YWBI - BACSU - GREMLIN Contacts

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YWBI - Uncharacterized HTH-type transcriptional regulator YwbI

UniProt:	P39592	Sequences: MDIRHLTYFLEVARLKSFTKASQSLYVSQPTISKMIKNLEEELGIELFYRNGRQVELTDAGHSMYVQAQEIIKSFQNLTSELNDIMEVKKGHVRIGLPPMIGSGFFPRVLGDFRENYPNVTFQLVEDGSIKVQEGVGDGSLDIGVVVLPANEDIFHSFTIVKETLMLVVHPSHRLADEKECQLRELKDEPFIFFREDFVLHNRIMTECIKAGFRPHIIYETSQWDFISEMVSANLGIGLLPERICRGLDPEKVKVIPLVDPVIPWHLAIIWRKDRYLSFAARAWLEHTKSYLWDPKKDSKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	301 (286)
Sequences:	79750 (57810)
Seq/√Len:	3418.4

ECOLI - OXYR CYSB LYSR YBHD CYNR TDCA YFER CBL NAC AAER YAFC TTDR DMLR HCAR ABGR YCAN YDHB YNFL ALLS LEUO PGRR ILVY YEEY YEIE YAHB METR YDCI YFIE YHJC XAPR YNEJ YBDO NHAR DSDC YBEF ICIA GCVA YIDZ YIAU YGFI YHAJ YJIE LRHA PERR HDFR
BACSU - YWBI ALSR YCGK GLTC CYSL YTLI YYBE BSDA GLTR CITR YVBU YWQM YUST YOFA YXJO YKUM CZCR 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
70_E	74_S	3.630	1.00
15_L	24_S	3.399	1.00
158_F	289_K	2.700	1.00
96_G	141_L	2.506	1.00
67_Q	81_E	2.461	1.00
11_E	24_S	2.350	1.00
231_V	238_G	2.257	1.00
159_T	162_K	2.227	1.00
162_K	266_H	2.221	1.00
92_H	123_Q	2.215	1.00
173_H	189_E	2.205	1.00
159_T	266_H	2.182	1.00
164_T	242_E	2.135	1.00
45_I	60_A	2.102	1.00
92_H	121_T	2.088	1.00
8_Y	35_M	2.083	1.00
20_K	23_Q	2.063	1.00
10_L	69_Q	2.019	1.00
162_K	264_P	2.017	1.00
112_D	287_H	2.013	1.00
182_Q	185_E	2.011	1.00
67_Q	74_S	1.997	1.00
232_S	252_K	1.995	1.00
14_R	69_Q	1.984	1.00
10_L	14_R	1.972	1.00
228_S	247_G	1.962	1.00
94_R	123_Q	1.951	1.00
10_L	65_Y	1.951	1.00
166_M	242_E	1.928	1.00
11_E	14_R	1.927	1.00
11_E	15_L	1.921	1.00
13_A	57_L	1.888	1.00
192_I	236_G	1.887	1.00
8_Y	32_I	1.886	1.00
169_V	256_I	1.866	1.00
71_I	75_F	1.860	1.00
65_Y	69_Q	1.825	1.00
18_F	36_I	1.733	1.00
232_S	247_G	1.732	1.00
166_M	255_V	1.731	1.00
190_P	218_I	1.729	1.00
49_Y	56_E	1.717	1.00
135_G	140_S	1.713	1.00
64_M	78_L	1.711	1.00
157_S	268_A	1.692	1.00
63_S	81_E	1.679	1.00
13_A	65_Y	1.649	1.00
132_V	144_G	1.633	1.00
15_L	20_K	1.605	1.00
113_F	284_W	1.572	1.00
14_R	24_S	1.564	1.00
156_H	273_K	1.564	1.00
10_L	68_A	1.556	1.00
134_E	138_D	1.526	1.00
178_E	185_E	1.523	1.00
9_F	65_Y	1.519	1.00
