P82854 - HALSA - GREMLIN Contacts

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P82854 - Thioredoxin

UniProt:	P82854	Sequences: MTEATADRTALTDGGRDVVEHRQLVIVGSGIAALSAATYAARSNNDPLLFEGDEPGGQLTLTSEVENYPGFPEGIAGAELIQEMKTQATRFGAEVEHGIVESVDDSGRPFRLTLTNGDVYTADAVIVASGASARTLGIPGEDELMGQGVSTCATCDGAFFRGEDMIVVGGGDAAAEEASFLTKFADTVYLVHRRDELRAEDYWADRIREHVADGDIEVLWNTEAVEVHGSPEEGVTGASLVRHPEGHPTAKLDADETEQLELDIGAFFIAIGHTPNTSFLADTGVVCDDAGYVQTVGGAGGGQTKTDVTGVFGAGDVVDYHYQQAVTAAGMGSKAAIDADEYLESVADGVTGETADATPADD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	362 (293)
Sequences:	57451 (40145)
Seq/√Len:	2345.3

ECOLI - AHPF TRXB STHA RCLA GSHR DLDH HCAD DHNA NORW GLTD PRET YGFT AEGA NIRB YGFK FADH
BACSU - DHNA TRXB FENR1 DLDH3 DLDH2 DLDH1 YPDA FENR2 YJLD YUMB GLTB CZCO YUTJ NASB NASD
HALSA - P82854 DLDH Q9HSN0 Q9HP48 Q9HR27 O54535
SULSO - Q97V69 Q97W27 Q97VD9 Q97XZ3 Q97WE3 Q97YT2 FENR Q97Z19 Q97WG1 Q97Z14 Q97VJ3 Q97VQ4 Q97Y24 Q980U1 Q97U72 Q97ZB4 Q97UP4 Q97UV0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
166_I	264_I	3.925	1.00
52_G	99_I	3.536	1.00
164_D	187_T	3.433	1.00
226_E	239_S	3.342	1.00
189_Y	219_L	3.215	1.00
228_H	239_S	3.069	1.00
187_T	217_E	2.986	1.00
23_Q	123_D	2.774	1.00
296_V	305_K	2.700	1.00
111_R	119_V	2.464	1.00
23_Q	46_D	2.440	1.00
242_R	260_L	2.425	1.00
219_L	260_L	2.418	1.00
24_L	40_A	2.387	1.00
164_D	265_G	2.385	1.00
239_S	261_E	2.381	1.00
108_R	310_G	2.354	1.00
139_P	226_E	2.294	1.00
36_A	126_I	2.291	1.00
166_I	191_V	2.280	1.00
48_L	96_E	2.263	1.00
286_V	294_Q	2.248	1.00
225_V	241_V	2.218	1.00
134_R	274_T	2.202	1.00
25_V	50_F	2.176	1.00
166_I	238_A	2.174	1.00
223_E	241_V	2.166	1.00
22_R	48_L	2.166	1.00
21_H	121_T	2.098	1.00
126_I	339_A	2.087	1.00
25_V	112_L	2.077	1.00
208_R	212_A	2.028	1.00
164_D	189_Y	2.012	1.00
50_F	120_Y	1.986	1.00
25_V	120_Y	1.966	1.00
23_Q	48_L	1.894	1.00
296_V	303_Q	1.879	1.00
21_H	123_D	1.839	1.00
113_T	119_V	1.834	1.00
105_D	308_V	1.812	1.00
225_V	239_S	1.808	1.00
32_A	314_A	1.764	1.00
132_S	276_N	1.689	1.00
124_A	310_G	1.687	1.00
193_R	223_E	1.677	1.00
222_T	242_R	1.677	1.00
228_H	261_E	1.674	1.00
143_E	229_G	1.674	1.00
132_S	274_T	1.661	1.00
122_A	125_V	1.658	1.00
164_D	263_D	1.618	1.00
132_S	278_S	1.613	1.00
189_Y	217_E	1.600	1.00
46_D	94_E	1.596	1.00
151_T	154_T	1.587	1.00
102_S	113_T	1.574	1.00
