YDCI - ECOLI - GREMLIN Contacts

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YDCI - Uncharacterized HTH-type transcriptional regulator YdcI

UniProt:	P77171	Sequences: MEKNSLFSQRIRLRHLHTFVAVAQQGTLGRAAETLNLSQPALSKTLNELEQLTGARLFERGRQGAQLTLPGEQFLTHAVRVLDAINTAGRSLHRKEGLNNDVVRVGALPTAALGILPSVIGQFHQQQKETTLQVATMSNPMILAGLKTGEIDIGIGRMSDPELMTGLNYELLFLESLKLVVRPNHPLLQENVTLSRVLEWPVVVSPEGTAPRQHSDALVQSQGCKIPSGCIETLSASLSRQLTVEYDYVWFVPSGAVKDDLRHATLVALPVPGHGAGEPIGILTRVDATFSSGCQLMINAIRKSMPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13752
Length:	307 (287)
Sequences:	79348 (57590)
Seq/√Len:	3399.4

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
80_R	84_A	3.685	1.00
25_Q	34_T	3.385	1.00
170_E	302_R	2.607	1.00
77_H	91_S	2.520	1.00
21_A	34_T	2.519	1.00
106_G	151_I	2.483	1.00
171_L	279_P	2.299	1.00
102_V	133_Q	2.243	1.00
171_L	174_L	2.228	1.00
174_L	279_P	2.216	1.00
55_A	70_P	2.204	1.00
185_H	200_W	2.191	1.00
20_V	79_V	2.153	1.00
243_T	250_W	2.148	1.00
18_T	45_T	2.122	1.00
20_V	24_Q	2.083	1.00
102_V	131_T	2.070	1.00
77_H	84_A	2.066	1.00
178_K	254_S	2.064	1.00
176_S	254_S	2.026	1.00
244_V	265_T	2.022	1.00
174_L	277_G	2.012	1.00
122_Q	300_A	1.998	1.00
21_A	25_Q	1.995	1.00
193_T	196_R	1.979	1.00
104_R	133_Q	1.968	1.00
30_R	33_E	1.952	1.00
21_A	24_Q	1.920	1.00
23_A	67_L	1.889	1.00
20_V	75_L	1.880	1.00
18_T	42_L	1.856	1.00
81_V	85_I	1.853	1.00
240_R	260_D	1.851	1.00
24_Q	79_V	1.849	1.00
203_V	248_Y	1.848	1.00
75_L	79_V	1.835	1.00
178_K	268_A	1.832	1.00
181_V	269_L	1.795	1.00
201_P	230_C	1.767	1.00
244_V	260_D	1.746	1.00
23_A	75_L	1.730	1.00
169_Y	281_G	1.722	1.00
73_Q	91_S	1.710	1.00
59_E	66_Q	1.689	1.00
145_G	150_E	1.679	1.00
74_F	88_A	1.655	1.00
25_Q	30_R	1.643	1.00
77_H	80_R	1.616	1.00
170_E	284_T	1.557	1.00
27_T	30_R	1.554	1.00
168_N	286_V	1.546	1.00
20_V	78_A	1.544	1.00
28_L	46_L	1.542	1.00
15_H	52_L	1.539	1.00
24_Q	34_T	1.508	1.00
15_H	45_T	1.507	1.00
144_A	148_T	1.495	1.00
15_H	48_E	1.475	1.00
284_T	298_I	1.457	1.00
77_H	87_T	1.445	1.00
113_L	237_S	1.442	1.00
38_S	41_A	1.440	1.00
61_G	66_Q	1.437	1.00
56_R	59_E	1.432	1.00
21_A	35_L	1.432	1.00
123_F	297_M	1.426	1.00
212_R	216_D	1.425	1.00
156_G	283_L	1.425	1.00
168_N	284_T	1.413	1.00
84_A	87_T	1.412	1.00
98_L	129_E	1.404	1.00
19_F	75_L	1.402	1.00
298_I	302_R	1.400	1.00
18_T	37_L	1.398	1.00
12_R	15_H	1.398	1.00
29_G	39_Q	1.395	1.00
158_M	281_G	1.389	1.00
145_G	151_I	1.384	1.00
126_Q	300_A	1.373	1.00
104_R	135_A	1.368	1.00
146_L	154_G	1.367	1.00
123_F	130_T	1.366	1.00
100_N	129_E	1.340	1.00
81_V	88_A	1.339	1.00
296_L	299_N	1.335	1.00
76_T	80_R	1.326	1.00
290_F	294_C	1.321	1.00
69_L	72_E	1.317	1.00
20_V	82_L	1.316	1.00
175_E	255_G	1.313	1.00
74_F	89_G	1.306	1.00
282_I	298_I	1.302	1.00
