Q9HNZ3 - HALSA - GREMLIN Contacts

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Q9HNZ3 - Thiamin-binding periplasmic protein homolog

UniProt:	Q9HNZ3	Sequences: MTSRRRFVAAVGSATAASLGLAGCVGDRETTTATEETTTTTEGTTTTTGGTTATQQGTPPRLRMGASETYVNAVSTSAGNWVKDAVQSEYTVDFDWVVAENGVTEFMRRAQQGVDLGADGYVGVTAADLARADRELSAPLFAAFDTDAVDNTDNVHDRFWIDGTDRMLPTGASYVTIIYDETVVDAPETLAALTTDEYSDGILVPNPQNTATGLAFVLWTVDAFGEDGFLEYWRRLADNGLQTAGSWNATYSAYSGGEAPMVMSYSTDQVYASQDPDVDMARHQVAFPGDSAYTYVSGTTKFESATNPALVDTFASFMLSGDTQRIVAEKNVGIPTVTNASLPAELREYVHVPEAPISHSAETLRQHADEWRAAVTRQIASQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	382 (314)
Sequences:	35807 (28265)
Seq/√Len:	1595.1

ECOLI - POTD YNJB THIB YDCS POTF MALE YCJN UGPB
BACSU - CYCB YTCQ MDXE ARAN LIPO YESO YURO MSME YVGL
HALSA - Q9HNZ3 Q9HMT5 Q9HR87 Q9HR04 Q9HHQ8 Q9HP00
SULSO - Q97ZC3 Q97YY1 Q97UZ1 Q97VC2 Q97UF5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_R	95_D	3.678	1.00
181_E	284_Q	3.653	1.00
63_R	95_D	3.523	1.00
142_A	308_P	3.212	1.00
61_R	93_D	3.022	1.00
194_T	235_R	2.926	1.00
143_A	164_T	2.783	1.00
182_T	282_R	2.683	1.00
234_R	238_D	2.518	1.00
87_Q	93_D	2.487	1.00
92_V	310_L	2.444	1.00
85_A	317_F	2.412	1.00
235_R	239_N	2.405	1.00
320_S	323_T	2.400	1.00
90_Y	313_T	2.372	1.00
189_T	192_A	2.346	1.00
63_R	97_V	2.211	1.00
104_T	107_M	2.159	1.00
85_A	88_S	2.148	1.00
80_N	84_D	2.132	1.00
313_T	316_S	2.131	1.00
183_V	260_P	2.094	1.00
85_A	89_E	2.088	1.00
179_Y	284_Q	2.077	1.00
181_E	185_D	2.055	1.00
85_A	326_I	2.034	1.00
119_D	307_N	2.030	1.00
325_R	329_E	2.029	1.00
307_N	310_L	1.988	1.00
60_P	310_L	1.961	1.00
141_F	300_T	1.946	1.00
232_Y	235_R	1.936	1.00
81_W	84_D	1.934	1.00
231_E	235_R	1.907	1.00
145_D	164_T	1.889	1.00
184_V	261_M	1.830	1.00
76_T	80_N	1.796	1.00
167_M	298_G	1.792	1.00
86_V	90_Y	1.783	1.00
147_D	312_D	1.783	1.00
142_A	303_E	1.770	1.00
321_G	325_R	1.760	1.00
86_V	313_T	1.747	1.00
84_D	88_S	1.736	1.00
308_P	312_D	1.735	1.00
83_K	314_F	1.732	1.00
83_K	87_Q	1.723	1.00
310_L	313_T	1.720	1.00
192_A	195_T	1.718	1.00
326_I	330_K	1.703	1.00
253_A	258_E	1.695	1.00
108_R	112_Q	1.694	1.00
231_E	234_R	1.674	1.00
323_T	326_I	1.667	1.00
59_P	93_D	1.652	1.00
309_A	313_T	1.644	1.00
100_E	104_T	1.642	1.00
121_Y	302_F	1.611	1.00
232_Y	236_L	1.609	1.00
65_G	112_Q	1.607	1.00
180_D	183_V	1.605	1.00
188_E	192_A	1.605	1.00
344_A	348_E	1.595	1.00
66_A	96_W	1.589	1.00
326_I	329_E	1.581	1.00
89_E	320_S	1.575	1.00
240_G	243_T	1.569	1.00