240_L	262_L	1.572	1.00
163_E	265_G	1.559	1.00
286_V	307_D	1.555	1.00
126_I	314_A	1.539	1.00
230_S	236_T	1.528	1.00
104_D	107_G	1.495	1.00
336_A	340_D	1.493	1.00
312_F	342_Y	1.492	1.00
25_V	122_A	1.478	1.00
25_V	48_L	1.476	1.00
76_A	79_E	1.470	1.00
114_L	120_Y	1.450	1.00
288_D	292_Y	1.443	1.00
222_T	240_L	1.442	1.00
219_L	222_T	1.427	1.00
111_R	121_T	1.424	1.00
191_V	262_L	1.420	1.00
227_V	267_F	1.416	1.00
164_D	186_D	1.393	1.00
26_I	37_A	1.392	1.00
222_T	260_L	1.387	1.00
99_I	115_T	1.386	1.00
150_S	154_T	1.384	1.00
124_A	312_F	1.351	1.00
201_D	205_D	1.344	1.00
129_S	317_V	1.332	1.00
124_A	339_A	1.326	1.00
332_G	336_A	1.324	1.00
288_D	294_Q	1.322	1.00
195_D	221_N	1.318	1.00
104_D	111_R	1.314	1.00
288_D	319_D	1.308	1.00
26_I	33_A	1.280	1.00
335_A	339_A	1.278	1.00
312_F	338_D	1.266	1.00
240_L	260_L	1.262	1.00
305_K	309_T	1.254	1.00
29_S	51_E	1.250	1.00
114_L	117_G	1.244	1.00
24_L	126_I	1.240	1.00
39_Y	337_I	1.224	1.00
137_G	141_E	1.219	1.00
230_S	234_G	1.218	1.00
165_M	181_L	1.218	1.00
154_T	157_G	1.205	1.00
85_K	89_T	1.204	1.00
295_T	318_V	1.194	1.00
128_A	314_A	1.193	1.00
37_A	49_L	1.184	1.00
48_L	120_Y	1.173	1.00
24_L	45_N	1.165	1.00
101_E	113_T	1.164	1.00
82_Q	86_T	1.164	1.00
229_G	236_T	1.164	1.00
191_V	240_L	1.157	1.00
296_V	302_G	1.150	1.00
196_E	204_A	1.146	1.00
182_T	216_I	1.146	1.00
189_Y	264_I	1.144	1.00
236_T	263_D	1.135	1.00
308_V	311_V	1.135	1.00
170_G	192_H	1.129	1.00
161_R	186_D	1.109	1.00
175_A	190_L	1.101	1.00
84_M	87_Q	1.100	1.00
334_K	338_D	1.095	1.00
210_H	213_D	1.094	1.00
192_H	220_W	1.092	1.00
114_L	118_D	1.089	1.00
105_D	311_V	1.079	1.00
155_C	158_A	1.072	1.00
50_F	96_E	1.058	1.00
86_T	89_T	1.058	1.00
40_A	336_A	1.055	1.00
293_V	317_V	1.052	1.00
293_V	313_G	1.051	1.00
22_R	25_V	1.044	1.00
165_M	266_A	1.039	1.00
168_V	267_F	1.038	1.00
39_Y	42_R	1.032	1.00
101_E	115_T	1.032	1.00
22_R	94_E	1.030	1.00
162_G	186_D	1.026	1.00
86_T	90_R	1.021	1.00
41_A	93_A	1.019	1.00
43_S	340_D	1.016	1.00
235_V	267_F	1.009	1.00
147_Q	151_T	1.006	1.00
150_S	158_A	1.004	1.00
32_A	328_A	1.001	1.00
153_A	157_G	0.997	1.00
152_C	155_C	0.993	1.00
165_M	186_D	0.991	1.00
102_S	282_D	0.991	1.00
147_Q	150_S	0.990	1.00
124_A	342_Y	0.989	1.00
210_H	214_G	0.988	1.00
104_D	113_T	0.979	1.00
182_T	187_T	0.973	1.00
88_A	91_F	0.972	1.00
43_S	337_I	0.972	1.00