5_H	35_M	1.510	1.00
67_Q	70_E	1.502	1.00
8_Y	27_V	1.499	1.00
5_H	42_E	1.486	1.00
17_S	20_K	1.482	1.00
158_F	271_W	1.480	1.00
88_V	119_N	1.476	1.00
5_H	38_N	1.471	1.00
28_S	31_T	1.468	1.00
19_T	29_Q	1.457	1.00
113_F	120_V	1.454	1.00
46_E	49_Y	1.445	1.00
127_D	131_K	1.438	1.00
11_E	25_L	1.425	1.00
59_D	62_H	1.423	1.00
285_L	289_K	1.422	1.00
146_V	270_I	1.409	1.00
103_S	225_D	1.403	1.00
156_H	271_W	1.397	1.00
271_W	285_L	1.393	1.00
201_H	205_M	1.390	1.00
148_L	268_A	1.388	1.00
67_Q	77_N	1.387	1.00
10_L	72_I	1.379	1.00
71_I	78_L	1.370	1.00
277_L	281_A	1.370	1.00
90_K	119_N	1.339	1.00
94_R	125_V	1.337	1.00
51_N	56_E	1.335	1.00
283_A	286_E	1.332	1.00
74_S	77_N	1.315	1.00
163_E	243_R	1.314	1.00
171_P	252_K	1.313	1.00
135_G	141_L	1.312	1.00
116_N	287_H	1.309	1.00
64_M	79_T	1.306	1.00
269_I	285_L	1.295	1.00
143_I	269_I	1.286	1.00
137_G	154_I	1.285	1.00
112_D	116_N	1.281	1.00
3_I	75_F	1.270	1.00
227_I	238_G	1.267	1.00
143_I	281_A	1.267	1.00
66_V	70_E	1.261	1.00
169_V	237_I	1.255	1.00
189_E	237_I	1.243	1.00
42_E	79_T	1.239	1.00
242_E	255_V	1.237	1.00
114_R	218_I	1.236	1.00
67_Q	78_L	1.230	1.00
171_P	254_K	1.212	1.00
229_E	232_S	1.210	1.00
159_T	268_A	1.209	1.00
114_R	190_P	1.201	1.00
63_S	66_V	1.191	1.00
9_F	48_F	1.190	1.00
27_V	31_T	1.186	1.00
111_G	115_E	1.182	1.00
157_S	270_I	1.163	1.00
34_K	38_N	1.163	1.00
247_G	252_K	1.163	1.00
242_E	246_R	1.160	1.00
111_G	233_A	1.158	1.00
62_H	66_V	1.156	1.00
9_F	13_A	1.150	1.00
37_K	41_E	1.136	1.00
179_K	254_K	1.129	1.00
34_K	37_K	1.127	1.00
174_R	189_E	1.121	1.00
180_E	259_V	1.118	1.00
123_Q	220_E	1.114	1.00
63_S	67_Q	1.095	1.00
9_F	47_L	1.091	1.00
190_P	216_H	1.089	1.00
117_Y	283_A	1.087	1.00
70_E	77_N	1.085	1.00
255_V	258_L	1.085	1.00
208_C	213_F	1.083	1.00
112_D	115_E	1.078	1.00
168_V	255_V	1.077	1.00
102_G	126_E	1.076	1.00
6_L	68_A	1.075	1.00
108_R	233_A	1.072	1.00
286_E	289_K	1.071	1.00
18_F	55_V	1.070	1.00
136_V	144_G	1.068	1.00
113_F	287_H	1.067	1.00
33_S	37_K	1.063	1.00
11_E	21_A	1.062	1.00
93_V	284_W	1.062	1.00
192_I	227_I	1.061	1.00
158_F	285_L	1.053	1.00
71_I	74_S	1.050	1.00
272_R	275_R	1.046	1.00
246_R	249_D	1.043	1.00
12_V	21_A	1.042	1.00
221_T	227_I	1.041	1.00
35_M	38_N	1.033	1.00
109_V	288_T	1.030	1.00
