YUTJ - BACSU - GREMLIN Contacts

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YUTJ - NADH dehydrogenase-like protein YutJ

UniProt:	O32117	Sequences: MKKLVLIGGGYGNMRVLHRLLPNQLPDDVSITLIDRNPYHCLKTEYYALAAGTISDHHIRVSFPEHPRLDVQYGDITSIDIVQKQVLFQDREPISYDDAIIGLGCEDKYHNVPGAPEFTYSIQTIDQSRETYQKLNNLSANATVAIVGAGLSGVELASELRESRDDLNIILFDRGNLILSSFPERLSKYVQKWFEEHGVRIINRANITKVEEGVVYNHDDPISADAIVWTAGIQPNKVVRDLDVEKDAQGRIVLTPHHNLPGDEHLYVVGDCASLPHAPSAQLAEAQAEQIVQILQKRWNGEALPESMPQFKLKGVLGSLGKKAGFGLVADRPLIGRVPRMLKSGLLWMYKHHNG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	355 (289)
Sequences:	56388 (40757)
Seq/√Len:	2397.5

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
145_A	224_A	4.298	1.00
143_T	168_N	3.555	1.00
36_R	75_D	3.412	1.00
3_K	30_S	3.141	1.00
170_I	202_I	3.072	1.00
168_N	200_R	2.865	1.00
211_E	215_V	2.754	1.00
3_K	97_D	2.600	1.00
32_T	72_Q	2.575	1.00
4_L	20_L	2.533	1.00
16_V	100_I	2.454	1.00
85_Q	93_P	2.442	1.00
108_K	234_Q	2.418	1.00
255_T	259_N	2.367	1.00
191_Q	195_E	2.348	1.00
145_A	172_F	2.347	1.00
143_T	225_D	2.312	1.00
84_K	265_H	2.290	1.00
143_T	170_I	2.287	1.00
215_V	221_P	2.266	1.00
34_I	94_I	2.259	1.00
209_K	215_V	2.226	1.00
245_E	253_V	2.214	1.00
86_V	90_D	2.129	1.00
202_I	220_D	2.114	1.00
5_V	34_I	2.106	1.00
87_L	93_P	2.015	1.00
113_P	209_K	1.989	1.00
81_I	263_D	1.966	1.00
170_I	200_R	1.944	1.00
3_K	32_T	1.940	1.00
100_I	295_L	1.926	1.00
211_E	221_P	1.921	1.00
80_D	83_Q	1.907	1.00
174_R	206_N	1.878	1.00
143_T	167_L	1.876	1.00
74_G	90_D	1.834	1.00
5_V	96_Y	1.833	1.00
98_D	265_H	1.824	1.00
247_D	251_R	1.821	1.00
12_G	269_V	1.777	1.00
85_Q	95_S	1.768	1.00
245_E	262_G	1.750	1.00
96_Y	99_A	1.745	1.00
5_V	94_I	1.737	1.00
142_A	225_D	1.706	1.00
30_S	70_D	1.686	1.00
55_S	58_H	1.683	1.00
106_E	234_Q	1.676	1.00
172_F	222_I	1.674	1.00
106_E	236_N	1.662	1.00
56_D	63_F	1.633	1.00
143_T	223_S	1.622	1.00
98_D	295_L	1.595	1.00
103_L	272_C	1.563	1.00
176_N	204_R	1.539	1.00
5_V	86_V	1.530	1.00
202_I	205_A	1.522	1.00
5_V	32_T	1.516	1.00
98_D	267_Y	1.512	1.00
60_R	63_F	1.492	1.00
56_D	60_R	1.478	1.00
100_I	269_V	1.477	1.00
78_S	87_L	1.467	1.00
208_T	215_V	1.464	1.00
205_A	218_H	1.410	1.00
267_Y	294_I	1.404	1.00
292_V	296_Q	1.390	1.00
