YBEQ - ECOLI - GREMLIN Contacts

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YBEQ - Uncharacterized protein YbeQ

UniProt:	P77234	Sequences: MIFTSSCCDNLSIDEIIERAEKGDCEAQYIVGFYYNRDSAIDSPDDEKAFYWLKLAAEQGHCEAQYSLGQKYTEDKSRHKDNEQAIFWLKKAALQGHTFASNALGWTLDRGEAPNYKEAVVWYQIAAESGMSYAQNNLGWMYRNGNGVAKDYALAFFWYKQAALQGHSDAQNNLADLYEDGKGVAQNKTLAAFWYLKSAQQGNRHAQFQIAWDYNAGEGVDQDYKQAMYWYLKAAAQGSVGAYVNIGYMYKHGQGVEKDYQAAFEWFTKAAECNDATAWYNLAIMYHYGEGRPVDLRQALDLYRKVQSSGTRDVSQEIRETEDLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13647
Length:	325 (254)
Sequences:	13374 (11915)
Seq/√Len:	747.6

ECOLI - YBEQ HEMY LPSRP YJCO PGAA NLPI YPHG
BACSU - YVCD YPIA RAPB RAPE RAPG RAPJ RAPH RAPA RAPF RAPK RAPI RAPD RAPC
SULSO - Q97VC4 Q97WM3 Q97V36 Q97ZS3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_D	84_Q	3.691	1.00
295_D	298_Q	3.637	1.00
259_D	262_A	3.628	1.00
151_D	154_L	3.599	1.00
223_D	226_Q	3.533	1.00
187_N	190_L	3.530	1.00
115_N	118_E	3.414	1.00
45_D	48_K	3.263	1.00
211_A	231_Y	2.356	1.00
37_R	53_L	2.288	1.00
139_G	159_Y	2.241	1.00
69_G	89_L	2.221	1.00
54_K	68_L	2.142	1.00
53_L	67_S	2.131	1.00
65_Q	88_W	2.125	1.00
243_Y	266_W	2.120	1.00
207_Q	230_W	2.102	1.00
247_G	267_F	2.088	1.00
174_L	194_W	2.082	1.00
175_A	195_Y	2.041	1.00
105_G	123_Y	2.021	1.00
68_L	88_W	2.018	1.00
283_A	303_Y	2.012	1.00
138_L	158_W	2.008	1.00
90_K	104_L	1.978	1.00
124_Q	138_L	1.946	1.00
123_Y	137_N	1.862	1.00
171_Q	194_W	1.834	1.00
246_I	266_W	1.825	1.00
101_S	122_W	1.795	1.00
89_L	103_A	1.777	1.00
210_I	230_W	1.745	1.00
279_W	302_L	1.715	1.00
104_L	122_W	1.665	1.00
196_L	210_I	1.663	1.00
135_Q	158_W	1.648	1.00
210_I	214_Y	1.638	1.00
160_K	174_L	1.632	1.00
195_Y	209_Q	1.597	1.00
232_L	246_I	1.595	1.00
68_L	72_Y	1.593	1.00
264_F	268_T	1.567	1.00
174_L	178_Y	1.543	1.00
192_A	196_L	1.518	1.00
159_Y	173_N	1.506	1.00
268_T	282_L	1.488	1.00
231_Y	245_N	1.403	1.00
50_F	71_K	1.391	1.00
178_Y	190_L	1.385	1.00
104_L	108_L	1.384	1.00
228_M	232_L	1.383	1.00
246_I	250_Y	1.367	1.00
282_L	286_Y	1.362	1.00
50_F	54_K	1.362	1.00
50_F	72_Y	1.343	1.00
282_L	302_L	1.339	1.00
72_Y	84_Q	1.334	1.00
250_Y	262_A	1.313	1.00
228_M	249_M	1.310	1.00
142_Y	154_L	1.302	1.00
72_Y	88_W	1.302	1.00
40_A	52_W	1.298	1.00
214_Y	223_D	1.277	1.00
72_Y	81_D	1.265	1.00
86_I	107_T	1.255	1.00
267_F	281_N	1.254	1.00
192_A	213_D	1.253	1.00
120_V	141_M	1.244	1.00
244_V	281_N	1.235	1.00
117_K	145_G	1.233	1.00
251_K	267_F	1.225	1.00
40_A	45_D	1.224	1.00
120_V	124_Q	1.222	1.00
233_K	236_A	1.209	1.00
