YCEB - BACSU - GREMLIN Contacts

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YCEB - Uncharacterized protein YceB

UniProt:	O34504	Sequences: MIHLSILDQAPVSKGESPVTTLQHSVELAQLSEQWGYKRYWFAEHHSTKGLASTAPEIMIARIAAQTNTIRVGSGGVLLPQYSPFKVAETFRQLEALYPNRIDLGVGRSPGGTTKTRLALTDGVKKSLTEFNRQLQDVSYFLTDSLPPDHPYAGIKAAPLIGTAPELWVLGLGENSARRAAHQGIGYVFGHFINPERGENAFRIYRESFRPSAHFSNPSALFTIFVICAKTDEEAEELALSQDLWLLRVGKGLDSRVPSIEEAKAHPYTASDKKLIEENRKRMVIGSPTTVKQQLLDLTGCYETNEIMVLCNVFDFEAKKESYERLAELFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	331 (286)
Sequences:	16496 (10429)
Seq/√Len:	616.7

ECOLI - YHBW RUTA SSUD
BACSU - YCEB YWCH YTMO YDDN YVBT SSUD YXEK MOXC
HALSA - Q9HQZ9
SULSO - Q97Y17

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
232_D	290_T	5.149	1.00
30_Q	66_Q	3.342	1.00
149_D	154_G	3.271	1.00
71_R	103_D	2.773	1.00
232_D	287_S	2.716	1.00
132_N	182_H	2.632	1.00
294_Q	297_D	2.535	1.00
33_E	69_T	2.531	1.00
31_L	34_Q	2.524	1.00
178_R	208_S	2.478	1.00
203_R	207_E	2.473	1.00
64_A	98_Y	2.471	1.00
232_D	236_E	2.418	1.00
231_T	234_E	2.355	1.00
60_I	72_V	2.347	1.00
287_S	290_T	2.259	1.00
229_A	234_E	2.257	1.00
136_Q	183_Q	2.251	1.00
296_L	300_G	2.229	1.00
202_F	206_R	2.188	1.00
177_A	204_I	2.166	1.00
207_E	211_P	2.166	1.00
129_T	151_P	2.140	1.00
23_Q	99_P	2.101	1.00
202_F	220_A	2.076	1.00
209_F	218_P	2.058	1.00
30_Q	34_Q	2.051	1.00
26_V	30_Q	2.036	1.00
199_E	203_R	2.024	1.00
204_I	208_S	2.003	1.00
29_A	63_I	1.999	1.00
233_E	237_E	1.948	1.00
143_T	164_A	1.916	1.00
40_Y	70_I	1.904	1.00
123_G	126_K	1.896	1.00
95_E	100_N	1.886	1.00
27_E	30_Q	1.879	1.00
91_F	102_I	1.872	1.00
284_V	291_V	1.863	1.00
41_W	73_G	1.847	1.00
55_A	90_T	1.808	1.00
114_T	118_L	1.801	1.00
64_A	72_V	1.795	1.00
26_V	66_Q	1.787	1.00
181_A	208_S	1.786	1.00
240_L	244_L	1.743	1.00
139_S	164_A	1.700	1.00
126_K	151_P	1.663	1.00
31_L	35_W	1.646	1.00
208_S	211_P	1.620	1.00
171_G	187_Y	1.611	1.00
91_F	104_L	1.605	1.00
178_R	211_P	1.603	1.00
63_I	72_V	1.600	1.00
29_A	40_Y	1.594	1.00
290_T	293_Q	1.579	1.00
204_I	207_E	1.560	1.00
228_C	291_V	1.544	1.00
200_N	203_R	1.529	1.00
274_K	277_E	1.526	1.00
289_T	293_Q	1.519	1.00
136_Q	140_Y	1.511	1.00
129_T	152_Y	1.510	1.00
139_S	183_Q	1.492	1.00
17_S	20_T	1.459	1.00
292_K	296_L	1.440	1.00
33_E	67_T	1.411	1.00
29_A	67_T	1.403	1.00
26_V	62_R	1.401	1.00
34_Q	68_N	1.398	1.00
178_R	182_H	1.394	1.00
296_L	299_T	1.385	1.00
62_R	65_A	1.384	1.00
139_S	167_L	1.367	1.00
234_E	238_L	1.356	1.00
62_R	97_L	1.346	1.00
222_F	304_T	1.318	1.00
23_Q	27_E	1.316	1.00
20_T	24_H	1.315	1.00
132_N	183_Q	1.303	1.00
293_Q	297_D	1.301	1.00
290_T	294_Q	1.299	1.00
55_A	58_I	1.297	1.00
136_Q	148_P	1.296	1.00
42_F	60_I	1.290	1.00
82_Y	90_T	1.288	1.00
126_K	129_T	1.287	1.00
140_Y	145_S	1.277	1.00
140_Y	144_D	1.273	1.00