124_T	127_Q	1.386	1.00
17_L	33_L	1.385	1.00
210_V	227_I	1.375	1.00
259_N	264_E	1.345	1.00
78_S	241_D	1.331	1.00
126_D	129_R	1.330	1.00
170_I	224_A	1.326	1.00
9_G	35_D	1.323	1.00
59_I	63_F	1.321	1.00
6_L	13_N	1.302	1.00
32_T	70_D	1.301	1.00
111_N	115_A	1.292	1.00
193_W	196_E	1.289	1.00
254_L	273_A	1.283	1.00
288_A	292_V	1.280	1.00
12_G	284_A	1.276	1.00
144_V	160_L	1.266	1.00
206_N	217_N	1.262	1.00
4_L	29_V	1.257	1.00
128_S	131_T	1.253	1.00
252_I	268_V	1.243	1.00
141_N	167_L	1.239	1.00
57_H	61_V	1.239	1.00
145_A	214_V	1.239	1.00
4_L	100_I	1.234	1.00
75_D	89_Q	1.231	1.00
205_A	220_D	1.228	1.00
55_S	59_I	1.219	1.00
21_L	69_L	1.216	1.00
149_A	173_D	1.207	1.00
45_E	48_A	1.193	1.00
74_G	89_Q	1.182	1.00
56_D	59_I	1.180	1.00
144_V	226_A	1.173	1.00
59_I	62_S	1.172	1.00
80_D	87_L	1.171	1.00
173_D	203_N	1.161	1.00
61_V	65_E	1.157	1.00
291_I	295_L	1.154	1.00
98_D	298_R	1.152	1.00
6_L	17_L	1.151	1.00
125_I	129_R	1.146	1.00
102_G	269_V	1.143	1.00
193_W	197_H	1.132	1.00
32_T	94_I	1.130	1.00
58_H	62_S	1.130	1.00
19_R	289_E	1.127	1.00
297_K	302_E	1.125	1.00
62_S	65_E	1.122	1.00
19_R	22_P	1.110	1.00
48_A	51_A	1.105	1.00
191_Q	203_N	1.104	1.00
127_Q	130_E	1.104	1.00
188_K	191_Q	1.098	1.00
76_I	79_I	1.096	1.00
290_Q	294_I	1.095	1.00
81_I	84_K	1.091	1.00
122_I	126_D	1.086	1.00
184_E	188_K	1.080	1.00
208_T	219_D	1.079	1.00
162_E	197_H	1.078	1.00
81_I	266_L	1.075	1.00
4_L	98_D	1.061	1.00
55_S	62_S	1.056	1.00
208_T	217_N	1.055	1.00
192_K	196_E	1.051	1.00
19_R	293_Q	1.051	1.00
269_V	291_I	1.051	1.00
161_R	199_V	1.042	1.00
124_T	128_S	1.040	1.00
154_V	171_L	1.039	1.00
170_I	222_I	1.036	1.00
267_Y	298_R	1.029	1.00
72_Q	94_I	1.023	1.00
88_F	94_I	1.022	1.00
80_D	85_Q	1.020	1.00
161_R	168_N	1.017	1.00
252_I	272_C	1.017	1.00
49_L	52_G	1.015	1.00
7_I	103_L	1.011	1.00
188_K	192_K	1.004	1.00
58_H	61_V	1.003	1.00
144_V	167_L	1.003	1.00
125_I	128_S	1.001	1.00
263_D	266_L	0.998	1.00
128_S	132_Y	0.998	1.00
7_I	76_I	0.996	1.00
189_Y	193_W	0.995	1.00
237_K	241_D	0.995	1.00
126_D	130_E	0.988	1.00
29_V	296_Q	0.984	1.00
157_A	171_L	0.979	1.00
50_A	53_T	0.976	1.00
77_T	89_Q	0.975	1.00
247_D	253_V	0.974	1.00
205_A	217_N	0.971	1.00
216_Y	222_I	0.970	1.00
192_K	195_E	0.968	1.00
145_A	222_I	0.967	1.00