252_S	256_G	1.555	1.00
156_H	159_F	1.540	1.00
87_Q	90_Y	1.523	1.00
191_A	194_T	1.491	1.00
179_Y	286_A	1.485	1.00
246_S	249_A	1.483	1.00
196_D	200_D	1.472	1.00
17_A	20_G	1.472	1.00
86_V	314_F	1.468	1.00
81_W	85_A	1.464	1.00
194_T	239_N	1.459	1.00
196_D	239_N	1.451	1.00
155_V	159_F	1.448	1.00
181_E	282_R	1.447	1.00
120_G	311_V	1.433	1.00
241_L	244_A	1.421	1.00
16_A	19_L	1.420	1.00
194_T	232_Y	1.417	1.00
60_P	307_N	1.402	1.00
253_A	259_A	1.392	1.00
305_A	308_P	1.390	1.00
197_E	201_G	1.382	1.00
194_T	236_L	1.373	1.00
187_P	192_A	1.372	1.00
84_D	87_Q	1.368	1.00
348_E	351_H	1.362	1.00
86_V	317_F	1.358	1.00
154_N	339_N	1.344	1.00
136_L	166_R	1.339	1.00
196_D	199_S	1.339	1.00
301_K	315_A	1.315	1.00
309_A	312_D	1.310	1.00
149_V	152_T	1.304	1.00
240_G	244_A	1.304	1.00
305_A	311_V	1.272	1.00
344_A	347_R	1.265	1.00
86_V	92_V	1.264	1.00
143_A	146_T	1.249	1.00
235_R	238_D	1.243	1.00
153_D	156_H	1.240	1.00
301_K	311_V	1.238	1.00
321_G	339_N	1.236	1.00
177_I	286_A	1.235	1.00
120_G	314_F	1.234	1.00
191_A	195_T	1.233	1.00
160_W	165_D	1.228	1.00
143_A	165_D	1.216	1.00
83_K	96_W	1.207	1.00
322_D	325_R	1.204	1.00
77_S	80_N	1.201	1.00
249_A	252_S	1.199	1.00
312_D	316_S	1.195	1.00
254_Y	283_H	1.182	1.00
178_I	264_S	1.181	1.00
176_T	285_V	1.152	1.00
99_A	108_R	1.151	1.00
180_D	282_R	1.148	1.00
83_K	94_F	1.143	1.00
278_V	281_A	1.135	1.00
14_A	18_S	1.114	1.00
348_E	352_V	1.113	1.00
349_Y	352_V	1.107	1.00
85_A	322_D	1.105	1.00
270_V	274_Q	1.099	1.00
150_D	153_D	1.098	1.00
198_Y	201_G	1.092	1.00
180_D	281_A	1.092	1.00
92_V	313_T	1.090	1.00
64_M	299_T	1.090	1.00
77_S	81_W	1.089	1.00
81_W	326_I	1.087	1.00
188_E	289_G	1.085	1.00
62_L	314_F	1.080	1.00
219_W	222_D	1.078	1.00
106_F	128_D	1.072	1.00
177_I	261_M	1.070	1.00
302_F	305_A	1.070	1.00
322_D	326_I	1.067	1.00
89_E	317_F	1.066	1.00
271_Y	274_Q	1.064	1.00
110_A	138_A	1.064	1.00
301_K	312_D	1.064	1.00
87_Q	91_T	1.063	1.00
89_E	322_D	1.063	1.00
108_R	111_Q	1.060	1.00
119_D	305_A	1.057	1.00
221_V	224_F	1.054	1.00
142_A	312_D	1.051	1.00
317_F	323_T	1.046	1.00
347_R	351_H	1.043	1.00
24_C	27_D	1.043	1.00
13_S	17_A	1.042	1.00
120_G	315_A	1.041	1.00
264_S	268_D	1.037	1.00
81_W	330_K	1.036	1.00
299_T	315_A	1.034	1.00
279_D	283_H	1.024	1.00
201_G	260_P	1.023	1.00
220_T	223_A	1.015	1.00
107_M	111_Q	1.005	1.00
221_V	226_E	1.005	1.00
86_V	310_L	1.004	1.00
314_F	318_M	0.999	1.00
321_G	337_V	0.998	1.00
153_D	157_D	0.997	1.00
248_N	251_Y	0.994	1.00
