YTLI - BACSU - GREMLIN Contacts

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YTLI - HTH-type transcriptional regulator YtlI

UniProt:	O35038	Sequences: MELRSIKTFHTIVKFGSFYKAAEILNYSQPTISMRMKQLEQDLGVLLFERGKSLQLTKAGKLFYERTGDLLMQYEALKHNLSDLKEEEAGIINIGVSEPTASLIFPEILKDFLMDYPKITVNIKVDDANTCSQKLLDGTIDFAVCGEPELILENYYHPFFYDTLNVIVSDQHPLAEKKAVHLSDLAEERFIFTPANCPIRLQIEQHLHRELGNRYKKMELTSSMSHEYYVRENIGISIFTSTAHSKPFNGTKVIPILNLDITPPIGLLTNQKEVHFDRATKDLIARITKRFQQRSKELEGTSDKTITG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	308 (284)
Sequences:	79678 (58280)
Seq/√Len:	3458.3

ECOLI - LYSR OXYR YFER CYNR AAER CYSB YBHD CBL ICIA YDHB YNFL TTDR TDCA YAFC NAC DMLR LEUO XAPR YCAN HCAR PGRR ILVY YEEY YDCI YFIE ABGR METR YAHB ALLS YHJC YEIE YIAU DSDC YBDO GCVA YNEJ NHAR YBEF YIDZ LRHA YGFI YHAJ PERR YJIE HDFR
BACSU - YTLI YCGK YWBI ALSR GLTC CYSL YYBE CITR BSDA GLTR YVBU YWQM YUST YOFA YOAU YXJO CZCR YKUM YRAN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
69_D	73_Q	3.614	1.00
15_F	24_I	3.460	1.00
157_H	288_T	2.760	1.00
95_G	140_I	2.656	1.00
66_R	80_N	2.443	1.00
230_V	237_S	2.361	1.00
163_T	241_S	2.310	1.00
172_H	188_E	2.266	1.00
111_D	290_R	2.264	1.00
11_T	24_I	2.212	1.00
161_Y	264_P	2.192	1.00
91_I	122_N	2.188	1.00
158_P	161_Y	2.186	1.00
20_K	23_E	2.166	1.00
14_K	68_G	2.166	1.00
91_I	120_T	2.114	1.00
227_E	247_P	2.071	1.00
181_H	184_D	2.065	1.00
158_P	264_P	2.057	1.00
8_T	35_R	2.037	1.00
45_V	59_A	2.037	1.00
10_H	64_Y	2.030	1.00
93_N	122_N	2.007	1.00
161_Y	262_T	1.989	1.00
66_R	73_Q	1.968	1.00
111_D	286_R	1.961	1.00
10_H	68_G	1.931	1.00
70_L	74_Y	1.929	1.00
191_I	235_G	1.920	1.00
8_T	32_I	1.920	1.00
11_T	14_K	1.918	1.00
18_F	36_M	1.915	1.00
13_V	56_L	1.904	1.00
11_T	15_F	1.886	1.00
10_H	14_K	1.877	1.00
64_Y	68_G	1.829	1.00
165_N	241_S	1.821	1.00
231_R	247_P	1.797	1.00
63_F	77_L	1.754	1.00
49_E	55_Q	1.731	1.00
189_R	217_K	1.710	1.00
177_K	184_D	1.681	1.00
62_L	80_N	1.673	1.00
112_F	283_L	1.668	1.00
156_Y	266_G	1.641	1.00
14_K	24_I	1.629	1.00
134_K	139_T	1.619	1.00
9_F	64_Y	1.615	1.00
13_V	64_Y	1.598	1.00
10_H	67_T	1.587	1.00
8_T	27_Y	1.579	1.00
15_F	20_K	1.566	1.00
112_F	119_I	1.555	1.00
19_Y	29_Q	1.547	1.00
87_E	118_K	1.529	1.00
58_K	61_K	1.520	1.00