166_D	169_I	0.964	1.00
254_L	268_V	0.962	1.00
237_K	240_R	0.957	1.00
60_R	64_P	0.954	1.00
88_F	92_E	0.948	1.00
56_D	62_S	0.948	1.00
254_L	258_H	0.947	1.00
177_L	187_S	0.943	1.00
106_E	237_K	0.938	1.00
147_V	227_I	0.936	1.00
3_K	95_S	0.932	1.00
34_I	72_Q	0.928	1.00
59_I	64_P	0.926	1.00
122_I	125_I	0.924	1.00
74_G	77_T	0.924	1.00
123_Q	126_D	0.923	1.00
257_H	294_I	0.919	1.00
124_T	129_R	0.918	1.00
258_H	273_A	0.918	1.00
41_C	44_T	0.916	1.00
100_I	291_I	0.914	1.00
55_S	63_F	0.903	1.00
123_Q	127_Q	0.902	1.00
61_V	64_P	0.902	1.00
50_A	54_I	0.902	1.00
247_D	274_S	0.901	1.00
21_L	68_R	0.900	1.00
7_I	101_I	0.891	1.00
48_A	52_G	0.886	1.00
78_S	84_K	0.883	1.00
178_I	203_N	0.877	1.00
122_I	128_S	0.877	1.00
123_Q	131_T	0.874	1.00
16_V	288_A	0.872	1.00
20_L	29_V	0.871	1.00
202_I	222_I	0.869	1.00
32_T	96_Y	0.859	1.00
20_L	292_V	0.858	1.00
189_Y	192_K	0.857	1.00
18_H	22_P	0.855	1.00
213_G	221_P	0.854	1.00
268_V	273_A	0.852	1.00
147_V	231_A	0.850	1.00
267_Y	295_L	0.847	1.00
105_C	233_I	0.842	1.00
258_H	290_Q	0.841	1.00
77_T	87_L	0.839	1.00
27_D	296_Q	0.836	1.00
51_A	54_I	0.835	1.00
129_R	132_Y	0.832	1.00
140_A	167_L	0.827	1.00
127_Q	131_T	0.826	1.00
120_Y	134_K	0.822	1.00
123_Q	128_S	0.819	1.00
34_I	74_G	0.818	1.00
146_I	157_A	0.817	1.00
205_A	216_Y	0.813	1.00
16_V	269_V	0.810	1.00
74_G	88_F	0.808	1.00
284_A	288_A	0.804	1.00
3_K	29_V	0.802	1.00
130_E	133_Q	0.801	1.00
258_H	291_I	0.801	1.00
78_S	81_I	0.796	1.00
114_G	209_K	0.794	1.00
16_V	291_I	0.791	1.00
268_V	272_C	0.791	1.00
20_L	31_I	0.791	1.00
47_Y	52_G	0.786	1.00
283_L	287_Q	0.783	1.00
56_D	64_P	0.778	1.00
101_I	272_C	0.771	1.00
74_G	78_S	0.765	1.00
259_N	265_H	0.761	1.00
57_H	63_F	0.758	1.00
6_L	16_V	0.758	1.00
117_E	120_Y	0.758	1.00
224_A	227_I	0.756	1.00
15_R	288_A	0.756	1.00
273_A	287_Q	0.755	1.00
49_L	53_T	0.753	1.00
259_N	294_I	0.752	1.00
291_I	294_I	0.752	1.00
17_L	31_I	0.751	1.00
74_G	79_I	0.751	1.00
99_A	266_L	0.750	1.00
39_Y	61_V	0.749	1.00
109_Y	116_P	0.747	1.00
57_H	60_R	0.747	1.00
13_N	102_G	0.746	1.00
296_Q	300_N	0.743	1.00
83_Q	93_P	0.742	1.00
172_F	216_Y	0.740	1.00
147_V	229_W	0.738	1.00
267_Y	291_I	0.738	1.00
253_V	262_G	0.737	1.00
158_S	162_E	0.734	1.00
115_A	229_W	0.733	1.00
21_L	31_I	0.732	1.00