239_S	250_W	1.294	1.00
13_L	85_I	1.289	1.00
77_H	88_A	1.283	1.00
241_Q	244_V	1.280	1.00
153_I	282_I	1.276	1.00
147_K	166_G	1.270	1.00
183_P	267_V	1.257	1.00
171_L	281_G	1.250	1.00
37_L	41_A	1.249	1.00
200_W	249_V	1.248	1.00
122_Q	126_Q	1.244	1.00
183_P	265_T	1.244	1.00
181_V	249_V	1.229	1.00
153_I	294_C	1.225	1.00
124_H	230_C	1.224	1.00
73_Q	76_T	1.223	1.00
124_H	201_P	1.221	1.00
260_D	265_T	1.219	1.00
44_K	48_E	1.214	1.00
254_S	268_A	1.208	1.00
121_G	245_E	1.205	1.00
19_F	58_F	1.192	1.00
121_G	125_Q	1.190	1.00
254_S	258_K	1.180	1.00
73_Q	77_H	1.175	1.00
19_F	23_A	1.163	1.00
169_Y	283_L	1.160	1.00
118_S	245_E	1.160	1.00
190_E	267_V	1.136	1.00
137_M	145_G	1.136	1.00
44_K	47_N	1.133	1.00
268_A	271_V	1.132	1.00
191_N	272_P	1.132	1.00
186_P	200_W	1.123	1.00
80_R	87_T	1.114	1.00
201_P	228_S	1.112	1.00
72_E	76_T	1.109	1.00
16_L	78_A	1.098	1.00
133_Q	232_E	1.089	1.00
127_Q	296_L	1.088	1.00
241_Q	245_E	1.086	1.00
170_E	298_I	1.086	1.00
192_V	196_R	1.084	1.00
47_N	51_Q	1.080	1.00
52_L	89_G	1.076	1.00
147_K	164_M	1.072	1.00
21_A	31_A	1.068	1.00
45_T	48_E	1.059	1.00
112_A	136_T	1.058	1.00
240_R	244_V	1.055	1.00
28_L	65_A	1.050	1.00
81_V	84_A	1.048	1.00
180_V	268_A	1.045	1.00
135_A	145_G	1.044	1.00
89_G	93_H	1.034	1.00
258_K	262_R	1.030	1.00
213_Q	217_A	1.029	1.00
43_S	47_N	1.025	1.00
259_D	263_H	1.022	1.00
295_Q	299_N	1.020	1.00
182_R	246_Y	1.018	1.00
176_S	277_G	1.017	1.00
14_R	17_H	1.014	1.00
299_N	302_R	1.014	1.00
122_Q	125_Q	1.012	1.00
285_R	288_A	1.007	1.00
123_F	300_A	1.007	1.00
19_F	57_L	1.007	1.00
83_D	87_T	1.006	1.00
103_V	297_M	0.996	1.00
213_Q	216_D	0.992	1.00
119_V	301_I	0.992	1.00
22_V	31_A	0.991	1.00
203_V	239_S	0.985	1.00
219_V	224_C	0.983	1.00
233_T	239_S	0.981	1.00
74_F	78_A	0.975	1.00
123_F	127_Q	0.974	1.00
204_V	229_G	0.972	1.00
48_E	51_Q	0.963	1.00
67_L	71_G	0.962	1.00
22_V	28_L	0.962	1.00
194_L	273_G	0.956	1.00
37_L	42_L	0.946	1.00
31_A	42_L	0.946	1.00
23_A	58_F	0.943	1.00
180_V	257_V	0.941	1.00
80_R	83_D	0.937	1.00
17_H	86_N	0.937	1.00
30_R	34_T	0.936	1.00
73_Q	95_K	0.936	1.00
86_N	89_G	0.934	1.00
179_L	249_V	0.927	1.00
85_I	89_G	0.926	1.00
181_V	185_H	0.920	1.00
300_A	303_K	0.919	1.00
18_T	35_L	0.916	1.00
145_G	148_T	0.913	1.00
233_T	242_L	0.912	1.00
19_F	67_L	0.909	1.00
19_F	49_L	0.909	1.00
109_P	235_S	0.904	1.00
106_G	154_G	0.896	1.00
119_V	300_A	0.893	1.00
70_P	73_Q	0.892	1.00
185_H	188_L	0.891	1.00
26_G	66_Q	0.889	1.00
126_Q	303_K	0.885	1.00
86_N	90_R	0.879	1.00
14_R	45_T	0.878	1.00
202_V	227_P	0.877	1.00
291_S	294_C	0.876	1.00
121_G	247_D	0.871	1.00
168_N	171_L	0.868	1.00
218_L	222_Q	0.867	1.00
11_I	52_L	0.866	1.00
158_M	279_P	0.865	1.00
244_V	263_H	0.858	1.00
76_T	79_V	0.858	1.00
55_A	92_L	0.856	1.00