5_S	35_R	1.512	1.00
133_Q	137_D	1.510	1.00
28_S	31_T	1.479	1.00
155_Y	272_K	1.476	1.00
10_H	71_L	1.461	1.00
200_R	204_E	1.458	1.00
5_S	42_D	1.453	1.00
157_H	269_T	1.450	1.00
46_L	49_E	1.450	1.00
276_F	280_T	1.445	1.00
17_S	20_K	1.440	1.00
5_S	38_Q	1.428	1.00
66_R	69_D	1.420	1.00
11_T	25_L	1.415	1.00
168_V	254_I	1.413	1.00
284_I	288_T	1.408	1.00
145_C	268_L	1.399	1.00
70_L	77_L	1.389	1.00
155_Y	269_T	1.387	1.00
66_R	76_A	1.373	1.00
147_E	266_G	1.361	1.00
136_L	153_E	1.354	1.00
111_D	115_D	1.351	1.00
102_S	224_M	1.344	1.00
142_F	280_T	1.342	1.00
93_N	124_K	1.335	1.00
89_A	118_K	1.334	1.00
267_L	284_I	1.324	1.00
42_D	78_K	1.310	1.00
135_L	143_A	1.306	1.00
282_D	285_A	1.299	1.00
134_K	140_I	1.293	1.00
63_F	78_K	1.285	1.00
162_D	242_T	1.284	1.00
168_V	236_I	1.281	1.00
188_E	236_I	1.279	1.00
3_L	74_Y	1.274	1.00
226_H	237_S	1.254	1.00
113_L	217_K	1.253	1.00
142_F	267_L	1.244	1.00
61_K	65_E	1.235	1.00
170_D	250_G	1.234	1.00
269_T	284_I	1.234	1.00
37_K	41_Q	1.232	1.00
115_D	286_R	1.210	1.00
73_Q	76_A	1.209	1.00
228_Y	231_R	1.201	1.00
241_S	245_S	1.198	1.00
65_E	69_D	1.196	1.00
62_L	65_E	1.193	1.00
207_L	212_G	1.192	1.00
66_R	77_L	1.190	1.00
191_I	226_H	1.189	1.00
113_L	189_R	1.187	1.00
111_D	114_M	1.186	1.00
110_K	114_M	1.175	1.00
9_F	48_F	1.172	1.00
173_P	188_E	1.155	1.00
92_I	283_L	1.150	1.00
158_P	266_G	1.149	1.00
170_D	252_K	1.149	1.00
156_Y	268_L	1.143	1.00
270_N	273_E	1.141	1.00
165_N	255_P	1.140	1.00
9_F	47_L	1.138	1.00
251_T	255_P	1.136	1.00
27_Y	31_T	1.129	1.00
9_F	13_V	1.129	1.00
33_S	37_K	1.122	1.00
122_N	219_E	1.118	1.00
34_M	37_K	1.117	1.00
7_K	75_E	1.114	1.00
110_K	232_E	1.100	1.00
34_M	38_Q	1.099	1.00
189_R	215_Y	1.098	1.00
220_L	226_H	1.097	1.00
241_S	255_P	1.097	1.00
12_I	21_A	1.097	1.00
285_A	288_T	1.092	1.00
112_F	286_R	1.091	1.00
126_D	134_K	1.090	1.00
18_F	54_L	1.087	1.00
116_Y	282_D	1.076	1.00
245_S	249_N	1.072	1.00
6_I	67_T	1.071	1.00
69_D	76_A	1.068	1.00
101_A	125_V	1.066	1.00
286_R	290_R	1.061	1.00
70_L	73_Q	1.056	1.00
56_L	60_G	1.052	1.00
281_K	285_A	1.050	1.00
108_I	287_I	1.049	1.00
169_S	233_N	1.049	1.00
11_T	21_A	1.044	1.00
231_R	252_K	1.043	1.00
227_E	231_R	1.039	1.00
4_R	7_K	1.031	1.00
35_R	38_Q	1.029	1.00