86_V	89_Q	0.728	1.00
248_A	253_V	0.728	1.00
74_G	92_E	0.726	1.00
123_Q	129_R	0.726	1.00
15_R	19_R	0.725	1.00
142_A	167_L	0.722	1.00
101_I	266_L	0.719	1.00
153_G	173_D	0.719	1.00
161_R	197_H	0.719	1.00
55_S	60_R	0.716	1.00
72_Q	92_E	0.716	1.00
187_S	191_Q	0.709	1.00
4_L	295_L	0.708	1.00
265_H	298_R	0.702	1.00
286_A	289_E	0.702	1.00
9_G	33_L	0.699	1.00
125_I	132_Y	0.698	1.00
259_N	267_Y	0.697	1.00
145_A	227_I	0.696	1.00
76_I	84_K	0.696	1.00
173_D	176_N	0.695	1.00
172_F	202_I	0.695	1.00
177_L	184_E	0.694	1.00
40_H	43_K	0.690	1.00
121_S	127_Q	0.689	1.00
48_A	53_T	0.688	1.00
17_L	69_L	0.687	1.00
186_L	189_Y	0.687	1.00
143_T	224_A	0.684	1.00
147_V	207_I	0.679	1.00
88_F	91_R	0.677	1.00
109_Y	115_A	0.676	1.00
259_N	298_R	0.675	1.00
190_V	194_F	0.672	1.00
129_R	133_Q	0.671	1.00
297_K	301_G	0.671	1.00
217_N	220_D	0.669	1.00
34_I	96_Y	0.669	1.00
83_Q	95_S	0.668	1.00
20_L	295_L	0.667	1.00
184_E	187_S	0.667	1.00
84_K	88_F	0.664	1.00
238_V	242_L	0.662	1.00
177_L	191_Q	0.661	1.00
98_D	299_W	0.657	1.00
76_I	86_V	0.657	1.00
156_L	159_E	0.657	1.00
34_I	88_F	0.656	1.00
70_D	73_Y	0.656	1.00
239_V	242_L	0.653	1.00
42_L	45_E	0.653	1.00
187_S	190_V	0.652	1.00
16_V	292_V	0.651	1.00
215_V	219_D	0.649	1.00
130_E	134_K	0.647	1.00
161_R	198_G	0.645	1.00
46_Y	49_L	0.639	1.00
110_H	229_W	0.638	1.00
13_N	17_L	0.638	1.00
34_I	76_I	0.636	1.00
246_K	253_V	0.635	1.00
15_R	285_E	0.633	1.00
158_S	197_H	0.633	1.00
240_R	246_K	0.633	1.00
109_Y	229_W	0.628	1.00
293_Q	297_K	0.628	1.00
47_Y	50_A	0.627	1.00
289_E	293_Q	0.626	1.00
112_V	115_A	0.625	1.00
242_L	246_K	0.625	1.00
156_L	230_T	0.623	1.00
46_Y	50_A	0.622	1.00
58_H	63_F	0.617	1.00
173_D	180_S	0.616	1.00
281_A	284_A	0.614	1.00
249_Q	274_S	0.613	1.00
157_A	199_V	0.603	1.00
243_D	246_K	0.602	1.00
244_V	252_I	0.602	1.00
103_L	238_V	0.600	1.00
246_K	252_I	0.599	1.00
293_Q	298_R	0.596	1.00
15_R	18_H	0.594	1.00
200_R	220_D	0.593	1.00
3_K	94_I	0.591	1.00
29_V	295_L	0.589	1.00
29_V	97_D	0.588	1.00
76_I	80_D	0.586	1.00
194_F	201_I	0.583	1.00
146_I	153_G	0.579	1.00
38_P	73_Y	0.578	1.00
80_D	84_K	0.574	1.00
86_V	91_R	0.573	1.00
108_K	111_N	0.571	1.00
149_A	178_I	0.570	1.00
271_D	284_A	0.569	1.00
282_Q	285_E	0.569	1.00
122_I	127_Q	0.568	1.00