179_S	183_K	0.969	1.00
87_Q	91_F	0.967	1.00
305_K	342_Y	0.967	1.00
209_E	213_D	0.967	1.00
96_E	120_Y	0.963	1.00
27_V	127_V	0.959	1.00
103_V	125_V	0.956	1.00
228_H	236_T	0.950	1.00
27_V	100_V	0.948	1.00
98_G	116_N	0.944	1.00
183_K	214_G	0.942	1.00
314_A	335_A	0.939	1.00
209_E	212_A	0.934	1.00
278_S	281_A	0.925	1.00
205_D	208_R	0.917	1.00
36_A	314_A	0.915	1.00
295_T	313_G	0.913	1.00
224_A	238_A	0.905	1.00
22_R	46_D	0.904	1.00
27_V	129_S	0.899	1.00
236_T	261_E	0.898	1.00
328_A	332_G	0.896	1.00
39_Y	43_S	0.895	1.00
222_T	241_V	0.894	1.00
217_E	260_L	0.893	1.00
313_G	317_V	0.891	1.00
305_K	310_G	0.890	1.00
178_A	190_L	0.889	1.00
208_R	220_W	0.889	1.00
230_S	263_D	0.886	1.00
304_T	318_V	0.885	1.00
40_A	45_N	0.884	1.00
304_T	334_K	0.881	1.00
316_D	328_A	0.881	1.00
83_E	86_T	0.880	1.00
24_L	124_A	0.878	1.00
50_F	114_L	0.877	1.00
227_V	238_A	0.873	1.00
48_L	122_A	0.871	1.00
83_E	87_Q	0.869	1.00
304_T	335_A	0.865	1.00
79_E	82_Q	0.862	1.00
202_Y	206_R	0.860	1.00
180_F	184_F	0.860	1.00
48_L	94_E	0.859	1.00
33_A	37_A	0.855	1.00
312_F	339_A	0.854	1.00
36_A	332_G	0.849	1.00
39_Y	333_S	0.848	1.00
80_L	83_E	0.845	1.00
166_I	262_L	0.843	1.00
21_H	46_D	0.842	1.00
125_V	311_V	0.841	1.00
318_V	331_M	0.834	1.00
23_Q	121_T	0.833	1.00
40_A	339_A	0.833	1.00
152_C	156_D	0.831	1.00
185_A	188_V	0.826	1.00
127_V	317_V	0.824	1.00
327_T	331_M	0.822	1.00
287_C	294_Q	0.821	1.00
22_R	124_A	0.818	1.00
231_P	234_G	0.812	1.00
77_G	81_I	0.811	1.00
23_Q	45_N	0.809	1.00
76_A	83_E	0.805	1.00
170_G	197_L	0.804	1.00
100_V	112_L	0.795	1.00
50_F	100_V	0.793	1.00
197_L	220_W	0.790	1.00
126_I	335_A	0.788	1.00
191_V	222_T	0.788	1.00
241_V	257_T	0.783	1.00
168_V	271_I	0.782	1.00
98_G	115_T	0.781	1.00
219_L	262_L	0.779	1.00
174_A	192_H	0.779	1.00
150_S	153_A	0.777	1.00
24_L	339_A	0.777	1.00
147_Q	153_A	0.775	1.00
37_A	93_A	0.772	1.00
140_G	143_E	0.772	1.00
67_N	71_F	0.768	1.00
234_G	263_D	0.767	1.00
196_E	201_D	0.766	1.00
166_I	267_F	0.766	1.00
38_T	42_R	0.763	1.00
153_A	156_D	0.760	1.00
36_A	335_A	0.760	1.00
78_A	82_Q	0.760	1.00
81_I	85_K	0.759	1.00
54_E	85_K	0.758	1.00
45_N	340_D	0.757	1.00
96_E	118_D	0.756	1.00
192_H	199_A	0.755	1.00
182_T	214_G	0.750	1.00
191_V	219_L	0.749	1.00
79_E	83_E	0.747	1.00
179_S	182_T	0.747	1.00
168_V	224_A	0.743	1.00
303_Q	338_D	0.738	1.00
168_V	269_I	0.735	1.00