178_K	254_I	1.019	1.00
180_V	184_D	1.019	1.00
62_L	66_R	1.019	1.00
157_H	284_I	1.006	1.00
228_Y	232_E	1.005	1.00
166_V	236_I	1.000	1.00
107_E	232_E	0.997	1.00
75_E	79_H	0.995	1.00
136_L	151_I	0.991	1.00
167_I	244_H	0.991	1.00
8_T	25_L	0.991	1.00
163_T	255_P	0.990	1.00
78_K	82_S	0.979	1.00
13_V	48_F	0.976	1.00
112_F	116_Y	0.975	1.00
163_T	262_T	0.973	1.00
75_E	78_K	0.971	1.00
27_Y	32_I	0.964	1.00
115_D	289_K	0.962	1.00
270_N	274_V	0.956	1.00
9_F	56_L	0.954	1.00
168_V	172_H	0.954	1.00
172_H	175_A	0.952	1.00
12_I	18_F	0.950	1.00
63_F	67_T	0.948	1.00
48_F	54_L	0.945	1.00
72_M	76_A	0.940	1.00
172_H	189_R	0.933	1.00
201_L	204_E	0.928	1.00
220_L	229_Y	0.923	1.00
134_K	137_D	0.923	1.00
108_I	286_R	0.921	1.00
277_D	280_T	0.920	1.00
201_L	205_Q	0.920	1.00
286_R	289_K	0.917	1.00
13_V	60_G	0.915	1.00
9_F	39_L	0.915	1.00
45_V	81_L	0.915	1.00
231_R	250_G	0.914	1.00
21_A	32_I	0.903	1.00
168_V	173_P	0.901	1.00
124_K	134_K	0.899	1.00
95_G	143_A	0.895	1.00
140_I	143_A	0.883	1.00
192_F	216_K	0.881	1.00
38_Q	41_Q	0.880	1.00
120_T	215_Y	0.880	1.00
172_H	176_E	0.878	1.00
153_E	272_K	0.873	1.00
95_G	145_C	0.870	1.00
251_T	254_I	0.870	1.00
20_K	24_I	0.864	1.00
119_I	279_A	0.859	1.00
65_E	68_G	0.859	1.00
94_I	142_F	0.857	1.00
285_A	289_K	0.856	1.00
154_N	268_L	0.855	1.00
248_F	251_T	0.853	1.00
184_D	187_E	0.853	1.00
19_Y	23_E	0.848	1.00
147_E	264_P	0.848	1.00
16_G	55_Q	0.843	1.00
190_F	214_R	0.842	1.00
132_S	136_L	0.841	1.00
98_E	222_S	0.840	1.00
167_I	237_S	0.836	1.00
244_H	247_P	0.832	1.00
176_E	189_R	0.831	1.00
12_I	36_M	0.830	1.00
167_I	253_V	0.827	1.00
25_L	32_I	0.823	1.00
173_P	178_K	0.820	1.00
179_A	257_L	0.819	1.00
247_P	250_G	0.817	1.00
247_P	252_K	0.815	1.00
69_D	72_M	0.814	1.00
124_K	140_I	0.808	1.00
246_K	250_G	0.801	1.00
203_I	207_L	0.799	1.00
12_I	48_F	0.798	1.00
9_F	63_F	0.797	1.00
13_V	16_G	0.794	1.00
37_K	46_L	0.792	1.00
155_Y	158_P	0.792	1.00
189_R	216_K	0.791	1.00
16_G	61_K	0.790	1.00
59_A	81_L	0.786	1.00
276_F	281_K	0.786	1.00
171_Q	175_A	0.785	1.00
90_G	119_I	0.780	1.00
206_H	210_E	0.778	1.00
90_G	279_A	0.774	1.00
110_K	234_I	0.772	1.00
88_E	116_Y	0.771	1.00
74_Y	77_L	0.768	1.00
29_Q	33_S	0.768	1.00
169_S	234_I	0.767	1.00
174_L	188_E	0.766	1.00
