_A	0.631	0.94
45_I	178_E	0.631	0.94
46_V	50_S	0.630	0.94
86_W	92_P	0.630	0.94
121_G	125_V	0.629	0.94
152_A	282_L	0.624	0.94
89_W	95_Y	0.624	0.94
175_A	179_S	0.621	0.94
275_L	279_I	0.619	0.94
94_N	97_L	0.619	0.94
141_G	156_L	0.619	0.94
87_L	97_L	0.616	0.94
105_L	110_I	0.616	0.94
49_F	178_E	0.615	0.93
89_W	97_L	0.613	0.93
210_M	213_V	0.612	0.93
105_L	108_L	0.609	0.93
86_W	102_C	0.609	0.93
96_L	100_F	0.607	0.93
42_W	272_H	0.607	0.93
39_I	42_W	0.603	0.93
177_T	265_S	0.602	0.93
205_T	247_F	0.597	0.92
38_R	265_S	0.591	0.92
39_I	190_S	0.590	0.92
142_W	146_V	0.590	0.92
173_L	282_L	0.589	0.92
70_L	266_G	0.586	0.92
114_G	125_V	0.585	0.92
88_Y	95_Y	0.585	0.92
99_G	103_F	0.583	0.92
178_E	282_L	0.582	0.91
253_M	256_I	0.581	0.91
112_L	116_L	0.580	0.91
141_G	144_M	0.579	0.91
146_V	149_L	0.577	0.91
92_P	98_I	0.576	0.91
209_L	213_V	0.574	0.91
170_V	252_V	0.573	0.91
274_G	277_D	0.573	0.91
92_P	101_N	0.573	0.91
96_L	99_G	0.571	0.91
95_Y	101_N	0.570	0.91
124_L	128_P	0.569	0.91
55_G	58_W	0.568	0.90
268_L	275_L	0.567	0.90
282_L	286_A	0.565	0.90
171_L	175_A	0.564	0.90
72_L	145_T	0.561	0.90
88_Y	100_F	0.560	0.90
41_T	45_I	0.560	0.90
201_S	273_G	0.557	0.90
155_L	290_F	0.557	0.90
123_V	128_P	0.554	0.89
194_R	199_K	0.553	0.89
197_V	203_G	0.552	0.89
89_W	93_L	0.547	0.89
91_I	94_N	0.545	0.89
61_L	65_A	0.543	0.88
87_L	101_N	0.542	0.88
88_Y	94_N	0.541	0.88
91_I	100_F	0.541	0.88
60_T	153_A	0.538	0.88
54_S	179_S	0.538	0.88
177_T	253_M	0.537	0.88
107_L	111_P	0.536	0.88
220_S	224_G	0.533	0.88
173_L	177_T	0.531	0.87
64_F	288_V	0.531	0.87
206_L	266_G	0.529	0.87
188_G	202_P	0.529	0.87
216_I	239_G	0.528	0.87
224_G	232_T	0.528	0.87
246_G	285_T	0.527	0.87
79_I	260_I	0.527	0.87
209_L	243_G	0.525	0.87
58_W	103_F	0.524	0.87
195_K	206_L	0.524	0.87
218_I	233_L	0.524	0.87
182_I	215_T	0.524	0.87
98_I	103_F	0.524	0.87
273_G	277_D	0.523	0.87
91_I	99_G	0.522	0.86
204_K	208_G	0.522	0.86
223_I	226_L	0.522	0.86
73_K	268_L	0.521	0.86
263_K	273_G	0.521	0.86
112_L	117_I	0.520	0.86
57_R	156_L	0.519	0.86
266_G	287_P	0.519	0.86
119_A	122_Q	0.517	0.86
207_E	272_H	0.516	0.86
95_Y	103_F	0.516	0.86
77_T	81_V	0.515	0.86
152_A	174_L	0.514	0.86
241_L	288_V	0.513	0.86
46_V	186_L	0.512	0.85
116_L	121_G	0.511	0.85
123_V	126_G	0.510	0.85
204_K	273_G	0.510	0.85
44_G	48_C	0.510	0.85
183_A	219_A	0.510	0.85
49_F	53_I	0.508	0.85
90_G	93_L	0.507	0.85
90_G	97_L	0.506	0.85
188_G	204_K	0.506	0.85
276_L	279_I	0.505	0.85
49_F	279_I	0.502	0.84
100_F	103_F	0.502	0.84
42_W	45_I	0.501	0.84
98_I	102_C	0.501	0.84
178_E	184_Q	0.500	0.84

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
4q2eA	2	0.849	100	0.209	Contact Map
2wswA	3	0.2819	9.5	0.965	Contact Map
3oufA	4	0.1275	5.5	0.969	Contact Map
2k1kA	2	0.1275	2.7	0.973	Contact Map
2q67A	3	0.094	2.5	0.974	Contact Map
2kogA	1	0.1946	2.2	0.975	Contact Map
3hd6A	3	0.8725	2.1	0.975	Contact Map
2mpnA	2	0.198	2	0.975	Contact Map
4ev6A	3	0.2584	1.8	0.976	Contact Map
4huqS	1	0.5168	1.8	0.976	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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