198_S	206_A	1.208	1.00
36_N	52_W	1.199	1.00
156_F	160_K	1.194	1.00
142_Y	158_W	1.184	1.00
145_G	151_D	1.183	1.00
37_R	56_A	1.178	1.00
214_Y	226_Q	1.177	1.00
108_L	118_E	1.174	1.00
36_N	40_A	1.172	1.00
40_A	48_K	1.165	1.00
138_L	142_Y	1.163	1.00
190_L	193_F	1.154	1.00
142_Y	151_D	1.149	1.00
203_N	206_A	1.148	1.00
86_I	90_K	1.138	1.00
192_A	210_I	1.138	1.00
120_V	138_L	1.135	1.00
47_E	79_H	1.135	1.00
300_L	304_R	1.133	1.00
286_Y	298_Q	1.131	1.00
33_F	52_W	1.130	1.00
269_K	272_E	1.130	1.00
192_A	221_D	1.125	1.00
120_V	142_Y	1.124	1.00
250_Y	259_D	1.118	1.00
228_M	257_E	1.108	1.00
172_N	209_Q	1.106	1.00
153_A	185_A	1.105	1.00
162_A	170_A	1.101	1.00
192_A	214_Y	1.100	1.00
69_G	92_A	1.098	1.00
197_K	200_Q	1.094	1.00
108_L	115_N	1.094	1.00
248_Y	267_F	1.091	1.00
286_Y	302_L	1.089	1.00
97_H	100_A	1.088	1.00
208_F	245_N	1.084	1.00
108_L	122_W	1.081	1.00
211_A	234_A	1.081	1.00
111_G	115_N	1.075	1.00
161_Q	164_L	1.072	1.00
126_A	134_A	1.070	1.00
57_A	65_Q	1.068	1.00
283_A	306_V	1.065	1.00
264_F	285_M	1.064	1.00
175_A	198_S	1.062	1.00
156_F	177_L	1.055	1.00
65_Q	91_K	1.054	1.00
247_G	270_A	1.047	1.00
139_G	162_A	1.047	1.00
38_D	67_S	1.032	1.00
91_K	94_L	1.028	1.00
127_A	134_A	1.028	1.00
270_A	278_A	1.022	1.00
264_F	282_L	1.021	1.00
33_F	56_A	1.015	1.00
239_S	242_A	1.015	1.00
50_F	79_H	1.010	1.00
136_N	173_N	1.010	1.00
264_F	286_Y	1.008	1.00
50_F	68_L	1.008	1.00
92_A	100_A	1.007	1.00
212_W	245_N	1.004	1.00
261_Q	289_G	1.003	1.00
61_H	64_A	0.999	1.00
235_A	242_A	0.994	1.00
305_K	308_S	0.993	1.00
178_Y	187_N	0.992	1.00
101_S	125_I	0.990	1.00
212_W	231_Y	0.985	1.00
57_A	64_A	0.981	1.00
66_Y	70_Q	0.978	1.00
154_L	157_F	0.977	1.00
83_E	111_G	0.973	1.00
132_S	162_A	0.971	1.00
135_Q	162_A	0.964	1.00
178_Y	194_W	0.963	1.00
207_Q	234_A	0.959	1.00
286_Y	295_D	0.947	1.00
93_A	101_S	0.947	1.00
86_I	111_G	0.945	1.00
215_N	231_Y	0.944	1.00
289_G	295_D	0.940	1.00
226_Q	229_Y	0.940	1.00
41_I	53_L	0.939	1.00
287_H	303_Y	0.938	1.00
56_A	64_A	0.938	1.00
275_D	278_A	0.935	1.00
262_A	265_E	0.933	1.00
199_A	207_Q	0.930	1.00
101_S	126_A	0.929	1.00
250_Y	266_W	0.929	1.00
271_A	279_W	0.927	1.00
156_F	174_L	0.927	1.00
244_V	248_Y	0.927	1.00
214_Y	230_W	0.925	1.00
199_A	206_A	0.924	1.00
298_Q	301_D	0.923	1.00
125_I	128_E	0.919	1.00
84_Q	87_F	0.917	1.00
41_I	71_K	0.916	1.00
225_K	257_E	0.911	1.00
86_I	104_L	0.910	1.00
131_M	134_A	0.910	1.00
140_W	159_Y	0.908	1.00
156_F	185_A	0.902	1.00
176_D	195_Y	0.901	1.00
118_E	121_V	0.896	1.00
264_F	289_G	0.896	1.00
102_N	137_N	0.896	1.00