181_C	185_E	1.029	1.00
229_E	233_A	1.025	1.00
127_D	135_G	1.024	1.00
228_S	232_S	1.022	1.00
282_R	286_E	1.019	1.00
137_G	152_E	1.017	1.00
7_T	76_Q	1.013	1.00
79_T	83_N	1.012	1.00
170_H	234_N	1.011	1.00
57_L	61_G	1.006	1.00
183_L	260_D	1.005	1.00
4_R	7_T	1.003	1.00
164_T	264_P	0.988	1.00
168_V	245_C	0.987	1.00
13_A	48_F	0.969	1.00
64_M	68_A	0.966	1.00
73_K	77_N	0.965	1.00
27_V	32_I	0.964	1.00
167_L	237_I	0.963	1.00
202_N	205_M	0.961	1.00
8_Y	25_L	0.959	1.00
287_H	290_S	0.957	1.00
193_F	217_I	0.955	1.00
113_F	117_Y	0.954	1.00
12_V	18_F	0.953	1.00
125_V	135_G	0.952	1.00
76_Q	79_T	0.948	1.00
135_G	138_D	0.940	1.00
169_V	173_H	0.935	1.00
76_Q	80_S	0.934	1.00
9_F	57_L	0.931	1.00
21_A	32_I	0.930	1.00
221_T	230_M	0.929	1.00
173_H	176_A	0.926	1.00
38_N	41_E	0.921	1.00
96_G	146_V	0.917	1.00
9_F	39_L	0.911	1.00
109_V	287_H	0.908	1.00
278_S	281_A	0.908	1.00
20_K	24_S	0.903	1.00
116_N	290_S	0.899	1.00
63_S	85_I	0.898	1.00
48_F	55_V	0.889	1.00
70_E	73_K	0.875	1.00
131_K	134_E	0.873	1.00
99_P	223_Q	0.873	1.00
45_I	82_L	0.866	1.00
202_N	206_T	0.865	1.00
148_L	266_H	0.863	1.00
16_K	56_E	0.862	1.00
13_A	61_G	0.857	1.00
66_V	69_Q	0.856	1.00
121_T	216_H	0.852	1.00
141_L	144_G	0.847	1.00
19_T	23_Q	0.844	1.00
190_P	217_I	0.837	1.00
177_D	190_P	0.836	1.00
120_V	280_A	0.836	1.00
25_L	32_I	0.828	1.00
156_H	159_T	0.828	1.00
60_A	85_I	0.824	1.00
51_N	54_Q	0.823	1.00
204_I	208_C	0.820	1.00
96_G	144_G	0.817	1.00
111_G	235_L	0.815	1.00
95_I	143_I	0.814	1.00
173_H	190_P	0.813	1.00
91_G	280_A	0.811	1.00
168_V	238_G	0.811	1.00
155_F	270_I	0.811	1.00
75_F	79_T	0.808	1.00
169_V	174_R	0.808	1.00
125_V	141_L	0.808	1.00
174_R	179_K	0.807	1.00
173_H	177_D	0.804	1.00
154_I	273_K	0.801	1.00
185_E	188_D	0.801	1.00
60_A	82_L	0.800	1.00
9_F	64_M	0.799	1.00
75_F	78_L	0.799	1.00
16_K	62_H	0.794	1.00
29_Q	33_S	0.792	1.00
286_E	290_S	0.792	1.00
13_A	16_K	0.792	1.00
133_Q	137_G	0.790	1.00
207_E	211_A	0.788	1.00
248_L	251_E	0.787	1.00
60_A	63_S	0.786	1.00
74_S	78_L	0.785	1.00
4_R	35_M	0.784	1.00
175_L	189_E	0.783	1.00
14_R	65_Y	0.783	1.00
77_N	81_E	0.782	1.00
277_L	282_R	0.781	1.00
3_I	72_I	0.774	1.00
37_K	46_E	0.774	1.00
279_F	283_A	0.769	1.00
12_V	48_F	0.768	1.00
15_L	21_A	0.767	1.00