228_C	288_P	1.271	1.00
174_E	204_I	1.266	1.00
229_A	235_A	1.261	1.00
168_W	221_L	1.243	1.00
261_E	264_K	1.228	1.00
227_I	238_L	1.226	1.00
27_E	31_L	1.225	1.00
297_D	300_G	1.224	1.00
178_R	204_I	1.202	1.00
87_V	134_Q	1.199	1.00
237_E	240_L	1.194	1.00
168_W	186_G	1.191	1.00
219_S	305_N	1.190	1.00
209_F	214_H	1.188	1.00
33_E	68_N	1.187	1.00
234_E	237_E	1.186	1.00
132_N	136_Q	1.178	1.00
60_I	74_S	1.173	1.00
139_S	185_I	1.168	1.00
239_A	243_D	1.158	1.00
73_G	103_D	1.157	1.00
135_L	183_Q	1.155	1.00
29_A	70_I	1.153	1.00
137_D	148_P	1.145	1.00
126_K	152_Y	1.143	1.00
237_E	241_S	1.129	1.00
286_G	291_V	1.127	1.00
94_L	102_I	1.125	1.00
182_H	212_S	1.124	1.00
157_A	160_L	1.124	1.00
197_R	200_N	1.121	1.00
272_D	275_L	1.120	1.00
104_L	138_V	1.119	1.00
140_Y	148_P	1.115	1.00
138_V	142_L	1.114	1.00
42_F	63_I	1.113	1.00
111_G	116_T	1.112	1.00
77_V	87_V	1.110	1.00
175_N	178_R	1.108	1.00
236_E	240_L	1.102	1.00
259_S	262_E	1.101	1.00
95_E	162_G	1.092	1.00
181_A	212_S	1.090	1.00
58_I	61_A	1.085	1.00
112_G	116_T	1.082	1.00
54_T	93_Q	1.080	1.00
57_E	90_T	1.080	1.00
178_R	212_S	1.079	1.00
137_D	153_A	1.075	1.00
230_K	234_E	1.074	1.00
76_G	170_L	1.073	1.00
161_I	164_A	1.071	1.00
199_E	302_Y	1.068	1.00
24_H	27_E	1.067	1.00
76_G	107_G	1.062	1.00
106_V	135_L	1.059	1.00
208_S	212_S	1.041	1.00
27_E	316_F	1.039	1.00
226_V	309_V	1.038	1.00
86_K	90_T	1.031	1.00
233_E	236_E	1.029	1.00
157_A	161_I	1.026	1.00
62_R	66_Q	1.021	1.00
195_P	297_D	1.017	1.00
30_Q	68_N	1.015	1.00
139_S	143_T	1.012	1.00
284_V	294_Q	1.012	1.00
24_H	316_F	1.008	1.00
275_L	278_E	1.007	1.00
194_N	197_R	1.003	1.00
219_S	306_E	0.999	1.00
158_A	161_I	0.989	1.00
57_E	77_V	0.985	1.00
58_I	94_L	0.978	1.00
180_A	187_Y	0.965	1.00
200_N	204_I	0.963	1.00
130_E	133_R	0.957	1.00
137_D	140_Y	0.955	1.00
39_R	73_G	0.954	1.00
132_N	179_R	0.952	1.00
129_T	175_N	0.951	1.00
224_I	284_V	0.950	1.00
179_R	183_Q	0.939	1.00
19_V	23_Q	0.933	1.00
126_K	130_E	0.933	1.00
133_R	151_P	0.930	1.00
239_A	285_I	0.930	1.00
133_R	150_H	0.923	1.00
229_A	238_L	0.920	1.00
241_S	244_L	0.919	1.00
95_E	163_T	0.914	1.00
247_L	250_G	0.914	1.00
188_V	221_L	0.909	1.00
272_D	277_E	0.906	1.00
274_K	278_E	0.906	1.00
195_P	199_E	0.905	1.00
177_A	208_S	0.895	1.00
113_T	116_T	0.893	1.00
258_P	262_E	0.891	1.00
148_P	153_A	0.889	1.00
22_L	97_L	0.886	1.00
27_E	34_Q	0.885	1.00
148_P	151_P	0.883	1.00
140_Y	146_L	0.882	1.00
150_H	153_A	0.880	1.00
23_Q	26_V	0.876	1.00
272_D	276_I	0.874	1.00
130_E	134_Q	0.871	1.00
257_V	260_I	0.866	1.00
206_R	220_A	0.866	1.00
84_P	137_D	0.852	1.00
231_T	235_A	0.845	1.00
95_E	164_A	0.842	1.00
224_I	295_L	0.842	1.00
61_A	65_A	0.833	1.00
133_R	137_D	0.830	1.00
39_R	306_E	0.826	1.00
293_Q	296_L	0.822	1.00
134_Q	138_V	0.821	1.00
64_A	102_I	0.821	1.00
169_V	180_A	0.819	1.00