58_F	65_A	0.854	1.00
106_G	156_G	0.854	1.00
29_G	33_E	0.850	1.00
61_G	64_G	0.845	1.00
143_L	147_K	0.843	1.00
151_I	154_G	0.840	1.00
101_D	293_G	0.833	1.00
87_T	91_S	0.831	1.00
292_S	296_L	0.829	1.00
85_I	88_A	0.829	1.00
201_P	229_G	0.826	1.00
135_A	151_I	0.826	1.00
185_H	189_Q	0.822	1.00
124_H	247_D	0.821	1.00
26_G	64_G	0.821	1.00
17_H	21_A	0.819	1.00
70_P	95_K	0.817	1.00
35_L	42_L	0.816	1.00
131_T	228_S	0.816	1.00
39_Q	43_S	0.815	1.00
70_P	92_L	0.814	1.00
23_A	26_G	0.813	1.00
25_Q	31_A	0.812	1.00
290_F	295_Q	0.811	1.00
105_V	153_I	0.810	1.00
130_T	293_G	0.808	1.00
24_Q	75_L	0.807	1.00
187_L	200_W	0.804	1.00
260_D	263_H	0.800	1.00
84_A	88_A	0.800	1.00
19_F	74_F	0.799	1.00
195_S	198_L	0.796	1.00
181_V	186_P	0.793	1.00
23_A	71_G	0.793	1.00
22_V	58_F	0.791	1.00
186_P	190_E	0.790	1.00
182_R	247_D	0.786	1.00
189_Q	201_P	0.786	1.00
193_T	272_P	0.782	1.00
26_G	72_E	0.781	1.00
167_L	283_L	0.777	1.00
13_L	82_L	0.776	1.00
188_L	267_V	0.775	1.00
176_S	275_G	0.771	1.00
72_E	75_L	0.771	1.00
79_V	83_D	0.770	1.00
215_S	219_V	0.770	1.00
257_V	260_D	0.768	1.00
180_V	250_W	0.767	1.00
242_L	247_D	0.765	1.00
47_N	56_R	0.761	1.00
15_H	18_T	0.759	1.00
235_S	238_L	0.757	1.00
88_A	92_L	0.756	1.00
261_L	264_A	0.750	1.00
28_L	42_L	0.748	1.00
176_S	270_P	0.746	1.00
107_A	112_A	0.745	1.00
22_V	42_L	0.744	1.00
78_A	81_V	0.742	1.00
182_R	185_H	0.740	1.00
59_E	68_T	0.739	1.00
17_H	20_V	0.739	1.00
184_N	246_Y	0.736	1.00
123_F	296_L	0.734	1.00
101_D	130_T	0.731	1.00
180_V	252_V	0.730	1.00
288_A	291_S	0.728	1.00
93_H	96_E	0.727	1.00
149_G	285_R	0.726	1.00
218_L	221_S	0.726	1.00
22_V	46_L	0.726	1.00
206_P	232_E	0.719	1.00
296_L	300_A	0.718	1.00
196_R	199_E	0.717	1.00
153_I	297_M	0.716	1.00
69_L	73_Q	0.716	1.00
166_G	286_V	0.716	1.00
214_H	218_L	0.714	1.00
185_H	201_P	0.711	1.00
299_N	303_K	0.711	1.00
147_K	167_L	0.710	1.00
126_Q	296_L	0.705	1.00
113_L	241_Q	0.700	1.00
181_V	267_V	0.693	1.00
152_D	294_C	0.692	1.00
184_N	188_L	0.691	1.00
70_P	74_F	0.690	1.00
217_A	221_S	0.687	1.00
99_N	127_Q	0.687	1.00
193_T	273_G	0.683	1.00
259_D	262_R	0.682	1.00
159_S	162_E	0.682	1.00
253_P	256_A	0.681	1.00
77_H	81_V	0.680	1.00
104_R	152_D	0.679	1.00
181_V	187_L	0.675	1.00
41_A	45_T	0.673	1.00
191_N	270_P	0.671	1.00
67_L	72_E	0.670	1.00
14_R	48_E	0.670	1.00
180_V	261_L	0.670	1.00
257_V	261_L	0.669	1.00
216_D	220_Q	0.667	1.00
74_F	92_L	0.666	1.00
17_H	82_L	0.664	1.00
104_R	151_I	0.663	1.00
213_Q	218_L	0.660	1.00
118_S	121_G	0.658	1.00
66_Q	72_E	0.657	1.00
205_S	239_S	0.657	1.00
202_V	249_V	0.656	1.00
214_H	217_A	0.654	1.00
59_E	64_G	0.654	1.00
19_F	71_G	0.653	1.00
179_L	251_F	0.653	1.00
215_S	218_L	0.650	1.00
87_T	90_R	0.644	1.00
33_E	36_N	0.644	1.00
11_I	89_G	0.642	1.00
198_L	224_C	0.639	1.00
