THIB - ECOLI - GREMLIN Contacts

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THIB - Thiamine-binding periplasmic protein

UniProt:	P31550	Sequences: MLKKCLPLLLLCTAPVFAKPVLTVYTYDSFAADWGPGPVVKKAFEADCNCELKLVALEDGVSLLNRLRMEGKNSKADVVLGLDNNLLDAASKTGLFAKSGVAADAVNVPGGWNNDTFVPFDYGYFAFVYDKNKLKNPPQSLKELVESDQNWRVIYQDPRTSTPGLGLLLWMQKVYGDDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGESDLVLSYTTSPAYHILEEKKDNYAAANFSEGHYLQVEVAARTAASKQPELAQKFLQFMVSPAFQNAIPTGNWMYPVANVTLPAGFEKLTKPATTLEFTPAEVAAQRQAWISEWQRAVSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11574
Length:	327 (290)
Sequences:	35636 (27905)
Seq/√Len:	1638.7

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_V	53_K	3.540	1.00
131_K	232_A	3.176	1.00
23_T	53_K	3.049	1.00
97_A	256_P	3.044	1.00
132_N	230_N	2.635	1.00
21_V	51_E	2.626	1.00
10_L	13_T	2.535	1.00
50_C	258_L	2.524	1.00
48_C	261_K	2.482	1.00
184_Q	188_K	2.481	1.00
8_L	11_L	2.422	1.00
43_A	265_F	2.385	1.00
145_V	185_K	2.313	1.00
181_Q	185_K	2.305	1.00
45_E	51_E	2.288	1.00
268_S	271_F	2.263	1.00
185_K	189_K	2.253	1.00
38_P	42_K	2.246	1.00
9_L	12_C	2.146	1.00
43_A	46_A	2.116	1.00
261_K	264_Q	2.114	1.00
140_S	143_E	2.048	1.00
43_A	274_A	2.009	1.00
7_P	10_L	1.943	1.00
62_S	65_N	1.941	1.00
273_N	277_T	1.921	1.00
134_L	211_L	1.895	1.00
77_D	255_Q	1.891	1.00
20_P	258_L	1.885	1.00
23_T	55_V	1.877	1.00
44_F	261_K	1.877	1.00
6_L	9_L	1.873	1.00
129_Y	232_A	1.868	1.00
178_D	181_Q	1.866	1.00
255_Q	258_L	1.851	1.00
133_K	210_D	1.848	1.00
39_V	42_K	1.829	1.00
96_F	248_A	1.828	1.00
25_Y	70_E	1.817	1.00
43_A	47_D	1.782	1.00
42_K	46_A	1.779	1.00
11_L	14_A	1.756	1.00
44_F	48_C	1.751	1.00
41_K	262_F	1.749	1.00
45_E	48_C	1.744	1.00
147_S	189_K	1.739	1.00
41_K	45_E	1.728	1.00
79_V	250_T	1.705	1.00
147_S	151_W	1.702	1.00
102_A	260_Q	1.693	1.00
131_K	135_K	1.688	1.00
143_E	146_E	1.679	1.00
257_E	261_K	1.677	1.00
107_N	286_N	1.656	1.00
182_A	185_K	1.652	1.00
58_E	62_S	1.649	1.00
117_F	246_V	1.649	1.00
196_G	199_E	1.636	1.00
190_T	193_V	1.608	1.00
5_C	8_L	1.586	1.00
130_D	133_K	1.586	1.00
269_P	273_N	1.585	1.00
132_N	136_N	1.565	1.00
66_R	70_E	1.546	1.00
203_L	208_E	1.540	1.00
256_P	260_Q	1.540	1.00
291_A	295_K	1.530	1.00
97_A	251_A	1.529	1.00
47_D	268_S	1.498	1.00
26_T	54_L	1.494	1.00
271_F	274_A	1.491	1.00
42_K	45_E	1.485	1.00
181_Q	184_Q	1.462	1.00
44_F	262_F	1.447	1.00
274_A	277_T	1.440	1.00
103_A	106_V	1.439	1.00
20_P	255_Q	1.438	1.00
44_F	265_F	1.432	1.00
139_Q	143_E	1.431	1.00
258_L	261_K	1.425	1.00
91_S	116_T	1.412	1.00
39_V	43_A	1.408	1.00
44_F	50_C	1.407	1.00
249_R	263_L	1.404	1.00
142_K	145_V	1.404	1.00
131_K	230_N	1.367	1.00
127_F	234_A	1.355	1.00
138_P	143_E	1.353	1.00
182_A	186_L	1.351	1.00
202_G	206_K	1.348	1.00
129_Y	234_A	1.332	1.00
110_G	113_N	1.323	1.00
274_A	278_G	1.313	1.00