245_W	248_R	0.815	1.00
177_A	181_A	0.812	1.00
187_Y	205_Y	0.810	1.00
79_L	134_Q	0.809	1.00
240_L	243_D	0.805	1.00
115_K	118_L	0.804	1.00
142_L	165_P	0.802	1.00
209_F	215_F	0.800	1.00
209_F	212_S	0.793	1.00
212_S	215_F	0.792	1.00
260_I	264_K	0.791	1.00
273_K	277_E	0.790	1.00
262_E	271_S	0.790	1.00
96_A	163_T	0.790	1.00
236_E	239_A	0.789	1.00
65_A	98_Y	0.787	1.00
21_T	24_H	0.786	1.00
60_I	64_A	0.786	1.00
205_Y	209_F	0.784	1.00
79_L	87_V	0.777	1.00
236_E	280_R	0.776	1.00
258_P	261_E	0.760	1.00
60_I	94_L	0.753	1.00
60_I	102_I	0.747	1.00
202_F	205_Y	0.746	1.00
260_I	263_A	0.746	1.00
132_N	175_N	0.743	1.00
22_L	62_R	0.743	1.00
103_D	168_W	0.741	1.00
169_V	176_S	0.741	1.00
174_E	178_R	0.741	1.00
238_L	241_S	0.740	1.00
244_L	248_R	0.740	1.00
169_V	184_G	0.738	1.00
64_A	94_L	0.736	1.00
257_V	263_A	0.736	1.00
252_G	258_P	0.735	1.00
203_R	303_E	0.735	1.00
95_E	161_I	0.734	1.00
41_W	75_G	0.732	1.00
141_F	146_L	0.729	1.00
264_K	271_S	0.728	1.00
133_R	152_Y	0.728	1.00
177_A	187_Y	0.727	1.00
209_F	216_S	0.723	1.00
182_H	208_S	0.722	1.00
117_R	121_T	0.720	1.00
174_E	208_S	0.719	1.00
257_V	261_E	0.715	1.00
247_L	251_K	0.714	1.00
205_Y	218_P	0.714	1.00
209_F	217_N	0.709	1.00
189_F	201_A	0.709	1.00
241_S	245_W	0.709	1.00
108_R	127_S	0.708	1.00
87_V	138_V	0.708	1.00
44_E	82_Y	0.704	1.00
24_H	28_L	0.701	1.00
128_L	175_N	0.700	1.00
84_P	134_Q	0.699	1.00
149_D	152_Y	0.698	1.00
178_R	207_E	0.697	1.00
221_L	306_E	0.697	1.00
26_V	63_I	0.695	1.00
46_H	89_E	0.694	1.00
140_Y	143_T	0.694	1.00
83_S	86_K	0.693	1.00
155_I	158_A	0.693	1.00
206_R	209_F	0.692	1.00
91_F	142_L	0.692	1.00
220_A	304_T	0.688	1.00
125_K	175_N	0.687	1.00
74_S	102_I	0.683	1.00
26_V	65_A	0.683	1.00
38_K	69_T	0.682	1.00
202_F	302_Y	0.680	1.00
133_R	148_P	0.678	1.00
71_R	166_E	0.677	1.00
39_R	308_M	0.674	1.00
42_F	59_M	0.670	1.00
136_Q	182_H	0.670	1.00
82_Y	86_K	0.668	1.00
92_R	155_I	0.667	1.00
263_A	271_S	0.659	1.00
171_G	176_S	0.657	1.00
73_G	168_W	0.655	1.00
61_A	98_Y	0.653	1.00
156_K	160_L	0.652	1.00
257_V	264_K	0.650	1.00
57_E	91_F	0.649	1.00
61_A	94_L	0.648	1.00
273_K	276_I	0.648	1.00
23_Q	65_A	0.647	1.00
108_R	131_F	0.647	1.00
130_E	153_A	0.647	1.00
77_V	91_F	0.645	1.00
99_P	160_L	0.644	1.00
206_R	305_N	0.643	1.00
206_R	210_R	0.639	1.00
245_W	249_V	0.638	1.00
299_T	304_T	0.638	1.00
232_D	235_A	0.635	1.00
259_S	263_A	0.635	1.00
196_E	199_E	0.634	1.00
236_E	285_I	0.634	1.00
133_R	136_Q	0.633	1.00
122_D	130_E	0.631	1.00
78_L	111_G	0.628	1.00
18_P	21_T	0.627	1.00
136_Q	139_S	0.626	1.00
169_V	179_R	0.625	1.00
118_L	121_T	0.625	1.00
295_L	307_I	0.623	1.00
230_K	288_P	0.622	1.00
23_Q	68_N	0.621	1.00
243_D	246_L	0.618	1.00
22_L	26_V	0.617	1.00
32_S	70_I	0.616	1.00
38_K	71_R	0.614	1.00
92_R	157_A	0.613	1.00
67_T	101_R	0.607	1.00