248_Y	281_N	0.894	1.00
271_A	278_A	0.891	1.00
156_F	178_Y	0.888	1.00
235_A	243_Y	0.888	1.00
39_S	43_S	0.887	1.00
93_A	100_A	0.886	1.00
171_Q	198_S	0.885	1.00
65_Q	92_A	0.883	1.00
167_H	170_A	0.878	1.00
86_I	108_L	0.878	1.00
55_L	58_E	0.873	1.00
281_N	284_I	0.872	1.00
280_Y	284_I	0.871	1.00
62_C	92_A	0.869	1.00
228_M	246_I	0.868	1.00
135_Q	161_Q	0.867	1.00
251_K	281_N	0.863	1.00
73_T	89_L	0.856	1.00
136_N	170_A	0.852	1.00
240_V	270_A	0.845	1.00
107_T	111_G	0.841	1.00
46_D	71_K	0.836	1.00
172_N	206_A	0.835	1.00
37_R	49_A	0.835	1.00
171_Q	197_K	0.832	1.00
168_S	198_S	0.832	1.00
228_M	250_Y	0.829	1.00
179_E	195_Y	0.829	1.00
105_G	119_A	0.825	1.00
139_G	158_W	0.818	1.00
70_Q	103_A	0.808	1.00
120_V	145_G	0.804	1.00
269_K	273_C	0.803	1.00
82_N	107_T	0.798	1.00
161_Q	165_Q	0.798	1.00
260_Y	285_M	0.797	1.00
243_Y	269_K	0.796	1.00
66_Y	103_A	0.794	1.00
176_D	209_Q	0.793	1.00
52_W	56_A	0.792	1.00
196_L	226_Q	0.791	1.00
208_F	212_W	0.790	1.00
194_W	198_S	0.790	1.00
249_M	257_E	0.787	1.00
71_K	79_H	0.785	1.00
233_K	237_Q	0.783	1.00
141_M	145_G	0.781	1.00
268_T	298_Q	0.778	1.00
247_G	266_W	0.777	1.00
163_A	171_Q	0.763	1.00
215_N	249_M	0.762	1.00
245_N	248_Y	0.757	1.00
127_A	135_Q	0.754	1.00
204_R	234_A	0.751	1.00
105_G	126_A	0.750	1.00
211_A	227_A	0.749	1.00
41_I	46_D	0.748	1.00
92_A	95_Q	0.743	1.00
177_L	185_A	0.734	1.00
270_A	273_C	0.732	1.00
73_T	107_T	0.730	1.00
213_D	221_D	0.729	1.00
52_W	55_L	0.725	1.00
251_K	285_M	0.725	1.00
109_D	137_N	0.721	1.00
264_F	295_D	0.721	1.00
234_A	237_Q	0.719	1.00
175_A	191_A	0.718	1.00
160_K	190_L	0.716	1.00
105_G	122_W	0.711	1.00
106_W	137_N	0.708	1.00
69_G	85_A	0.705	1.00
207_Q	233_K	0.703	1.00
66_Y	100_A	0.702	1.00
109_D	141_M	0.701	1.00
247_G	263_A	0.701	1.00
234_A	242_A	0.698	1.00
135_Q	165_Q	0.697	1.00
179_E	213_D	0.696	1.00
189_T	221_D	0.695	1.00
116_Y	141_M	0.692	1.00
152_Y	177_L	0.691	1.00
140_W	173_N	0.686	1.00
98_T	126_A	0.684	1.00
279_W	305_K	0.680	1.00
158_W	162_A	0.677	1.00
54_K	84_Q	0.669	1.00
208_F	242_A	0.666	1.00
139_G	155_A	0.664	1.00
188_K	192_A	0.661	1.00
232_L	262_A	0.661	1.00
41_I	67_S	0.661	1.00
38_D	53_L	0.661	1.00
136_N	140_W	0.661	1.00
66_Y	97_H	0.659	1.00
248_Y	251_K	0.659	1.00
85_A	89_L	0.651	1.00
193_F	197_K	0.651	1.00
64_A	67_S	0.649	1.00
127_A	138_L	0.648	1.00
91_K	95_Q	0.647	1.00
143_R	159_Y	0.645	1.00
243_Y	270_A	0.644	1.00
232_L	236_A	0.643	1.00
163_A	174_L	0.642	1.00
163_A	170_A	0.639	1.00
266_W	269_K	0.638	1.00
106_W	110_R	0.636	1.00
301_D	305_K	0.636	1.00