154_I	209_S	1.312	1.00
253_S	256_P	1.308	1.00
185_K	188_K	1.296	1.00
105_A	113_N	1.295	1.00
142_K	146_E	1.292	1.00
41_K	54_L	1.283	1.00
78_V	259_A	1.281	1.00
104_D	107_N	1.272	1.00
145_V	189_K	1.266	1.00
291_A	294_E	1.260	1.00
41_K	52_L	1.259	1.00
126_A	233_A	1.250	1.00
78_V	262_F	1.240	1.00
148_D	152_R	1.236	1.00
145_V	186_L	1.233	1.00
203_L	209_S	1.233	1.00
269_P	286_N	1.213	1.00
190_T	194_T	1.210	1.00
171_M	176_G	1.209	1.00
171_M	174_V	1.204	1.00
260_Q	264_Q	1.203	1.00
257_E	260_Q	1.201	1.00
44_F	258_L	1.201	1.00
145_V	182_A	1.174	1.00
172_Q	175_Y	1.174	1.00
249_R	259_A	1.167	1.00
50_C	261_K	1.158	1.00
247_A	263_L	1.143	1.00
171_M	175_Y	1.133	1.00
22_L	258_L	1.129	1.00
43_A	270_A	1.123	1.00
9_L	13_T	1.121	1.00
170_W	175_Y	1.120	1.00
249_R	260_Q	1.110	1.00
39_V	274_A	1.095	1.00
130_D	229_D	1.090	1.00
94_G	251_A	1.088	1.00
98_K	101_V	1.081	1.00
269_P	285_A	1.081	1.00
262_F	266_M	1.080	1.00
22_L	262_F	1.067	1.00
77_D	253_S	1.066	1.00
47_D	270_A	1.066	1.00
127_F	211_L	1.064	1.00
68_R	93_T	1.059	1.00
57_L	66_R	1.059	1.00
152_R	210_D	1.052	1.00
270_A	273_N	1.045	1.00
147_S	150_N	1.042	1.00
108_V	113_N	1.041	1.00
183_W	187_A	1.037	1.00
108_V	112_W	1.030	1.00
133_K	136_N	1.022	1.00
199_E	202_G	1.021	1.00
133_K	149_Q	1.020	1.00
78_V	263_L	1.007	1.00
82_L	248_A	1.004	1.00
191_V	194_T	1.002	1.00
265_F	271_F	1.002	1.00
20_P	49_N	1.000	1.00
79_V	248_A	0.989	1.00
250_T	253_S	0.989	1.00
270_A	274_A	0.984	1.00
225_E	228_K	0.983	1.00
130_D	230_N	0.981	1.00
64_L	86_L	0.977	1.00
67_L	79_V	0.977	1.00
149_Q	152_R	0.975	1.00
24_V	247_A	0.970	1.00
251_A	256_P	0.966	1.00
120_F	247_A	0.965	1.00
107_N	285_A	0.965	1.00
40_V	271_F	0.965	1.00
88_D	92_K	0.961	1.00
172_Q	177_D	0.961	1.00
128_V	214_S	0.960	1.00
75_K	250_T	0.960	1.00
8_L	13_T	0.955	1.00
178_D	182_A	0.952	1.00
132_N	229_D	0.952	1.00
109_P	112_W	0.950	1.00
191_V	195_K	0.948	1.00
249_R	253_S	0.945	1.00
105_A	108_V	0.945	1.00
39_V	278_G	0.942	1.00
47_D	265_F	0.940	1.00
273_N	287_V	0.938	1.00
117_F	248_A	0.937	1.00
296_L	299_P	0.934	1.00
97_A	253_S	0.933	1.00
204_F	231_Y	0.932	1.00
153_V	156_Q	0.931	1.00
7_P	11_L	0.928	1.00
253_S	259_A	0.928	1.00
43_A	271_F	0.927	1.00
290_P	294_E	0.926	1.00
149_Q	210_D	0.925	1.00
129_Y	137_P	0.921	1.00
109_P	113_N	0.914	1.00
13_T	17_F	0.912	1.00
25_Y	76_A	0.911	1.00
8_L	12_C	0.910	1.00
247_A	266_M	0.907	1.00
97_A	260_Q	0.903	1.00
96_F	116_T	0.898	1.00
262_F	265_F	0.895	1.00
89_A	93_T	0.894	1.00
52_L	262_F	0.892	1.00
13_T	16_V	0.890	1.00
292_G	295_K	0.888	1.00
132_N	135_K	0.885	1.00
14_A	18_A	0.884	1.00
45_E	49_N	0.877	1.00
10_L	14_A	0.875	1.00
98_K	116_T	0.868	1.00
134_L	149_Q	0.863	1.00
297_T	300_A	0.861	1.00
200_A	212_V	0.860	1.00
66_R	69_M	0.859	1.00
90_A	96_F	0.854	1.00
45_E	52_L	0.853	1.00
104_D	264_Q	0.844	1.00
19_K	51_E	0.840	1.00