200_R	219_E	0.765	1.00
183_S	186_A	0.765	1.00
73_Q	77_L	0.765	1.00
14_K	64_Y	0.763	1.00
163_T	260_D	0.759	1.00
82_S	85_K	0.752	1.00
15_F	21_A	0.750	1.00
4_R	35_R	0.747	1.00
142_F	283_L	0.742	1.00
229_Y	234_I	0.740	1.00
62_L	84_L	0.740	1.00
278_R	282_D	0.738	1.00
56_L	61_K	0.736	1.00
59_A	84_L	0.733	1.00
76_A	80_N	0.731	1.00
115_D	282_D	0.731	1.00
165_N	253_V	0.731	1.00
3_L	71_L	0.730	1.00
16_G	53_S	0.730	1.00
136_L	154_N	0.729	1.00
113_L	234_I	0.725	1.00
59_A	62_L	0.724	1.00
111_D	289_K	0.720	1.00
31_T	35_R	0.717	1.00
167_I	239_F	0.717	1.00
55_Q	61_K	0.714	1.00
144_V	287_I	0.713	1.00
67_T	70_L	0.712	1.00
93_N	140_I	0.711	1.00
205_Q	209_R	0.711	1.00
108_I	290_R	0.708	1.00
5_S	8_T	0.707	1.00
244_H	248_F	0.705	1.00
74_Y	78_K	0.704	1.00
169_S	172_H	0.704	1.00
174_L	177_K	0.701	1.00
77_L	81_L	0.701	1.00
112_F	282_D	0.698	1.00
7_K	11_T	0.696	1.00
12_I	32_I	0.694	1.00
167_I	248_F	0.693	1.00
18_F	32_I	0.690	1.00
240_T	243_A	0.687	1.00
49_E	57_T	0.687	1.00
40_E	45_V	0.686	1.00
96_V	101_A	0.685	1.00
18_F	53_S	0.684	1.00
182_L	258_N	0.683	1.00
183_S	210_E	0.682	1.00
206_H	209_R	0.682	1.00
222_S	225_S	0.681	1.00
186_A	212_G	0.681	1.00
187_E	215_Y	0.678	1.00
205_Q	208_H	0.677	1.00
92_I	279_A	0.673	1.00
59_A	63_F	0.673	1.00
96_V	105_F	0.671	1.00
93_N	141_D	0.671	1.00
218_M	229_Y	0.662	1.00
252_K	255_P	0.661	1.00
68_G	72_M	0.660	1.00
49_E	53_S	0.660	1.00
193_T	226_H	0.659	1.00
141_D	280_T	0.658	1.00
194_P	219_E	0.657	1.00
72_M	75_E	0.653	1.00
181_H	258_N	0.652	1.00
76_A	79_H	0.651	1.00
168_V	174_L	0.651	1.00
202_Q	206_H	0.648	1.00
67_T	71_L	0.646	1.00
135_L	268_L	0.643	1.00
251_T	257_L	0.643	1.00
40_E	50_R	0.639	1.00
21_A	25_L	0.637	1.00
58_K	62_L	0.636	1.00
203_I	206_H	0.635	1.00
282_D	286_R	0.635	1.00
61_K	64_Y	0.634	1.00
120_T	219_E	0.633	1.00
63_F	81_L	0.629	1.00
89_A	120_T	0.627	1.00
12_I	17_S	0.620	1.00
246_K	249_N	0.618	1.00
36_M	40_E	0.618	1.00
171_Q	233_N	0.618	1.00
23_E	26_N	0.614	1.00
171_Q	174_L	0.612	1.00
138_G	270_N	0.611	1.00
173_P	177_K	0.611	1.00
201_L	206_H	0.610	1.00
98_E	127_D	0.606	1.00
166_V	185_L	0.606	1.00
66_R	70_L	0.605	1.00
102_S	228_Y	0.605	1.00
7_K	10_H	0.604	1.00
173_P	176_E	0.603	1.00
190_F	236_I	0.601	1.00
207_L	214_R	0.599	1.00