62_L	310_L	0.987	1.00
82_V	323_T	0.985	1.00
78_A	81_W	0.985	1.00
351_H	354_E	0.982	1.00
182_T	281_A	0.981	1.00
121_Y	300_T	0.981	1.00
130_A	137_S	0.980	1.00
117_G	302_F	0.974	1.00
139_P	303_E	0.972	1.00
170_T	299_T	0.970	1.00
193_L	261_M	0.966	1.00
325_R	340_A	0.966	1.00
82_V	85_A	0.965	1.00
85_A	323_T	0.961	1.00
343_P	347_R	0.955	1.00
124_V	300_T	0.954	1.00
303_E	308_P	0.953	1.00
131_R	138_A	0.953	1.00
198_Y	202_I	0.952	1.00
234_R	237_A	0.950	1.00
94_F	314_F	0.946	1.00
24_C	28_R	0.946	1.00
112_Q	116_L	0.945	1.00
337_V	340_A	0.939	1.00
301_K	305_A	0.938	1.00
211_A	214_L	0.928	1.00
109_R	121_Y	0.925	1.00
252_S	255_S	0.914	1.00
350_V	354_E	0.912	1.00
136_L	161_I	0.910	1.00
179_Y	186_A	0.906	1.00
197_E	200_D	0.904	1.00
154_N	337_V	0.897	1.00
132_A	141_F	0.894	1.00
230_L	234_R	0.888	1.00
65_G	118_A	0.884	1.00
167_M	300_T	0.878	1.00
65_G	99_A	0.876	1.00
16_A	20_G	0.876	1.00
18_S	21_L	0.874	1.00
17_A	21_L	0.871	1.00
202_I	205_P	0.869	1.00
345_E	348_E	0.866	1.00
203_L	259_A	0.864	1.00
233_W	237_A	0.864	1.00
218_L	222_D	0.858	1.00
24_C	29_E	0.856	1.00
107_M	110_A	0.855	1.00
222_D	225_G	0.854	1.00
190_L	194_T	0.854	1.00
183_V	198_Y	0.849	1.00
106_F	110_A	0.845	1.00
152_T	155_V	0.841	1.00
220_T	224_F	0.838	1.00
55_Q	58_T	0.829	1.00
128_D	131_R	0.821	1.00
104_T	108_R	0.820	1.00
154_N	157_D	0.820	1.00
125_T	128_D	0.820	1.00
255_S	275_D	0.814	1.00
97_V	108_R	0.811	1.00
206_N	209_N	0.811	1.00
13_S	16_A	0.806	1.00
219_W	223_A	0.805	1.00
145_D	165_D	0.804	1.00
144_F	315_A	0.801	1.00
143_A	166_R	0.801	1.00
222_D	226_E	0.797	1.00
141_F	166_R	0.797	1.00
217_V	221_V	0.795	1.00
182_T	185_D	0.789	1.00
15_T	19_L	0.788	1.00
12_G	16_A	0.788	1.00
271_Y	275_D	0.787	1.00
24_C	30_T	0.785	1.00
57_G	60_P	0.782	1.00
142_A	302_F	0.781	1.00
311_V	315_A	0.779	1.00
196_D	201_G	0.779	1.00
154_N	158_R	0.778	1.00
142_A	305_A	0.773	1.00
316_S	320_S	0.773	1.00
314_F	317_F	0.772	1.00
299_T	318_M	0.771	1.00
136_L	141_F	0.766	1.00
173_S	295_Y	0.765	1.00
178_I	269_Q	0.764	1.00
204_V	207_P	0.763	1.00
247_W	250_T	0.763	1.00
186_A	286_A	0.761	1.00
13_S	19_L	0.760	1.00
223_A	226_E	0.758	1.00
14_A	20_G	0.757	1.00
60_P	92_V	0.752	1.00
79_G	82_V	0.750	1.00
121_Y	141_F	0.749	1.00
15_T	18_S	0.749	1.00
19_L	22_A	0.748	1.00
87_Q	94_F	0.747	1.00
198_Y	260_P	0.747	1.00
349_Y	353_P	0.745	1.00
270_V	273_S	0.739	1.00
62_L	307_N	0.738	1.00
341_S	344_A	0.737	1.00
115_D	304_S	0.736	1.00
186_A	192_A	0.735	1.00
122_V	299_T	0.733	1.00