40_V	43_A	0.837	1.00
91_S	96_F	0.833	1.00
167_L	171_M	0.828	1.00
14_A	17_F	0.820	1.00
20_P	50_C	0.819	1.00
198_S	201_Y	0.812	1.00
140_S	238_E	0.810	1.00
49_N	261_K	0.803	1.00
106_V	109_P	0.800	1.00
144_L	211_L	0.799	1.00
65_N	68_R	0.798	1.00
25_Y	57_L	0.795	1.00
97_A	249_R	0.785	1.00
65_N	69_M	0.783	1.00
97_A	250_T	0.782	1.00
264_Q	268_S	0.781	1.00
15_P	18_A	0.778	1.00
295_K	298_K	0.778	1.00
259_A	263_L	0.777	1.00
123_G	243_Q	0.777	1.00
166_G	169_L	0.776	1.00
64_L	68_R	0.776	1.00
103_A	264_Q	0.771	1.00
154_I	157_D	0.769	1.00
16_V	19_K	0.769	1.00
55_V	66_R	0.768	1.00
141_L	145_V	0.767	1.00
170_W	174_V	0.760	1.00
184_Q	187_A	0.759	1.00
202_G	205_L	0.759	1.00
99_S	263_L	0.759	1.00
36_P	39_V	0.758	1.00
148_D	151_W	0.756	1.00
106_V	110_G	0.750	1.00
149_Q	211_L	0.748	1.00
229_D	232_A	0.746	1.00
97_A	101_V	0.745	1.00
9_L	14_A	0.743	1.00
64_L	90_A	0.739	1.00
139_Q	237_S	0.730	1.00
100_G	260_Q	0.729	1.00
232_A	235_N	0.726	1.00
106_V	113_N	0.724	1.00
70_E	74_S	0.720	1.00
80_L	247_A	0.718	1.00
169_L	172_Q	0.714	1.00
79_V	96_F	0.709	1.00
22_L	255_Q	0.705	1.00
220_A	223_I	0.704	1.00
137_P	143_E	0.703	1.00
180_P	184_Q	0.700	1.00
192_T	195_K	0.699	1.00
48_C	258_L	0.695	1.00
45_E	50_C	0.690	1.00
173_K	176_G	0.686	1.00
169_L	173_K	0.684	1.00
5_C	9_L	0.683	1.00
129_Y	134_L	0.682	1.00
87_L	117_F	0.678	1.00
64_L	89_A	0.677	1.00
221_Y	224_L	0.676	1.00
40_V	265_F	0.676	1.00
168_L	171_M	0.675	1.00
153_V	157_D	0.674	1.00
6_L	11_L	0.674	1.00
83_D	86_L	0.672	1.00
128_V	233_A	0.672	1.00
97_A	252_A	0.672	1.00
180_P	183_W	0.664	1.00
296_L	300_A	0.664	1.00
103_A	107_N	0.663	1.00
108_V	267_V	0.661	1.00
82_L	90_A	0.659	1.00
12_C	15_P	0.657	1.00
20_P	261_K	0.656	1.00
137_P	234_A	0.654	1.00
179_A	183_W	0.653	1.00
154_I	159_R	0.652	1.00
272_Q	284_V	0.652	1.00
40_V	266_M	0.646	1.00
217_T	281_M	0.645	1.00
203_L	206_K	0.644	1.00
102_A	257_E	0.643	1.00
170_W	173_K	0.642	1.00
99_S	249_R	0.642	1.00
12_C	16_V	0.642	1.00
201_Y	205_L	0.641	1.00
134_L	210_D	0.638	1.00
166_G	170_W	0.634	1.00
229_D	235_N	0.633	1.00
256_P	259_A	0.631	1.00
168_L	172_Q	0.630	1.00
12_C	18_A	0.630	1.00
73_N	252_A	0.629	1.00
11_L	15_P	0.624	1.00
132_N	207_G	0.624	1.00
174_V	177_D	0.624	1.00
13_T	19_K	0.623	1.00
99_S	260_Q	0.619	1.00
219_P	223_I	0.617	1.00
198_S	202_G	0.616	1.00
11_L	17_F	0.615	1.00
91_S	94_G	0.613	1.00
220_A	224_L	0.613	1.00
25_Y	55_V	0.612	1.00
86_L	89_A	0.611	1.00
154_I	158_P	0.610	1.00
7_P	12_C	0.609	1.00
12_C	19_K	0.608	1.00
23_T	77_D	0.607	1.00
28_D	32_A	0.606	1.00
135_K	230_N	0.605	1.00
77_D	254_K	0.603	1.00
166_G	171_M	0.602	1.00
127_F	213_L	0.601	1.00
62_S	66_R	0.601	1.00
249_R	256_P	0.600	1.00
141_L	182_A	0.600	1.00
10_L	16_V	0.599	1.00
124_Y	216_T	0.597	1.00
123_G	245_E	0.596	1.00
15_P	19_K	0.595	1.00
51_E	54_L	0.595	1.00