142_F	284_I	0.598	1.00
62_L	81_L	0.598	1.00
4_R	38_Q	0.597	1.00
166_V	190_F	0.597	1.00
166_V	238_I	0.593	1.00
283_L	287_I	0.592	1.00
125_V	221_T	0.591	1.00
92_I	142_F	0.591	1.00
204_E	208_H	0.591	1.00
174_L	180_V	0.590	1.00
278_R	281_K	0.589	1.00
125_V	222_S	0.588	1.00
229_Y	235_G	0.587	1.00
160_F	265_I	0.586	1.00
226_H	230_V	0.584	1.00
56_L	64_Y	0.581	1.00
30_P	34_M	0.578	1.00
95_G	126_D	0.577	1.00
79_H	83_D	0.573	1.00
31_T	34_M	0.573	1.00
274_V	277_D	0.570	1.00
135_L	154_N	0.568	1.00
107_E	111_D	0.568	1.00
164_L	238_I	0.567	1.00
194_P	221_T	0.563	1.00
48_F	56_L	0.562	1.00
45_V	49_E	0.561	1.00
28_S	34_M	0.560	1.00
105_F	108_I	0.559	1.00
155_Y	273_E	0.555	1.00
109_L	121_V	0.552	1.00
146_G	263_P	0.551	1.00
43_L	81_L	0.550	1.00
186_A	213_N	0.547	1.00
43_L	63_F	0.544	1.00
204_E	207_L	0.541	1.00
4_R	8_T	0.541	1.00
202_Q	205_Q	0.539	1.00
220_L	225_S	0.538	1.00
195_A	219_E	0.536	1.00
162_D	263_P	0.535	1.00
65_E	80_N	0.535	1.00
251_T	256_I	0.534	1.00
100_T	104_I	0.534	1.00
179_A	184_D	0.534	1.00
95_G	124_K	0.533	1.00
107_E	110_K	0.532	1.00
269_T	281_K	0.530	1.00
8_T	36_M	0.530	1.00
36_M	48_F	0.529	1.00
168_V	175_A	0.528	1.00
71_L	74_Y	0.527	1.00
67_T	74_Y	0.525	1.00
239_F	244_H	0.525	1.00
43_L	46_L	0.521	1.00
90_G	118_K	0.520	1.00
172_H	236_I	0.515	1.00
7_K	71_L	0.514	1.00
66_R	81_L	0.513	1.00
18_F	50_R	0.513	1.00
116_Y	119_I	0.512	1.00
159_F	267_L	0.512	1.00
71_L	75_E	0.511	1.00
144_V	267_L	0.511	1.00
223_S	240_T	0.507	1.00
102_S	222_S	0.504	1.00
200_R	206_H	0.503	1.00
114_M	175_A	0.503	1.00
46_L	59_A	0.502	1.00
8_T	21_A	0.502	1.00
147_E	156_Y	0.502	1.00
181_H	257_L	0.502	1.00
90_G	116_Y	0.502	1.00
175_A	252_K	0.500	1.00
27_Y	35_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
1ixcA	4	0.9448	100	0.112	Contact Map
3fzvA	4	0.9253	100	0.123	Contact Map
2esnA	3	0.9416	100	0.126	Contact Map
1uthA	2	0.7305	100	0.127	Contact Map
4x6gA	4	0.974	100	0.128	Contact Map
1al3A	1	0.724	100	0.129	Contact Map
2h98A	2	0.6883	100	0.129	Contact Map
2h9bA	2	0.6916	100	0.131	Contact Map
3fxqA	3	0.9383	100	0.137	Contact Map
3szpA	3	0.9318	100	0.15	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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