YWQM - BACSU - GREMLIN Contacts

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YWQM - Uncharacterized HTH-type transcriptional regulator YwqM

UniProt:	P96725	Sequences: MELKQLITFITAAEHVNFTLTAKMLNYAQSSVTSQIKSLEEEIGTPLFERLGKRLILTEAGKTFKSYAQKIIALTEEAKMATNQVRETTGTLKIGATESQCTYRLPPIIKEFKQAFPQVKLIFKPYISNEQAKEQLLQGQLDITFILDVNRMEDALHVESLIQDEIKMVAANDHPFPADLPVTLKDLQNETLLLTEDGCSYRTLFENNLHDSGIYPNKLEFVSIEAIKQCVMAGLGIGILPEMTVKDDIAAGRMKELNWQSDCPVFTQLAWHKDKWMSAPLKAFIDLTRKTFK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	293 (283)
Sequences:	79497 (57864)
Seq/√Len:	3439.7

ECOLI - METR OXYR LYSR YFIE PGRR CYSB NHAR CYNR YDCI YBDO TTDR DMLR HCAR LEUO YBHD CBL YFER YBEF YEIE YAFC ABGR ILVY YIDZ YHJC NAC AAER XAPR DSDC YNFL TDCA YCAN YAHB YNEJ YEEY YDHB ALLS GCVA YIAU YHAJ ICIA YGFI HDFR PERR YJIE LRHA
BACSU - YWQM CYSL YCGK YWBI YVBU GLTC CITR YYBE GLTR BSDA ALSR YTLI YUST YOFA YXJO CZCR YKUM YOAU 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
70_K	74_L	3.713	1.00
15_H	24_M	3.390	1.00
11_T	24_M	2.603	1.00
159_E	289_R	2.583	1.00
67_Y	81_A	2.540	1.00
95_G	141_L	2.369	1.00
160_S	266_F	2.365	1.00
91_T	122_I	2.278	1.00
160_S	163_Q	2.257	1.00
45_T	60_A	2.248	1.00
163_Q	266_F	2.231	1.00
10_I	69_Q	2.200	1.00
174_H	190_E	2.162	1.00
8_T	35_Q	2.152	1.00
10_I	14_E	2.136	1.00
231_V	238_G	2.133	1.00
167_K	242_E	2.129	1.00
67_Y	74_L	2.089	1.00
91_T	120_K	2.077	1.00
11_T	15_H	2.039	1.00
232_M	253_R	2.015	1.00
165_E	242_E	2.007	1.00
111_E	287_L	1.994	1.00
183_T	186_D	1.958	1.00
93_K	122_I	1.952	1.00
11_T	14_E	1.927	1.00
20_L	23_K	1.914	1.00
13_A	57_L	1.907	1.00
167_K	256_E	1.889	1.00
228_K	248_D	1.880	1.00
8_T	32_V	1.867	1.00
193_L	236_G	1.866	1.00
10_I	65_K	1.853	1.00
232_M	248_D	1.847	1.00
65_K	69_Q	1.846	1.00
71_I	75_T	1.842	1.00
14_E	69_Q	1.805	1.00
191_T	218_K	1.801	1.00
13_A	65_K	1.772	1.00
170_A	257_L	1.765	1.00
158_V	268_Q	1.739	1.00
135_Q	140_Q	1.709	1.00
63_T	81_A	1.703	1.00
49_E	56_I	1.676	1.00
15_H	20_L	1.670	1.00
67_Y	70_K	1.650	1.00
64_F	78_A	1.626	1.00
17_N	20_L	1.574	1.00
132_A	144_T	1.571	1.00
10_I	68_A	1.551	1.00
159_E	271_W	1.547	1.00
134_E	138_Q	1.544	1.00
157_H	273_K	1.539	1.00
163_Q	264_P	1.527	1.00
5_Q	42_E	1.516	1.00