80_L	120_F	0.593	1.00
128_V	231_Y	0.592	1.00
101_V	260_Q	0.592	1.00
153_V	158_P	0.591	1.00
138_P	211_L	0.591	1.00
24_V	54_L	0.590	1.00
165_L	171_M	0.589	1.00
12_C	17_F	0.587	1.00
131_K	229_D	0.586	1.00
107_N	110_G	0.584	1.00
60_G	86_L	0.584	1.00
36_P	40_V	0.584	1.00
23_T	26_T	0.583	1.00
261_K	265_F	0.581	1.00
79_V	82_L	0.581	1.00
121_D	245_E	0.580	1.00
107_N	269_P	0.579	1.00
155_Y	158_P	0.578	1.00
24_V	41_K	0.577	1.00
289_L	294_E	0.575	1.00
173_K	177_D	0.574	1.00
255_Q	259_A	0.573	1.00
190_T	195_K	0.573	1.00
24_V	78_V	0.573	1.00
11_L	18_A	0.571	1.00
69_M	72_K	0.571	1.00
289_L	292_G	0.571	1.00
130_D	207_G	0.570	1.00
165_L	168_L	0.568	1.00
55_V	76_A	0.568	1.00
11_L	16_V	0.567	1.00
260_Q	263_L	0.567	1.00
78_V	247_A	0.567	1.00
201_Y	214_S	0.564	1.00
214_S	219_P	0.563	1.00
118_V	263_L	0.563	1.00
26_T	31_A	0.563	1.00
105_A	109_P	0.563	1.00
219_P	222_H	0.563	1.00
77_D	259_A	0.560	1.00
169_L	175_Y	0.560	1.00
97_A	102_A	0.560	1.00
222_H	226_E	0.559	1.00
168_L	175_Y	0.559	1.00
118_V	267_V	0.557	1.00
125_F	215_Y	0.556	1.00
99_S	118_V	0.556	1.00
87_L	91_S	0.555	1.00
41_K	51_E	0.554	1.00
252_A	256_P	0.554	1.00
20_P	23_T	0.552	1.00
172_Q	176_G	0.552	1.00
90_A	95_L	0.552	1.00
9_L	15_P	0.551	1.00
20_P	48_C	0.551	1.00
87_L	248_A	0.547	1.00
24_V	262_F	0.545	1.00
104_D	109_P	0.544	1.00
60_G	64_L	0.543	1.00
112_W	122_Y	0.543	1.00
13_T	18_A	0.543	1.00
40_V	274_A	0.541	1.00
199_E	203_L	0.540	1.00
269_P	272_Q	0.539	1.00
204_F	212_V	0.537	1.00
139_Q	144_L	0.537	1.00
22_L	259_A	0.536	1.00
197_W	200_A	0.536	1.00
128_V	220_A	0.536	1.00
22_L	77_D	0.535	1.00
45_E	262_F	0.535	1.00
75_K	252_A	0.534	1.00
277_T	292_G	0.532	1.00
174_V	178_D	0.527	1.00
26_T	37_G	0.526	1.00
272_Q	276_P	0.526	1.00
200_A	209_S	0.526	1.00
68_R	89_A	0.525	1.00
22_L	52_L	0.524	1.00
171_M	177_D	0.523	1.00
272_Q	285_A	0.523	1.00
169_L	174_V	0.520	1.00
158_P	161_S	0.516	1.00
77_D	256_P	0.514	1.00
122_Y	284_V	0.514	1.00
6_L	10_L	0.513	1.00
267_V	272_Q	0.513	1.00
102_A	256_P	0.513	1.00
91_S	114_N	0.511	1.00
108_V	111_G	0.509	1.00
48_C	265_F	0.508	1.00
159_R	163_P	0.505	1.00
63_L	79_V	0.504	1.00
88_D	91_S	0.502	1.00
167_L	172_Q	0.502	1.00
164_G	171_M	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
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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
2qryA	1	0.9725	100	0.233	Contact Map
3pu5A	1	0.9297	100	0.285	Contact Map
3rpwA	1	0.9113	100	0.291	Contact Map
4edpA	1	0.9083	100	0.303	Contact Map
3uorA	1	0.9205	100	0.307	Contact Map
3qufA	1	0.9358	100	0.315	Contact Map
4r6kA	1	0.9358	100	0.317	Contact Map
2pt1A	1	0.9205	100	0.32	Contact Map
3c9hA	1	0.9511	100	0.32	Contact Map
3waeA	2	0.8899	100	0.321	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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