142_A	146_T	0.732	1.00
251_Y	255_S	0.731	1.00
341_S	345_E	0.729	1.00
14_A	17_A	0.727	1.00
18_S	22_A	0.723	1.00
248_N	252_S	0.720	1.00
350_V	353_P	0.716	1.00
269_Q	273_S	0.712	1.00
206_N	212_T	0.711	1.00
106_F	131_R	0.711	1.00
219_W	224_F	0.711	1.00
110_A	131_R	0.710	1.00
182_T	257_G	0.708	1.00
65_G	97_V	0.708	1.00
142_A	301_K	0.706	1.00
21_L	24_C	0.705	1.00
217_V	222_D	0.702	1.00
245_G	249_A	0.701	1.00
229_F	233_W	0.699	1.00
119_D	311_V	0.696	1.00
268_D	271_Y	0.691	1.00
230_L	233_W	0.691	1.00
63_R	119_D	0.689	1.00
279_D	282_R	0.688	1.00
93_D	96_W	0.686	1.00
250_T	262_V	0.686	1.00
178_I	283_H	0.684	1.00
346_L	349_Y	0.683	1.00
239_N	242_Q	0.683	1.00
189_T	290_D	0.680	1.00
180_D	257_G	0.678	1.00
211_A	215_A	0.677	1.00
185_D	282_R	0.676	1.00
178_I	285_V	0.673	1.00
346_L	350_V	0.671	1.00
156_H	338_T	0.671	1.00
284_Q	287_F	0.670	1.00
349_Y	354_E	0.669	1.00
20_G	23_G	0.668	1.00
64_M	122_V	0.667	1.00
199_S	202_I	0.667	1.00
136_L	139_P	0.665	1.00
341_S	347_R	0.665	1.00
313_T	317_F	0.662	1.00
245_G	253_A	0.661	1.00
12_G	19_L	0.660	1.00
147_D	150_D	0.659	1.00
145_D	312_D	0.659	1.00
179_Y	184_V	0.658	1.00
142_A	147_D	0.657	1.00
27_D	30_T	0.654	1.00
343_P	346_L	0.651	1.00
63_R	66_A	0.650	1.00
208_Q	212_T	0.649	1.00
151_N	154_N	0.647	1.00
342_L	347_R	0.644	1.00
60_P	63_R	0.640	1.00
64_M	120_G	0.640	1.00
253_A	256_G	0.639	1.00
28_R	31_T	0.638	1.00
209_N	212_T	0.637	1.00
238_D	241_L	0.636	1.00
160_W	163_G	0.636	1.00
212_T	215_A	0.634	1.00
179_Y	261_M	0.628	1.00
308_P	311_V	0.626	1.00
62_L	311_V	0.621	1.00
9_A	12_G	0.621	1.00
218_L	224_F	0.619	1.00
161_I	164_T	0.618	1.00
147_D	309_A	0.618	1.00
206_N	210_T	0.615	1.00
345_E	349_Y	0.613	1.00
13_S	20_G	0.613	1.00
215_A	219_W	0.612	1.00
97_V	112_Q	0.612	1.00
220_T	225_G	0.612	1.00
207_P	210_T	0.611	1.00
154_N	159_F	0.611	1.00
218_L	221_V	0.611	1.00
105_E	109_R	0.610	1.00
190_L	232_Y	0.609	1.00
218_L	223_A	0.607	1.00
247_W	251_Y	0.606	1.00
142_A	304_S	0.606	1.00
321_G	324_Q	0.605	1.00
184_V	198_Y	0.602	1.00
22_A	26_G	0.601	1.00
298_G	302_F	0.601	1.00
12_G	15_T	0.601	1.00
260_P	263_M	0.601	1.00
22_A	25_V	0.600	1.00
236_L	239_N	0.600	1.00
301_K	308_P	0.599	1.00
203_L	206_N	0.595	1.00
97_V	118_A	0.595	1.00
8_V	11_V	0.594	1.00
210_T	214_L	0.594	1.00
29_E	32_T	0.593	1.00
129_L	167_M	0.591	1.00
155_V	158_R	0.590	1.00
229_F	234_R	0.588	1.00
216_F	220_T	0.586	1.00
82_V	318_M	0.585	1.00
236_L	241_L	0.582	1.00
347_R	350_V	0.582	1.00