5_Q	35_Q	1.513	1.00
18_F	36_I	1.504	1.00
5_Q	38_S	1.503	1.00
102_T	225_E	1.490	1.00
14_E	24_M	1.488	1.00
51_L	56_I	1.468	1.00
74_L	77_E	1.456	1.00
67_Y	77_E	1.454	1.00
28_A	31_S	1.451	1.00
11_T	25_L	1.448	1.00
146_I	270_A	1.436	1.00
271_W	285_I	1.432	1.00
157_H	271_W	1.422	1.00
135_Q	141_L	1.420	1.00
46_P	49_E	1.417	1.00
179_D	186_D	1.416	1.00
9_F	65_K	1.384	1.00
19_T	29_Q	1.381	1.00
112_F	284_F	1.381	1.00
202_R	206_E	1.380	1.00
93_K	124_K	1.380	1.00
148_D	268_Q	1.376	1.00
8_T	27_Y	1.373	1.00
71_I	78_A	1.373	1.00
285_I	289_R	1.358	1.00
66_S	70_K	1.357	1.00
64_F	79_K	1.354	1.00
115_A	287_L	1.351	1.00
112_F	119_V	1.342	1.00
136_L	144_T	1.335	1.00
248_D	253_R	1.327	1.00
126_Y	131_Q	1.327	1.00
229_Q	232_M	1.308	1.00
277_M	281_L	1.306	1.00
164_D	243_M	1.305	1.00
10_I	72_I	1.302	1.00
269_L	285_I	1.301	1.00
143_I	269_L	1.301	1.00
67_Y	78_A	1.300	1.00
283_A	286_D	1.297	1.00
227_I	238_G	1.297	1.00
59_E	62_K	1.295	1.00
27_Y	31_S	1.277	1.00
160_S	268_Q	1.274	1.00
137_L	155_A	1.267	1.00
89_T	118_Q	1.257	1.00
172_N	255_K	1.256	1.00
172_N	253_R	1.253	1.00
170_A	237_I	1.246	1.00
242_E	256_E	1.238	1.00
110_K	233_A	1.238	1.00
34_S	38_S	1.233	1.00
190_E	237_I	1.231	1.00
113_K	191_T	1.226	1.00
143_I	281_L	1.223	1.00
113_K	218_K	1.222	1.00
63_T	66_S	1.221	1.00
3_L	75_T	1.214	1.00
63_T	67_Y	1.210	1.00
110_K	114_Q	1.202	1.00
181_P	260_Q	1.193	1.00
111_E	115_A	1.191	1.00
42_E	79_K	1.187	1.00
9_F	13_A	1.181	1.00
9_F	48_F	1.172	1.00
107_P	233_A	1.163	1.00
242_E	246_K	1.153	1.00
256_E	259_W	1.146	1.00
158_V	270_A	1.142	1.00
70_K	77_E	1.137	1.00
6_L	68_A	1.122	1.00
34_S	37_K	1.118	1.00
228_K	232_M	1.111	1.00
191_T	217_N	1.109	1.00
159_E	285_I	1.107	1.00
175_P	190_E	1.105	1.00
116_F	283_A	1.100	1.00
229_Q	233_A	1.094	1.00
182_V	186_D	1.092	1.00
11_T	21_T	1.092	1.00
62_K	66_S	1.089	1.00
122_I	220_E	1.081	1.00
124_K	135_Q	1.077	1.00
246_K	250_A	1.068	1.00
180_L	255_K	1.065	1.00
137_L	153_E	1.065	1.00
169_V	256_E	1.063	1.00
37_K	41_E	1.057	1.00
71_I	74_L	1.049	1.00
18_F	55_L	1.048	1.00
247_D	251_A	1.036	1.00
35_Q	38_S	1.034	1.00
101_C	125_P	1.029	1.00
79_K	83_N	1.027	1.00
33_T	37_K	1.027	1.00
73_A	77_E	1.012	1.00
126_Y	135_Q	1.008	1.00
282_K	286_D	1.006	1.00