184_R	187_K	0.767	1.00
114_R	235_L	0.767	1.00
164_T	262_V	0.765	1.00
170_H	235_L	0.762	1.00
16_K	54_Q	0.761	1.00
182_Q	259_V	0.759	1.00
12_V	36_I	0.756	1.00
96_G	132_V	0.752	1.00
91_G	120_V	0.750	1.00
5_H	8_Y	0.748	1.00
143_I	284_W	0.745	1.00
164_T	257_P	0.742	1.00
230_M	235_L	0.739	1.00
232_S	250_P	0.737	1.00
172_S	176_A	0.736	1.00
7_T	11_E	0.736	1.00
78_L	82_L	0.734	1.00
12_V	32_I	0.731	1.00
18_F	32_I	0.727	1.00
168_V	240_L	0.726	1.00
247_G	250_P	0.725	1.00
113_F	283_A	0.723	1.00
116_N	283_A	0.723	1.00
176_A	254_K	0.721	1.00
68_A	71_I	0.719	1.00
131_K	135_G	0.719	1.00
89_K	117_Y	0.718	1.00
97_L	102_G	0.717	1.00
49_Y	58_T	0.717	1.00
83_N	86_M	0.714	1.00
137_G	155_F	0.712	1.00
69_Q	73_K	0.711	1.00
170_H	173_H	0.710	1.00
49_Y	54_Q	0.707	1.00
62_H	65_Y	0.706	1.00
139_G	272_R	0.703	1.00
223_Q	226_F	0.699	1.00
203_R	207_E	0.697	1.00
206_T	210_K	0.695	1.00
60_A	64_M	0.694	1.00
169_V	254_K	0.692	1.00
207_E	210_K	0.689	1.00
31_T	35_M	0.688	1.00
241_P	244_I	0.687	1.00
94_R	141_L	0.684	1.00
57_L	62_H	0.684	1.00
56_E	62_H	0.684	1.00
187_K	213_F	0.683	1.00
195_R	220_E	0.682	1.00
275_R	278_S	0.679	1.00
169_V	175_L	0.678	1.00
283_A	287_H	0.678	1.00
94_R	142_D	0.675	1.00
205_M	209_I	0.675	1.00
184_R	211_A	0.674	1.00
142_D	281_A	0.671	1.00
201_H	220_E	0.670	1.00
191_F	215_P	0.669	1.00
194_F	227_I	0.669	1.00
180_E	257_P	0.668	1.00
59_D	63_S	0.668	1.00
204_I	207_E	0.667	1.00
7_T	10_L	0.662	1.00
172_S	234_N	0.652	1.00
40_E	45_I	0.650	1.00
64_M	82_L	0.650	1.00
127_D	132_V	0.648	1.00
112_D	290_S	0.647	1.00
103_S	229_E	0.646	1.00
172_S	175_L	0.644	1.00
40_E	50_R	0.644	1.00
168_V	248_L	0.643	1.00
191_F	237_I	0.642	1.00
219_Y	230_M	0.638	1.00
206_T	209_I	0.637	1.00
73_K	76_Q	0.635	1.00
67_Q	71_I	0.635	1.00
202_N	207_E	0.634	1.00
77_N	80_S	0.632	1.00
121_T	220_E	0.631	1.00
36_I	40_E	0.631	1.00
23_Q	26_Y	0.622	1.00
97_L	106_F	0.621	1.00
126_E	222_S	0.621	1.00
182_Q	260_D	0.620	1.00
68_A	72_I	0.619	1.00
167_L	239_L	0.616	1.00
93_V	280_A	0.615	1.00
248_L	255_V	0.611	1.00
279_F	282_R	0.610	1.00
167_L	186_L	0.609	1.00
203_R	206_T	0.609	1.00
134_E	140_S	0.608	1.00
171_P	251_E	0.605	1.00
134_E	137_G	0.604	1.00
12_V	17_S	0.604	1.00
4_R	38_N	0.602	1.00
188_D	216_H	0.601	1.00
18_F	54_Q	0.599	1.00