150_S	157_G	0.731	1.00
178_A	216_I	0.729	1.00
26_I	36_A	0.729	1.00
148_G	151_T	0.728	1.00
208_R	218_V	0.727	1.00
189_Y	262_L	0.727	1.00
41_A	47_P	0.724	1.00
88_A	93_A	0.722	1.00
305_K	338_D	0.721	1.00
150_S	155_C	0.720	1.00
167_V	178_A	0.719	1.00
22_R	123_D	0.717	1.00
150_S	266_A	0.716	1.00
152_C	158_A	0.715	1.00
124_A	343_L	0.713	1.00
77_G	84_M	0.712	1.00
181_L	184_F	0.711	1.00
313_G	318_V	0.711	1.00
310_G	342_Y	0.711	1.00
74_G	77_G	0.711	1.00
140_G	226_E	0.709	1.00
131_A	273_H	0.708	1.00
335_A	338_D	0.706	1.00
66_E	70_G	0.705	1.00
33_A	128_A	0.704	1.00
227_V	235_V	0.696	1.00
333_S	337_I	0.694	1.00
37_A	47_P	0.694	1.00
331_M	335_A	0.687	1.00
264_I	267_F	0.686	1.00
151_T	156_D	0.686	1.00
228_H	231_P	0.685	1.00
100_V	103_V	0.684	1.00
107_G	111_R	0.683	1.00
66_E	69_P	0.682	1.00
229_G	235_V	0.681	1.00
36_A	336_A	0.681	1.00
29_S	49_L	0.679	1.00
152_C	157_G	0.678	1.00
219_L	240_L	0.678	1.00
40_A	47_P	0.678	1.00
150_S	156_D	0.678	1.00
147_Q	154_T	0.677	1.00
314_A	339_A	0.675	1.00
164_D	264_I	0.674	1.00
35_S	332_G	0.673	1.00
135_T	142_D	0.672	1.00
212_A	217_E	0.670	1.00
68_Y	71_F	0.670	1.00
151_T	155_C	0.662	1.00
23_Q	122_A	0.662	1.00
154_T	158_A	0.661	1.00
306_T	313_G	0.661	1.00
75_I	79_E	0.660	1.00
77_G	80_L	0.658	1.00
60_T	63_S	0.655	1.00
82_Q	85_K	0.653	1.00
192_H	195_D	0.650	1.00
314_A	332_G	0.649	1.00
76_A	80_L	0.649	1.00
149_V	227_V	0.642	1.00
67_N	70_G	0.642	1.00
70_G	73_E	0.641	1.00
205_D	209_E	0.639	1.00
305_K	308_V	0.638	1.00
169_G	272_G	0.637	1.00
280_L	283_T	0.637	1.00
294_Q	307_D	0.636	1.00
295_T	304_T	0.635	1.00
287_C	293_V	0.631	1.00
234_G	265_G	0.630	1.00
304_T	338_D	0.629	1.00
41_A	92_G	0.628	1.00
171_G	272_G	0.627	1.00
105_D	108_R	0.627	1.00
77_G	83_E	0.625	1.00
236_T	239_S	0.624	1.00
163_E	186_D	0.619	1.00
84_M	88_A	0.618	1.00
23_Q	120_Y	0.615	1.00
177_E	268_F	0.611	1.00
136_L	269_I	0.611	1.00
45_N	123_D	0.610	1.00
242_R	257_T	0.610	1.00
206_R	209_E	0.609	1.00
163_E	187_T	0.607	1.00
178_A	188_V	0.602	1.00
231_P	261_E	0.597	1.00
100_V	104_D	0.597	1.00
312_F	335_A	0.597	1.00
196_E	208_R	0.596	1.00
196_E	199_A	0.595	1.00
289_D	294_Q	0.595	1.00
35_S	39_Y	0.592	1.00
330_G	333_S	0.592	1.00
279_F	283_T	0.590	1.00
51_E	95_V	0.589	1.00
24_L	336_A	0.589	1.00
180_F	183_K	0.589	1.00
29_S	55_P	0.588	1.00
135_T	151_T	0.588	1.00
136_L	141_E	0.581	1.00