171_A	234_G	1.004	1.00
9_F	47_L	0.995	1.00
64_F	68_A	0.988	1.00
111_E	114_Q	0.984	1.00
12_A	21_T	0.981	1.00
112_F	287_L	0.979	1.00
108_I	288_T	0.978	1.00
272_H	275_K	0.977	1.00
184_L	261_S	0.974	1.00
112_F	116_F	0.973	1.00
12_A	18_F	0.971	1.00
4_K	7_I	0.967	1.00
38_S	41_E	0.966	1.00
57_L	61_G	0.963	1.00
75_T	79_K	0.963	1.00
21_T	32_V	0.959	1.00
92_L	284_F	0.958	1.00
221_F	227_I	0.955	1.00
174_H	177_P	0.955	1.00
70_K	73_A	0.953	1.00
286_D	289_R	0.953	1.00
209_L	214_I	0.948	1.00
63_T	85_V	0.945	1.00
193_L	227_I	0.945	1.00
169_V	245_V	0.942	1.00
20_L	24_M	0.939	1.00
27_Y	32_V	0.936	1.00
76_E	79_K	0.929	1.00
203_T	206_E	0.929	1.00
135_Q	138_Q	0.928	1.00
8_T	25_L	0.926	1.00
13_A	48_F	0.919	1.00
9_F	39_L	0.918	1.00
168_M	237_I	0.914	1.00
60_A	63_T	0.909	1.00
7_I	76_E	0.907	1.00
170_A	174_H	0.905	1.00
16_V	56_I	0.901	1.00
221_F	230_C	0.901	1.00
278_S	281_L	0.898	1.00
157_H	160_S	0.897	1.00
98_E	223_S	0.895	1.00
148_D	266_F	0.894	1.00
108_I	287_L	0.889	1.00
9_F	57_L	0.883	1.00
76_E	80_M	0.876	1.00
77_E	81_A	0.875	1.00
248_D	251_A	0.873	1.00
110_K	235_L	0.871	1.00
131_Q	134_E	0.865	1.00
203_T	207_N	0.865	1.00
19_T	23_K	0.862	1.00
208_N	212_S	0.857	1.00
75_T	78_A	0.855	1.00
45_T	82_T	0.855	1.00
66_S	69_Q	0.850	1.00
113_K	235_L	0.850	1.00
178_A	191_T	0.847	1.00
16_V	54_R	0.841	1.00
48_F	55_L	0.841	1.00
60_A	85_V	0.839	1.00
51_L	54_R	0.838	1.00
90_G	280_P	0.836	1.00
29_Q	33_T	0.835	1.00
95_G	146_I	0.835	1.00
25_L	32_V	0.827	1.00
7_I	11_T	0.826	1.00
176_F	190_E	0.826	1.00
141_L	144_T	0.825	1.00
279_A	283_A	0.823	1.00
183_T	260_Q	0.819	1.00
74_L	78_A	0.818	1.00
15_H	21_T	0.817	1.00
133_K	137_L	0.814	1.00
14_E	65_K	0.812	1.00
60_A	82_T	0.805	1.00
4_K	35_Q	0.804	1.00
13_A	16_V	0.802	1.00
277_M	282_K	0.798	1.00
95_G	144_T	0.797	1.00
205_F	209_L	0.794	1.00
185_K	188_Q	0.793	1.00
62_K	65_K	0.792	1.00
165_E	262_D	0.791	1.00
119_V	280_P	0.790	1.00
12_A	48_F	0.790	1.00
124_K	141_L	0.788	1.00
120_K	217_N	0.786	1.00
9_F	64_F	0.786	1.00
94_I	143_I	0.785	1.00
186_D	189_N	0.784	1.00
245_V	248_D	0.781	1.00
171_A	235_L	0.777	1.00
7_I	10_I	0.776	1.00
230_C	235_L	0.775	1.00
78_A	82_T	0.772	1.00
175_P	180_L	0.772	1.00
69_Q	73_A	0.772	1.00
192_L	216_P	0.769	1.00