230_W	234_A	0.635	1.00
88_W	92_A	0.631	1.00
121_V	125_I	0.631	1.00
215_N	252_H	0.627	1.00
268_T	272_E	0.624	1.00
33_F	55_L	0.623	1.00
34_Y	38_D	0.623	1.00
209_Q	212_W	0.622	1.00
173_N	176_D	0.619	1.00
82_N	86_I	0.618	1.00
73_T	103_A	0.612	1.00
248_Y	252_H	0.610	1.00
224_Y	249_M	0.608	1.00
211_A	230_W	0.607	1.00
70_Q	74_E	0.606	1.00
109_D	123_Y	0.605	1.00
196_L	214_Y	0.605	1.00
57_A	68_L	0.604	1.00
283_A	299_A	0.604	1.00
48_K	51_Y	0.602	1.00
196_L	200_Q	0.602	1.00
260_Y	289_G	0.596	1.00
162_A	165_Q	0.595	1.00
122_W	125_I	0.594	1.00
244_V	278_A	0.591	1.00
119_A	141_M	0.587	1.00
49_A	71_K	0.585	1.00
160_K	164_L	0.583	1.00
157_F	161_Q	0.581	1.00
102_N	106_W	0.575	1.00
49_A	56_A	0.570	1.00
102_N	134_A	0.563	1.00
244_V	270_A	0.562	1.00
136_N	162_A	0.560	1.00
131_M	135_Q	0.560	1.00
61_H	65_Q	0.559	1.00
49_A	53_L	0.559	1.00
143_R	152_Y	0.559	1.00
278_A	281_N	0.558	1.00
230_W	233_K	0.556	1.00
251_K	288_Y	0.556	1.00
67_S	70_Q	0.555	1.00
172_N	203_N	0.555	1.00
143_R	177_L	0.555	1.00
109_D	116_Y	0.553	1.00
296_L	300_L	0.553	1.00
285_M	289_G	0.550	1.00
215_N	227_A	0.550	1.00
267_F	285_M	0.548	1.00
304_R	308_S	0.547	1.00
120_V	151_D	0.547	1.00
283_A	302_L	0.546	1.00
62_C	69_G	0.545	1.00
106_W	123_Y	0.545	1.00
36_N	39_S	0.544	1.00
93_A	104_L	0.543	1.00
37_R	41_I	0.543	1.00
224_Y	252_H	0.542	1.00
164_L	200_Q	0.539	1.00
53_L	68_L	0.538	1.00
122_W	126_A	0.537	1.00
86_I	93_A	0.537	1.00
124_Q	128_E	0.536	1.00
208_F	234_A	0.535	1.00
51_Y	55_L	0.531	1.00
284_I	303_Y	0.528	1.00
66_Y	92_A	0.528	1.00
73_T	82_N	0.527	1.00
90_K	118_E	0.526	1.00
179_E	216_A	0.525	1.00
157_F	160_K	0.524	1.00
302_L	305_K	0.523	1.00
211_A	245_N	0.523	1.00
37_R	52_W	0.522	1.00
54_K	58_E	0.520	1.00
188_K	213_D	0.520	1.00
203_N	239_S	0.515	1.00
229_Y	233_K	0.511	1.00
106_W	109_D	0.511	1.00
175_A	194_W	0.510	1.00
279_W	306_V	0.510	1.00
305_K	309_S	0.510	1.00
280_Y	283_A	0.509	1.00
137_N	140_W	0.509	1.00
275_D	279_W	0.503	1.00
102_N	131_M	0.502	1.00
265_E	269_K	0.502	1.00
70_Q	89_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
1ouvA	1	0.7969	100	0.284	Contact Map
3e4bA	1	0.9415	100	0.297	Contact Map
4bwrA	1	0.9877	100	0.299	Contact Map
4ui9J	2	0.9169	100	0.308	Contact Map
4ui9C	2	0.9138	100	0.309	Contact Map
1w3bA	2	0.9108	100	0.314	Contact Map
4jsnB	1	0.8	100	0.326	Contact Map
2xpiA	2	0.9046	100	0.328	Contact Map
4rg9A	2	0.7508	100	0.345	Contact Map
4ui9F	2	0.9108	100	0.348	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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