282_R	294_Q	0.606	1.00
182_H	211_P	0.606	1.00
289_T	292_K	0.605	1.00
294_Q	298_L	0.605	1.00
156_K	161_I	0.600	1.00
215_F	218_P	0.597	1.00
271_S	274_K	0.597	1.00
85_F	141_F	0.595	1.00
40_Y	63_I	0.593	1.00
62_R	98_Y	0.592	1.00
82_Y	87_V	0.590	1.00
20_T	23_Q	0.590	1.00
106_V	138_V	0.589	1.00
95_E	98_Y	0.589	1.00
26_V	29_A	0.589	1.00
33_E	70_I	0.588	1.00
175_N	179_R	0.587	1.00
59_M	93_Q	0.586	1.00
248_R	251_K	0.586	1.00
226_V	284_V	0.585	1.00
174_E	200_N	0.585	1.00
72_V	98_Y	0.582	1.00
211_P	215_F	0.581	1.00
206_R	303_E	0.581	1.00
92_R	142_L	0.581	1.00
223_T	308_M	0.578	1.00
114_T	117_R	0.577	1.00
207_E	210_R	0.575	1.00
177_A	205_Y	0.574	1.00
111_G	117_R	0.573	1.00
246_L	249_V	0.572	1.00
272_D	278_E	0.571	1.00
56_P	74_S	0.570	1.00
156_K	159_P	0.569	1.00
58_I	90_T	0.568	1.00
235_A	239_A	0.567	1.00
197_R	201_A	0.566	1.00
231_T	237_E	0.564	1.00
105_G	170_L	0.563	1.00
295_L	309_V	0.562	1.00
88_A	142_L	0.560	1.00
168_W	306_E	0.558	1.00
75_G	188_V	0.556	1.00
160_L	163_T	0.556	1.00
225_F	310_L	0.555	1.00
95_E	165_P	0.555	1.00
271_S	276_I	0.554	1.00
172_L	191_H	0.554	1.00
288_P	292_K	0.553	1.00
172_L	201_A	0.553	1.00
112_G	117_R	0.546	0.99
228_C	287_S	0.546	0.99
217_N	305_N	0.545	0.99
166_E	219_S	0.544	0.99
181_A	209_F	0.544	0.99
198_G	201_A	0.543	0.99
206_R	216_S	0.543	0.99
25_S	28_L	0.543	0.99
106_V	167_L	0.540	0.99
298_L	302_Y	0.540	0.99
135_L	169_V	0.539	0.99
112_G	115_K	0.539	0.99
113_T	117_R	0.538	0.99
203_R	206_R	0.534	0.99
155_I	160_L	0.533	0.99
143_T	146_L	0.533	0.99
67_T	70_I	0.531	0.99
84_P	138_V	0.531	0.99
79_L	106_V	0.531	0.99
168_W	219_S	0.531	0.99
243_D	248_R	0.530	0.99
259_S	264_K	0.529	0.99
111_G	121_T	0.528	0.99
227_I	239_A	0.528	0.99
246_L	250_G	0.527	0.99
27_E	317_E	0.527	0.99
258_P	271_S	0.526	0.99
148_P	154_G	0.525	0.99
195_P	302_Y	0.523	0.99
172_L	190_G	0.520	0.99
196_E	200_N	0.519	0.99
273_K	278_E	0.519	0.99
61_A	64_A	0.516	0.99
244_L	247_L	0.515	0.99
92_R	96_A	0.515	0.99
84_P	153_A	0.513	0.99
206_R	217_N	0.511	0.99
98_Y	102_I	0.511	0.99
131_F	169_V	0.510	0.99
176_S	179_R	0.509	0.99
242_Q	247_L	0.508	0.99
114_T	121_T	0.508	0.99
127_S	130_E	0.503	0.99
58_I	97_L	0.502	0.99
205_Y	220_A	0.502	0.99
179_R	182_H	0.502	0.99
74_S	77_V	0.501	0.99
111_G	119_A	0.500	0.99

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
1lucA	1	0.9396	100	0.201	Contact Map
4us5A	3	0.9668	100	0.202	Contact Map
2wgkA	2	0.9728	100	0.205	Contact Map
1lucB	1	0.9426	100	0.206	Contact Map
2i7gA	2	0.9637	100	0.229	Contact Map
1rhcA	2	0.9305	100	0.247	Contact Map
3raoA	2	0.9607	100	0.249	Contact Map
1z69A	4	0.9366	100	0.251	Contact Map
1ezwA	3	0.9366	100	0.252	Contact Map
3b9oA	2	0.9728	100	0.258	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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