5_Q	8_T	0.767	1.00
13_A	61_G	0.764	1.00
16_V	62_K	0.763	1.00
12_A	32_V	0.763	1.00
49_E	58_T	0.759	1.00
68_A	71_I	0.758	1.00
173_D	234_G	0.756	1.00
156_L	270_A	0.755	1.00
18_F	32_V	0.754	1.00
170_A	175_P	0.753	1.00
96_A	101_C	0.751	1.00
37_K	46_P	0.748	1.00
165_E	264_P	0.747	1.00
275_K	278_S	0.746	1.00
223_S	226_A	0.746	1.00
139_G	272_H	0.745	1.00
169_V	238_G	0.741	1.00
171_A	174_H	0.740	1.00
165_E	258_N	0.738	1.00
3_L	72_I	0.737	1.00
196_E	220_E	0.737	1.00
112_F	283_A	0.737	1.00
90_G	119_V	0.735	1.00
137_L	156_L	0.731	1.00
208_N	211_D	0.726	1.00
188_Q	214_I	0.724	1.00
204_L	208_N	0.718	1.00
177_P	255_K	0.716	1.00
169_V	240_L	0.715	1.00
59_E	63_T	0.714	1.00
283_A	287_L	0.712	1.00
131_Q	135_Q	0.711	1.00
12_A	36_I	0.708	1.00
170_A	255_K	0.706	1.00
102_T	229_Q	0.702	1.00
60_A	64_F	0.701	1.00
142_D	281_L	0.698	1.00
207_N	211_D	0.696	1.00
95_G	132_A	0.695	1.00
83_N	86_R	0.692	1.00
9_F	61_G	0.689	1.00
174_H	191_T	0.688	1.00
67_Y	71_I	0.688	1.00
107_P	110_K	0.684	1.00
7_I	72_I	0.680	1.00
183_T	261_S	0.680	1.00
88_T	116_F	0.679	1.00
181_P	258_N	0.677	1.00
174_H	178_A	0.675	1.00
93_K	142_D	0.673	1.00
192_L	237_I	0.673	1.00
241_P	244_T	0.673	1.00
155_A	273_K	0.671	1.00
143_I	284_F	0.671	1.00
31_S	35_Q	0.669	1.00
168_M	239_I	0.666	1.00
205_F	208_N	0.665	1.00
206_E	210_H	0.665	1.00
64_F	82_T	0.663	1.00
57_L	62_K	0.661	1.00
173_D	177_P	0.657	1.00
120_K	220_E	0.657	1.00
49_E	54_R	0.652	1.00
115_A	283_A	0.652	1.00
170_A	176_F	0.646	1.00
56_I	62_K	0.644	1.00
23_K	26_N	0.643	1.00
173_D	176_F	0.642	1.00
195_T	227_I	0.641	1.00
232_M	251_A	0.639	1.00
93_K	141_L	0.634	1.00
204_L	207_N	0.632	1.00
185_K	212_S	0.631	1.00
77_E	80_M	0.630	1.00
147_L	265_V	0.630	1.00
105_L	108_I	0.624	1.00
279_A	282_K	0.624	1.00
72_I	76_E	0.623	1.00
40_E	50_R	0.622	1.00
219_L	230_C	0.621	1.00
125_P	222_V	0.620	1.00
196_E	222_V	0.620	1.00
13_A	62_K	0.614	1.00
4_K	38_S	0.606	1.00
43_I	64_F	0.606	1.00
128_S	131_Q	0.602	1.00
201_Y	205_F	0.601	1.00
247_D	250_A	0.599	1.00
73_A	76_E	0.596	1.00
143_I	285_I	0.594	1.00
80_M	84_Q	0.591	1.00
4_K	8_T	0.588	1.00
36_I	40_E	0.585	1.00
126_Y	132_A	0.581	1.00
12_A	17_N	0.578	1.00
40_E	45_T	0.577	1.00
107_P	111_E	0.575	1.00