106_F	132_A	0.579	1.00
58_T	61_R	0.579	1.00
215_A	218_L	0.576	1.00
229_F	232_Y	0.576	1.00
62_L	94_F	0.574	1.00
317_F	320_S	0.572	1.00
87_Q	92_V	0.571	1.00
144_F	312_D	0.571	1.00
203_L	208_Q	0.570	1.00
204_V	210_T	0.570	1.00
82_V	326_I	0.569	1.00
342_L	346_L	0.568	1.00
324_Q	336_T	0.567	1.00
59_P	91_T	0.565	1.00
151_N	316_S	0.565	1.00
208_Q	213_G	0.564	1.00
204_V	208_Q	0.563	1.00
154_N	338_T	0.563	1.00
146_T	164_T	0.561	1.00
304_S	308_P	0.561	1.00
12_G	18_S	0.561	1.00
60_P	91_T	0.558	1.00
21_L	25_V	0.557	1.00
206_N	211_A	0.557	1.00
9_A	13_S	0.556	1.00
210_T	213_G	0.556	1.00
165_D	168_L	0.556	1.00
64_M	96_W	0.556	1.00
144_F	147_D	0.555	1.00
207_P	212_T	0.555	1.00
267_T	270_V	0.554	1.00
15_T	20_G	0.553	1.00
168_L	319_L	0.553	1.00
249_A	253_A	0.551	1.00
111_Q	114_V	0.549	1.00
80_N	83_K	0.549	1.00
177_I	263_M	0.549	1.00
144_F	301_K	0.547	1.00
173_S	297_S	0.547	1.00
90_Y	310_L	0.544	1.00
82_V	317_F	0.544	1.00
26_G	29_E	0.542	1.00
324_Q	328_A	0.541	1.00
56_Q	59_P	0.540	1.00
171_G	297_S	0.539	1.00
217_V	220_T	0.538	1.00
122_V	170_T	0.536	1.00
345_E	351_H	0.534	1.00
347_R	353_P	0.534	1.00
23_G	26_G	0.534	1.00
188_E	193_L	0.532	1.00
342_L	345_E	0.531	1.00
83_K	93_D	0.531	1.00
64_M	83_K	0.531	1.00
181_E	281_A	0.530	1.00
208_Q	211_A	0.529	1.00
155_V	319_L	0.527	1.00
152_T	316_S	0.526	1.00
345_E	350_V	0.523	1.00
131_R	137_S	0.523	1.00
217_V	224_F	0.521	1.00
58_T	313_T	0.521	1.00
105_E	121_Y	0.520	1.00
24_C	31_T	0.520	1.00
63_R	118_A	0.518	1.00
143_A	147_D	0.518	1.00
268_D	272_A	0.517	1.00
22_A	28_R	0.517	1.00
347_R	354_E	0.517	1.00
214_L	217_V	0.517	1.00
9_A	20_G	0.513	1.00
333_G	336_T	0.511	1.00
154_N	321_G	0.511	1.00
174_Y	266_S	0.511	1.00
20_G	24_C	0.510	1.00
119_D	306_T	0.509	1.00
68_E	71_V	0.506	1.00
14_A	19_L	0.505	1.00
251_Y	264_S	0.504	1.00
119_D	308_P	0.503	1.00
259_A	263_M	0.503	1.00
120_G	299_T	0.503	1.00
92_V	96_W	0.502	1.00
140_L	143_A	0.501	1.00
65_G	105_E	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
3uorA	1	0.8115	100	0.308	Contact Map
4r9fA	1	0.8063	100	0.318	Contact Map
4r2fA	1	0.8141	100	0.324	Contact Map
4mfiA	1	0.8272	100	0.326	Contact Map
3vxbA	1	0.8168	100	0.329	Contact Map
4edpA	1	0.7958	100	0.339	Contact Map
3woaA	1	0.8874	100	0.352	Contact Map
2w7yA	1	0.8089	100	0.352	Contact Map
4r6kA	1	0.8115	100	0.355	Contact Map
4g68A	1	0.8246	100	0.356	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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