157_R	278_E	0.635	1.00
50_E	60_R	0.634	1.00
217_A	220_Q	0.625	1.00
184_N	187_L	0.624	1.00
206_P	234_L	0.623	1.00
131_T	232_E	0.622	1.00
261_L	268_A	0.622	1.00
116_L	119_V	0.621	1.00
136_T	234_L	0.620	1.00
292_S	295_Q	0.615	1.00
231_I	242_L	0.612	1.00
83_D	86_N	0.611	1.00
53_T	74_F	0.609	1.00
23_A	72_E	0.602	1.00
153_I	298_I	0.600	1.00
82_L	86_N	0.596	1.00
22_V	27_T	0.595	1.00
233_T	238_L	0.594	1.00
122_Q	303_K	0.593	1.00
179_L	197_V	0.593	1.00
195_S	222_Q	0.590	1.00
90_R	94_R	0.589	1.00
14_R	18_T	0.586	1.00
127_Q	130_T	0.583	1.00
109_P	138_S	0.582	1.00
107_A	116_L	0.580	1.00
31_A	35_L	0.579	1.00
199_E	228_S	0.577	1.00
46_L	50_E	0.577	1.00
118_S	122_Q	0.575	1.00
106_G	135_A	0.575	1.00
78_A	82_L	0.573	1.00
146_L	167_L	0.572	1.00
212_R	232_E	0.571	1.00
103_V	153_I	0.570	1.00
284_T	295_Q	0.570	1.00
177_L	251_F	0.570	1.00
55_A	59_E	0.567	1.00
185_H	249_V	0.567	1.00
50_E	55_A	0.567	1.00
106_G	137_M	0.565	1.00
184_N	267_V	0.562	1.00
183_P	264_A	0.558	1.00
100_N	131_T	0.558	1.00
158_M	169_Y	0.557	1.00
41_A	44_K	0.557	1.00
53_T	92_L	0.556	1.00
175_E	278_E	0.556	1.00
216_D	219_V	0.554	1.00
91_S	94_R	0.554	1.00
58_F	67_L	0.553	1.00
212_R	218_L	0.551	1.00
73_Q	92_L	0.551	1.00
252_V	257_V	0.551	1.00
103_V	293_G	0.551	1.00
297_M	301_I	0.550	1.00
12_R	52_L	0.549	1.00
224_C	227_P	0.548	1.00
115_I	119_V	0.546	1.00
28_L	39_Q	0.546	1.00
239_S	243_T	0.544	1.00
172_L	282_I	0.544	1.00
40_P	44_K	0.542	1.00
113_L	235_S	0.538	1.00
53_T	56_R	0.538	1.00
117_P	121_G	0.538	1.00
219_V	227_P	0.537	1.00
146_L	283_L	0.536	1.00
101_D	129_E	0.535	1.00
37_L	45_T	0.535	1.00
147_K	150_E	0.535	1.00
38_S	44_K	0.531	1.00
56_R	70_P	0.530	1.00
90_R	93_H	0.529	1.00
26_G	65_A	0.528	1.00
293_G	296_L	0.528	1.00
136_T	235_S	0.528	1.00
94_R	99_N	0.526	1.00
107_A	134_V	0.525	1.00
187_L	192_V	0.523	1.00
67_L	75_L	0.522	1.00
111_A	115_I	0.522	1.00
125_Q	188_L	0.522	1.00
118_S	241_Q	0.520	1.00
28_L	64_G	0.515	1.00
179_L	202_V	0.515	1.00
207_E	232_E	0.515	1.00
121_G	124_H	0.515	1.00
18_T	46_L	0.514	1.00
173_F	280_I	0.511	1.00
242_L	248_Y	0.511	1.00
88_A	91_S	0.511	1.00
294_C	298_I	0.510	1.00
237_S	241_Q	0.509	1.00
131_T	230_C	0.507	1.00
40_P	43_S	0.506	1.00
265_T	268_A	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
2esnA	3	0.9739	100	0.088	Contact Map
1uthA	2	0.7264	100	0.088	Contact Map
3fxqA	3	0.9642	100	0.101	Contact Map
4x6gA	4	0.9707	100	0.113	Contact Map
3fzvA	4	0.9381	100	0.113	Contact Map
2h98A	2	0.658	100	0.114	Contact Map
1ixcA	4	0.9479	100	0.116	Contact Map
1al3A	1	0.6775	100	0.117	Contact Map
2h9bA	2	0.658	100	0.12	Contact Map
3szpA	3	0.9414	100	0.128	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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