37_N	47_Y	0.567	1.00
126_D	132_Y	0.561	1.00
44_T	48_A	0.561	1.00
172_F	205_A	0.561	1.00
12_G	102_G	0.560	1.00
286_A	290_Q	0.558	1.00
6_L	102_G	0.557	1.00
110_H	115_A	0.554	1.00
131_T	134_K	0.553	1.00
101_I	238_V	0.553	1.00
125_I	130_E	0.553	1.00
142_A	226_A	0.552	1.00
191_Q	201_I	0.549	1.00
251_R	279_P	0.549	1.00
259_N	263_D	0.549	1.00
121_S	124_T	0.548	1.00
157_A	169_I	0.548	1.00
200_R	203_N	0.548	1.00
78_S	99_A	0.547	1.00
131_T	226_A	0.545	1.00
46_Y	52_G	0.541	1.00
122_I	130_E	0.540	1.00
261_P	268_V	0.539	1.00
35_D	73_Y	0.539	1.00
122_I	131_T	0.539	1.00
47_Y	51_A	0.538	1.00
122_I	129_R	0.538	1.00
200_R	222_I	0.538	1.00
40_H	71_V	0.538	1.00
109_Y	121_S	0.537	1.00
154_V	194_F	0.535	1.00
125_I	131_T	0.533	1.00
9_G	40_H	0.533	1.00
248_A	251_R	0.532	1.00
282_Q	286_A	0.530	1.00
285_E	289_E	0.529	1.00
190_V	193_W	0.529	1.00
15_R	289_E	0.528	1.00
3_K	96_Y	0.526	1.00
153_G	230_T	0.524	1.00
18_H	67_P	0.523	1.00
145_A	170_I	0.523	1.00
57_H	64_P	0.520	1.00
274_S	287_Q	0.520	1.00
19_R	292_V	0.519	1.00
253_V	261_P	0.516	1.00
247_D	250_G	0.516	1.00
175_G	180_S	0.516	1.00
5_V	84_K	0.514	1.00
139_S	142_A	0.513	1.00
58_H	65_E	0.512	1.00
212_E	223_S	0.512	1.00
156_L	228_V	0.512	1.00
294_I	297_K	0.511	1.00
12_G	100_I	0.510	1.00
127_Q	132_Y	0.510	1.00
134_K	226_A	0.510	1.00
44_T	47_Y	0.509	1.00
39_Y	60_R	0.507	1.00
269_V	288_A	0.507	1.00
113_P	116_P	0.506	1.00
96_Y	265_H	0.506	1.00
6_L	31_I	0.506	1.00
159_E	162_E	0.506	1.00
48_A	54_I	0.505	1.00
280_S	283_L	0.504	1.00
244_V	262_G	0.503	1.00
79_I	84_K	0.502	1.00
171_L	201_I	0.500	1.00
258_H	294_I	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)
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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
4g6hA	2	0.9887	100	0.262	Contact Map
4nwzA	2	0.9775	100	0.278	Contact Map
3h8lA	2	0.8789	100	0.344	Contact Map
3l8kA	3	0.9465	100	0.345	Contact Map
1ojtA	2	0.9493	100	0.345	Contact Map
3ntdA	2	0.9803	100	0.35	Contact Map
3sx6A	2	0.9915	100	0.351	Contact Map
2yquA	2	0.9493	100	0.352	Contact Map
3kljA	1	0.9352	100	0.352	Contact Map
3icsA	2	0.9831	100	0.352	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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