195_R	222_S	0.599	1.00
143_I	285_L	0.598	1.00
172_S	254_K	0.597	1.00
137_G	140_S	0.595	1.00
108_R	111_G	0.594	1.00
145_V	288_T	0.593	1.00
99_P	128_G	0.593	1.00
21_A	25_L	0.590	1.00
205_M	208_C	0.589	1.00
7_T	72_I	0.589	1.00
147_V	265_W	0.584	1.00
175_L	178_E	0.583	1.00
93_V	143_I	0.580	1.00
106_F	109_V	0.579	1.00
63_S	82_L	0.578	1.00
43_L	64_M	0.577	1.00
90_K	121_T	0.577	1.00
80_S	84_D	0.576	1.00
126_E	223_Q	0.573	1.00
245_C	248_L	0.572	1.00
221_T	226_F	0.569	1.00
9_F	61_G	0.566	1.00
161_V	267_L	0.564	1.00
43_L	82_L	0.563	1.00
30_P	34_K	0.563	1.00
4_R	8_Y	0.560	1.00
284_W	288_T	0.559	1.00
208_C	215_P	0.559	1.00
167_L	191_F	0.558	1.00
31_T	34_K	0.557	1.00
28_S	34_K	0.556	1.00
45_I	49_Y	0.555	1.00
227_I	231_V	0.554	1.00
163_E	265_W	0.552	1.00
175_L	181_C	0.552	1.00
165_L	239_L	0.550	1.00
48_F	57_L	0.549	1.00
117_Y	120_V	0.549	1.00
57_L	65_Y	0.549	1.00
72_I	76_Q	0.548	1.00
108_R	112_D	0.548	1.00
196_E	220_E	0.543	1.00
101_I	105_F	0.542	1.00
174_R	178_E	0.541	1.00
200_L	204_I	0.541	1.00
230_M	236_G	0.540	1.00
271_W	282_R	0.536	1.00
156_H	274_D	0.533	1.00
173_H	237_I	0.531	1.00
136_V	155_F	0.531	1.00
96_G	125_V	0.525	1.00
160_I	269_I	0.524	1.00
43_L	46_E	0.523	1.00
13_A	62_H	0.523	1.00
148_L	157_S	0.522	1.00
103_S	223_Q	0.520	1.00
110_L	122_F	0.519	1.00
240_L	245_C	0.518	1.00
224_W	241_P	0.518	1.00
8_Y	36_I	0.517	1.00
18_F	29_Q	0.515	1.00
139_G	275_R	0.511	1.00
96_G	127_D	0.510	1.00
84_D	89_K	0.509	1.00
66_V	81_E	0.509	1.00
80_S	83_N	0.508	1.00
91_G	119_N	0.507	1.00
8_Y	21_A	0.507	1.00
27_V	35_M	0.507	1.00
72_I	75_F	0.504	1.00
16_K	55_V	0.504	1.00
46_E	60_A	0.504	1.00
115_E	176_A	0.501	1.00
108_R	229_E	0.500	1.00
281_A	285_L	0.500	1.00
168_V	253_V	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
1al3A	1	0.7176	100	0.088	Contact Map
1ixcA	4	0.9701	100	0.089	Contact Map
4x6gA	4	1	100	0.091	Contact Map
2esnA	3	0.9701	100	0.096	Contact Map
1uthA	2	0.7508	100	0.096	Contact Map
2h9bA	2	0.6977	100	0.098	Contact Map
2h98A	2	0.6977	100	0.099	Contact Map
3fxqA	3	0.9668	100	0.099	Contact Map
3fzvA	4	0.9502	100	0.1	Contact Map
3szpA	3	0.9601	100	0.121	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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