168_M	187_L	0.573	1.00
206_E	209_L	0.570	1.00
221_F	226_A	0.570	1.00
21_T	25_L	0.569	1.00
202_R	220_E	0.565	1.00
172_N	252_G	0.564	1.00
92_L	143_I	0.564	1.00
116_F	119_V	0.564	1.00
207_N	210_H	0.561	1.00
271_W	282_K	0.560	1.00
203_T	208_N	0.559	1.00
96_A	105_L	0.559	1.00
63_T	82_T	0.559	1.00
45_T	49_E	0.558	1.00
90_G	118_Q	0.558	1.00
104_R	108_I	0.558	1.00
173_D	255_K	0.557	1.00
284_F	288_T	0.557	1.00
148_D	158_V	0.556	1.00
188_Q	215_Y	0.556	1.00
80_M	83_N	0.555	1.00
81_A	84_Q	0.554	1.00
18_F	29_Q	0.554	1.00
202_R	208_N	0.554	1.00
166_I	239_I	0.553	1.00
68_A	72_I	0.552	1.00
43_I	82_T	0.552	1.00
164_D	265_V	0.551	1.00
31_S	34_S	0.549	1.00
89_T	120_K	0.548	1.00
174_H	237_I	0.546	1.00
136_L	156_L	0.546	1.00
137_L	140_Q	0.545	1.00
48_F	57_L	0.544	1.00
95_G	124_K	0.542	1.00
209_L	216_P	0.542	1.00
227_I	231_V	0.541	1.00
84_Q	88_T	0.540	1.00
92_L	280_P	0.539	1.00
110_K	113_K	0.537	1.00
43_I	46_P	0.537	1.00
100_Q	104_R	0.535	1.00
161_L	269_L	0.534	1.00
280_P	283_A	0.532	1.00
96_A	123_F	0.528	1.00
134_E	140_Q	0.528	1.00
46_P	60_A	0.527	1.00
175_P	179_D	0.527	1.00
106_P	110_K	0.527	1.00
30_S	34_S	0.526	1.00
125_P	223_S	0.523	1.00
253_R	256_E	0.521	1.00
16_V	55_L	0.521	1.00
27_Y	35_Q	0.519	1.00
84_Q	87_E	0.517	1.00
224_I	241_P	0.516	1.00
38_S	42_E	0.516	1.00
120_K	218_K	0.515	1.00
195_T	224_I	0.515	1.00
88_T	118_Q	0.515	1.00
202_R	205_F	0.514	1.00
225_E	229_Q	0.514	1.00
107_P	229_Q	0.513	1.00
97_T	100_Q	0.513	1.00
281_L	285_I	0.512	1.00
240_L	245_V	0.511	1.00
28_A	34_S	0.510	1.00
201_Y	204_L	0.509	1.00
78_A	81_A	0.509	1.00
176_F	179_D	0.507	1.00
6_L	64_F	0.507	1.00
30_S	33_T	0.506	1.00
10_I	76_E	0.504	1.00
57_L	65_K	0.500	1.00
45_T	86_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
1uthA	2	0.7474	100	0.088	Contact Map
2esnA	3	0.9863	100	0.088	Contact Map
3fxqA	3	0.9898	100	0.096	Contact Map
2h98A	2	0.6826	100	0.097	Contact Map
1al3A	1	0.7031	100	0.098	Contact Map
1ixcA	4	0.9829	100	0.102	Contact Map
2h9bA	2	0.6826	100	0.102	Contact Map
3fzvA	4	0.9659	100	0.103	Contact Map
4x6gA	4	0.9932	100	0.104	Contact Map
3szpA	3	0.9795	100	0.117	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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