285_V	293_V	0.579	1.00
50_F	122_A	0.579	1.00
175_A	218_V	0.577	1.00
278_S	282_D	0.577	1.00
138_I	141_E	0.576	1.00
35_S	329_A	0.575	1.00
324_Q	327_T	0.575	1.00
305_K	312_F	0.575	1.00
160_F	163_E	0.574	1.00
100_V	114_L	0.574	1.00
45_N	339_A	0.571	1.00
151_T	158_A	0.568	1.00
204_A	208_R	0.567	1.00
339_A	343_L	0.567	1.00
141_E	269_I	0.566	1.00
277_T	287_C	0.566	1.00
167_V	174_A	0.565	1.00
32_A	128_A	0.561	1.00
203_W	206_R	0.559	1.00
190_L	218_V	0.557	1.00
129_S	279_F	0.557	1.00
76_A	81_I	0.555	1.00
229_G	234_G	0.554	1.00
77_G	87_Q	0.551	1.00
182_T	215_D	0.550	1.00
277_T	317_V	0.545	1.00
201_D	204_A	0.543	1.00
41_A	46_D	0.542	1.00
179_S	184_F	0.541	1.00
151_T	157_G	0.538	1.00
55_P	95_V	0.538	1.00
211_V	218_V	0.538	1.00
147_Q	152_C	0.536	1.00
197_L	204_A	0.534	1.00
99_I	102_S	0.534	1.00
135_T	269_I	0.534	1.00
55_P	97_H	0.533	1.00
51_E	97_H	0.533	1.00
206_R	210_H	0.532	1.00
337_I	341_E	0.532	1.00
101_E	104_D	0.531	1.00
202_Y	205_D	0.531	1.00
175_A	211_V	0.531	1.00
60_T	64_E	0.530	1.00
39_Y	336_A	0.526	1.00
136_L	271_I	0.525	1.00
26_I	128_A	0.525	1.00
221_N	242_R	0.525	1.00
165_M	268_F	0.524	1.00
138_I	227_V	0.524	1.00
107_G	119_V	0.523	1.00
174_A	270_A	0.523	1.00
319_D	331_M	0.522	1.00
98_G	101_E	0.520	1.00
148_G	154_T	0.520	1.00
115_T	118_D	0.520	1.00
76_A	84_M	0.520	1.00
53_D	62_T	0.519	1.00
25_V	125_V	0.518	1.00
153_A	158_A	0.517	1.00
326_V	329_A	0.517	1.00
49_L	93_A	0.516	1.00
127_V	280_L	0.516	1.00
78_A	81_I	0.515	1.00
127_V	279_F	0.514	1.00
35_S	38_T	0.514	1.00
192_H	197_L	0.513	1.00
57_G	60_T	0.512	1.00
330_G	334_K	0.510	1.00
147_Q	158_A	0.509	1.00
127_V	313_G	0.508	1.00
33_A	49_L	0.507	1.00
285_V	307_D	0.504	1.00
36_A	40_A	0.503	1.00
192_H	198_R	0.503	1.00
26_I	47_P	0.502	1.00
49_L	95_V	0.501	1.00
148_G	152_C	0.501	1.00
104_D	108_R	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
2q7vA	2	0.8536	100	0.299	Contact Map
2a87A	2	0.8619	100	0.304	Contact Map
2q0lA	2	0.8425	100	0.306	Contact Map
3ctyA	2	0.8425	100	0.308	Contact Map
3r9uA	2	0.8425	100	0.312	Contact Map
3f8dA	2	0.8508	100	0.312	Contact Map
1trbA	2	0.8702	100	0.316	Contact Map
1vdcA	2	0.8536	100	0.319	Contact Map
4up3A	2	0.8425	100	0.319	Contact Map
4jnqA	2	0.8619	100	0.323	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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